Biology Full Review

Pumping Cycle of P-Type SR Ca Transporter

-Resting state is open to cytosol -Binding of ATP and calcium -ATP phosphorylates nextdoor aspartate site, inducing conformational change and opening transporter to lumen -Calcium released into lumen -Dephosphorylation induces conformational change that re-opens pump to inside

Pumping Cycle of P-Type Na/K Pump

-Sodium and ATP bind from inside -Phosphorylation of Aspartate induces conformational change (ADP RELEASED IN THIS PROCESS! unlike with Ca) -Sodium releases to exterior and Potassium binds -Dephosphorylation causes conformational change reverting opening to inside -Potassium releases to restart cycle

What was Lyon's experiment?

-Took skin samples from a women heterozygous for fast and slow G6PD alleles to determine if X-chromosome inactivation was random and persistent -he separated and grew the cells in vitro to see if the ones with slow and fast alleles would continue to produce only their kind, and when they did indeed produce only their kind it demonstrated that the X-chromoosmes were inactivated randomly and when that happened, they stayed inactive (random because equal quantities and not favoring more evolutionarily beneficial one)

What are reciprocal translocations? another name for them?

-Two non-homologous chromosomes exchange genetic material as result of chromosomal breakage and repair or abnormal crossovers -usually phenotypically normal, occasional position effects -AKA balanced translocations because they lead to a rearrangement of genetic material, not change in total amount

What is a Robertsonian Translocation? Example?

-Unbalanced (simple) translocation arising from breaks near centromeres of two non-homologous acrocentric chromosomes -small acentric fragments are lost -larger fragments fuse at centromeric regions to form single chromosome -most common rearrangement in humans! approximately 1 in 900 births! -Familial Down Syndrome

What is the endosymbiosis theory?

-mitochondria and chloroplasts once separate free prokaryotes that were absorbed and taken over by eukaryotes for their energy-producing and converting purposes -mitochondria from purple bacteria and chloroplasts from cyanobacteria (they have genomes closer to these than eukaryotic genomes, missing things like introns)

What is extranuclear inheritance? Mitochondria and chloroplasts roles? Patterns of inheritance?

-non-Mendelian inheritance of genes outside the genome in organelles like chloroplasts and mitochondria -maintain separate prokaryotic-like genome not sorted during meiosis and with its own inheritance rules specific to the species

What are some key tenets of protein folding? (requirements, process)

-requires correct temp, pH, and time (slow enough) to fold correctly? -folds as it comes out of the ribosome -evolved so final correct fold is most stable and lowest energy, raising likelihood of it going smoothly

What is an inversion and its usually phenotypic effect?

-segment of DNA that has been flipped to opposite direction -usually no phenotypic consequences

(3) Roles of energy in mitochondrial import mechanism

1. After cytosolic hsp70 chaperon proteins hold protein in unfolded conformation reach TOM complex, ATP required for their release as they are fed through 2. Membrane potential across inner leaflet then facilitates initial transport across inner membrane due to positively-charged N-terminal sequence 3. Mitochondrial hsp70 proteins than bind in interior and hydrolyze ATP pull in like a rope

4 Principles of Natural Selection

1. Allelic variation from mutations provides raw material 2. Some alleles may encode proteins the enhance individual's survival/reproductive capacity 3. Individuals with beneficial alleles are more likely to survive and reproudce 4. Net result of natural selection is population that is better adapted to its environment and/or more successful at reproduction

What is the cycle of induction and repression of lac operon?

1. Allolactose available, small amount taken up and converted to allolactose by beta-galactosidase, allolactose binds to repressor causing it to fall off operator site 2. Lac operon proteins synthesized -> uptake and metabolism of lactose 3. Lactose depleted, allolactose level decreases, allolactose released from repressor and repressor binds to operator 4. most protein involved with lactose utilization degraded

What is the process of Muscle Contraction from the viewpoint of actin/myosin interactions

1. Attached - myosin head lacking bound nucleotide is locked tightly onto actin filament in Rigor configuration; short-lived 2. Release - ATP binds the large cleft on back of myosin head, causing slight conformational change and allowing release 3. Cocking - Cleft closure around ATP molecule hydrolyzes ATP, displacing myosin head towards positive side of actin filament about 5nm. ADP/P remain bound 4. Force-Generation - Myosin binds weakly to spot on actin further towards plus end from before, causing phosphate to dissociate and triggering power stroke as myosin head pulls towards positive end. ADP dissociates during power stroke.

How does telomerase add telomeres?

1. Binding 2. Polymerization 3. Translocation

Mechanisms (2) of translational repressors?

1. Binding next to Shine-Dalgarno sequence and/or start codon to sterically hinder ribosome 2. Binding outside Shine-Dalgarno/stard codon to stabilize mRNA secondary structure that prevents initiation

What are the five "cool stuff microbes do"?

1. Bioluminescence - produce light through chemical reactions 2. Photosynthesis - ATP from light energy 3. Use weird molecules as food (sulfur, photons, nitrogen, waste) 5. Sense magnetic fields 5. Form biofilms

What are the 4 enzymatic methods of lowering Ea and what do they have in common?

1. Bring reactants together 2. Expose to altered environments 3. Change reactant shape 4. Use cofactors or coenzymes Relation: all increase unstability

Full Breakdown of Steps of Genetic Code Experiment in 7G:3U Ratio

1. Cell-Free translation system into 20 tubes 2. Add random synthetic mRNA polymers of G and U made via polynucleotide phosphorylase using 70% G and 30% U 3. In each of 20 tubes, add 1 radio labeled amino acid and 19 other normal amino acids 4. Incubate 60 min at body temp to allow cell-free translation 5. Add 15% trichloroacetic acid (TCA) to precipitate polypeptides but not amino acids 6. Filter solution from tubes so that amino acids go through and precipitated polypeptides are collected 7. Measure radioactivity on filtered precipitate and use to calculate amount of radio labeled amino acids as percentage 8. Resultant radio labeled amino acids must be encoded by combinations of G and U in this case; use probability to determine which likely to be which

What are the steps of Sporulation?

1. DNA Replication 2. 'Asymmetric' cell division where the plasma membrane divides the cell into two unequally-sized compartments inside of the cell wall. 3. Additional membranes form a forespore 4. Layers of calcium and dipicolinic acid form between layers of membrane forming a 'cortex' shell 5. A protein coat forms around the cortex 6. The bacterial cell degrades releasing the endospore

What are the goals of oxidative phosphorylation?

1. ETC - move electrons to final acceptor 2. Chemiosmosis - build proton motive gradient to create ATP

What is the process for light dependent reactions?

1. Energy from pigment molecules transferred with electrons form H2O splitting to chlorophyll a 2. Chlorophyll a oxidized and gives excited electrons to primary acceptor 3. Electron is passed from Plastoquinone (PQ) to Cytochrome Complex to Plastocyanin (PC) to Photosystems I (PS1) 4. Light Energy excited electrons in PS1 -> passed tp primary acceptor -> Ferredoxin -> final acceptor NADP+ -> NADPH 5. Protons pumped from stroma to lumen with energy released down ETC 6. Creates Proton Motive Force to drive ATP Synthase

What is the Epinephrine G-protein-coupled process?

1. Epinephrine -> G-protein receptor 2. GDP -> GTP + G-Protein 3. Activation of Adenylyl Cyclase (effector) 4. Effector catalyzes ATP to cAMP 5. CAMP activates protein kinase A (PK(A)) 6. PK(A) phosphorylates glycogen phosphorylase -> glycogen to glucose -> adrenaline response

What are 4 major ideas Mendel was credited with?

1. For each gene, organism inherits 1 allele from each parent 2. If individual's pair of genes are different, 1 allele is dominant to the other, which is recessive 3. Principle of Segregation - pair of alleles that Control a trait segregate as gametes are formed, and half of gametes carry each allele 4. Principle of Independent Assortment - alleles of genes segregate Independent during formation of the gametes (Randomness)

What are the steps of transcription?

1. Initiation - TF binds to promoter and recruit RNA polymerase; DNA unwinds, RNA polymerase begins Synthesis in 5'->3' direction 2. Elongation - RNA polymerase moves along DNA, extending RNA chain, behind the enzyme DNA returns to double helix 3. Termination in Prokaryotes - RNA polymerase reaches termination sequence and is removed, mRNA released to cytoplasm Termination in Eukaryotes - polyadenylation sequence transcribed into the RNA, proteins cleave RNA at this point

What are the steps of conjugation?

1. Physical contact between F+ and F- 2. Formation of Conjugation Bridge 3. Relaxosome Formation, separation of DNA strands transfer only one of them so both cells can become F+ 4. T DNA/Relaxosome complex recognized by coupling factor and molecular motor push/pull T DNA into F- cell 5. Replication of T DNA into double-stranded plasmid

What are the 4 "harmful things microbes can do"?

1. Produce toxins in bodies and environments 2. Invade or kill cells 3. Steal food 4. Cause immune responses

What are the mechanisms of correcting mistakes in DNA replication?

1. Proofreading by DNA Polymerase III - reduces error in E. Coli from about 1 in 1,000-10,000 to 1 in a million - recognizes 99% of errors 2. Mismatch Repair - occurs after proofreading, finding distortions in backbone from incorrect pairing (2 or 4 rings across instead of 3), marks them with cut (methyl group), and then uses polymerase I to remove and Ligase to stich back together - reduces error to 1 in billion 3. Pyrimidine Dimer (T-T or C-C) caused by UV damage after replication, results in senescent (G0) cell then apoptosis or else skin cancer / melanoma

What are the three categories of proteins required for basal transcription?

1. RNA Polymerase II 2. 5 General Transcription Factors (GTFs) 3. Protein Complex called the Mediator

What are the four major steps in the process of first messengers?

1. Reception of Ligand 2. Transduction (protein kinase activation, amplification, deactivation) 3. Response (phosphorylation of target protein) 4. Ending Response (endocytosis of signal into lysosomes)

What is the process of activation for internal steroid/hormone receptors?

1. Receptor begins in cytoplasm with 2 binding domains (signal binding and DNA binding) 2. Signal needs hydrophilic carrier protein to get through PM to receptor 3. Once ligand in cytoplasm, binds to signal binding domain 4. Ligand and receptor travel to nucleus, enter nucleus, and DNA binding region alters transcription through gene activation

How did Mendel accomplish cross-fertilization?

1. remove stamen/pollen from one flower to prevent "selfing" 2. paint pollen onto stigma from another plant

How do double crossovers play into using asci to determine linkage?

1/2 of double crossovers -> T 1/4 of double crossovers -> PD 1/4 of double crossovers -> NPD

Structure of P-Type Pumps

10 transmembrane alpha helices connected to 3 globular cytosolic domains: 1. Nucleotide-Binding Domain 2. Activator Domain 3. Phosphorylation Domain

How long are RNA primers?

10-12 nucleotides

How many nucleotides long on average is a single strand of a human chromosome?

100 million nucleotides

How many genes on average are in a chromosome?

1000 genes

What's the magnification limit for light microscopy?

1000-1500X

What is the magnification of the ocular lens on the microsocopes in lab?

10X (objective ones varied)

Which aneuploid trisomy are viable?

13 - Patau Syndrome 18 - Edward Syndrome 21 - Down syndrome

What is the structure of fatty acids? Their significance?

14-22 carbons, can be polar or nonpolar Extremely important signaling molecule (hence omega-3 craze)

How man enzymatic relaxations occur before oxidative phosphorylation?

18! 10 in glycolysis alone

How was lacI discovered experimentally?

1950s - Jacob and Monad and their colleague Arthur Pardee identified few rare mutant strains of bacteria with abnormal lactose adaptation, one of which involved defective lacI gene (denoted lacI-) that mapped very close to lac operon They found that this lacI- gene resulted in the constitutive expression of the lac operon with or without lactose

What was Experiment 11a? (Meselson and Stahl)

1958 Meselson and Stahl method to determine mechanism of DNA replication Grew E. coli in presence of 15N (heavy nitrogen) for many generations, switch to 14N medium, collect samples of cells at various times and analyze density of DNA by centrifugation using CsCl gradient

When was gene expression first identified?

1961 in prokaryotes with E. Coli and the lac operon

How many electrons are in the first 3 orbital shells?

1st: 2 2nd: 8 3rd: 8

What is the equation for the Krebs Cycle?

2 AcetylCoA + 6 NAD+ + 2 FAD + 2 ADP + 2 P --> 2 ATP + 4 CO2 + 2 FADH2 + 6 NADH + 2 CoA

What is generated per molecule of Acetyl-CoA in Kreb's cycle?

2 CO2 3 NADH 1 FADH2 1 ATP (double it for glucose)

What is the end product of Meiosis I?

2 haploid cells that contain non-identical sister chromatids Complicated because they are haploid since they have one copy of chromosome 2 cells with non-identical sister chromatids

What L value do we use in the cotransduciton formula for E. Coli (at least in the book)?

2 minutes because the assumption is made that it is 2% of the total E. Coli genome which is 100 minutes

What percentage of genes encode TFs in humans?

2-3%

What is Sarin Gas and how does it act?

26X more dearly than cyanide Lung paralysis in 1-10 minutes by acting as noncompetitive irreversible inhibitor so Acetylcholine Esterase cannot break down ACh and muscles can't relax

What is the structure of a nucleotide?

3 Main Parts: 1. Nitrogenous Base - Adenine, Guanine, Thymine, or Cystosine 2. Deoxyribose - pentose sugar that has lost oxygen group 3. Phosphate Group

How many base pairs are in total human haploid DNA?

3 billion base pairs

Role of ABC genes in plant development and what happens if they are all defective

3 classes of genes (A, B, C) govern formation of sepals, petals, stamens, and carpels (4th class has been found since that is required called SEP genes) through encoding TFs A,B,C all defective -> produces "flower" composed of leaves, the default

How do unfolded proteins in the ER stimulate their own correction?

3 parallel intracellular pathways -> stimulate nucleus to express genes to deal with them

How does the acceptor stem differ between tRNAs?

3' ACC acceptor stem found in all tRNAs (counterintuitive to specificity for amino acid binding)

What is antiparallel?

3' end of one strand is paired with 5' of paired strand Strands have polarity as a result

How many carbons are in monosaccharides?

3-7 carbons

What is glycerol structurally?

3-carbon nonpolar molecule

Difference in half-life of monomer association within treadmilling filament in vitro vs. in non-muscle vertebrate cell

30 min in vitro 30 seconds in non-muscle vertebrate cell

How much pigments and which ones do most chloroplasts contain?

300 chlorophyll and about 40 carotenoid

How is translation initiated in bacteria?

30S (small) subunit binds to mRNA facilitated by ribosomal-binding site AKA Shine-Dalgarno Sequence that is complementary to sequence in 16S rRNA The mRNA, Initiator tRNA, and ribosomal subunits associate to form an initiation complex

What is the efficiency of cellular respiration?

33%, rest lost as heat

What is the net ATP created per glucose molecule and per NADH/FADH2 (for this class)?

34 ATP total with 3 ATP per NADH and 2 ATP per FADH2 (for MCAT, 30-32 ATP for glucose, 2.5 per NADH, 1.5 per FADH2)

How does olfaction utilize GPCRs?

350 possible GPCRs for smells, each on their individual modified cilia of olfactory epithelium Various odorants activate specific combinations of them that allow distinguishing of much more than 350 smells Interaction with odorant stimulates cAMP cascade -> cAMP-gated cation channels cause influx of calcium cations -> depolarization

What are the measurements for the length of full DNA rotation, rise per base pair, and width?

36 Angstroms full rotation 3.4-3.6 Angstroms rise per base pair 20 Angstroms width

Which types of leukocytes extravasate into tissues? Integrin Defective Pathology?

4 Types of Leukocytes Exstravasate into tissues: Neutrophils Monocytes T and B Lymphocytes Human Leukocyte-Adhesion deficiency disease causd by defect in integrin Beta-2 synthesis causes susceptability to repeated bacaterial infections because leukocytes cannot extravasate properly

Speed and Diagram of Elongation/RNA Synthesis

43 Nucleotides per second

How many codons are there?

4^3 = 64, 61 sense and 3 nonsense

What is added at the 5' and 3' ends of pre-mRNA before it becomes mature mRNA?

5' cap - 7-methylguanosine cap that is applied as pre-mRNA is being synthesized by RNA Pol II and is only 20-25 bases long 3' poly A tail - String of adenine nucleotides added enzymatically after gene is completely transcribed

What is the purpose of the 5' cap?

5' cap - movement of some RNAs into cytoplasm, early stages of translation, splicing of introns

Which positions do wobble bases recognize in the codon?

5' wobble bases recognize 3' codon positions, allowing for multiple bases at the 3' position to encode for the same amino acid (redundancy)

In which direction are nucleotides added?

5'->3' direction

Which direction do ribosomes read mRNA molecules?

5'->3' direction (so be careful with this one!)

What ratio do cells maintain for F-actin/G-actin

50-50

Structure/mechanism/abundance of Nuclear Pore Complexes (NPCs)? What kind of molecules can be transported through them? Which sides are the nuclear basket and fibrils on?

500-1000 subunits of ~30 diff proteins spanning both membranes (transmembrane proteins spanning nuclear envelope and anchoring, scaffolding proteins, channel porins) 3-4K of them in typical cell Mechanism not fully understood, but the FG (residues) regions lining the pore provide selectivity They transports up to 1K molecules/second selectively, allowing <5kDa molecules to diffuse freely 5-60kDa molecuels - smaller = faster >60kDa require active transport

How many elements occur naturally? Synthesized?

98 naturally; 99-118 synthesized

How does this show that lac repressor is actually a repressor and not an activator?

???

Who was Mendel?

A Serendipitous Augustinian Monk who grew up in a farming family Founder of genetics Studied pea plants Found predictability 1822-1884

What are the 3 sites on a ribosome?

A Site - where tRNAs come into the mix with amino acids P Site - where polypeptide are added to the chain and where start methionine tRNA binds to start translation E Site - Empty site where tRNAs have already given up their amino acids and are released

What is binary fission?

A form of asexual reproduction in which the parent divides into two approximately equal parts

What is a tumor suppressor gene?

A gene that protects a cell from one step (often proliferation or growth) on the path to cancer

What is a proto-oncogene?

A gene that regulates cell division

What is the makeup of a triglyceride?

A glycerol and 3 fatty acids

Four ways of restricting lateral mobility of specific plasma membrane proteins

A. Self-Assembly into aggregates B. Macromolecular assembly outside of cell C. Macromolecular assembly inside of cell D. Cell Surface Interactions

What is differential interference contrast (DIC)?

AKA Nomarski optics Type of phase contrast that further enhances contrast by using two beams of light with different polarization, giving 3D appearance

What are multi-drug-resistant microbes?

AKA Superbugs Resistant to many and sometimes all antimicrobials

Define antigen-presenting cells

APCs - macrophages and dendritic phagocytes engulf and digest pathogens, then display their antigens via MHC II glycoproteins

How many H bond connections are between base pairs?

AT-2 GC-3 (cuz there's 3 good Clayburn's)

What are the three types of significant DNA sequences in the OriC?

AT-rich region - weaker bonds allow strand separation DnaA boxes - regions of specific sequences recognized by DnaA proteins GATC Methylation Sites

What creates ATP in oxidative phosphorylation and how?

ATP Synthase, a large channel membrane protein that uses the energy given off by the protons flowing down their proton gradient AKA proton motive force back into the matrix

How do chloroplasts and mitochondria work together in plants? Why is this necessary? How does this affect the placement of mitochondria/chloroplasts?

ATP and NADPH produced in chloroplasts cannot escape since inner chloroplast membrane is impermeable to them Only sugars are transported out and then stored as polysaccharides or used by mitochondria for cellular energy This separation is necessary to prevent futile cycling of intermediates within the chloroplasts Result is localization of mitochondria to regions near chloroplasts to optimize this transport

What is the mechanism of SNARE proteins? What does SNARE stand for? Types?

ATP hydrolysis coupled to conformational changes of these proteins facilitate the membranes being pulled into one another and all of the water forced out Hemifusion intermediate forms first when outer membrane leaflets form, then inner membrane leaflets form to complete process Soluble NSF Attachment protein REceptors vSNAREs - incoming Vesicle tSNAREs - Target membrane

Why do we call ATP the "energy currency" of the cell? What does it do for cells?

ATP is the energy currency because its breakdown into ADP and P fuels most anabolic reactions. It acts as a rechargeable battery in the cell

What is pathogenicity?

Ability of microbe to cause a disease

What is phosphorescence? Difference from fluorescence?

Ability of object to absorb energy and emit them later, i.e. glow in the dark Fluorescence is immediate transmission and when light is removed it immediately stops emitting, but phosphorescence is glow in the dark in that it will continue to emit without a light source Jellyfish fluoresce

What is the leading cause of chromosomal duplication? Result?

Abnormal events during recombination such as repetitive sequences causing misalignment between homologous chromosomes Result - non allelic homologous recombination

What is aneuploidy?

Abnormal number of chromosomes

Mechanism of inducers with repressors

Absence - repressor blocks transcription Presence - conformational change that inhibits ability of repressor protein to bind to DNA -> transcription proceeds

What is the difference between absorption, diffraction, refraction, and reflection?

Absorption - when light captured by material (can be reradiated after) Diffraction - light waves interact with material causing bending or scattering of some or all of waves Refraction - when light changes direction as it enters new medium Reflection - light bounces off surface

How are vesicles pinched off?

Accessory proteins such as dynamin form helical structures around the neck of the budding vesicles and utilize GTP hydrolysis to change conformation and constrict the neck until the two edges of membrane fuse and the vesicle blebs off as one distinct membrane

How are chromosomes numbered?

According to length (1 biggest, 22 smallest, last X-Y)

Why aren't there 61 tRNA molecules?

According to wobble hypothesis, the 5' base in the anticodon region of tRNA can recognize one or more codons in the 3' position of mRNA

Which happens first, acetylcholine CoA creation or NADH and FADH2 creation?

Acetylcholine CoA created first NADH and FADH2 created second align cycle

What is the structure and function of lysosomes?

Acid-filled vesicles Waste removal

What are acidophiles, neutrophiles, alkaliphiles, mesophiles, psychotrophs, psychorphiles, thermophiles, and hyperthermophiles?

Acidophiles - thrive in pH 1-5.5 Neutrophiles - thrive in pH 5.5-8.5 Alkaliphiles - thrive in pH 7.5-11.5 Mesophiles - thrive in 20-45 deg C Psychotrophs - thrive in 4-25 deg C Psychrophiles - thrive in 0-15 deg C Thermophiles - thrive in 50-80 deg C Hyperthermophiles - thrive in 80+ deg C

Difference in energy source of Actin vs. Tubulin

Actin - ATP Tubulin - GTP

How do the three types of filaments work together in the lining of the small intestines?

Actin microfilaments generate microvilla, stabilized by circumferential band of microfilaments below Intermediate filaments anchor to adhesive structures that connect adjacent epithelial cells into a sturdy sheet Microtubule run vertically to help provide a cellular GPS to move components to proper locations

Primary Role of Arps

Actin related proteins Structurally similar to actin (as shown); used to generate a plus end mimicking complex that stimulates chain growth as they become the minus end Pseudo-nucleation to drive polymerization Arp2/Arp3 form complex that is activated to form site of nucleation upon which plus end grows from

How does actin differ among eukaryotic species? What is the evolutionary significance of this?

Actins from different eukaryotic species are about 90% identical This means that the structure/function of actin is very critical, and variation was mostly non-viable

What are the two types of allosteric activity?

Activation - increases enzyme activity (i.e. oxygen and hemoglobin) Inhibition - feedback inhibition, down-regulation (i.e. strychnine)

Active vs. Passive Immunity

Active - adaptive immunity derived from activation of hosts own immune system Passive - transmission of adaptive immune response from another person or animal

What must happen in order for cellular respiration to proceed from the cytoplasm to the mitochondria? When does this occur?

Active transport into mitochondrial matrix Happens between glycolysis and pyruvate oxidation

What are acute, chronic, and latent diseases?

Acute - Rapid onset and relatively short duration of pathological changes (hours, days, few weeks) Chronic - Pathological changes happen over longer times (months, years, decades, entire life) Latent - Dormant pathogens with no replication, signs, or symptoms

Compare and Contrast Acute and Chronic Inflammation

Acute - short-lived; histamine-mediated (mast cells and other phagocytes); vasodilation and increased vascular permeability Chronic - When acute doesn't clear pathogens and long-term/chronic inflammation manifests; can cause many problems and waste resources

Define autoimmune disorder

Adaptive immune response to one's own cells i.e. celiac, diabetes I, MS

Are adaptive immune responses faster or slower than nonspecific immune responses

Adaptive response is much slower than nonspecific

What is the role adaptor proteins in vesicle formation?

Adaptor proteins interact with cargo proteins through signaling domains to aid in the recruitment of specific coat proteins They also act as Coincidence Detectors (detecting the coincidence that enough valuable cargo accumulates)

How can they be used to interpret the presence or absence of plaques in a lawn of cells infected with a virus?

Add known virus and patient serum in serial dilution like described above Count plaques

What is Alloploidy? Allodiploid? Allotetraploid? Allopolyploid?

Additional chromosomes as result of interspecies crosses Allodiploid - one set of chromosomes from two different species Allotetraploid - contains two complete sets of chromosomes from two different species Allopolyploid - combination of autopolyploidy and alloploidy

What does the outer layers beyond prokaryotic cell walls contain?

Additional protective layers: Glycocalyx - capsule and slime layer for adherence; protects against hose defense like phagocytes S-layer - contains proteoglycans, unknown function but believed to be related to protection

What are the components of ATP?

Adenosine (nucleotide base) Ribose (Sugar) 3 phosphate groups (negatively charged, high potential)

Describe adherens junction formation. What is the role of adherens junctions? Where do they form on the cell-cell interface?

Adherens junctions provide lateral stability between cells within a sheet and connection points for the cytoskeleton through cadherin interactions combined with microfilaments attached intracellularly Formation: Cis then Trans -CAM cis interactions form first, forming lateral clusters within the plasma membrane through cis interactions between cadherins on the same cell -Trans interactions then form intercellularly genearting strong, velcro-like adhesions between cells These trans and cis interactions are mutually reinforcing and form just below tight junctions but can also form puncta for specific interactions between cells

Bacterial Virulence Factors from class

Adhesins - pathogens make proteins, glycoproteins, lipoproteins, etc to facilitate adhesion to host or even particular cell type in host Exoenzymes Toxins Capsules to prevent digestion and phagocytosis Proteases to degrade antibodies Coagulase to cause blood clotting and distract host immune system

Viral Virulence Factors

Adhesins - spike proteins which allow vision to attach to proper host cells Antigenic Variation to affect immune recognition

What are the various types of energy generation in prokaryotic cells?

Aerobic - use oxygen to generate ATP Obligate Anaerobes - cannot tolerant or liver n presence of oxygen Facultative Anaerobes - can use oxygen when present or switch to anaerobic means Aerotolerant Anaerobes - do not perform any aerobic respiration but can live in presence of oxygen

How does glycolysis compare to the full oxidation of glucose energetically? How does this relate to mitochondria?

Aerobic provides about 15X energy of anaerobic Acquisition of mitochondria was essential to the development of complex life, as without it we could not fund (energetically) the complex processes required

Ultimate goal of steroid hormones generally and pathway

Affect gene transcription

How does fever help immune system rid body of pathogens?

Affects enzyme function and raises average kinetic energy of molecules May kill microbes that can't handle the heat like mesophiles

How is simultaneous contraction facilitated in muscle cells?

After Acetylcholine binds to muscle cell at NMJ and causes depolarization to initiate calcium release from SR, T-Tubules linking SRs surrounding myofibrils formed from invaginations of PM propagate this signal rapidly throughout muscle This leads to signal passing in milliseconds, and combined with the extremely brief period of time that myosin motors spend attached to actin, facilitates simultaneous contraction

GPCR Mechanism of Activation/Deactivation

After binding signaling molecule, receptor changes conformation and acts as GEF for G-Protein, releasing its GDP so a GTP can bind to it Resultant conformational change in alpha subunit of G protein causes it to dissociate from both the Beta-Gamma subunit and the receptor The rate at which the GTP bound to the active alpha subunit hydrolyzes to GDP is extremely slow, so after the signal is sent, RGS (regulator of G protein signaling) proteins act as GAPs to hydrolyze GTP and turn off the alpha subunit, causing reformation of the inactive GPCR complex (there are about 25 different RGS proteins in humans that can each act on various G proteins)

What were the results of experiment 11a?

After one generation, DNA half-heavy (support semiconservative and dispersive) After two generations, DNA is light and half-heavy -> must be semiconservative

Q Cycle Breakdown

All of this occurs through Complex III Process: 1. One QH2 (CoQ) comes in and Complex III splits its electrons, giving one through Fe-S to cytochrome C (which can only take one at a time) and the other through a fully oxidized Q 2. Another QH2 comes in, and Complex III again splits the electrons, giving one through Fe-S to cytochrome C again and the other to the semiquinone QH from step 1 to finish reducing it and recycling one total QH2 per two QH2 used Key Points: -Pumps total of 4 H+ into IMS, 2 in each step -per cycle, two QH2 oxidized and one Q reduced -Net oxidation of 1 CoQ and reduction of two cytochrome Cs (can only take one e- at at a time)

What types of organisms can take DNA -> RNA -> protein?

All organisms

What are proteoglycans and how are they synthesized?

All other GAGs are covalently linked to proteins Protein components of proteoglycans (core proteins) synthesized on membrane-bound ribosomes into ER Polysaccharide chains added to core proteins prior to delivery to extracellular space during transit through Golgi in addition to many mods like epimerization, sulfonation Linkage tetrasaccharides provide initial point for chain growth

Which direction do the myosin heads pull on actin, and how does this directionality lead to contraction?

All the heads pull toward the plus end of the actin filament, and the orientation of myosin heads in opposite directions in thick filaments allows this structure to shorten sarcomeres

Which of the aforementioned 3 domains of life are microbes found in?

All three

Differences in torpedo and allosteric model of transcriptional termination in eukaryotes?

Allosteric - Poly A sequence causes conformational change in RNA polymerase that reduces processivity Torpedo - RNase attaches to carboxyl end and degrades residual RNA till it reaches enzyme

What's the genetic advantage of allotetraploid as compared to allodiploid?

Allotetraploid has extra copies of everything (2 from each species), allowing it greater chance to be fertile than the allodiploid individual since it has Homologues that can pair up during meiosis

What is the purpose of eukaryotic multiple origins of replication?

Allow eukaryotic cells to replicate their long linear chromosomes in reasonable time period as compared to prokaryotic (much more to replicate)

What is the advantage of the additional steps of G-Protein receptors?

Allows additional specificity and requirements for activation

Structure/Function of respirasome/supercomplex

Allows minimization of ROS production and increased efficiency of ETC through aggregation of all the ETC complexes into single location

How universal is the genetic code?

Almost completely, same nucleotides linking to same amino acids across species

Mechanism of antisense RNA

Alternative method of regulating translation Antisense RNA is RNA strand complementary to mRNA that binds to create double-stranded mRNA to prevent translation initiation and ribosomal binding

How are G-bands numbered?

Always counting out from centromere

What is meant by genes being constitutive? What type of genes are constitutive?

Always on at same level; consistently expressed Essential genes are constitutive

How are DNA and RNA sequences written (directionally)?

Always written 5'->3' left to right

Why are metal-ion cofactors necessary in the ETCs?

Amino acid side chains are not capable of undergoing the type of redox reactions required for electron transport (except cysteine which can only undergo once)

How do proteins play into cellular respiration?

Amino acids contribute as pyruvate molecules, acetyl groups, and intermediates in citric acid/Krebs cycle

How are tRNAs charged? Error rate?

Aminoacyl-tRNA Synthetases specific to each amino acid catalyze a two-step reaction between the amino acid, tRNA, and ATP Error rate less than 1 in 10,000

Define heritability

Amount of phenotypic variation within a group of individuals that is due to genetic variation

What is Chargaff's rule?

Amount of pyrimidines matches amount of purines -> base pairing

Sterols

Amphipathic Nonpolar carbon rings with nonpolar side chain at one end and single polar -OH group at the other end

What are detergents and their significance for membranes?

Amphipathic molecules that are much more solubles in water than lipids and have polar groups that can be charged or uncharged When they reach critical micelle concentration, the hydrophobic ends with with membrane proteins and displace lipid molecules with a collar of detergent molecules, bringing the membrane proteins into solution as detergent-protein complexes with some attached lipids, and allowing isolation of NON-denatured proteins from membrane (SDS PAGE)

What is the Nuclear matrix? Role of radial loops attachment to nuclear matrix?

Anchors chromosomes to regions (see picture) Composed of two parts: Nuclear Lamina - 30 nm fibers that line inner nuclear membrane Internal Matrix Proteins - connect to nuclear lamina and fill interior of nucleus Role of radial loops attachment to nuclear matrix is compaction and organization

What are the two regions of photosystems and their purposes?

Antenna Complexes - light-harvesting regions with high numbers of chlorophyll molecules that allow frequent excitation and a source of high energy electrons Reaction Center - Receives energy from antenna complexes via resonance energy transfer to special pair, allowing splitting of water and sending down ETC

Structure of IgG Antibody

Antibody AKA Immunoglobins Have 4 polypeptide chains held together by disulfide bonds (2 heavy, 2 light)

Process of neutralization

Antibody binds to pathogen antigen, preventing it form attaching to target cells Facilitate phagocytosis by marking cells

What are antiseptics?

Antimicrobial agents safe for use on living skin or tissues

What is a somatic cell?

Any cell other than reproductive cell

Sodium glucose cotransport mechanism

Any system in which any molecule moves against its gradient = active transport

What is matter?

Anything that has mass and takes up space

Apical and Basal Lamina

Apical - faces lumen / external environment Basal - attachment and holding together to basement membrane that separates from connective tissues; anchored side

What are apoenzymes and holoenzymes?

Apoenzymes - inactive enzymes without their cofactors/coenzymes Holoenzymes - active enzymes with cofactor/coenzyme

What happens if a cell is tagged at one of the checkpoints?

Apoptosis - Programmed cell death

Apoptosis vs. Necrosis

Apoptosis - programmed/regulated cell death in which cells form membrane-enclosed apoptotic bodies and then are consumed by macrophages or neighboring cells Necrosis - cell death in response to acute insult (damage) in which cell spills contents into neighbors resulting in inflammation

How large is the open complex that moves along in elongation?

Approximately 17 bases long

How does age relate to Down's syndrome?

As woman ages, her primary oocytes (produced in ovary of female fetus prior to birth, arrested in prophase of meiosis I until time of ovulation) have been arrested in prophase I for a progressively longer period of time Added length of time may contribute to increased frequency of nondisjunction Paternal non-disjunction causes Down syndrome 5% of the time

What is scurvy and its mechanism of action?

Ascorbic Acid (Vitamin C) deficiency that causes defects in pro-alpha chains hydroxylation -> prevents stabilizing of triple-helical procollagen This is because a one-and-done enzyme make hydroxyproline, and vitamin C is required to regenerate it or it cannot be re-used

What is the Prereplicaiton Complex (preRC)

Assembled in eukaryotes to begin replication includes Origin Recognition Complex (ORC), MCM Helicase

Spectrum of Membrane Permeability of Varied Substances

Assuming Simple Diffusion

What is the second most common mechanism for activation upon signaling binding for RTKs?

Asymmetric Dimerization - EGF binds two previously inactive monomers and brings them together, but instead of trans-autophosphorylation, activator pushes on receiver causing the receiver to phosphorylate the activator and then itself

What is Catenation?

At end of DNA replication sometimes catenanes, or intertwined circular molecules of DNA, form, and topoisomerase II has to introduce temporary cuts and unwind them

What are the types of collagen found in the ECM? How are they different in structure and function? What structures would you find each type in?

At least 40 collagen alpha chains that are theoretically capable of multimerizing in a variety of different conditions but only a small combination are physiologically existent or relevant Fibril-forming collagen -> structural support Fibril-associated collagen -> lateral associations Network-forming and Transmembrane Collagen -> basal lamina and cell anchoring

Mechanism of Autophagy (5 Steps)

Autophagy = self-eating 1. Induction by Activation of signaling molecules 2. Nucleation and extension of double membrane around target organelles 3. Closure of double membrane complex to form autophagosome 4. Fusion of the autophagosome with lysosomes utilizing SNAREs 5. Digestion of inner membrane and lumenal contents

What are bacteremia, viremia, toxemia, septicemia?

Bacteremia - presence of bacteria in blood Viremia - presence of visions in blood Toxemia - presence of toxins in blood Septicemia - bacteria present AND reproducing in blood (patients are "septic")

What is the process of translation elongation? Rate in eukaryotes and bacteria? Where does peptidyltransferase act?

Bacteria - 15-20 amino acids per second Eukaryotes - 2-6 amino acids per second Peptidyltransferase catalyzes bond formation between the polypeptide in the P-site and the amino acid in the A site, transferring the polypeptide toe the A site BEFORE it is moved over to the P site

What are the two divisions of prokaryotes?

Bacteria and Archaea

What two kingdoms make up prokaryotes?

Bacteria and Archaea

What is the process of transduction in bacteria?

Bacteria are infected by a bacteriophage virus DNA is transferred from virus to bacteria Results in new Recombinants

What is the process of conjugation in bacteria?

Bacteria contact each other with sex pilus Form cytoplasmic bridge Copy of donor DNA moves to recipient Donor DNA pairs with homologous regions in the recipient

How do bacteria and archaea differ?

Bacteria have peptidoglycan in their cell walls while archaea do not Archaea also tend to be found in more extreme environments, though bacteria are also found everywhere Archaea are also always non-pathogenic while bacteria are only usually non-pathogenic

What is the process of transformation in bacteria?

Bacteria take up pieces of DNA that are released as other bacterial cells disintegrate (can happen in lab or nature settings)

What is the study of bacteria? study of fungi? protozoa? parasites like helminths? viruses?

Bacteriology Mycology Protozoology Parasitology Virology

What are some considerations when choosing bactericidal vs. bacteriostatic?

Bacteriostatic is the reversible inhibition of bacterial growth, ideally allowing maintenance of healthy microbiome, ideal when patient has healthy immune system Bactericidal is sometimes required when patient is immunocompromised and is faster acting but can leave patient susceptible to superinfection

3 Categories of chemical mutagens

Base Modifiers - covalent modification or alkylation of bases Intercalating Agents - directly interfere with replication process Base Analogues - incorporate into DNA and disrupt structure; often tautomerize at high rate

Role of Basophils

Basophils - contain histamine in granules; involved in inflammation and allergic response; open gaps between cells of blood vessels during inflammation

What are the three families of Bcl2 related proteins and specifics within them? What are their roles in apoptosis?

Bcl2 Family - regulators of intracellular initiation of apoptosis that act by control of cytochrome c release Three Classes: -Anti-Apoptotic (Bcl2, BclX) - located in OMM and interact with effector Bcl2 proteins to prevent aggregation -Prop-Apoptotic Effectors (Bax, Bak) - when activated, aggregate in OMM to form pores for cytochrome c to escape IMS triggering apoptosome formation -Pro-Apoptotic BH3-Only (Bad, Bim, Bid, Puma, Noxa) - bind anti-apoptotic Bcl2 proteins and prevent their interaction with effector Bcl2 proteins

What chemical indicator test identifies simple carbs?

Benedict's Solution Orange positive Blue negative

Beneficial vs. Deleterious Mutation and Influences on which

Beneficial - enhance survival or reproductive success Deleterious - decrease chances of survival Environment can affect whether given mutation is deleterious or beneficial

What is the clamp protein? Clamp loader?

Beta subunit of DNA Pol III that forms a dimer with itself in the shape of a ring around template DNA, promoting association with the DNA Clamp loader is complex of several subunits that function to set it up

Vesicles, Micelles, Bilayer Sheets, and Bicelles

Bicelles useful in makeup

How do the membrane leaflets (inner and outer) differ?

Bilayer is aymmetric Some lipids preferably found inside, others outside Carbohydrate moieties always outside Membrane Polarization (outer leaflet more positively charged)

How do heavy metals control microbes?

Bind to and denature proteins little goes a long way e.g. Hg, Ag, Cu, Ni, Zn

What is the role of small effector molecules in transcription regulation?

Bind to regulatory proteins but not to DNA directly Types: Inducers - Increase transcription by binding activators and causing them to bind to DNA or binding repressors and preventing them Corepressors - Inhibit transcription by binding to repressors and causing them to bind to DNA or binding to activators and preventing

How does DNA replication licensing work?

Binding of MCM to preRC completes licensing, allowing licensed origins to begin DNA synthesis

What are the remaining steps in transcription initiation?

Binding of RNA polymerase to promoter forms Closed Complex Open Complex formed when TATA box in -10 region is unwound Short RNA strand made within the open complex and then sigma factor releases, marking end of transcription

Define cross-reactivity

Binding of antibody with multiple antigens with similar properties

What is the role of the promoter in gene expression?

Binds RNA polymerase to transcribe lac genes

What is the role of the operator in gene expression?

Binds depressors and activators to prevent or assist binding of RNA polymerase and expression of lac genes

What is the function of the trp repressor?

Binds to tryptophan High tryptophan -> repressor bound to tryptophan (acting as corepressor) and DNA -> Decreases transcription Low Tryptophan -> no tryptophan bound -> dissociates from DNA -> increases transcription

What is the difference between the two subtypes of indirect viral transmission?

Biological - virus gets inside vector and is transmitted wen vector bites host Mechanical Transmission - virus on outside of vector and falls onto new host

How long are human telomeres at bitch compared to elderly?

Birth ~ 8000 bp Elderly ~ 1500 bp

What chemical indicator test identifies proteins?

Biuret's Solution (copper sulfate and sodium hydroxide) Violet Positive Blue negative

Hyponatremia

Blood becomes hypotonic from either low sodium or ingestion of hypotonic solution like water -> lysis of tons of red blood cells Death from drinking too much water is because of this (hold your wii for a wii)

How does EPO (erythropoietin) act?

Blood doping agent - increases red blood cells which increases oxygen carrying capacity thus producing more ATP and empowering patient Side effect - blood clotting

Define fever and describe role of pyrogens and hypothalamus in its generation

Body-Wide Inflammatory Response of Increased Body Temperature Pyrogens - released by some viruses and bacteria to cause body to increase body temp set-point Hypothalamus - homeostasis

Are transcription factors used in prokaryotes or eukaryotes?

Both

What is the difference between Fimbriae and Pili?

Both filamentous proteins protruding from cell surface Fimbriae - short, numerous, for cell attachment to host cells Pili - longer, less numerous, aid in attachment to fellow bacteria for transferring genetic material

What are the differences in the abilities of DNA Polymerases I and III?

Both have 5'->3' direction polymerization I - 5'->3' exonuclease ability (removing RNA primers and replacing with DNA) III - 3'->5' exonuclease ability (back-up ability to proofread)

Describe two similarities between transmission electron microscopy and scanning electron microscopy.

Both involve a beam of electrons Both require the imaging to be done in a vacuum with a completely dehydrated specimen

What is the difference between latent and chronic infections?

Both persistent, but latent remains dormant without causing symptoms and chronic remains active constantly causing symptoms

Two types of genetic drift

Bottleneck Effect - population reduced dramatically in size by natural disaster and elimination is random Founder Effect - small group establishes new colony in new location

What is beta-galactosidase?

Breaks down lactose to inducer Allolactose

What are the "nicks" referred to in DNA replication?

Breaks in the sugar-phosphate backbone that remain between newly synthesized Okazaki fragments before being sealed by DNA Ligase

What is true-breeding?

Breeding with pure-bred, homozygous alleles for all genes organisms that Mendel lucked into

What is a cytoplasmic bridge?

Bridge connecting bacteria in conjugation that allow them to exchange DNA

How do sphingolipids differ from phospholipids?

Built from sphingosine rather than glycerol Sphingosine does not have any O sites for esterification of fatty acid tails - it has directly attached fatty acid chain, an additional unused OH group on the opposite side, and an amine that can form an amide bond with a fatty acid tail

How were the multiple origins of replication discovered?

By Huberman and Riggs

How are transport vesicles guided to their target membranes?

By Rab proteins

How is RNA editing accomplished?

By changing one type of base to another through processes like deamination

How is directionality of integration into the ER membrane achieved?

By charges on the start transfer sequences Which terminus (c or n) and the charges on the ends of the protein determine how it is placed within the membrane

How and why can polyploidy be induced?

By introducing chemicals like colchicine to bind to tubulin (spindle apparatus protein) to promote nondisjunction or by using abrupt temperature changes Study and use of plants

What does C4 and CAM plants do?

C4 uses alternative way to make ATP since it gan't get it from photorespiration pathway CAM plants avoid photorespiration in first place by only doing light dependent in day and light independent at night

What is the typical trinucleotide repeat and how does this contribute to the disease?

CAG (glutamine, so encoded protein contains long tracks of glutamine that causes aggregation to one another leading to disease) (Huntington's -> aggregated plaques of protein in brain)

What is another way (other than morphogens) that cells receive positional information?

CAMs (cell adhesion molecules)

What happens when the stomata build up oxygen from staying closed?

CO2 and O2 constantly compete for Rubsico's fixing, so whichever is present in greater concentration gets fixed by Rubisco When oxygen -> toxic product phosphoglycolate produced, and plant gets rid of it only way it can, by mixing and releasing with CO2, which in tern causes more loss of carbon and makes original O2 problem worse

What are cis and trans interactions in the context of cadherin binding? What type of other cahderins to cadherins bind to? What is strand swapping and how is it related to cadherin interactions?

Cadherin groups have protruding and interlocking segments that facilitate binding between cadherins on opposing cells (trans binding) Cis binding also occurs via specific interactions between EC1 and EC2 domains that allows for aggregation of cadherins into junction structures Cadherins almost exclusively bind to other cadherins of the same type STRAND SWAPPING????? Guessing from picture/class referring to mention of trans interaction in which strands wind around one another to facilitate interaction

How does caffeine affect the epinephrine pathway?

Caffeine inhibits phosphodiesterase, allowing continuation of glycogen release and thus glucose stimulation while caffeine remains in sufficient quantity to keep acting as inhibitor

Role/Purpose of calcium in nuclear transport? Example with T Cells?

Calcium and other methods can be used to selectively expose/hide signals depending on roles of cell In the case of T-cells, NF-AT (nuclear factor of activated T-cells) are typically phosphorylated in the resting state, allowing its export to the cytosol. However, when they are activated by a foreign antigen, resulting increased calcium concentration in the cell facilitates a phosphatase to dephosphorylate NF-AT, blocking the nuclear export signal and exposing the import signal so that it can move into the nucleus and activate the appropriate gene transcription

What is the light independent reaction?

Calvin cycle in which carbons are fixed to a carbohydrate

What are the major features of fungi?

Can be pathogenic, medically beneficial, and environmentally important Wide variety of reproductive means including sexual and asexual

Result of genetic defects of Filamin proteins

Can result in nerve cell migration defects -> Periventricular Heterotopia: Condition in which nerve cells fail to migrate, leading to neuron-depleted spaces in brain causing things like epilepsy Remarkably, little affect on overall intelligence!

What are the side effects of the loss of carbon in phosphorespiration?

Can't fix carbon Can't make glucose Can't run CR and thus cannot make ATP

What accessory proteins make up the Z-disc?

CapZ and Alpha-Actinin to anchor actin

Roles of CapZ and Tropomodulin

Capping proteins CapZ - binds to plus end of actin, stabilizing it and allowing only polymerization at minus end; if used on Arp2/3 nucleated filament, accomplishes capping at both ends Tropomodulin - binds at minus end in combination with tropomyosin to create especially long-lived muscle actin filaments

What is the most naturally-abundant molecule?

Carbohydrates

Which ends of the polypeptide chain are amino acids added to?

Carboxyl group (C-terminus) of growing chain is bonded to amino group (N-terminus) of incoming chain (Read 5'->3', Synthesized N-terminus to C-terminus)

Define analytical epidemiology and contrast retrospective and prospective analytical epidemiological studies

Carefully gathering data and random to test hypotheses about causes of outbreaks Retrospective - gather data from past to inform present Prospective - gather data from present time

What is the mechanism of clathrin vesicle formation?

Cargo receptors in the donor membrane bind cargo to signal the need for budding They cytosolic domain of said cargo receptors then binds adaptor proteins as they bud A Clathrin Triskelion then forms around the adaptor proteins to bend the membrane and form the vesicle After vesicle formation, the clathrin dissociates

What is Linnaean taxonomy?

Carolus Linnaeus (1701-1778) proposed system for organizing, describing, and naming organisms by dividing into animal, plant, and mineral kingdoms and developing class, order, family, genus species

GPCR-cAMP mechanism

Case shown is adenylyl cyclase activator, but same effect could be achieved through cAMP phosphodiesterase inhibitor Mechanism involves signaling molecule, 2nd messengers, effectors, and intracellular proteins (PKA) which are NOT 2nd messengers

What is the other way (than lac repressor) for regulating lac operon?

Catabolite Repression through CAP site used as E. coli is using glucose first since it is more efficient energy

How does DNA polymerase add nucleotides?

Catalyzes formation of ester bonds between innermost phosphate group of incoming nucleotide and 3' hydroxyl group of sugar using power source of nucleotide triphosphate and releasing pyrophosphate (PPi) byproduct

Catabolism vs. Anabolism Mnemonic

Cats break stuff by knocking it down Anabolism Assemble

Diseases related to NER mutations

Causes various syndromes with common characteristic of increased sensitivity to sunlight and inability to remove thymine dimer

Types of connections between cells and between cell and ECM

Cell-Cell - mediated by cell-adhesion molecules (CAMs) Cell-Matrix - Adhesion Receptors

What is the central dogma of biology? In what ways is it correct and incorrect?

Central dogma is information flow goes from DNA -> RNA -> protein Correct in that this is generally what occurs Inconsistencies: 1. 1 gene -> 1 polypeptide 2. Reverse Transcriptase can take RNA and transcribe it back into complimentary DNA (used by HIV) 3. RNA Viruses exist like SARS, Influenza, and Measles 4. Non-coding RNA -> rRNA Epigenetics - same DNA can be modified to get different phenotypes

What is a polyribosome complex?

Chain of ribosomes that act on a single mRNA as they are directed to form a chain of ribosomes on rER by SRPs Free ribosomes can also form these, allowing ribosomes to cycle between free cycle and membrane-bound depending on which mRNA they bind

Plasmodesmata

Channels through cell walls that connect the cytoplasms of adjacent cells Only in plant cells

What are chemokine and interferons?

Chemokine - special cytokine which signals for activation of adaptive immune response by attracting immune cells Interferons - released by cells to signal need for immune response and to let nearby cells know to protect themselves

What are the types of bacterial movement?

Chemotaxis - movement towards or away from chemical cue Magnetotaxis - movement towards or away from or along magnetic field Phototaxis - movement towards or away from sources of light

What is cystic fibrosis?

Chloride channel mutation caused by excess mucous that leads to inability of lungs to maintain necessary elasticity and expand. Recessive inherited disease

What are the types of pigment molecules in photosystems?

Chlorophyll Pigments - absorbs blue/red strongly Carotenoid - absorbs violet to green strongly Chlorophyll A - absorbs most all wavelengths

How is chlorophyll a different than carotenoid and chlorophyll?

Chlorophyll a is the primary source of excited electrons, located in the reaction center. The antenna complex around the reaction center is filled with chlorophyll and carotenoid. The photons of light are absorbed in the antenna complex by those molecules, bounced around in resonance, then when have right energy are absorbed in reaction center by chlorophyll a along with electrons from water splitting and sent to the ETC through primary electron acceptor

Structure/Function of Chlorophyll

Chlorophyll contains a highly conjugated porphyrin ring complexing magnesium to allow closer energy states between electron excitation levels so that they can be excited by lower energy photons of light (680 nm, or red light) They also have a hydrophobic tail region

How do ETCs within the mitochondria and chloroplasts differ in structure/location of pumping?

Chloroplasts have more compartments within them Within chloroplasts are thylakoids, and they have the membranes in which ETC proteins are located. The pumping direction is from the chloroplast stroma into the thylakoid spaces

What is ChIP-Seq? Mechanism?

Chromatin Immunoprecipitaiton Sequencing Method of determining location of nucleosomes, where histone variants found, and where covalent mods occur Can be applied to any DNA-binding protein, not just histones

Mucus Transportation Mechanisms

Ciliate epithelial cells Mucociliary Escalator moves pathogen-trapping mucus up respiratory tract and either down digestive tract or expulsion follows

What is the nucleoid of a prokaryotic cell?

Circular ring of genetic material

What are the compartments/structure of the Golgi?

Cis Golgi - entry face closest to ER/nucleus Trans Golgi - Exit face closest to plasma membrane Cisternae - series of flattened membrane enclosed compartments that make up Golgi Golgis usually consist of 4-6 stacks of cisternae but can get up to 20 depending on organism

How would we allow Cl- through a membrane but block Na+? Glucose through, block Cl-? Na+ through, block Ca2+? K+ through, block Na+?

Cl-, no Na+: use positive residues Glucose, no Cl-: Use negative/polar residues Na+, no Ca2+: Make too small for Ca to get through K+, no Na+: Have to use specificity of size utilizing solvation shell (since K+ bigger than Na+, so can't just go by too small for the other)

How are MHC II receptors involved in antigen-presenting cellular processes?

Class II MHC bind to fragments of exogenous antigens that are then recognized by specific Helper T cells that proliferate once they bind to their target

What are the two distinct mechanisms of pinocytosis and how often does this occur?

Clathrin-Dependent and Calveolin-Dependent Calveolin are different in that they form from lipid rafts, and they are static for most of their life cycles, forming vesicles that just remain within the lipid rafts and must be induced to bud off Clathrin coated vesicles are much more transient and also more common as they are constantly forming 1-3% of the PM is endocytosed every minute

How are channels in tight junctions created and why?

Claudin proteins can create channels through which ions can pass depending on tissue requirements

What is sanitation?

Cleansing formites to remove enough microbes to achieve levels safe for public health

What are coating proteins? 3 Main types and their roles?

Coatings are regions of specific protein aggregation that cause conformational changes to properties of regions of membrane to facilitate responses like budding Clathrin - transport between plasma membrane and endosomal/Golgi COPI - transport FROM golgi COPII - transport FROM ER (because ER has two letters)

What are antisense codons?

Codons that do NOT code for an amino acid but instead are a stop signal - there are 3 of them: UAG, UAA, UGA and NO tRNA is associated with these

Do the given genetic code sequences like AUG start refer to codons for associated amino acids or anticodons?

Codons, be careful!

What is the difference between cofactors and coenzymes?

Cofactors - inorganic molecules like magnesium Coenzymes - organic molecules

What are cofactors and coenzymes? What do they do?

Cofactors - nonprotein components of enzymes that contribute to enzyme function Coenzymes - organic cofactors Cofactors help the reactants fit better and coenzymes can do further catalyzation with additional active site as well.

What is colinearity and how does it apply to eukaryotic and prokaryotic transcription?

Colinearity - Coding strand of DNA identical to sequence of mRNA Prokaryotes - exhibit colinearity Eukaryotes - don't because of Introns and RNA splicing

What are transcription factors?

Collection of proteins and enzymes that bind to promoter region and recruits RNA polymerase

What is the microbiome?

Combination of resident and transient prokaryotic and eukaryotic microorganisms associated with an organism

Does RNA splicing occur in prokaryotes?

Common in eukaryotes, very rare in prokaryotes

What is the difference between communicable and contagious infectious disease?

Communicable - spreadable between hosts (directly or indirectly) Contagious - EASILY spread between hosts

What is the 30nm fiber? Theoretical models?

Compact structure of nucleosomes that shortens total length of DNA another 7-fold through its compaction

What is the phenol coefficient method of testing effectiveness of antiseptics and disinfectants?

Compare effectiveness to that of phenol

What are competent cells? Competence factors?

Competent Cells - cells capable of accepting DNA through transformation Competence Factors - genes that encode proteins allowing for DNA uptake

What is the difference between competitive and non-competitive inhibition?

Competitive inhibition - another molecule binds the same receptor active site to prevent substrate from bonding Noncompetitive Inhibition - another molecule binds to another site on molecule to allosterically prevent the target molecule from binding

Significance of complementary regions in mRNA for attenuation. trp Regions

Complementary regions allow the formation of stem loops between different segments of the mRNA to either prevent or allow attenuation In trp operon, region 2 is complementary to 1 and 3, but cannot bind to both simultaneously When 3-4 bound, allows U-rich attenuator sequence to attenuate, but when 3-4 cannot bind (because 2-3 bound), cannot attenuate transcription

Define Sterilization

Complete removal or killing of all vegetative cells, endospores, and viruses from an item or an environment Difficult and expensive to achieve

Mitochondrial ETC Breakdown

Complex 1 - NADH Dehydrogenase - huge complex that accepts from NADH, passes through Fe-S clusters to CoQ, and pumps 4 H+ into IMS Complex 2 - Succinate Dehydrogenase, oxidizes succinate to fumarate to reduce FAD to FADH2 inside the complex, then those electrons passed to CoQ as well with NO pumping of e- Complex 3 - Cytochrome Reductase - accepts electrons from CoQ and passes them onto soluble cytochrome C Complex 4 - Cytochrome Oxidase - accepts electrons one at a time from cytochrome c and passes them onto O2, generating H2O

What is the primosome?

Complex of DNA helicase and primase that coordinates their actions

What are Hox Genes?

Complexes of adjacent homeotic genes in vertebrates are homologous to those in the fruit fly

What makes up the basal lamina? Functions?

Composed of four ubiquitous highly conserved components that each contain multiple distinct repeating domains -Type IV Collagen and Laminin each form 2D networks -Nidogen/Entactin and Perlecan molecules crosslink basal lamina networks Functions include: -organizing cells into tissues and distinct compartments -protecting cells -repairing tissues -forming permeability barriers -guiding migrating cells during development One side is linked to cells by adhesion receptors including hemidesmosome integrins that bind to laminin in the basal lamina The other side is anchored to adjacent connective tissue by a layer of collagen fibers embedded in a proteoglycan-rich matrix

Spliceosome

Composed of subunits known as snRNPs (small nuclear RNA and a set of proteins) that bind to intron sequence, precisely recognize intron-exon boundaries, hold pre-mRNA in correct configuration, catalyze chemical reactions that remove introns and covalently link exons

What is a histone octamer?

Composition of two copies of each of four different histone proteins (H2A, H2B, H3, and H4)

What is the difference in effects of a convex and concave lens?

Concave - expands image by divergence Convex - focuses light to single point and can be used to magnify by producing larger image

What is the Critical Concentration (Cc) and how is it calculated? How is it affected by adjusting the initial concentration?

Concentration of G-actin at which steady-state is reached Changes to initial concentration of actin only changes average length, but not Cc Cc=koff/kon = ~0.2uM for a solution containing only actin

What is the purpose of the following microscope parts: condenser iris diaphragm

Condenser - lens beneath specimen that focuses light from the light source to a point on the specimen Iris Diaphragm - opens and closes size of beam of light coming through condenser

What are the roles of Condensin and Cohesin? (both individually and collectively)

Condensin - Chromsomes condensation; in cytoplasm during interphase, then travels to nucleus to bind to chromosome and compact radial loop Cohesin - Sister chromatid alignment Combined Role - Use their Strucal Maintenance of Chromosome (SMC) proteins and energy form ATP to catalyze changes in chromosome structure

How are K+ channels gated?

Conformational change induced by binding of accessory proteins

What are the three types of genetic transmission?

Conjugation (physical transfer) Transduction (viral transfer) Transformation (mobile genetic info)

What proteins make up gap junctions? What are the role of gap junctions in the cell? Pathology? Structure? Sensitivity?

Connexins (coded by 21 human connexin genes) facilitate tissue-dependent gap junctions They allow small molecules to pass directly between cytosol of adjacent cells Mutations can cause at least 8 diseases including nuerosensory deafness, cataracts, heart malformations, C-linked Charcot-Marie-Tooth disease (progressive degeneration of peripheral nerves) Structurally six dumbell-shaped connexin molecules from hemichannels on each membrane, and must connect with another hemichannel to open Sensitive to environmental changes such as pH, calcium concentration, potential, etc.

What are constitutive and alternative exons?

Constitutive - always found in mature mRNA from all cell types Alternative - vary from one cell to another and subtly change function of protein to meet needs of cell type

Difference between the constitutive and regulated secretory pathways

Constitutive - operates continuously in all cells Regulated - mainly in specialized secretory cells - useful for rapid secretion of things like hormones, NTs, and digestive enzymes Main Difference in constitutive vs. regulated secretory is constitutive automatically exported when hit PM, regulated has to wait for signal

What are the two types of heterochromatin?

Constitutive Heterochromatin - Always heterochromatic, permanently inactive transcriptionally and usually highly repetitive Facultative Heterochromatin - Interconverts between euchromatin and heterochromatin

Four general forms of extracellular signaling

Contact Dependent - who are my neighbors? Paracrine - What are my neighbors doing and how are they? Synaptic - Nerve specific Endocrine - What's going on in the world? Systemic info for all

Define and briefly describe contact, vehicle, and vector transmissions of infections

Contact Transmission - direct/indirect contact of infected hosts and soon-to-be-infected individuals involving body fluids, environmental liquids, formites Vehicle Transmission - transmission of pathogens through "vehicles" (non-biological or living objects or substances suitable to spread such as water, food, air) Vector Transmissions - Transmission via biological intermediate like insects

What is unique about mitochondria compared to other organelles?

Contain their own DNA similar to bacterial genome (may have developed from bacteria)

Amphipathic

Containing hydrophobic and hydrophilic regions

What is the difference between continuous and discontinuous replication?

Continuous replication refers to the faster replication on the leading strand that continues in the direction of the unwinding Discontinuous replication refers to the slower replication that moves away from the unwinding direction and thus must constantly create fragments to be later brought together by DNA Ligase

What are the various arrays that actin organizes into and how are they established?

Contractile Bundle of anti-parallel strands or tight bundles of parallel strands by bundling proteins cross-linking Dendritic networks by Arp2/Arp3 proteins permitting angular reactions Gel-like loose meshwork facilitated by gel-forming proteins holding actin filaments together at large angles

What is the Random Mutations Theory?

Contrast to physiological adaptation proposal of genetic variation all being due to random chance Natural Selection -> better-adapted organisms

What is combinatorial control with TFs? Methods?

Control of transcription through multiple players Methods Include: -Multiple activators/repressors -Binding of small effector molecules -Protein-Protein interactions -Covalent Modifications -Altering of nucleosomes near promoter -DNA methylation inhibition of transcription by prevention of activator protein binding or recruitment of proteins for compaction -Various combinations of the above methods

What is the role of glucose and galactose in the lac operon?

Control the amount of the lac genes expressed (presence leads to less expression, lack of them leads to much more expression of lac operon)

How are homeotic genes regulated?

Controlled by gap and pair-rule genes, interactions between different homeotic genes and other genes

What is the function of the cytoskeleton?

Controls movement Controls intracellular traffic Shape and support

How is caspase-9 accidental runaway apoptosis activation prevented?

Conversion to active form by reversible dimerization is used instead of irreversible proteolytic cleavage

What are the various types of symbiosis?

Cooperative - one food or raw material for another (i.e. nitrogen-fixing bacteria for plants) Commensalism - waste of one is food or raw material for another (one indifferent other benefits) Parasitism - one harmed one benefits

What are basal transcription, core promoter, and regulatory elements of eukaryotic transcription?

Core Promoter - relatively short promoter consisting of TATA box and transcriptional start site Basal Transcription - transcription only under regulation of core promoter Regulatory Sequences - more complex (than prokaryotic) system of regulators to control rate of transcription

What is the order of electromagnetic waves from greatest to lowest energy?

Cosmic radiation > gamma rays > X-Rays > UV > Visible > Infrared > Radar > Radio > AC Circuits

What is the importance of coupling reactions? In the case of ATP?

Coupling reactions are important because they allow exergonic reactions to fuel endergonic reactions. In the case of ATP, the exergonic reaction of ATP breaking down into ADP + P fuels many critical biological reactions and is the primary cellular energy source

What is the difference between a cross and a reciprocal cross?

Cross = between two phenotypes Reciprocal cross = successive cross between same two phenotypes with male/female switched

What is a monohybrid cross?

Cross of 2 HT for one gene Results: phenotypic ratio of 3:1 and genotype ratio of 1:2:1

What is a dihybrid cross?

Cross of 2 organisms HT for 2 genes Results: Phenotype Ratio of 9(Dom):3(HT):3(HT):1(Rec)

What was the Nilsson-Ehle Experiment?

Cross of true breeding red and true breeding white F1: Intermediate red F2: white, light red, intermediate red, medium red, dark red Conclusion -> must be multiple genes that control hull color

Structure/Function/Purpose of Gel-like meshworks of actin and what proteins help form them

Crucial for developing strong yet flexible protrusions of cell membrane as well as organizing structure in the cell membrane Filamin - promotes loose viscous gel formation by clamping filaments together at right angles; common at leading edge of cell protrusions involved in cell movement Spectrin - Organize cell membrane by interacting with inner leaflet, crisscrossing networks of actin filaments closely held to the membrane with the help of associated ERM proteins; membrane domain organization

What is the small effector molecule for catabolite repression? Mechanism?

Cyclic AMP, produced from ATP via adenylyl cyclase cAMP binds to activator protein known as Catabolite Activator Protein (CAP) in inducible, positive control mechanism cAMP-CAP complex binds to CAP site near lac promoter to increase transcription Presence of glucose inhibits adenylyl cyclase enzyme

Which amino acids form disulfide bridges?

Cysteine and Cysteine form Cystine disulfide bridge

Structure/Function of Cytochrome b6f

Cytochromes are all heme-containing proteins Reduced CoQ (plastoquinone) from PSII diffuses through the stacked grana thylakoid membranes through cytochrome b6f to the soluble cytochrome carrier plastocynanin Cyt b6f pumps protons into the thylakoid space as plastoquinone passes electrons through it to plastocyanin

What is the equation for cellular respiration?

C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + energy

What happens in the absence of the beta subunit?

DNA pol III falls of DNA template after about 10 nucleotides have been polymerized, slowing rate to ~20 nucleotides per second (as opposed to staying on long enough to polymerize 500,000 nucleotides and moving at 750 nucleotides per second)

Why are telomeres needed?

DNA polymerase can only synthesize 5'->3' direction, so 3' ends of linear chromosomes cannot be replicated!

What are promoters?

DNA regions upstream of the coding DNA that the initiation complex of transcription binds to

Double-Strand Break Repair Mechanisms

DS breaks are very dangerous and caused by some ionizing radiation and chemical mutagens Cause chromosomal rearrangements and deficiencies Repaired by Homologous Recombination Repair and Nonhomologous End Joining

What's the different in a darkfield and bright field microscope?

Darkfield - bright objects on dark background with special condenser Brightfield - dark image on bright background

Define observed epidemiological study and describe the essential features and usefulness

Data gathered by conducting studies of randomly chosen individuals using surveys or interviews including infected and non-infected individuals Cannot establish strict causation Helps explain progression of disease and determine future directions of outbreaks

Which experiment provided visible evidence of chromosomal rearrangement?

Demonstrated first visible evidence that chromosomal rearrangement isn't just small sections of crossover but large regions responsible for recombinant genotypes

How does pressure control microbes?

Denatures Usually used in conjunction with other methods

How does heat control microbes? Methods?

Denatures proteins and disrupts their molecular interactions and integrity Useful for pathogenic ones since they are typically mesophiles Dry-Heat Sterilization - lab incinerators, ovens Moist-Heat Sterilization - penetrates cells better than above (specific heat of water higher than air)

How does alcohol control microbes? What % most effective and why?

Denatures/coagulates proteins Disrupts membranes Most effective at 70% concentration because 100% coagulates proteins too fast and thus 70% penetrates cell better

What are the visible morphological changes an apoptosing cell undergoes?

Dense chromatin condensation at nuclear periphery Cell body shrinkage (most organelles remain intact) Nucleus and cytoplasm fragmentation -forms membrane-enclosed apoptotic bodies -no loss of intracellular contents into ECM Apoptotic bodies phagocytosed by surrounding cells

What is the nucleolus?

Dense region within eukaryotic nucleus containing rRNA

Why is it important that response timing be adjustable?

Depending on the process, may want fast or slow effect. i.e. when telling cells to stay alive through active signaling, don't want cells to quickly respond to a brief loss of that signal and apoptose in seconds

3 Ways spontaneous mutations can occur?

Depurination Deamination Tautomeric Shift

In a DNA isolation protocol, why do we use salt? Detergent? Isopropyl alcohol? Meat tenderizer?

Detergent - breaks apart cell membrane with its polar and nonpolar heads Salt - ionizes it by binding to and neutralizing negative phosphate groups; helps DNA stick together and allows it to precipitate out of solution (insoluble in salty after) Cold isopropyl alcohol - causes DNA to uncoil and precipitate and provides layer for it to defuse into Meat tenderizer - cuts histones out as enzyme to free DNA strands

Joshua and Esther Lederberg Experiment on Random Nature of Mutation

Developed Replica Plating Method in 1950s 1. Bacteria plated on master plate under nonselective conditions 2. Replica created by using sterile velvet cloth and pressing to master plate then two secondary plates with T1 bacteriophage 3. Only ton(r), resistant to T1, can survive to form new colonies Results: colonies grew in same places on secondary plates, demonstrating the mutations conferring ton(r) occurred randomly without the selective pressure of T1 while the cells were growing on the master plate -> Support for Random Mutation Theory

Ames Test for Mutagenicity

Developed by Bruce Ames Uses strain of Salmonella typhimurium that cannot synthesize amino acid histidine due to point mutation Second mutation may occur restoring ability to synthesize histidine Test monitors rate at which this second mutation occurs Test can be used for a variety of reasons including to provide evidence for randomness of mutations, demonstrate frequency of reversion, and to tell if something is a mutagen

Process of Segmentation

Developmental step after axes formation Initially shallow grooves partition embryo into 14 Parasegments Grooves then disappear and new boundaries are formed that divide embryo into morphologically discrete Segments

What is the difference in DNA major grooves and minor grooves?

Difference in groove sizes are because side sugars point to is more crowded and thus minor groove, other side is major

How do the ends of actin differ in T-actin and D-actin concentration and why?

Differences between Cc(D) and Cc(T) result in higher concentrations of T-actin at the plus end and vice versa

What does heterozygous refer to in genetics?

Different alleles for a gene

What is meant by topologically distinct?

Different content and separated

What is local signaling? Examples?

Diffusion of signal molecules to a specific target Signal has to make it to the target Taste buds and neurons

What is the difference between direct and indirect viral transmission?

Direct - virion travels directly host to host by itself, can happen via objects or water too though Indirect - virion travels by transmission vectors (such as intermediary animals)

What are the 3 major types of signaling?

Direct, local, and long distance signaling

Four patterns of natural selection

Directional Selection Balancing Selection Disruptive Selection Stabilizing Selection

What is the role of parasites in infectious disease including roles of definitive and intermediate hosts?

Disease carriers using host to help transmit Definitive Host - preferred host to parasite that actually carries and transmits disease and allows parasitic sexual maturation Intermediate Hosts - parasite infects and leaves before becoming sexually mature

What is a noninfectious disease? Causes?

Disease not caused by pathogen (i.e. genetic, environmental)

What is zoonotic disease?

Disease transmitted from animals to humans

Describe the four patterns of incidence discussed in class

Diseases SEEP through Sporadic Disease - occasional, often small geographical region Endemic Disease - spreads constantly Epidemic Disease - spreads to larger number of individuals than expected in short amount of time Pandemic Disease - epidemic on world-wide scale

Mechanism of Antiviral Drugs

Disrupt gene transcription Activated by viral enzyme thymidine kinase (inactive otherwise) Irreversibly binds to to viral DNA polymerase in these cells, halting viral DNA replication (unpleasant for patient though)

How do halogens control microbes?

Disrupts chemical properties of biomolecules

How does radiation control microbes?

Disrupts réplication and certain biomolecules UV Radiation used to sterilize petri dishes

What are photons?

Distinct amounts of energy that occur when energy of light interacts with matter

Different between broad-spectrum and narrow-spectrum antibiotic?

Diversity of bacterial species affected Narrow - safer, but requires specificity Broad - risk of superinfection

What is the goal of eukaryotic mitosis?

Divide DNA equally and preisely

How is replication in prokaryotic DNA initiated?

DnaA proteins bind to DnaA boxes and to each other, creating complex and separating strands in DnaA region DnaB/Helicase - six subunits that travel along DNA in 5'->3' direction using ATP to separate further strands

What is a protein's domain(s)?

Domains refer to a functional globular region of a protein

What is incomplete penetrance? (Impact and molecular mechanism)

Dominant trait that lacks phenotypic expression in certain heterozygous individuals Presents a challenge in determining from pedigree molecular mechanism unknown

What are endospores?

Dormant states of bacteria when environmental conditions unfavorable allowing them to survive harsh conditions for thousands of years Dormant state means completely dehydrated, no activity, cannot gram stain, and mother cell disintegrates Can even survive autoclaves!

What are dosage and route of administration and their significance?

Dosage - amount and time interval of drug administration; maximize effectiveness against pathogen but minimize harm ROA - method used to get drug to target; maximize effectiveness while minimizing patient inconvenience and cost

What is the only way to form non parental ditypes in asci?

Double crossover including all four chromatids

Chloroplasts structure

Double membrane Thylakoids - contain chlorophyll

Structure of the mitochondria

Double membranes similar to nucleus Lack NPCs Outer membrane much "leakier" than inner membrane Like nucleus, space between topologically similar to exterior, but matrix similar to cytosol

What are the defaults of protein transport?

ER to Golgi to outside of cell Must have KDEL to remain trapped in ER Must have M6P to go to lysosome and avoid excretion

What does each Calvin Cycle turn create and from what? 3? 6?

Each turn creates 2 G3P (3-C) with 1 carbon from CO2 that is fixed to RuBP (5-C) by rubisco. The 2 G3Ps dont make RuBP or at least are not thought of as doing so at this point because we think about it in terms of 5 -> at the end of the 3rd cycle, we have 6 G3Ps and thus 6 X 3 = 18 carbons. 15 -> 3 RuBP and 3 are put aside as half of what needed for glucose 6 cycles: 12 G2Ps = 12 *3 = 36 carbons. 30 -> 6 RuBP, 6 -> 1 Glucose

What is pangenesis?

Early theory proposed by Hippocrates that suggested an organism requires skills and traits through experience and then passes them on, supporting familial jobs, skills, etc.

What is cerumen and what is its effect?

Earwax Has antimicrobial proteins and also plays role in slowly moving things out of ears, like how headphone are slowly pushed out over time

What is elastin and what is its role in the ECM? What structural features does it have the contribute to its properties? Where in the body would you find high concentrations of elastin and why? Precursor? Stability?

Elastin is a fiber that allows resistance to expansive forces and provides contraction following expansion Enriched in vessels and the aorta Made of elastin protein which contains a disproportionate amount of glycine and proline like collagen Tropoelastin - soluble precursor excreted into extracellular space adjacent to cell membrane that is processed into complex entangled weave of elastin proteins Hydrophobic nature of elastin monomers -> compressive force to minimize surface area Tensile strength upon expansion provided by cross-linking of lysine residues Fibrils exist on the order of 70 years!!

Signaling events at neuromuscular junction requiring multiple interactions

Electric signals get converted to chemical signals at synapses Ligand-gated, voltage-gated, and mechanically-gated channels all play role in Neuromuscular junction

What type of force is a proton gradient?

Electrochemical Force

What type of energy is produced by the ETC?

Electrochemical gradient both from concentration (pH) across IMM and charge separation (more negative matrix than IMS)

What role do Cytochrome C and Ubiquinone play?

Electron shuttles - small, highly mobile electron carriers that help pass electrons down along ETC

What are redox reactions?

Electron transfer reactions in which one reactant loses electrons (oxidation) and one gains them (reduction)

How do we differentiate endergonic/exergonic vs. endothermic/exothermic vs. spontaneous/non-spontaneous for this exam?

Endergonic/Exergonic - energy absorbed/released Spontaneous/Not - overall negative/positive free energy change Exothermic/Endothermic - heat released/absorbed

What is the difference between endergonic/exergonic and endothermic/exothermic?

Endergonic/exergonic refers to free energy wile endothermic/exothermic refers to enthalpy

What are Trisomy Disorders? Examples?

Ending up with 3 copies of a gene Down syndrome - 3 copies of 21 Patou's - 3 of 13 Edward's 3 of 16 Smaller the gene, higher the number, longer the lifespan

Endocytosis Pathway from PM to lysosomes Purpose of intralumenal vesicles Distinguishing early from late endosomes

Endocytic vesicles fuse with early endosomes that sort them From there the sorted particles can be recycled back to the PM through recycling endosomes, transported to the TGN, or held until fusion with lysosomes All of this sorting back and forth with the PM, recycling endosomes (that can store until needed), and TGN, happens as lysosomes mature and are moved along microtubules toward interior of cell Proteins destined for degradation are held in intralumenal vesicles Early endosomes have tubular projections that are lost by the time they mature to late endosomes

What is the difference between endocytosis and macropinocytosis?

Endocytosis - take up of macromolecules in ECF Macropinocytosis - nonspecific uptake of fluids, membrane, and particles attached to the plasma membrane

What is the name for the system that holds all the organelles together?

Endomembrane system (similar to peritineum)

What is the 1st law of thermodynamics?

Energy is neither created nor destroyed; energy of the universe is constant

What is the process and effect of ATP-dependent Chromatin Remodeling?

Energy of ATP hydrolysis is used to drive change in location and/or composition of nucleosomes to make more transcriptionally active or inactive

Process of macropinocytosis

Engulfment of large amounts non-selectively Cell Signal -> reprogramming of Actin -> formation of cell-surface ruffles -> ruffles collapse back on surface, trapping ECF non-specifically forming large vacuoles/macropinosomes

What is the effect of enhancers and silencers?

Enhancers - DNA Region that TF binds to causing Up-regulation of gene (increase rate of transcription 10- to 1000-fold) Silencers - DNA region TF binds to causing down-regulation of gene

What are the enriched, chemically-defined, and complex types of growth media?

Enriched - contains growth factors, vitamins, nutrients Chemically-Defined - exact chemical composition known Complex - exact composition unknown (extracts of yeast, meat, or plants added)

What is the relationship of enthalpy and entropy?

Enthalpy is chemical potential energy, while entropy is disorder

What are alternative methods of extracting energy from glucose?

Entner-Doudoroff Pathway - alternative mechanism used by some bacteria for similar yield PPP - evolutionarily basal, used by nearly all cells to make NADPH, nucleotides, amino acids

What are alternative methods to extract energy from glucose?

Entner-Doudoroff Pathway - used by bacteria with similar yield as glycolysis with different mechanism Pentose Phosphate Pathway - most evolutionarily basal pathway used to make nucleotides and amino acids

What are some causes of chromosome breakage?

Environmental - ionizing radiation, replication errors, oxidizing agents Endogenous - meiotic recombination

Direct Repair Mechanism and what types of Enzymes conduct it

Enzymatic repair by reversal of covalent modification off nucleotides Photolyase - repairs thymine dimers Alkyltranfserase - repairs alkylated bases and permanently inactivates alkyl transferase

What is the mechanism of DNA Methyltransferase?

Enzyme that methylates chromatin structure to silence gene expression Methylation inhibits binding of activator proteins

Define exoenzyme

Enzymes released outside of pathogen cells that are used to breakdown host cell components, fight host immune system, etc.

Role of Eosinophils

Eosinophils attack Eukaryotes and are involved in allergic reactions; granulocytes with granules containing MBP (major basic protein) that binds to surface carbs and disrupts cell membranes

What is the difference between an epidemic and a pandemic?

Epidemic - disease which affects many people over a large geographical area or affects a large number of people in a population Pandemic - disease which sweeps across multiple continents infecting people over large areas of the earth (bigger)

Which types of signal messaging was studied first? What did the substance activate?

Epinephrine - activated glycogen phosphorylase -> liver releases glycogen in form of glucose into the bloodstream

Antigens vs. Epitopes?

Epitopes are subsections of antigens that are the specific part the antibody attaches to

How does oxidative phosphorylation and ETC compare with energy of combustion obtained through combusting glucose? Why is combustion not a good option?

Essentially equivalent amount of energy from OP as from combustion Reason for ETC and OP is to do it gradually and efficiently to contain and utilize the energy released, while combustion just releases it all at once making it very hard to efficiently capture and utilize (i.e. gasoline engines)

What is the process of formation of synaptic vesicles in a nerve cell?

Essentially synaptic vesicle membrane proteins are delivered to the PM, synaptic vesicles are budded off from the PM with these proteins and loaded with NTs, then they fuse and release

What do the words eukaryote and prokaryote derive from?

Eukaryote = with nucleus (eu is with, karaoke is nucleus) Prokaryote = before nucleus

How are eukaryotes regulated differently in terms of gene expression?

Eukaryotes don't have operons

Are prokaryotic or eukaryotic cells typically larger?

Eukaryotic

What is the difference between euploidy and aneuploidy?

Euploidy - variation in number of complete sets of chromosome (occur occasionally in animals and frequently in plants) Aneuploidy - variation in number of particular chromosomes within a set (regarded as abnormal)

What is the 2nd law of thermodynamics?

Every energy transfer or transformation increases the entropy (disorder) of the universe; during every transfer of energy, some of energy is lost to heat

What is the difference between endonuclease and exonuclease?

Exonuclease - enzymes that work by cleaving nucleotides one at a time by the end (exo) of the chain Endonuclease - cleaves phosphodiester bonds in the middle (endo) of the chain

What experiment was conducted to demonstrate digit development by apoptosis? What proteins are involved? Conclusion?

Experiment examining development of vertebrate limbs using chicken feet Left shows development with bone morphogenic proteins (BMPs) expressed by interdigit cells that induce apoptosis Right shows under condition of dominate negative type I BMP receptor expression that results in webbed foot -> surviving interdigital cells that were supposed to apoptose differentiate into web and BMPs not expressed Conclusion - BMP signaling medaites interdigital cell death in the embryonic limb

What were the Griffith experiments?

Experiment with nonlethal R-type and lethal S-type streptococcus infection of mice in which dead S-type mixed with live R-type still killed mice, demonstrating Transforming Principle and that something could be transferred from dead S-type to R-type to change R-type's phenotype

What is the result of gain-of-function mutations in homeotic genes?

Expression of genes in additional places in embryo These cause a gene to expressed in the wrong place, wrong time, and/or at an abnormal level i.e. antennapedia

How are the two apoptosis pathways interconnected?

Extrinsic pathways are coupled to intrinsic pathways through Bid TNF Alpha death signals on the surface of one cell activate trimer formation of TNF alpha death receptors on adjacent cell Activated TNF Alpha recruits TNF receptor-associated death domain protein (TRADD) and Fas-associated death domain protein (FADD) adapter proteins FADD recruits and activates initiator caspase-8 Caspase-8 dimerizes to activate and then cleaves caspases 3, 6, and to activate them Caspase-8 also generates the tBid fragment that binds to Bcl-2 on the OMM to release cytochrome C, simultaneously activating intrinsic pathway

What is F factor?

F stands for fertility, and the F factor is something the donor has in bacterial conjugation. The donor is fertile, or F+, having the F factor, and is thus the one who reaches out with the sex pilus

Fab vs. Fc regions of antibodies

Fab - antigen-binding, variable region unique to specific epitopes Fc - Immune cell signaling, constant region that binds complement and is recognized by phagocytes and common to all antibodies

Which region of antibody binds to antigen? Which one interacts with other immune cells?

Fab region binds to antigen Fc interacts with other immune cells

What is the process of rho-independent termination?

Facilitated by two sequences in RNA: -Uracil-rich sequence located at 3' end of RNA -Stem-loop structure upstream of uracil-rich sequence

How are lipids synthesized in the cytosolic leaflet of the ER?

Fatty acids are placed in the cytosolic leaflet CoAs are ligated onto the fatty acids Glycerol 3-phosphate is attached and removes the CoAs The 3rd phosphate is removed from G3P and replaced with a hydroxyl group CDP-Choline transfers a choline group to the hydroxyl group

What is Balancing Selection? Means for calculation?

Favors maintenance of 2+ alleles (heterozygote advantage) Selection Coefficient = 1 - w(fitness) Calculate equilibrium allele frequency

Attenuation and the trp operon

First gene in trp operon is trpL that encodes short peptide termed Leader peptide

Intergenic Suppressor Mechanisms - Transcription Factor

First mutation causes loss of function of particular protein, second mutation may alter transcription factor and cause it to activate expression of another gene that encodes a protein that can compensate for loss of function cause by first mutation

How is a fixed specimen prepared?

Fixation is process of attaching cells to slide, usually killing them but not disrupting their morphology Methods - heating or chemical treatment

Plant cells and tonicity

Flaccid in isotonic Plasmolysis (death) in hypertonic Normal turgor pressure in hypotonic

Where are lysosomes formed?

Formed by budding from the Golgi complex

Role/Mechanism of Formins

Formins form dimers to nucleate growth of unbranched actin filaments that can be cross-linked with other unbranched filaments to create bundles Each monomer binds actin and then to another monomer to hold everything together while it "walks" up the plus end, grabbing actin with its "whiskers" and throwing it on top

What is the role of peptidyl transferase in translation?

Forms peptide bonds between adjacent amino acids using tRNAs

Forward vs. Reverse Mutation

Forward Mutation - changes wild-type into some new variation Reverse Mutation - changes mutant allele back into wild type (AKA Reversion)

MHC I features/location?

Found on all nucleated cells (not RBCs) and signal that cell is not an enemy Can be adjusted when cell compromised to ask for suicide

What are the membranes/spaces of the mitochondria and their functionalities?

From outside to in: Porous outer membrane with many porin proteins that allows for free movement of ions and small molecules up to 5kDa; results in IMS having same pH/ionic composition as the cytosol Inter Membrane Space (IMS) - narrow gap of about 20-30nm between inner and outer membranes that's small size and cristae spaces permit the effective building of the proton gradient Highly selective inner membrane with highly invaginated regions called cristae and all the ETC machinery Matrix - Interior of mitochondria in which Krebs cycle happens

Three classes of segmentation genes? Effects of mutations in each?

Gap Genes - rough segmentation; identify major regions Pair-Rule Genes - Interfaces Segment-Polarity Genes - within segment actions

What does gene transformation mean? What are the steps in the protocol? How is the pGLO plasmid regulated?

Gene transformation is when bacteria take up pieces of DNA released as other bacterial cells disintegrate 1. Scrape up bacteria colonies with inoculating loop 2. Mix bacteria into transformation buffer (CaCl2) 3. Finger vortex tube 4. Add in plasmid and incubate on ice 30 min 5. Heat shock at 42 C for 50 seconds 6. Incubate on ice for 5 minutes 7. Mix in LB medium and incubate at 37 degrees for 30 min 8. Spread on Petri dishes and allow growth and response PGLO regulated by pBAD promoter, araC inducer w/arabinose, and GFP and bla ampicillin resistance on transcription unit with it

What is the function of the trp ("trip") operon?

Generate proteins responsible for tryptophan synthesis

What are genetic linkage and synteny?

Genetic Linkage - transmission of more than one gene as a unit Synteny - genes located on same chromosome

What is Mosaicism?

Genetic abnormalities that occur after fertilization leading to organism having subset of cells genetically different from rest of cells

What are the two things present in all viruses?

Genetic material and capsid protein

What is Fast Flush?

Genetic polymorphism found often in Asian cultures that results in less of this second enzyme in ethanol processing and natural inability to break down ethanol -> less alcoholism, but redder faces when drinking

What is the difference between genetic recombination and crossing over?

Genetic recombination is the phenomenon by which non parental, or recombinant, offspring are produced as a result of genetic material being exchanged by DNA. Crossing over is the actual crossing that happens during prophase I that can lead to recombination

Calculate impact of inbreeding on population

Gentoypes: AA = p^2 + fpg Aa = 2pq(1-f) aa = q^2+fpq f is a measure of how much the frequencies vary from HW equilibrium due to nonrandom mating and varies from -1 to 1

Germ-line cells vs. Somatic cells

Germ-line - cells that give rise to gametes such as eggs and sperm Somatic - all others

What is permease?

Gets lactose into the cell

What are fitness values applied to? What affects these values?

Given genotypes Whether they are: -more likely to survive -more likely to mate -more likely to be fertile

Give an example of gene families and paralogs

Globin Family - all encode subunits of proteins that bind oxygen Now 14 paralogs of the ancestral globin gene on three different chromosomes

Glucocorticoids vs. Gonadocorticoids

Glucocorticoids - influence nutrient metabolism Gonadocorticoids - influence growth and function of gonads

If we produce 3 ATP per 10 H+ pumped, then why does NADH only make 2.5 ATP instead of 3? How is ATP moved back out to the cell?

H+ is also used in the H/P Phosphate Translocase Symporter ATP is moved back out by being coupled with influx of ADP through Adenine Nucleotide Translocase Antiporter

What type of bonding bonds the middle of the double helix of DNA?

H-bonding

HRR vs. NHEJ

HRR - unbroken strands used as templates to synthesize DNA, then strands broken and rejoined in way that produces separate chromatids; can be error-free NHEJ - last ditch effort in which broken ends recognized by end-binding proteins, forms cross bridge, stitches up with potential deletions

How do enzyme-coupled receptors differ/relate to GPCRs and what is their function and most common type?

Have EC and IC domains that process wide variety like GPCRs Major difference is they don't interact with G-protein complexes to translate the signal across the membrane, but rather utilize inherent enzymatic activity in their cytosolic domains to propagate the signal Most common type = receptor tyrosine kinases = RTKs

What is the difference between homologous and sister chromosomes?

Homologous - 1 paternal, 1 maternal, different alleles Sister - exact chromosomal replicatoin

What are paralogs?

Homologous genes within a single species

At Anaphase I, what separates to poles and what stays together?

Homologues separate to poles, sister chromatids stay together

What are the differences between homophilic and heterophilic interacting proteins?

Homophilic - between two of same molecule, most often cell-cell; helps to organize similar cell types Heterophilic - between two different types of molecule, most often cell-ECM; facilitates interactions between cell and surrounding environment

Role of cholesterol in cold and hot conditions?

Hot Conditions - cholesterol holds fast moving lipids together to maintain membrane rigidity Cold Conditions - cholesterol wedged between lipids to prevent crystallization and maintain fluidity

What are antiretrovirals and their significance?

Hot topic of research involving utilizing reverse transcriptase inhibitors and integrase inhibitors Targeting HIV

Which type of quasi-ionic bonding is weak alone but strong in groups?

Hydrogen bonding

How does the sigma factor bind tightly to the promoter sequence when it crosses it?

Hydrogen bonding to the nucleotide bases of the promoter sequences

How is ATP broken down to couple other reactions?

Hydrolysis (addition of water to break off phosphate)

Are transport proteins hydrophilic or hydrophobic?

Hydrophilic

What are the 3 phases of the Calvin cycle?

I. Fixation - carbon from CO2 is fixed to RuBP by Rubisco and together create 6-carbon molecule II. Reduction - 3-PGA increases in energy by ATP hydrolysis (adds phosphate group) III. Regeneration - Generation of RuBP

What are IAPs and how do they function? In what organisms are they found? Cons and how those cons are mediated?

IAPs - inhibitors of apoptosis that bind to and inhibit caspase activity XIAP is an IAP in humans that binds to caspases 3, 7, and 9 IAPs also in mammals and flies but absent in nematodes First discovered in baculoviruses to prevent apoptosis of infected cells Can prevent issue when cells need to apoptosis - SMAC/DIABLO proteins released with cyt C from IMS inhibit XIAP and allow for apoptosis to proceed

What are the five periods of a disease?

IPIDC Incubation - pathogen enters host and begins reproducing; no signs, symptoms, or knowledge Prodromal - Reproduction continues as sign/symptoms and immune response occur Illness - signs and symptoms most severe, culminates in maximal number of pathogens Decline - Pathogenic decline, symptoms/signs decline, increased risk of secondary/opportunistic infection Convalescence - pathogen numbers decrease and are eliminated, signs/symptoms decrease and subside

What is the focal point?

Image point where parallel light rays meet after passing through a lens

Mechanism of nuclear import via cargo proteins and role of importins

Importins are nuclear import receptors that recognize nuclear localization signals on proteins Certain families of cargo proteins have nuclear localization signals recognized by a certain importin or by a important adaptor protein that is in turn recognized by an import receptor (when this is the case, the adaptor proteins are only able to bind the import receptors after binding their cargo proteins) This mechanism plays a role in preventing de novo synthesis of organelles (info in the membrane)

How did the introduction of copolymers help finish cracking the genetic code?

In 1960s, Khorana and colleagues developed new way to synthesize copolymers of RNA so that sequence is not random assortment of given nucleotides but consistent pattern (like creating UC and then enzymatically inking to make synthetic UCUCUCUCUCUCUC

When in the 5 phases can pathogens be contagious?

In ALL of them and even sometimes after convalescence if some cells/particles remain

Attenuation Mechanism in trp

In bacteria, soon after mRNA synthesis begins, ribosomes attach to 5' end and begin translation Attenuation is the early stopping of this transcription before entire mRNA is made Formation of 3-4 stem-loop happens naturally and favorably when region 2 not bound to region 3, allowing attenuation and inhibiting synthesis of trp; however, when tryptophan levels low and coupling of translation/transcription occurring, ribosome pauses at trp-sites in trpL since it cannot find charged trp tRNA (since low trp present) and this keeps 1 out of way while 2 bonds to 3, preventing 3-4 loop and preventing attenuation

Where is glycogen kept in the body?

In complex storage in places like the liver

How is eukaryotic DNA packaged in the nucleus?

In form of chromatin, linear DNA and proteins

What are the purposes of RNA?

In living cells, intermediate info storage and part of ribosomes nucleoprotein complex Viruses - genome

What is an activated amino acid?

In the context of translation, an activated amino acid has had AMP attached to it. This provides necessary energy so that the amino acid can be attached to the correct tRNA.

Where does the light independent reaction take place?

In the stroma

Main process of phospholipid synthesis

Individual fatty acids synthesized in cytosol and migrate to cytosolic leaflet of ER as result of entropy and non-favorable interactions in aqueous cytosol After arrival in ER, activated with CoA and then acyl transferases exchange these for glycerol 3-P to produce phosphatidic acid (this the only step that enlarges ER cytosolic leaflet) Head group then modified to whatever through appropriate phosphotransferases They can blebbed off to other membranes as necessary

What are the three phases of DNA replication?

Initiation, Elongation, Termination

Difference between integral and peripheral proteins?

Integral - has region within membrane (nonpolar region) Peripheral - anchored to membrane without spanning it 1, 2, 3, 4 - integral, embedded 5, 6, 7, 8 - peripheral, associated 1, 5, 6 - use lipid anchors

Are surface receptors integral or peripheral proteins?

Integral proteins

What is integrate and how is it involved in life cycle of HIV?

Integrase is an enzyme that catalyzes the insertion of HIV into a host CD4 cell's genome

What are inclusion bodies?

Internal storage containers that store nutrients or energy molecules for later use such as gas, magnetic iron, or enzymes Can have quasi-membrane around them or protein shells

What is the function of WHO?

International public health manager that is part of UN and monitors significant epidemics and pandemics and establishes best practices to help prevent outbreaks

Explain mechanotransduction and its role in outside-in information transfer. What is the physical mechanism of mechanotransduction? How is it read on the inside of the cell?

Intracellular cadherin domains provide an attachment point for mediator proteins and cytoskeletal proteins that generates lateral strength within the sheet and connects adjacent cells to one another Mechanotransduction refers to the transfer of forces between cells through adaptor proteins and cytoskeletal filaments that allow them to respond It is read intracellularly by tension sensing systems in which pulling on cadherin causes opening of folded alpha-catenin protein -> exposed site on unfolded protein allows binding of vinculin -> actin filament connects to structure mechanotransducing tension to myosin

Intragenic vs. Intergenic Suppressors

Intragenic - within gene, second mutant site is within same gene as first mutation Intergenic - different genes, second mutation site in different gene from first mutation

What are the two pathways that initiate apoptosis? How are they related? How are they different?

Intrinsic and Extrinsic Intrinsic - Mitochondrial - relies on intracellular signaling to regulate release of cytochrome c into cytosol from IMS of mitochondria Extrinsic - relies on cell-cell interactions via surface receptors (death receptors) for initiation

Intrinsic Apoptosis Pathway

Intrinsic signal -> mitochondrial release of cytochrome C into cytosol from IMS Cyt C interacts with adaptor protein Apoptotic Protease Activating Factor-1 (Apaf1) to form active monomer Monomers oligomerize to form hepatmeric structure called apoptosome or "wheel of death" that recruits initiator caspase-9 Caspase-9 activates executioner caspases

What is the name for the pieces spliced out and kept in in eukaryotic splicing?

Introns - spliced out Exons - remain

What is the energy investment and energy payoff of glucose?

Investment - 2 ATP per glucose used to phosphorylate Payoff - 4 ATP (2 net) and 2 NADH per glucose (2 pyruvate molecules produced)

What is the purpose of GATC methylation?

Involved in regulating replication by ensuring only one round of replication DNA Adenine Methyltransferase (DAM) methylates the A on both strands to distinguish the daughter strand by its lack of methylation, allowing blocking of second round of initiation

Define Humoral Immunity (and relation to intracellular vs. extracellular pathogens)

Involving antibodies interacting with pathogens in the blood and between cells Extracellular Pathogens

Define Cellular Immunity (and relation to intracellular vs. extracellular pathogens)

Involving identifying and eliminating pathogens that have gained access to inside of cell Intracellular Pathogens

How do cells lining ducts of exocrine glands (mammary, pancreas, liver, sweat, salivary) secrete their fluids?

Ion pumps and channels situated in the basolateral and apical plasma membrane of the epithelial cells move ions into the lumen of the exocrine ducts, creating an osmotic gradient for water to rush through following them through aquaporins

Difference between ionizing and non-ionizing radiation?

Ionizing Radiation includes gamma and x rays and it refers to radiation that is more damaging and can actually cause double strand breaks Non-Ionizing Radiation refers to radiation like UV light that modifies bases and structures without actually tearing them apart such as the formation of thymine dimers

What is the significance of quaternary structure of proteins?

It allows multiple proteins to form one and thus have multiple functions in one protein

What is special about the LPS in gram negative bacteria?

It allows the bacteria to cause sickness even after they die

Does the lac I gene sit upstream or downstream from the lac operon? (does the regulatory gene sit up or downstream from its operon?)

It binds upstream, or before in the direction of polymerization

What is the mechanism of DNA Helicase?

It breaks the hydrogen bonds between strands to unwind the DNA (as opposed to topoisomerase that breaks covalent bonds and reseals them)

How can fluorescence be used in light microscopy?

It can be used by staining specimens with fluorochromes and only allowing emission from those fluorochromes to pass through microscope (filter out other wavelengths, dark background) Can be used to view sub-structures of the specimen

What is Allolactose?

It inactivates the lac repressor in the presence of lactose and absence of glucose

What is the significance of the 23S rRNA?

It is a component of the large subunit and the ACTUAL peptide transferase (making the ribosome a ribozyme)

What is receptor tyrosine kinase?

It is a dimer receptor of the amino acid tyrosine that comes together when activated, thus requiring twice the amount of ligand (i.e. more signal) to activate

What is Disulfiram (Anatabuse) and how does it work?

It is a drug given to people trying to overcome alcohol abuse Acts by inhibiting second enzyme in ethanol breakdown, causing buildup of acetyl aldehyde intermediate that is normally broken down to acetic acid and released in urine

What is a falsifiable hpothesis and why is it important?

It is a hypothesis that can be confirmed incorrect through tests and is important so that one's hypothesis isn't only either true or unknown. E.g. "There are other inhabited plants in universe" is testable but not falsifiable because we cannot prove it untrue

Why is the oocyte critical in determining the pattern of development?

It is an elongated cell with pre-established axes created by asymmetric depositing of certain gene products

Why is it difficult for microtubules to nucleate and how do they overcome it?

It is difficult because of the complex array of interactions between tubulin monomers that is necessary for the nucleation to initiate, driving the nucleation up very high

Is the critical concentration higher for D-actin or T-actin? Why? What effect does this have?

It is higher for D-actin than T-actin because D-actin has a lower affinity for the polymer than T-actin does. This is a result of the energy released by ATP hydrolysis from T-actin to D-actin that is absorbed by the polymer As a result, a higher concentration of D-actin is required for steady state polymerization than T-actin, and it is usually the T form that adds to the polymer while the D form later leaves.

What is a methionine tRNA and it's special role?

It is the tRNA that is part of the translation initiation complex with GTP and the small ribosomal subunit

What is the role of primase?

It makes an RNA primer on which DNA polymerase III can initiate replication (in prokaryotes)

What is the lac I gene?

It makes or doesn't make the lac repressor to induce or not induce lactose

What is the direction of reading and synthesizing for DNA polymerase?

It reads 3'->5' and synthesizes 5'->3'

What is the role of phosphatase?

It turns off the PK cascade by removing phosphate groups

How does a lac operon work?

It turns on and off 3 genes depending on presence or lack of lactose so that E. Coli only produce enzymes to break down lactose when they need it

How does phase contrast light microscopy work? What is uniquely advantageous about it?

It uses refraction and interference caused by structures of the specimen to create images with high contrast and resolution Does NOT require staining

What shape do transport vesicles form into?

It varies, not always spherical Image is of procollagen COPII vesicle formation

What is progeria?

It's a disease in children where they appear to age incredibly fast and die young believed to be connected to a lack of telomerase dearly on in development

Structure/Function of Complex III

It's proton pumping mechanism is unique and utilizes the Q Cycle Uses Q cycle to oxidize CoQ and reduce cytochrome C Pumps 4 H+ into IMS

Persistence/Turnover of cAMP?

Its concentration can change very rapidly, making it a low persistence high turnover messenger

6 major functions of membrane proteins

JERSTA Intercellular Joining Enzymatic Activity Cell-Cell Recognition Signal Transduction Transport Attachment to cytoskeleton and ECM

What is the difference between GTP and ATP?

Just the nucleotide base, guanine vs. adenine

What is the difference between reversible and irreversible inhibition?

Just what it sounds like: reversible involves weak bonding so it can be undone, but irreversible inhibition involves strong permanent bonds to enzyme

Which amino acids are typically methylated?

K, H, and R Lysine, Histidine, and Arginine (positive, basic ones)

What is the ER return sequence for proteins destined to remain in ER ?

KDEL sequence (lysine, aspartate, glutamate, leucine-C-Terminus)

Where do KT MTs and Non-KT MTs attach?

KT MTs - to centromere Non-KT MTs - to opposite pole

What is the pH of lysosomes as compared to the rest of the cell and how is it maintained?

Kept low compared to cytosol through function of V-Type ATPase pumps

cAMP responses table

Key is the variety

Mechanism of synaptic vesicles

Key is they are staged in a primed status synaptic vesicles full of things like NTs are docked and primed for rapid response with partially paired SNAREs

How can refrigeration/freezing be used to control microbes?

Kills or slows growth depending

What are examples of kinetic energy? Potential?

Kinetic - Waves, heat energy, radiant energy, electrical energy Potential - locational/structural, chemical bonds, nuclear, gravitational

What is the relationship between kinetic and potential energy?

Kinetic energy is energy in motion while potential energy is in bonds and gravitational and springs etc. Ball has potential energy while holding it out a window, but its converted to kinetic after letting go

Pathway of electron movement in photosynthesis and the name for the pattern

Known as Z-Scheme

How do Koch's postulates and etiology of a disease relate?

Koch's postulates are used as a guide for etiology to figure out cause of disease and sort through correlations and try to determine causation

What are the two types of fermentation? What occurs in each?

Lactate Fermentation - pyruvate is broken down into lactate in process that oxidizes NADH, producing ATP. Lactate stores electrons from NADH until oxygen returns, i.e. lactic acid buildup in muscles Alcoholic Fermentation - same except alcohol stores electron instead, producing byproduct of carbon dioxide

What is the difference between lactate and lactic acid?

Lactate is reduced by oxidation of NADH into lactic acid

What is the microbe that increases in concentration prior to birth to coat and initiate the fetal microbiome upon entrance to the world? Where else is it found?

Lactobacillus (many species of it) Also found in active cultures in yoghurt

What are the four stages of the bacterial growth curve?

Lage Phase - no increase, acclimating to environment Log Phase - exponential increase of cells, cell death minimal Stationary Phase - plateau where rate of cell division = rate of cell death, reaching density limits and accumulating waste Death or Decline Phase - exponential decrease in number of living bacterial cells

Describe the structure and function of laminin. What does it interact with and what structure does it help to organize? What structural features are associated with its function?

Laminin - heterotrimeric multi-adhesive matrix protein found in all basal laminae with 16 isoforms in vertebrates Structure: -Coiled-coil region - three peptides covalently linked by several disulfide bonds -Globular domains - bind to/crosslink adhesion receptors and various matrix components -Five alpha subunit C-terminal globular LG domains that mediate calcium dependent binding to cell-surface laminin receptors including integrins, sulfated glycolipids, syndecan, and dystroglycan -Inset: laminins assemble into a lattice via interactions between their N-terminal globular domains Overall shape is characteristic cross

How does RI difference relate to the degree of refraction?

Large RI Difference -> greater refraction -> greater angle change

What is the structure of G-protein coupled receptors?

Large glycoproteins said to have serpentine structure snaking back and forth through PM

Do larger or smaller N help the rejection of null hypotheses in correlation?

Larger N makes for easier null hypothesis rejection to prove correlations

Hoes does genetic drift relate to population size?

Larger population = less susceptibility to genetic drift

Structure/Prevalence of GPCRs

Largest family of cell-surface receptors with wide functional diversity but all having 7-membrane-spanning helix Binding pockets are sequestered a bit into the protein into the membrane The outsides of the transmembrane helices have to be hydrophobic, but the insides can have varying properties as they do not interact with the membrane

Pro-Apoptotic BH3-Only Proteins Mechanism

Largest subclass of Bcl2 family that provide crucial link between apoptotic stimuli and activation Promote apoptosis by binding anti-apoptotic Bcl2 proteins and preventing their interaction with effector Bcl2 proteins Expression/Inhibition of these provides multiple input system to regulate initiation of apoptosis Non-Apoptotic state - inactive, allowing anti-apoptotic pathways to prevent effector aggregation Apoptotic Signals -> activate BH3-only -> inactivate anti-apoptotic -> allows effector aggregation -> cyt c release

What types of movements of fatty acids are possible in membrane?

Lateral Diffusion - uncatalzed lateral movement of phospholipids that occurs very fast (1 um/s) Transverse Diffusion - can occur uncatalyzed very slowly or be catalyzed by flippase/floppase/scramblase

How does skin establish physical barriers to pathogens?

Layered with outer layers dead and falling off Stuck together and well-sealed to prevent pathogens from entering Keratin-rich

What's the difference between leading strand and lagging strand synthesis?

Leading - Continuous one piece Lagging - Conducted in Okazaki fragments, stitched together by DNA Ligase

What is the difference between the leading and lagging strands?

Leading strand is the 3'->5' strand that after unwinding DNA polymerase III can just run across in the 5'->3' direction and make a strand on in one go Lagging Strand - 5'->3' strand in which multiple primers must be made to create Okazaki fragments

What is a perfect lens?

Lens through which all entering light rays meet at a single focal point to cause no blurriness whatsoever

What are the magnification limits on light microscopy? Transmission Electron microscopy? Scanning electron microscopy? Scanning tunneling microscopy?

Light - 1000X-1500X TEM - 10^6X SEM - 50,000X STM - 10^8X

Vision Activation Pathway through GPCR

Light -> GPCR Activation -> PDE activation -> cGMP production -> opening of cGMP-gated ion channels All very fast (fastest ones in body I think?) and rapid process acts as amplification cascade

What is the process from light to ETC?

Light -> thylakoids -> produce photons -> resonance as they are bounced around efficiently -> reach primary acceptor -> electrons to ETC

What are the two sets of reactions in photosynthesis and how do they relate?

Light Dependent [LD] (light energy to chemical energy) and Light independent [LI] (Calvin cycle) Relation: LD takes in photons and splits water to create ATP and NADPH that feed into LI with CO2 to produce G3P

Chloroplasts Cycles and Light and Dark Reactions Locations and Overview of Function

Light Reactions happen in the thylakoid and use light to split water, producing O2, high energy electrons that reduce/create NADPH, and the proton gradient -> ATP Dark Reactions occur in the stroma and use ATP and NADPH to fix carbon from CO2 to make sugars

What are the two models of transport through the Golgi?

Likely that actual transport involves bits and pieces from both models Cisternal Maturation Model - each Golgi cisternae forms from vesicular tubular clusters then matures as it migrates through the stack from cis to medial to trans cisternae, a process mediated by the acquisition and loss of proteins/enzymes along the way; Trans cisternae then bud off vesicles until they disappear and are replaced Vesicle Transport Model - Static cisternae containing characteristic complement of resident enzymes; passing from cis to trans accomplished by forward-moving transport vesicles that bud and fuse from one to the next; key difference is that the cargo proteins are moved, not the cisternae, as opposed to the previous model

What is the role of DNA Ligase?

Linking segments of DNA together either after repair or Okazaki fragments of lagging strand

How does the Golgi conduct its sorting?

Localization from microtubule interactions and other factors The Golgi then functions to complete the protein modification and sorting within its cisternae and then sorts and exports

Where specifically are the ETC and respiratory chain proteins localized and why?

Localized to cristae to create unique chemical environments within the mitochondria to facilitate efficient electron transport Specialized proteins bind to regions where inner and outer membranes are closest to prevent free diffusion of the cristae

Which strand are promoters located on and in which positions and what are they recognized by?

Located on Sense Strand -10 and -35 sequences recognized by Sigma Factors

Structure of microtubules and basic roles

Long hollow cylinders of tubulin that are more rigid than actin in these tube-shaped formations Formation of cilia, intercellular highways, cell division, mitotic spindle

What are flagella? What are their two functions?

Long rigid proteins protruding from cell for motility in liquid environments Tumbling - clockwise rotation - random directional change Running - counterclockwise rotation - propel them forward

Microfilaments

Long, thin fibers that function in the movement and support of the cell

How are Chi Square results analyzed?

Low values - high probability observed deviations due to random chance High values - low probability less than 0.05 -> hypothesis is rejected

What chemical indicator test identifies complex carbohydrates?

Lugol's Solution (iodine) Dark blue positive Amber negative

What is the most heterogenous organelle and what does that mean?

Lyosomes meaning they vary the greatest in size, shape, and content

Define cytolysis as it pertains to the complement system

Lysing of foreign invading cells

What is the fate of lysosomal hydrolases outside of the lysosome?

Lysosomal hydrolases dont function outside of the lysosome due to high pH

What is the difference between lysosomes and peroxisomes?

Lysosomes - derived from endomembrane system, filled with enzymes that digest organic material Perixosomes - NOT part of endomembrane system, synthesize hydrogen peroxide and break down biomolecules

Sarcomere Structure/Function

M-line of myosin thick (dark) filaments drive the actin thin (light) filaments towards the M-line as they pull along the sarcomere structure Light-band is length of actin filaments, dark band is length of myosin filaments, M-line is center of myosin, Z-disc anchors actin Filaments themselves do not change length

How are RTK and Ras Activation signals amplified?

MAP Kinase modules function in signal amplification by each one activating multiple of the next The first level is MAP3Ks, then MAPKKs, then MAPKs

What is pre-mRNA?

MRNA transcript before all of the eukaryotic modifications such as splicing and adding the poly A tail and 5' caps

Basic Structure of Microtubules. Differences between subunits. Prevalence in cells

Made up with tubulin monomers that are almost always found in heterodimers of Alpha-Tubulin and Beta-Tubulin Subunits 445-450 AAs long and each binds one GTP Beta subunit can hydolyze GTP, but Alpha unit GTP is physically trapped at dimer interface and never hydrolyzed 6 isoforms, found in all cells Also has +/- ends

What are magnification and resolution?

Magnification - ability of lens to enlarge image Resolution - ability to separate two points in an image

What are the two main factors that determine the property of a lens?

Magnification and Resolution

Ribosome Composition in bacteria and eukaryotes

Main Points: Bacteria - 30-50-70S Eukaryotes - 40-60-80S These sedimentation coefficients are based on density

How do Ran proteins establish concentration gradients and which types serve which functions?

Main purpose is to provide the gradient for transport They couple GTP hydrolysis and binding to facilitate the creation of this gradient Ran-GTP diffuses out of the cell, Ran-GAP (GTPase-activating protein) in the cytosol bind and hydrolyzes GTP removing a phosphate, then Ran-GDP re-enters nucleus, where nuclear Ran-GEF (guanine exchange factor) exchanges GDP for GTP, recycling process

Purpose of cholesterol in cell membrane

Maintain fluidity of membrane

What does MHC stand for?

Major Histocompatibility Complex

Three major classes of cell-surface receptors

Major difference between GPCR and enzyme-coupled is GPCR causes a change in a protein which then has the downstream effect and catalytic activity, while enzyme-coupled has that activity itself on its intracellular domain

What is the lac Z gene?

Makes beta galactosidase in presence of lactose

What is the lac Y gene?

Makes permease in the presence of lactose

What is the lac A gene?

Makes transacetylase in the presence of lactose

Define experimental epidemiological study

Makes use of lab/clinical studies to manipulate study subjects Goal - establish links between disease and causative agents

What is a genotype? How it is determined?

Makeup of genes and alleles determined by either crossing or otherwise determining what set of alleles, both dominant and recessive, a person has

Males vs. Hermaphrodite Nematodes

Males - produce sperm Hermaphrodites - produce sperm and eggs

Limitations on understanding of proteins confined to certain regions of cell membrane

Many situations in which we can examine cells like the sperm and visualize the differentiation of proteins to certain regions, but are unable to determine the molecular nature of the "fence" that prevents the molecules from leaving their domains

What is the second genetic code?

Matching of tRNA to appropriate amino acids that aminoacyl-tRNA synthetases are responsible for

Order of activation of segmentation genes?

Maternal genes activate gap genes Gap and Maternal activate pair-rule Pair-rule genes then regulate segment polarity genes

What is the ultimate fate of endolysosomes?

Mature into lysosomes as hydrolyases complete their digestion

What are the measurements of the DNA double helix?

Max distance between strands - 2 nm 10 base pairs per twist Each twist 3.4 nm apart 0.34 nm between each base pair

Effects of chromosomal rearrangement mutations

May affect gene because chromosomal breakpoint occurs within gene Gene may be left intact, but its expression may be altered because of its new location (Position Effect)

What is polycistronic and which type of mRNA exhibits this?

Means it mRNA encodes two or more polypeptides Prokaryotic mRNA may be polycistronic

Correlation Coefficient and what makes positive/negative correlation

Measure of strength of association between two variables If r>0, positive correlation If r<0 negative if r=0 no correlation

What is the difference between a mechanical and biological vector?

Mechanical - carries pathogen between hosts but is not infected Biological - becomes infected with pathogen and transmits it to another host through fluid transfer, biting, etc.

What are the mechanical barriers to pathogens and their mechanisms of defense? Examples?

Mechanisms that physically remove pathogens from the body (skin cells fall off, hair falls out, mucus expelled, urine/feces excreted, tears flush eyes)

What is the role of the Mediator?

Mediates interactions between RNA Pol II and various regulatory TFs that bind enhancers or silencers

What are the three mechanisms of chromosomal mis-segregation?

Meiotic Nondisjunction Mitotic Nondisjunction Interspecies Nondisjunction

Fluid Mosaic Model

Membrane is fluid structure with mosaic of various proteins embedded in it

Tight junctions

Membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid

What were the three theories of DNA replication and who developed them? What experiment did they use?

Meselson and Stahl (1958) - Heavy Nitrogen Experiments Conservative - original strand stays original, new strand stays new, no mixing Semi-Conservative - products are made of part old part new, half and half products Dispersive - within each strand is part old and part new Semi-Conservative is the correct theory

What is mRNA?

Messenger RNA

How does cyanide act?

Messes with final movement of electrons from complex IV to oxygen, making it impossible to create proton gradient and create ATP -> patient dies form hypoxia (lack of oxygen)

What is the significance of metaphase in terms of compaction?

Metaphase compaction allows visualization of chromosomes By end of prophase, sister chromatids are entirely heterochromatic

What is karyotyping?

Method of identifying, counting, and examining chromosomes

What is plate counting?

Method of serial dilutions and plating then counting colony forming units (CFU) per mL

Mechanism of Methyl-CpG binding proteins?

Methyl-CpG-binding proteins may recruit factors that lead to compaction of chromatin

How does methylation play into genomic imprinting?

Methylated DNA sequences are inherited during cell division Specific genes are methylated in gametes from mother or father, and pattern of one copy of gene being methylated and the other not is maintained in resulting offspring

How is pathway 3 for excited electrons in chlorophyll facilitated?

Mg of chlorophyll in the reaction center in PSII is specifically positioned to induce electron transfer due to an interaction with a His in the chlorophyll-protein complex This is the "special pair"

What is a more modern way (than comparative genomic hybridization) to detect deletions and duplications?

Microarray

How does filtration control microbes?

Microbes can't fit through HEPA air filters

Peroxisomes

Microbodies that produce hydrogen peroxide as byproduct

What are the 3 protein fibers of the cytoskeleton?

Microtubules Intermediate filaments Microfailments

What is the persistence length of actin?

Minimum filament length at which the filament can bend

How do unfolded proteins in the ER stimulate their own correction? (Part II, one of specific IRE1 pathway)

Misfolded ER proteins bind to ER receptors sensing for them Kinase cytosolic domain of same receptors activates ribonuclease to cleave cytosolic pre-mRNA to mature mRNA that produce designated transcription factors TFs in nucleus produce appropriate chaperon mRNA that is leave nucleus and are co-translocationally translated into ER lumen to fold proteins correctly

What are prions? Common diseases associated with them?

Misfolded, rogue forms of normal proteins Proteinaceous Infectious Particles Can cause Transmissible Spongiform Encephalopathy (rapid neural degeneration) and mad cow disease (degeneration of cerebral cortex)

What are the types of amino acid mutations?

Missense - new (incorrect) amino acid substituted in the polypeptide (e.g. hemoglobin, albinism, sickle cell, and achondroplasia/dwarfism) Nonsense - amino acid changed to a stop codon, early stop Silent - new sense codon, same amino acid, so mutation doesn't change expression Frameshift - deletion or insertion that creates a non-functional amino acid sequence (messes up the reading frame)

What are the point four basic translational mutations types?

Missense - wrong single base, swapped amino acid Silent - wrong single base, still same amino acid Nonsense - mistakenly placed stop codon cuts off polypeptide chain early Frameshift - Everything slides down or up one so that everything is off

Which organelle acts as the major energy converter?

Mitochondria

What are the energy transforming mechanisms of mitochondria and chloroplasts

Mitochondria: 2H+ + 2 e- + 1/2 O2 -> H2O Chloroplasts Light + H2O + CO2 -> carbohydrates + O2

What is binary fission?

Mitosis and meiosis accomplished in one process Cytoplasmic Growth - DNA replication starting at Ori - cell division - 2 exact replicate haploid cells

What are the two types of mitotic nondisjunction?

Mitotic Nondisjunction Chromosome Loss

Why are the majority of cancers environmental not genetic?

Mitotic mutations cannot be passed on since sex cells are only ones passed

What happens in telophase?

Mitotic spindle breaks down 2 new nuclei form Chromosome de-condense

What is used to accomplish PCR?

Mix the following in a thermal cycler: ○ Template - DNA to be amplified ○ Primers - short specific pieces of DNA whose sequences flank the target sequence to be copied, one facing in the forward direction and the other in the reverse direction § Tons of this thrown in there, ordered from company, to increase chances of binding to desired DNA § The primers attach outside of the desired gene ○ Nucleotides - Deoxyadenosine Triphosphate (dAPT), dCTP, dGTP, and dTTP ○ Magnesium Chloride - enzyme cofactor ○ Buffer - maintain pH and contains salt to create needed conditions ○ Heat-Stable DNA Polymerase - enzyme

What was Marshall Nirenberg and Philip Leder's Triplet-Binding Assay in 1964?

Mixed one triplet in 20 tubes each with a different radio labeled amino acid and then filtered to identify only amino acids stuck to ribosomes Discovered that 3 nucleotide RNA could cause ribosome to bind a tRNA and tube with large amount of retained radioactivity was the corresponding amino acid

What was the Lederberg and Tatum Experiment?

Mixing of complementary auxotrophs resulting in them canceling out their needs and being able to grow on agar plates lacking amino acids, biotin, and thiamine Evidence of genetic transfer!

What molecule is on the 3' and 5' ends of DNA?

Mnemonic - Five prime Phosphate (F-F) 3' - hydroxyl group

Mechanisms of Drug Resistance

Modification or inactivation Prevention of cellular uptake or efflux of drug Change structure of molecule targeted Overproduction of drug target to outpace the drug Enzyme bypass - alternative method to complete pathway Target Mimicry - synthesis of "dummy molecule" for drug

How do autoclaves control microbes?

Moist-heat sterilizers that have high heat AND high pressure Stats: 121 deg C, 15-20 psi, 20-60 minutes

What are the three pillars of modern genetic studies?

Molecular Genetics - most modern field, molecular features underlying gene expression; genetic approach to research, linking genes/mutations and abnormal function Transmission Genetics - how traits passed from one generation to the next; oldest pillar Population Genetics - relation of genetic variation of population to environment and prevalence of phenotypes

Define antigen? Examples?

Molecules on or in pathogen that are specific to that particular pathogen i.e. glycoproteins, LPS, flagella/pili, capsules, capsid proteins, spike proteins, other biomolecules

What are examples of monosaccharides and polysaccharides?

Mono - glucose and fructose Poly - glycogen and starch

Polyclonal vs. Monoclonal Antibodies

Monoclonal - purified antibody from single B cell that recognizes only one specific epitope of an antigen Polyclonal - collection of antibodies from different B cells that recognize multiple epitopes of the same antigen

What is the significance of the complexity of antigens?

More complex antigens = better specificity and more efficient defense

How do microtubules differ from actin?

More rigid in structure due to tube-shaped bundles they organize into Use GTP instead of ATP Alternative roles like cell division, mitotic spindle, cilia formation, intracellular transport

What is meant by the genetic code being degenerate?

More than one codon can specify the same amino acid

What is multiple alleles?

More than two options for alleles, but individual can still only have 2 I.e. A, B, AB, and O options for blood but individual still only has 2 of these

Who provided first direct evidence for chromosomal crossover and how?

Morgan - studied X-linked patterns of inheritance and flies and noted that body color, eye color, and wing shape did NOT assort independently

What is Morgan's experiment an what does it tell us about the impact of sex chromosomes?

Morgan induced mutation to fly to produce white eye'd male flies, then discovered through the non-Mendelian results of crosses that the gene was X-linked

What is long distance signaling? Examples?

Most common type in which signal crosses circulatory system E.g. hormones to target

Where are enhancers/silencers for genes located and what is their directionality?

Most located within a few hundred nucleotides upstream of the promoter, but in extreme cases up to 100,000 away or downstream from promoter or with introns Can exhibit bidirectional capability (orientation independent, meaning function in forward or reverse)

Structure/Function/Regulation of Non-Muscle Actin-Myosin

Most non-muscle cells contain small amounts of contractile actin-myosin II bundles that form transiently Regulated by MLCK, not tropnin Bundles form stress fibers that connect cell to ECM through Focal Adhesions or by Forming Circumferential Belt in epithelia that helps connect adjacent cells through Adherens Junctions Also form contractile ring that helps split daughter cells during last stage of cell division

What happens to M6P modified proteins that escape targeting and are exported by default?

Most of them are recaptured by M6P receptors missegregated to the plasma membrane

What is the process of protein glycosylation and where does it occur?

Most proteins synthesized in rER are glycosylated by the addition of common N-linked precursor oligosaccharides catalyzed by Oligosaccharyl Transferase in ER that transfers chunk of sugars from membrane lipid to side chain in protein (usually Asn) Glycosyltransfer Reaction happens almost immediately following translocation and prior to protein folding

cell walls

Mostly found in plants Provide structural strength, water resistance, and protection

What is a TF motif?

Motifs are domains or portions of domains that have very similar structure in many different proteins

Simple Diffusion

Movement down concentration gradient based on size and lipid solubility

What is Migration?

Movement of individuals between two ESTABLISHED populations that can alter allele frequencies

What is the purpose of lipids?

Movement of substances and energy storage

Two common reasons for position effects

Movement to position next to regulatory sequences so it is regulated by a different region Movement to heterochromatic/euchromatic region to up or down regulate transcription levels

What happens to the polypeptide after release from the ribosome?

Moves on to Golgi Apparatus for various modifications such as: Folding Addition or removal of amino acid Addition or removal of carbohydrates

What places in the body are protected by mucous membranes?

Mucous MURND Mouth Urinary Tract Respiratory Tract Nose Digestive Tract

What are the major features of molds?

Multicellular Fungi Hyphae - filaments of multicellular molds Mycelium - tangled network of hyphae Thallus - fleshy body

How do we calculate expected double crossovers on a three gene mapping?

Multiply the two m.u. Numbers by one another

How do you determine total magnification from power of ocular lens and power of objective lens?

Multiply them

What are multivesicular bodies? Purpose of ubiquitin tags?

Multivesicular Bodies - maturing endosomes that carry endocytosed membrane proteins destined for degradation in their intralumenal vesicles in addition to soluble content from early endosomes that is also destined for degradation Ubiquitin tags are added to the cytosolic domains of membrane proteins to dictate sorting into intralumenal vesicles The tags are then recognized by a series of cytosolic ESCRT protein complexes that bind sequentially and ultimately mediate the sorting process into intralumenal vesicles Receptors and signaling proteins bound to them are sequestered into endosomes to prevent continued action in cytosol and made available to digestive enzymes

Interpretation of Jacob and Monad's results?

Mutants - 100% because of constitutive expression in lacI- strain Merozygotes: Lac(-) - both lac operons repressed, <1% Lac(+) - both lac operon induced, 220%

Intergenic Suppressor Mechanisms - Multimeric Protein

Mutation in gene encoding one protein subunit that inhibits function may be suppressed by a mutation in a gene that encodes a different subunit. Double mutant has restored function AKA Compensatory Mutation

What is a heterochronic mutation?

Mutation that affects the timing of development in the cell Timing of fate of a specific cell lineage becomes out of harmony with the development of the rest of the cells of the organism

What was the first motor protein discovered and where was it discovered? Structure/Function?

Myosin II in skeletal muscle Two heavy and two light-chains: Heavy Chains - globular domain for force generation and elongated C-terminal tail that is responsible for dimerization Light Chains - regulation of myosin interaction Forms coiled-coil interactions between heavy chain tails that organize adjacent myosin molecules together via tail-tail interactions

Simplified Mitochondrial Important Mechanism

N-terminal import sequence recognized by TOM complex TOM scans across membrane to find TIM23 complex Unfolded protein fed through TOM and TIM complexes into matrix Peptidase cleaves of signal peptide

How many total ATP produced and Protons pumped per NADH and FADH2 molecule?

NADH - 10 protons pumped, 2.5 ATP per molecule FADH2 - 6 protons pumped (skips Complex I) and 1.5 ATP per molecule

Which protein complexes do NADH and FADH2 give their electrons to?

NADH - I and III FADH2 - II

What are the soluble intermediates of the ETC and why are they necessary?

NADH/NADPH/Succinate, necessary to move electrons from point of generation to points of usage

What type and with what selectivity do the NLSs direct nuclear proteins to the nucleus?

NLSs for import consist of a series of positively-charged amino acids placed anywhere on the protein Anything with the sequence will be imported Point mutations in just one of the set of 5 will prevent import (highly selective for this span)

Is lac I part of the lac operon

NO!

Is there any RNA primer in transcription?

NO!

What is the lacI gene of the lac operon?

NOT part of lac operon has own promoter, "i" promoter Constitutively expressed at fairly low levels Encodes lac repressor that functions as tetramer and only requires small amount to repress lac operon

How are SNAREs reset?

NSF and accessory proteins work together utilizing ATP to to dissociate the vSNAREs from the tSNAREs so they can be reused

What is the life cycle of the brain-eating amoeba and its scientific name?

Naeglaeria fowleri Starts out as cyst in warm waters, then activated to mobile Trophozoite. When humans in warm waters like natural hot springs, they penetrate the nasal mucosa to hang out in the CSF and brain tissue and cause Primary Amebic Meningoencephalitis

How are tRNAs named and how do they relate to their codons?

Named according to amino acid they bear Their anticodon is anti-parallel to the mRNA codon

Natural vs. Artificial Immunity

Natural - originating from natural exposure of pathogen Artificial - transfer of antibodies from a person or animal to a different person

Structure/Function of Nebulin and Titin

Nebulin - determines the length of each actin filament by extending the Z-disc toward the minus end of the filament and interacting with tropomodulin caps (half-lives of actin filaments in muscle are extremely long on the order of days, allowing very little turnover here) Titin - series of immunoglobulin-like domains that nfold one at a time when strain is applied and refold when pressure is released, creating spring-like structure - Anchor thick filaments to Z-discs

What are the three levels of compaction of the eukaryotic genome?

Negative Supercoiling around histones 30 nm fiber Nuclear Matrix

Which type of supercoiling would left-hand twisting introduce to DNA?

Negative Supercoiling, making it more compact but also promoting DNA functions involving strand separation

How does the timing of negative feedback result in different responses?

Negative feedback makes overall less sensitive systems Longer the delay, longer the oscillations

Which direction are amino acids always read?

Negus Clay N->C

What's the difference between neutral lipids and phospholipids?

Neutral lipids - energy storage, nonpolar (oils and fats) Phospholipids - polar unit, membrane structure

Which types of cells are phagocytes

Neutrophils Macrophages Monocytes (phagocytes that leave bloodstream and become tissue specific like dendritic cells, mast cells, osteoclasts, etc. and produce cytokines)

What is a conglomerate in gene flow?

New, recipient population is the conglomerate

What are Nick's in DNA replication?

Nicks are Ligase identifiers for fragments but also little methylation made in mismatch Repair that mark the areas for protein action

How was the genetic code experimentally determined in the 1960s? What type of science was used?

Nirenberg and colleagues used cell-free translation system and added radio labeled amino acids to these extracts so that the synthesized polypeptides would be easy to detect Discovery-based science

What are complimentary base pairs? How are they matched

Nitrogenous base pairs that match up with one another in DNA Terrible Mnemonic inappropriate for the internet Adenine - Thymine Guanine - Cytosine

Do prokaryotes have introns?

No

Does splicing require additional energy from external source?

No

What is the role of DNA pol Beta?

No DNA replication Removal of incorrect bases from damaged DNA

How does smooth muscle contraction initiation differ?

No Troponin Calcium still used, but through different signaling pathway leading to slow, sustained contractions as opposed to rapid transient contractions of skeletal muscle Smooth muscle myosin II hydrolyzes ATP 10X slower -> slower fire rate Ca release -> Ca binds Calmodulin -> activates myosin light chain kinase (MCLK) -> phosphorylates myosin light chain -> smooth muscle myosin II interacts with actin

Coordination/Action of Myosin in Sarcomeres

No direct coordination between heads - they must just remain bound for extremely short periods of time to avoid opposing contractile forces Each head cycles approximately 5 times/sec causing contraction rates of 15 um/sec and shortening by 10% in 1/5th of a second Heads do not all fire with every contraction

How many ribosomes can move across a single strand of mRNA?

No limit!

Can all bacteria form endospores?

No!

Can a chi square test prove a hypothesis correct?

No! just evaluates whether or not data and hypothesis have good fit

Are the DnaA boxes and AT-rich region the same thing?

No, DnaA boxes are bound by DnaA protein, but the regions next to them are the AT-rich regions that they strain to separate

Does the signal enter the cell in the first messenger process of epinephrine?

No, NEVER

Is supercoiling an issue in elongation? Why or why not?

No, as the DNA reminds back into double helix behind open complex

Do enzymes change the reaction or get consumed by it?

No, they do not do either

Are cytotoxic T cells phagocytes?

No, they inject a chemical to cause apoptosis

Are all microbes alive?

No, viruses are an example of acellular microbes

What are the maternal effects? example? mechanism and impact?

Non-mendelian genetics in which reciprocal crosses exhibit different genes i.e. the snail shells, genotype of mother determines phenotype of offspring and male has no effect

What are virusoids?

Non-self-replicating ssRNA molecules that require helper virus to cause disease Can be carried inside helper virus capsid Affect plants almost exclusively

What are intergenic regions?

Non-transcribed DNA between adjacent genes

What is nondisjunction? How does it play into Down's?

Nondisjunction - failure to separate chromosomes appropriately during anaphase Downs - failure of chromosome 21 to segregate properly

What type of catalytic function to the Receptors of GPCRs exhibit?

None

What molecules diffuse simply?

Nonpolar inorganic gases Small organic molecules

What is the two hit hypothesis?

Normal people have two healthy copies of alleles - 5% chance of cancer from environment If a person inherits one mutated allele towards a cancer, then they are heterozygous for that mutation and their risk increases to 80% since they only require one additional mutation from environment to induce cancer

What is the role of nosocomial infections in epidemiology?

Nosocomial infections are diseases acquired acquired by healthcare facilities

Are all nondisjunctions trisomy? All trisomy nondisjunctions?

Not all nondisjunctions are trisomy, but all trisomy disorders are nondisjunctions

What makes sex chromosomes unique?

Not fully homologous, only homologous on very short region

Which eukaryotic DNA have primary function of replicating DNA and which types?

Nuclear DNA - alpha, delta, epsilon Mitochondria DNA - Gamma

What happens in prometaphase?

Nuclear envelope breaks down Mitotic spindle beings to capture chromosomes

What distinguishes Eukarya?

Nuclei Membrane-bound organelles with specialized functions Can be multi or unicellular

Which type of macromolecule contains a phosphodiester bond?

Nucleic Acids

Nucleosides vs. Nucleotides

NucleoSides are Single NucleoTides can have Three phosphates

What is the name for the region of prokaryotic DNA containing the bacterial chromosome?

Nucleoid

What is a relaxosome?

Nucleoprotein complex encoded by F factor that recognizes oriT and catalyzes separation of DNA strands

What is the difference between nucleotides and nucleosides?

Nucleotides - sugar, phosphate group, nitrogenous base Nucleosides - just base and sugar (no phosphate)

What is the largest organelle?

Nucleus

Which organelle is the genetic control center?

Nucleus

What is culture density?

Number of cells / Volume

Mutation Frequency

Number of mutant genes divided by total number of genes in a population

Define incidence of morbidity

Number of new infections per some proportion of population

What is median infectious disease (ID50)?

Number of organisms needed to cause disease in 50% of inoculated subjects

What is median lethal does (LD50)?

Number of organisms required to kill 50% of inoculated subjects

What is a viral titer?

Number of virions per unit volume (concentration of viruses)

Define prevalence

Number or proportion of diseased individuals in population at particular point in time

What is the name of the feature that describes the resolution properties of a lens?

Numerical Aperture Higher NA = more resolution

How do maternal genes affect the directionality of the oocyte? What are the morphogens that set up body axes?

Nurse cells are localized asymmetrically towards the anterior end of the oocyte, and maternal gene products enter one side of the oocyte that becomes the anterior of the embryo Bicoid, Nanos, Torso, and Toll

What are the three operator sites for lac repressor binding? How do they function?

O1 - next to promoter (slightly downstream) O2 - downstream in the lacZ coding region O3 - slightly upstream of promoter Lac repressor must bind to two of the three operators to cause repression, but must be O1/O2 or O1/O3

Between donors and acceptors in cellular respiration, which are oxidized and which are reduced?

OIL RIG - oxidation is loss reduction is gain (of electrons) Donors are oxidized Acceptors are reduced

Reasons why cells may undergo apoptosis? (4)

OREQ Organ size regulation Removal of unwanted neurons during development Elimination of cells between digits to create fingers (or some other kind of necessary developmental elimination such as pruning useless nerve connections, loss of human embryonic tail) Quality Control

What is a phenotype and can they change over time?

Observable characteristic Yes, may change in response to cell's environment or life cycle (genotype remains constant)

How did Antonie van Leeuwenhoek (1632-1723) contribute to microbiology?

Observe tiny organisms he called "animalcules" in rain water

What volume of the average cell is mitochondria? What shape are they? How are they transported?

Occupy up to 20% of the volume of the cell Shape is constantly changing as they are constantly moving, dividing, and merging Transported along micotubules

Define outbreak

Occurrence of a disease in a significant portion of the population

Where does synthesis of lipids occur in the cell, how does it occur, how are the phospholipids placed, and how are the head groups added?

Occurs in cytosol Grown on acetyl groups Synthesized in ER, transported in vesicle or small soluble lipid-transfer protein to membrane, then floppase to place in outer leaflet if needed Polar head specialization happens after already in membrane Membranes can be fattened up, blebbed off, then transferred between membranes through cytosol in vesicles

What is the result of odd polyploidy? Benefits?

Odd number of chromosomes usually results in sterility due to unequal segregation in formation of gametes However, we often seek it out despite this sterility for desirable seedless fruit (triploid watermelon and bananas) and seedless flowers

How do plants maintain pH balance and turgor pressure?

Often through many special lysosomes (vacuoles) within cell wall that balance maintain these gradients

What role do oligosaccharides play in the quality control of misfolded proteins?

Oligosaccharide trimming provides ticking clock for protein folding Trimming occurs at fixed rate, and if protein hasn't successfully folded by time that it is targeted for degradation, it is exported to cytosol and degraded Calnexin is membrane-bound chaperon protein that keeps unfolded proteins in the ER and binds to incompletely folded proteins, removing a terminal glucose before releasing it back to ER where glucosyl transferase checks them for correct folding If they are still uncorrectly folded, it transfers a new glucose on to them and cycles them back to calnexin (by increasing their affinity for it with the glucose attachment)

Purposes/Method of membrane protein glycolsylation

Oligosaccharides added in lumen of ER and Golgi to mark for transport, then always positioned on extracellular side Protects cells against mechanical and chemical damage and prevents unwanted cell-cell interactions Also antigen-communication for immune system

What hypothesis did George Beadle and Edward Tatum develop in regards to the central dogma and how did they test it?

One Gene - One Enzyme Hypothesis Analyzed more than 2,000 strains of Neurospora crassa (bread mold) that had been irradiated to produce mutations and analyzed enzyme pathways for synthesis of vitamins and amino acids They tested the mutants on various nutrient plates to see what enzymes in the pathways were missing Results: defect in one gene prevented synthesis of one protein (enzyme) at one step in the pathway

What is the disk-diffusion method of testing effectiveness of antiseptics and disinfectants?

One in lab where apply agent to sterile disc and place in bacterial lawn and measure

Structure/Function of Complex IV

One of most dangerous reaction centers in all of biology as must receive one e- at a time to reduce O2, and each of the intermediates along the way are highly reactive oxygen species (ROS) Requires 4 cytochrome C's to fully reduce O2, and pumps 4 H+ in the process Per NADH, only 2 e' provided, providing only 2 cytochrome C's to this complex and thus only half-reducing O2 and pumping 2 H+ per NADH from this complex (half the other complexes) For complete O2 reduction (from 2 NADH molecules), 4 protons are pumped, 4 are used in formation of water, for a total of 8 protons lost.

What is a processive enzyme?

One that remains bound to any of its substrates In the case of polymerase, processivity refers to the ability of the enzyme to remain bound longer to synthesize for longer periods of time before falling off, speeding the rate of synthesis

What does it mean for DNA to by polycistronic? Which domains demonstrates this quality

One transcript has instructions for multiple proteins Only in prokaryotes

What types of cells respond to signaling molecules?

Only cells with the appropriate receptor for the signaling molecules will respond directly to that signal

Which domains have mRNA that undergoes splicing?

Only eukaryotes

What does recessive refer to in genetics?

Only expressed when containing two of this allele, otherwise subservient to dominant traits

How does DNA Pol Alpha in eukaryotes operate?

Only polymerase to associate with primase, and does so by creating a complex with primase to synthesize a short RNA-DNA hybrid primer (10 RNA nucleotides followed by 20-30 DNA nucleotides) before DNA epsilon or delta takes over

Gap junctions

Open direct channels that allow ions and small molecules to pass directly from one cell to another

What is the general trend of inducible vs. repressible regulation?

Operons involved in catabolism typically inducible (substance to be broken down substance acts as inducer) Operons involved in anabolism typically repressible (like tryptophan preventing its own overproduction by its presence as corepressor)

What is photophosphorylation?

Opposite of oxidative phosphorylation in which water makes NADPH and ATP

What is the name for the origin of replication in E. coli?

OriC (ORIgin of Chromosome Replication)

How can conjugation be useful for genetic mapping?

Orientation of incorporated F factor into genome is random Closer to F Factor - higher likelihood of transfer

Smooth muscle organization

Oriented in various directions to allow overall narrowing and shrinkage

What is the ER Signal Hypothesis? How was it tested?

Originally proposed simplification of translocation across ER membrane Essentially signal peptide directs free ribosome to translocator that opens up and feeds through while cleaving off peptide signal -Set up in vitro translation system -Made proteins with signal sequence on them, then added microsomes, then incubated together and then removed microsomes and checked if anything was in there. Showed that none of those proteins made it into the microsomes, thus there was not Post-translational co-translation -Reconducted with microsomes and ribosomes all together -Also showed that proteins in the microsome in this second part of the experiment lacked the signal sequence - proof of cleavage

Attenuation beyond trp and summarized

Other operons for amino acids also have Leader genes (i.e. hisL) with codons encoding their own amino acid within them for the same reason - to allow pausing at these codons in low presence of the amino acid to facilitate production of more of the amino acid

How does genetic drift relate to fixation?

Over long run, genetic drift favors loss or fixation of an allele Fixed allele is monomorphic and cannot flucturate

What role might telomerase play in cancer?

Overactive telomerase and long telomeres may be viewed by cell as signal to replicate since cell is still very young, leading to uncontrollable cell proliferation

What is a Type III Immune Hypersensitivity?

Overproduction of IgG, IgM, and IgA antibodies form immune complexes in tissues, leading to tissue damage Excess recruitment, activation, and inflammation Can lead to autoimmune diseases

What is the difference between oxygenic and an oxygenic photosynthesis?

Oxygenic - water as electron donor -> O2 byproduct Anoxygenic - other electron donors like H2S (sulfur byproduct) and thiosulfate (sulfate byproduct, egg smell)

What are the four types of chromosomes based on centromere location and how are the arms labeled/drawn?

P arm (petite) = shorter arm, always drawn on top Q arm always drawn on bottom as longer arm

Types of ATP-Driven Pumps

P-Type - Phosphorylate themselves - primarily pump ions ABC Transporters - ATP-Binding Cassette Transporters - primarily pump small molecules V-Type - Multi-subunit, turbine-like proteins that pump protons into various membranes to change pH or electric gradient F-Type - reverse, using H+ to drive ATP production i.e. PMF in oxidative phosphorylation

Structure/Function of PSII and its P680 Special Pair

P680 special pair uses Mn cluster to have extremely powerful redox potential (1270 mV) to conduct four sequential electron and proton removals from two molecules of water to create oxygen High potential for ROS's again Mn cluster does this by sequestering water and reactive intermediates within the complex until the reaction is complete

Types of quantitative traits

PBAD Physiological Behavioral Anatomical Diseases

Phagocytic Process

PIPs stimulate actin polymerization which then stimulates the formation of pseudopods that extend and engulf large particles

What is the role of Phosphoinositides?

PIs are modified membrane lipids with the inositol head group that aid in the recruitment of the adaptor proteins They go through a series of phosphorylation and dephosphorylation at various carbons that result in recognition by different proteins and are named by these interactions

Roles/Locations of Photosystems?

PS II is the first in the chain (named in order of discovery) that is found in stacked grana thylakoids and is responsible for charge separation functionality at the heart of photosynthesis PS I is the second in chain that is found in unstacked stroma thylakoids and provides a boosts to the electrons produced in PSII to make them high enough energy to reduce NADP to NADPH

Special function of effector B-cells? (what do they release)

Packed with extra rER to produce tons of the correct antibody and spitting them out at rate of 2000/second into blood for 4-5 days until they die

What are the two types of local signaling?

Paracrine - one cell to another cell Autocrine - within same cell

Parallel vs. Contractile Bunding Formation. Reason for nomenclature and which proteins utilized

Parallel - held together by Fimbrin proteins that closely hold actin together, preventing access to motor proteins and therefore prevneting them from being contractile Contractile - cross-linked by Alpha-Actinin dimers that interact with each other through elongated dimerization domain, facilitating motor protein association and contraction

What are Chromalveolata and their major features?

Parasitic, singe-celled eukaryotes with complex life cycles Has apical complex on one end with organelles, vacuoles, and cytoskeleton that help them infect their hosts

What are the three possible outcomes for asci?

Parental Ditype (PD) - same pairs of genotypes as parental cells (no crossover) Tetratype (T) - two parental pairs, two recombinant pairs (single crossover between two chromosomes) Nonparental Ditype (NPD) - all recombinant offspring (double crossover between all four chromosomes)

What is a sex pilus?

Part of bacteria that reaches out in conjugation to contact the other bacteria and form the cytoplasmic bridge

What are merozygotes?

Partial Diploids that have two copies of a gene, one in a plasmid and one in the chromosome

Role/Process of ESCRT proteins in formation of multivesicular bodies

Passed along from one ESCRT complex to the next ultimately mediating the formation of intralumenal vesicles

Structure/Function of Complex I

Passes electrons from NADH to FMN (a quinone), then through 8 Fe-S clusters in the matrix arm each with increasing redox potentials then to CoQ This pumping of electrons causes a conformational shift between the membrane and matrix arms, and that shift is what leads to the pumping of the 4 H+ into the IMS CoQ moves through the membrane arm on to Complex III through the membrane

What is the histone code?

Patterns of covalent histone modifications that occur together and act as code for overall chromatin modification

Ionizing Radiation Mechanism

Penetrate deeply into biological molecules creating chemically reactive molecules termed free radicals and causing base deletions, oxidized bases, single nicks in DNA strands, cross-linking, chromosomal breaks, etc.

What type of bond forms proteins?

Peptide bonds

What is the difference between pericentric inversion and paracentric inversion?

Pericentric - inversion over centromere ParAcentric - A single side of the chromosome

Persistence and Turnover in Biosignaling

Persistence - duration of effects caused by signal Turnover - rate at which molecule is removed from a system Generally, they are inversely correlated

What is endoploidy? Example in humans?

Phenomenon in which diploid animals produce tissues that are polyploid i.e. liver cells can be 3n, 4n, 8n

What is coupling and in which domains is it found?

Phenomenon of translation beginning before transcription ends Occurs only in bacteria since these processes occur in same place, unlike eukaryotes

What is incomplete dominance?

Phenotype of the HT somewhere between phenotypes of HM-d and HM-r I.e. red and white snapdragon flowers producing pink ones

Structure/Mechanism/Derivation/Regulation of cAMP?

Phosphate Group triple-bound to ribose of adenosine It binds to regulatory subunits of cAMP dependent PKA causing them to dissociate as activated kinases Regulated by competing reactions of adenylyl cyclase and cAMP phosphodiesterase

What is the major component of most eukaryotic cell membranes? (what specific phospholipid)

Phosphatidylcholine

What type of bonds hold together base pairs? Phosphate groups and sugars?

Phosphodiester Bonds exist between sugar and phosphate groups to connect nucleotides together on the same strand Hydrogen Bonds pair the nitrogenous bases between strands

What converts cAMP back to ATP to slow down or reverse glycogen storage release?

Phosphodiesterase

Mechanism of Gq GPCRs

Phospholipids are the second messengers The activated alpha subunit activates phospholipase C's (in this case, C-Beta) Action of phospholipase C-Beta is to remove phosphoinositide headgroup from PIP2 groups creating 2nd messengers of both DAG and PIP3 that are involved in activating PKC

How does vision utilize GPCRs?

Photon of light -> Rhodopsin GPCR changes conformation as shift to all-trans-retinal -> hyperpolarization (opposite of other senses) -> NT release

Where does energy in electrons moved during cellular respiration originate from?

Photosynthesis

Chloroplasts Function

Photosynthesis in plant cells Synthesize fatty acids and amino acids Immune response

3 Types of Nonspecific Immunity Defenses

Physical (barriers, mechanical defenses, microbiome) Chemical (cytokines, antimicrobial peptides) Cellular (granulocytes, agranulocytes)

What is a kinetochore?

Piece of protein on centromere where kinetochore microtubules bind

How does the Etest dilution test work to determine the effective dose of an antibiotic?

Place strip on lawn culture with gradient of antimicrobial concentration

Define reservoir in the context of epidemiology

Place where active infectious agents reside Can be living/nonliving, natural/artificial, long-lasting/transient

What commonly exhibits polyploidy and how is it beneficial?

Plants commonly do and these strains of plants display agricultural benefits like larger size and more robust that we select and breed for ideal crop

What are the differences between plant and animal cells?

Plants have cell walls, chloroplasts, and plasmodesmata

What are plasma protein mediators? Examples?

Plasma - Fluid (non-cell) part of blood Numerous proteins in this plasma among other substances have antimicrobial properties allowing that can be increased and activated by inflammation and start a complement cascade leading to opsonization, inflammation, chemotaxis, or cytolysis

Where do prokaryotes conduct photosynthesis?

Plasma membrane NOT the cell wall!

Where is the F factor encoded?

Plasmid, extrachromosomal and encoding for own survival

What does the presence of phosphatidylserine in the outer leaflet signal for various types of cells (2)?

Platelets - activates blood clotting Others - marks cell for destruction

What is different about the asymmetric ends of actin in terms of structure and function?

Plus end - barbed - grows faster Minus end - pointed end - slower growing

State and define the key features of three types of common source spread infections

Point Source Spread - common source is present for short time Continuous Source Spread - Common source is present for extended periods of time Intermittent - source appears, disappears, and reappears multiple times; most difficult to track down

What's the difference in constitutive secretory pathway of polarized vs. unpolarized cells?

Polarized (i.e. endothelial with apical and basement membranes) - secretion specific to correct side Unpolarized - truly unregulated and randomly excreted to PM

How do voltage-gated sodium channels activate one another?

Polarized cell - closed, stable channel Depolarization -> positive alpha helices attract to exterior and open channel in state that is only energetically favorable when membrane depolarized Repolarization -> refractory period induced by inactivation gate that flips closed

How are lab animals used to generate polyclonal and monoclonal antibodies to an antigen?

Polyclonal - Injecting pathogen or antigen into lab animal and having their immune system make antibodies for the pathogen, then extracting their blood serum Monoclonal - produced in vitro in tissue culture; isolation of B cells that produce specific antibody for epitope and fusion with cancerous cell in culture to multiply (more expensive)

What is the role of the Polycomb and Trithorax Genes?

Polycomb Gene represses expression of homeotic genes in regions of embryo where they should not act by remodeling chromatin into closed conformation Trithorax Gene promotes expression of homeotic genes in regions where they should act by remodeling chromatin into an open conformation

What is PCR used for and what are the steps?

Polymerase Chain Reaction is used to replicate DNA Steps: Replicatin DNA all DAE, every DAE 1. Denaturation - heat to 95-96 C to uncoil DNA 2. Annealing - cool to around 55 C for primers to bind each side of desired strand 3. Extension - polymerase extends chain Repeat to 2^n desired copies

What is it called when DNA pol alpha is switched for epsilon or delta?

Polymerase Switch

What is the role of DNA Polymerase III?

Polymerizes in 5' -> 3' direction and proofreads strands

Monomorphic vs. Polymorphic Genes? Threshold for Monomorphism?

Polymorphic - most genes - many traits display variation within a population; result of two or more alleles that influence phenotype; commonly exists as 2+ alleles in a population Monomorphic - Predominantly exists as single allele in population; when single allele found at least 99% of all cases, gene is monomorphic

How is synthetic RNA created?

Polynucleotide Phopshorylase used to catalyze covalent linkage of ribonucleotides into RNA in random order

What is the difference between polyunsaturated and monounsaturated fats?

Polyunsaturated fats have multiple double bonds and monounsaturated fats have a single double bond

How do portals of exit relate to the spread of infectious disease?

Portals of exit are places where infectious agents leave host i.e. orifices, body fluids, coughing/sneezing, etc.

Two types of assortative (nonrandom) mating?

Positive - occurs when individuals more likely to mate due to similar phenotypic characteristics Negative - when individuals with dissimilar phenotypes mate more frequently

What is the difference between positive and negative control in transcriptional regulation?

Positive Control - regulation by activator proteins Negative Control - regulation by repressor proteins

What is the purpose of precipitin reactions? How are antibodies involved?

Precipitin - visual antibody-antigen complex (need right ratio of antigen and antibody for maximal visibility) Ouchterclony Assay - way to determine whether antiserum has antibodies against particular pathogen by placing antigens in central well and antisera in outer wells and viewing for precipitin ring formation (agar gel holds antigen/antibodies in place but allows precipitin rings to form between them) Diagram - only Well 1 is positive for antibody

Animal Cells and Tonicity

Prefer isotonic Shrivel/die in hypertonic Cell lysis in hypotonic (Explode)

What is the role of topoisomerase? Another name for it?

Prevents supercoiling from unwinding Gyrase

What is the purpose of primary and secondary antibodies used in enzyme immunoassays?

Primary - bound to inside of plate wells Secondary - recognizes only primary antibody/antigen complex (has marker molecule attached to it, fluorescent or color developing)

Primary vs. Opportunistic Pathogen

Primary - causes disease regardless of host's microbiota or immune system Opportunistic - causes disease only when host's defenses are compromised (by other pathogen, noninfectious disease, stress, malnutrition, etc.)

What is the difference between primary and opportunistic pathogens?

Primary - causes disease regardless of host's microbiota or immune system Opportunistic - causes disease only when host's immune system is compromised

Primary vs secondary active transport

Primary - direct use of energy Secondary - uses favorable concentration gradient created by primary active transport to move another molecule with diffusion

Primary vs. Secondary Immunodeficiency

Primary - inherited/genetic Secondary - acquired impairment of B/T cell Function (either or both) - commonly caused by malnutrition, diabetes, hepatitis, HIV, immunosuppressive treatments, chronic illness

What are the purposes of the reagents in a gram stain?

Primary Stain - crystal violet, stain purple Gram's Iodine - chemically bond alkaline dye to bacterial cell wall, if possible Decolorizer - alcohol to wash off any unbound crystal violet Counterstain - safranin, to color decolorized cells pink (but not strong enough to overcome the violet stained cells)

What are Excavata and their major features?

Primitive, typically non-pathogenic, metabolically-limited eukaryotes with complex shape, structure, lifestyle Has stigmata (eye spots)

What are lysosomes and what do they contain?

Principle site of intracellular digestion Composed of hydrolytic enzymes including proteases, nucleases, glycosidases, lipases, phospholipases, phosphatases, sulfatases (essentially all the -ases)

What is the function of the Golgi Apparatus?

Processes proteins and lipids and carbohydrates Packages molecules

What is Combinatorial Regulation?

Processing of multiple signals to elicit response and requiring of specific combinations of external signals to determine how to behave

When are the product rule and sum rule used?

Product Rule - 2 independent events occurring together Sum Rule - if there are 2+ ways to obtain same outcome, chance event will occur; not specific to order

What is pathogenesis and its 4 stages?

Progression of Disease 1. Exposure - encounter with pathogen 2. Adhesion - attaching to parts of the host 3. Invasion - pathogen disseminates through tissue near portal of entry 4. Infection - pathogen establishes itself within the host

How many types of ribosomes do prokaryotes and eukaryote have?

Prokaryotes - one type in cytoplasm Eukaryotes - one type in cytoplasm and another found in organelles (mitochondria, chloroplasts)

Differences between prokaryotes and eukaryotes

Prokaryotes have circular DNA in their nucleotide, eukaryotes have linear dna in their nuclei Prokaryotes do NOT have membrane bound organelles

What are methanogens?

Prokaryotes that produce methane gas

What is the start codon and associated amino acid in prokaryotic and eukaryotic?

Prokaryotic - AUG, formylmethionine Eukaryotic - AUG, methionine

How do prokaryotic and eukaryotic reproduction differ?

Prokaryotic - asexual - fast and accurate Eukaryotic - sexual - goal to divide DNA equally and precisely

Where do eukaryotic and prokaryotic transcription take place?

Prokaryotic - cytoplasm Eukaryotic - nucleus

What are the key differences in prokaryotic vs. eukaryotic gene expression mechanisms?

Prokaryotic - immediate needs handled by operon mechanism Eukaryotic - has more time sensitive needs, some immediate and some over long term, so does not use operon but instead more complicated mechanisms involving crazy folds and many different transcription factors and players along complicated gene expression mechanism

What are the key differences in prokaryotic vs. eukaryotic transcription/translation?

Prokaryotic - no nucleus, free ribosome, RNA polymerase stops are terminal sequence, and mRNA includes only coding mRNA and 3 and 5' UTRs Eukaryotic - start in nucleus, RNA polymerase reaches polyadenylation sequence to stop, must leave for rER, must splice pre-mRNA to mRNA, mRNA has 5' cap and poly A tail in addition to UTRs and exon

What are the sizes of prokaryotic ribosomal subunits? Eukaryotic?

Prokaryotic: 30S small subunit and 50S large subunit make 70S complete ribosome Eukaryotic: 40S small and and 60S large make 80S complete ribosome

What are the DNA elements of the lac operon?

Promoter - bind RNA polymerase Operator - bind lac repressor protein CAP site - bind Catabolite Activator Protein

Process of complement activation

Promotes inflammation and recruits phagocytes

In which direction is DNA Pol I's proofreading ability? Exonuclease ability?

Proofreading - 3'->5' (backup) Exonuclease - 5'->3' (remove RNA primers, replace with DNA) This is referred to as a 5' exonuclease!

How is the nuclear membrane broken down and reformed during mitosis?

Prophase - Lamins, the nuclear anchors that bind chromosomes and the inner leaflet of the nuclear membrane, are phosphorylated to along with NPC proteins, breaking down membrane and freeing chromosomes Early Telophase - Lamins are dephosphorylated and rebind inner nuclear membrane and chromosomes, establishing pieces of initial nuclear membranes around individuals chromosomes Late Telophase - Nuclear membranes around individual chromosomes fuse together to complete nuclear membranes Interphase - Fusion of enveloped chromosomes to reform complete nucleus

At what stage of meiosis does crossover occur?

Prophase I

What is Jean Baptiste Lamarck's Theory of Physiological Adaptation?

Proposal that physiological effects (e.g. use/disuse) determine whether traits are passed along to offspring

What is the wobble hypothesis?

Proposed by Francis Crick in 1966 3rd base of codon most variable to retain fidelity and is the wobble base Allows tolerating certain types of mismatches

What are the many purposes of glycosylation?

Protect proteins from degradation by adding oligosaccharides Make folding intermediates soluble to prevent their aggregation Provide the ticking clock by glyco-code that encodes folding progress Cell-cell recognition/signaling Sorting of proteins in the Golgi

How are GPI-anchors attached to proteins?

Protein is initially membrane bound through C-terminal peptide Protein is then cleaved from C-terminal peptide and reattached to amino group on GPI in membrane

What is the process of rho-dependent transcription termination?

Protein knows as rho binds to "rut" site in RNA and moves toward 3' end RNA polymerase transcribes a region that forms a stem-loop and then proceeds to the terminator; stem loop causes RNA polymerase to pause Rho protein takes advantage of pause to catch up to open complex and separate RNA-DNA hybrid

Define exotoxin

Protein molecules released by pathogenic bacteria, usually Gram-positive but some Gram-negative

What are structural genes?

Protein-encoding genes or genes encoding actual amino acid sequence of polypeptide

How do the kinetics of protein-mediated transport differ form simple diffusion?

Protein-mediated transport approaches a vmax the same way an enzyme would, while simple diffusion maintains a relatively linear relationship between concentration gradient and transport speed

What are the two types of interactions that coating proteins must facilitate?

Protein-protein - drive coat formation and structure of resulting vesicle Protein-Lipid - retain lipid proportions and provide barrier to free diffusion of contents

What is unique about the reading of major grooves? What uses this technique?

Proteins can read these major grooves without unzipping to identify which bases Can read hydrogen bond donors, acceptors, and polar hydroxyl groups, and determine and interact Restriction enzymes and transcriptional regulating proteins use this technique

What are viral protein spikes?

Proteins protruding from capsid protein involved in attachment and host entry

What is a regulatory unit?

Proteins that bind to the DNA and control transcription in an operon; regulatory sequence of the lac operon is the operator and promoter

What are Maturases?

Proteins that enhance rate of splicing

What is a caretaker gene?

Proteins that scan DNA and check for mutations before it goes into the cell cycle

Types of forces mediated by proteoglycans vs. collagen?

Proteoglycans - Compressive Collagen - Tensile

What are the protofilaments of microtubules? How are they arranged and stabilized?

Protofilaments are the chains of stacked tubulin heterodimers that make up the length of the microtubules, with 13 arranged in a circle to form the hollow ring Stabilized by longitudinally between heterodimers and laterally between protofilaments Slightly staggered between protofilaments

What are the purines? Pyrimidines?

Pure And Godly = #Extra (rings) Purines - Adenine and Guanine - double (extra) ring structure Pyrimidines - single ring structure - cytosine and thymine

Which of the nitrogenous bases are the purines and pyrimidines?

Purines - Pure And Godly - #Extra rings (adenine and guanine are two-ringed) Pyrimidines - Cytosine, Thymine, Uracil

What is the purpose of viral neutralization assays? Process?

Purpose - quantify antibodies in patient serum for virus by serum neutralize virions 1. Serial dilution is carried out on a serum sample 2. Each dilution then mixed with standardized amount of suspect virus 3. Any virus-specific antibodies in serum will neutralize some of virus 4. Suspension added to host cells in culture to allow any non-neutralized virus to infect cells and form plaques after several days 5. Titer = Reciprocal of highest dilution showing 50% reduction in plaques

What is the purpose and method of staining?

Purpose is to increase contrast and/or visibility by applying stain color to specimen

What are some methods for cancer to develop?

Pyrimidine Dimer from UV rays causes two pyrimidines to link in DNA chain, causing mutation Genetic mutations in cell replication Environmental damage

What is the purpose of a microbial death curve? D-value?

Quantitative measure of how effective an antimicrobial regiment is D-Value - DRT - Decimal Reduction Time - Time it takes to produce 90% reduction

What are continuous traits

Quantitative traits that don't fall into discrete categories like height and weight

What are the components and purpose of the endomembrane system?

RER (but NOT sER) Vehicle Golgi Apparatus Lysosomes Synthesize cell components and move materials around

Is the double helix considered right or left-handed in terms of twist?

RIght-handed

What are the three RNA polymerases involved in eukaryotic transcription?

RNA Pol I - transcribes all rRNA genes (except for 5S rRNA) RNA Pol II - transcribes all structural mRNAs and some snRNA genes needed for splicing RNA Pol III - transcribes all tRNA genes and 5S rRNA gene and microRNA genes

How is Prokaryotic transcription initiated? Role of Helix-Turn-Helix Structure?

RNA Polymerase Holoenzyme composed of core enzyme of 5 subunits and Sigma Factor of one alpha subunit binds loosely to DNA and then scans along DNA until it encounters promoter SIgma factor recognizes -10 and -35 sequences Helix-Turn-Helix Structure within sigma factor involved in tighter binding to DNA

What is the role of RNA polymerase in lac operon?

RNA binds to the promoter of the lac operon and creates proteins that break down lactose and transport it

How does transcription/translation differ from replication?

RNA created (uracil replaces thymine, deoxyribose replaces ribose) Purpose is to create proteins instead of additional DNA

What are introns?

RNA that is removed by enzyme complex called Spliceasome

What are exons?

RNA that will be kept in the final mRNA going to be translated

What are Reactive Oxygen Species and their role in mutations?

ROS include Hydrogen peroxide, superoxide, and hydroxyl radicals Buildup blocked by superoxide dismutase, catalase, antioxidants like NADPH ROS cause Oxidative Stress - imbalance between production of ROS and organism's ability to break them down which in extreme levels can lead to oxidative DNA damage

Persistence/Turnover of RTK and Ras activation

RTK and Ras activation are short-lived and rapidly reversed by tyrosine-specific protein phosphatases and Ras-GAPs, so another step is required for signal propagation (next card)

What is the mechanism of Rab proteins guiding destination?

Rab proteins can localize to the vesicle itself, the target membrane, or both In the shown example, a Rab-GTP on the vesicle docks to a Rab effector protein on the target membrane, pulling it to the membrane with the help of SNARE proteins from the membrane and vesicle together to facilitate fusion of hte membranes Rab-GAP hydrolyzes the Rab-GTP on the vesicle to dissociate it, and then Rab-GDP is bound by a GDI protein to keep Rab soluble and inactive

What type of energy is light?

Radiant energy (kinetic)

What is genetic drift?

Random and rapid change in allele frequencies due to random fluctuations i.e. natural disasters

What are the break point and position effects

Rare cases in which inversion alter phenotype Break Point Effect - inversion break point occurs in a vital gene Positon Effect - gene repositioned in way that alters its gene expression

What are Ras proteins and their role in RTKs?

Ras proteins are monomeric GTPases that function as molecular switches RTKs often contain Ras-GEFs that act via Ras proteins

Where is chlorophyll a located?

Reaction center

What protein kinase does insulin use?

Receptor Tyrosine Kinase

receptor-mediated endocytosis

Receptors recognize specific molecules Receptors collect in coated pit - network of proteins (clathrin) coat and reinforce cytoplasmic side

Essential features of natural killer cells and how they participate in nonspecific immune responses

Recognize abnormal cells by not MHC markers and kill them by releasing Perforin (creating pores in target cell) and Granzymes (proteases that lead to apoptosis) Infected cells can signal they have been invaded and ask for the nK cells to kill them

Where does genetic variability stem from?

Recombination (PI) - incalculable Fertilization (which haploid cell) - chances of same genetic gamete 1 in 70 trillion Anaphase I (which chromosomes to which pole) - 8 million options

Define chemotaxis as it pertains to the complement system

Recruitment of more adaptive immune cells

Define inflammation as it pertains to the complement system

Recruitment of more plasma mediators

How do surfactant control microbes?

Reduces surface tension of water, disrupting cell membranes Gets in between fatty acids

What are Nucleosome Free Regions and their significance?

Region free of histones typically about 150 bp in length Many genes are flanked by NFRs and well-positioned nucleosomes forming transcription activation site with enhancer and promoter regions

What region in prokaryotic DNA is the promoter?

Region from -35 to -1 with -35 and -10 sequences that direct exact location for initiation of transcription -10 = TATA Box

What is a TATA box?

Region of successive thymine and adenine nucleotides within promoter about 30 base pairs up from the start that tells TF where to begin

What are CpG islands?

Regions 1,000-2,000 nucleotides long that contain C's paired to Gs Common in housekeeping genes Un-methylated so they tend to be highly expressed in most cell types May be methylated to silence the genes

What are UTRs?

Regions of mRNA surrounding the coding region that are not read

What is allosteric regulation?

Regulation of enzymatic activity by reversible binding of regulatory molecules to allosteric site

What are TF steroid receptors?

Regulatory TFs that respond to steroid hormones in which hormone binds TF

What is Darwinian fitness?

Relative likelihood that genotype will survive and contribute to gene pool of next generation Measure of reproductive superiority

What are redox potentials? What patterns of redox potentials are observed in the ETC? What has the higher redox potential in the ETC?

Relative measures of affinity of compound for electrons Each redox potential is higher than the last as electrons are shuttled down the ETC O2 at the end has highest redox potential in the ETC, as higher redox potential means greatest oxidizing agent (hence oxygen, what oxidizing is named after)

Structure of Proton-Driven APTases. Which part of F-Type pumps is the F0 and F1 components?

Remember F-ONE is Free (from the membrane) to make ONE ATP 2 Turbines connected F0 - membrane-spanning, proton-powered motor F1 - receives energy from F0 motor and uses it to phosphorylate ADP to ATP 3 Protons = 1 ATP https://www.youtube.com/watch?v=b_cp8MsnZFA

Mechanism and Frequency of Depurination

Removal of purine from DNA forming apurinic site In mammalian cells, lose approximately 10,000 purines/24 hours at physiological temp 37C Regularly repaired, but if not polymerase adds random base with 75& chance of mutation occurring (due to 4 base choices)

What is the role of DNA Polymerase I?

Removes RNA primers and replaces them with complimentary DNA

Mismatch Repair Mechanism. Which strand does it operate on? How does it identify it?

Repairs base mismatches in all species by detecting mismatch and directing its removal from newly made strand Specifically operate on newly made strands! IDs that strand by less methylation (methylation = DNA age-indicator) Diagram is for E. coli mechanism

Nucleotide Excision Repair Uses and Prevalence

Repairs many types of DNA damage including thymine dimers, chemically modified bases, missing bases, crosslinks, and is found in all eukaryotes and prokaryotes

What are the two main types of regulatory proteins in transcriptional regulation?

Repressors - Bind to DNA and inhibit transcription Activators - Bind to DNA and increase transcription

What is the role of Splicing Factors?

Repressors - prevent splice site recognition, eclipsed repressed exon from mRNA Enhancers - promote splice site recognition, include enhanced exon in mRNA

What are spores? Cycle?

Reproductive cells on fungi that can be part of sexual or asexual reproductive phases Often microscopic and can cause disease or allergic reactions

What is the role of calcium in cadherin structure and function?

Required for cadherins to form structures necessary for cell-cell adhesion Absence of Ca2+ -> prevents appropriate cadherin structure formation as well as interactions between cadherins on adjacent cells More specifically, calcium ions bind to site near each hinge and prevent it from flexing so that the whole string of cadherin domains behaves as a rigid and slightly curved rod

NER Mechanism in E. coli

Requires four key proteins (UvrA, UvrB, UvrC, UvrD, standing for UV light repair) These proteins recognize and remove a short segment of damaged DNA and then DNA polymerase and ligase finish the repair job

What is the mechanism of transport for ER proteins with the signal sequence on the C-terminus? (tail-anchored)

Requires special set of proteins since SRP proteins cannot be utilized to associate these with the ER membrane

How is the bacterial initiation complex formed

Requires three Initiation Factors 1. IF1 and IF3 bind to 30S 2. mRNA binds to 30S 3. GTP-bound IF2 promote binding of initiator tRNA to P site 4. IF1/IF3 released 5. IF2 hydrolyzes GTP and is released 6. 50S subunit associates to form 70S initiations complex

What are polytene chromosomes?

Resultant bundle of chromosomes that lie together in parallel fashion when repeated rounds of chromosome replication occur without cellular division observed in Drosophila (double nine times, 2^9 = 512 copies!) -So large they can be seen in interphase (helped study of chromosome structure), and they exhibit characteristic banding pattern shown

Define case-control studies

Retrospective type of study in which Individuals with and without disease are comapred

What are suppressor mutations?

Reverse phenotypic effects of another mutation

What is water ionization?

Reversible dissociation of H2O into hydroxide and hydronium ions

How is the start codon determined in eukaryotes? What rules govern optimal translation initiation?

Ribosome scans from 5' end of mRNA until it finds the AUG start codon (not all AUGs can act as start though, but usually its the first AUG after the 5' cap) Kozak's Rules

What constitutes a cell-free translations system?

Ribosomes tRNAs Other factors required for translation including supportive enzymes to attach amino acids to tRNAs (initiation and elongation factors)

What are the three sites of ribosomes?

Ribosomes go APE on protein synthesis Aminoacyl Site (A) Peptidyl Site (P) Exit Site (E)

What is rubisco short for?

Ribulose Bisphosphate Carboxylase

What is the structure of DNA polymerase and its limitations?

Right hand-like structure that threads DNA through the palm, but is unable to link two individual nucleotides (Primase), can only lengthen strands

Hydropathy Index Plots for Proteins

Right is probably G-protein with 7 membrane-spanning helices

What is Escherichia coli?

Rode-shaped, gram-negative, LPS-containing, catalase-positive, non-sport lasting, flagella containing bacteria found throughout human microbiome that can do horizontal gene transfer, are mostly non-pathogenic but can cause food poisoning

What is the role of ER and what determines sections of rough vs. smooth ER?

Role of ER is production fo all transmembrane proteins and lipids for most cell organelles and most of proteins that will be secreted or retained in ER lumen as well Rough ER and Smoother ER are interchangeable as ribosomes transiently react with the membrane

Where are the enzymes of lysosomes synthesized?

Rough ER

What are the six common shapes of bacteria and their names?

Round-Spherical - Coccus Rods - Bacillus Curved Rods - Vibrio Mix between rod and sphere - Coccobacillus Twists - Spirillum Spiral - Spirchoete

What are Nematoda and their major features?

Roundworms Most abundant animals on Earth Intestinal parasites

Which amino acids typically get phosphorylated, methylated, and acetylated?

S, T, and Y have their OH's P'd K, H, and R (basic) get methylated All N-termini can be acetylated, but K, H, and R can have additional acetylation on their extra N's (think relationship with histones)

Which amino acids have hydroxyl groups that are typically phosphorylated in eukaryotes?

S, Y, and T Serine, Tyrosine, and Threonine

In which phase of the cell cycle does chromosomal replication occur?

S-Phase

What does homozygous refer to in genetics?

Same allele for a gene

How do we calculate map distance from cotransformation data?

Same as cotransduction data, divide second plating colonies by initial plating colonies to get cotransformation frequency and equate that to (1 - d/L)^3

Isotonic

Same outside and inside, no net water movement

What is the purpose of the other non-template strand in DNA?

Same, both strands can be template strands

What is the difference between saturated and unsaturated fats?

Saturated fats are solid and have no double bonds. Unsaturated fats are liquid at room temp and have at least one double bond.

What is the role of scaffold proteins in metaphase?

Scaffold forms from nuclear matrix and anchors chromosomes by radial loops to maintain compaction

What types of intracellular responses occur in RTKs?

Scaffolding usually occurs in various forms that facilitate multiple proteins involved in the pathway to be brought together This helps prevent crosstalk between pathways and increase efficiency of signal transduction

What are the methods of scanning probe microscopy?

Scanning Tunneling Microscope - probe measures current between probe and specimen and stays at constant height above specimen Atomic Force Microscope - probe generates its own constant current and moves up and down accordingly to maintain it and detect chemical bonds and molecular forces across molecule Both use probe that is scanned over surface of specimen

What are sebum and sweat? Production Areas?

Sebum - oil produced by sebaceous glands in skin with antimicrobial factors that makes it hard for microbes to attach to skin Sweat - salty, watery substance from sudoriferous glands that can also have antimicrobial effect from salinity

What is the sec61 complex and its mechanism?

Sec61 complex forms a plugged translocator channel in the ER membrane It binds to the signal sequence, displacing its plug It also has a lateral seam that can open up to allow translocation Hydrophobic amino acids line the interior of the channel to prevent ion movement when the channel is inactive

Mechanisms of second messengers and moleculear switches

Second messengers are small non-protein molecules that are up or downregulated in the signaling pathway to change environment to relay signal Molecular Switches - proteins whose functionality changes upon receipt of external signal through modification i.e. kinases/phosphatases

How do mucous membranes establish physical barriers to pathogens?

Secrete mucus to cover fragile or infection-prone cells Mucus helps absorb or import materials

Name these parts

See answers on next card

What are tapeworms?

Segmented type of Platyhelminthes with Scolex - complex of hooks and suckers) lay eggs inside host and form protective cyst

What are Insulators and their mechanism?

Segments of DNA that insulate a gene from regulatory effects of other genes by various mechanisms

What is the difference between selective and differential growth media?

Selective - inhibits growth of unwanted organisms with chemical agents and antibiotics Differential - distinguish between different organisms without killing by methods like dying and causing other distinguishing patterns to occur

General strategy of antibiotic development

Selective toxicity - kill/inhibit with minimal damage to host Modes of action like inhibiting cell wall synthesis, inhibiting protein synthesis, disrupting membranes, inhibiting nucleic acid synthesis, inhibiting metabolism, etc.

Process of Receptor-Mediated Endocytosis

Selective uptake of proteins bound to cell surface receptors Method similar to receptor proteins in ER with coating and adaptor proteins etc. Shown is endocytosis of LDL to early endosome and through that pathway with recycling of LDL receptors to PM

What are two exceptions amino acids not included in the 20 and what are their codes?

Selenocysteine - UGA (one of the nonsense) Pyrrolysine - UAG (one of the nonsense) Found in speciality enzymes Means only UAA is true always nonsense codon

What is a termination sequence?

Sequence of DNA that signals the end of transcription (not to be confused with stop codons that signify end of translation)

What is a telomere?

Sequence of non-coding DNA that adds to end of DNA to protect from shortening during replication

What are Riboswitches?

Sequences in RNA that regulate expression discovered in 2001 Involve switching of RNA between active and inactive conformations Can regulate transcription or translation

What is a consensus sequence?

Sequences with some conserve bases and some variable bases that are mostly amongst all organisms like the -10 and -35 regions that constitute the promoter region

What do telomeric sequences typically have high numbers of and what is the human telomeric sequence?

Several guanine and many thymine on the 3' ends overhang, typically 12-16 nucleotides long Humans - TTAGGG

What is the difference between sex-influenced, sex-limited, and sex-linked traits?

Sex-Influenced - autosomal traits in which allele appears dominant in one sex, recessive in the opposite Sex-Limited - traits that occur only in one of the two sexes like development of specific genitalia Sex-Linked - genes found on one of two types of sex chromosomes but not both

What determines whether bicelles, micelles, bilayered sheets, or other structures form?

Shape/Structure of the amphipathic molecules

What is chemiosmotic coupling and which organelles utilize it?

Shared mechanism of mitochondria and choloroplasts of utilizing an ETC to shuttle electrons to build up a protein gradient, then coupling the movement of those protons down that gradient with ATP synthesis Generally it is the conversion of external energy sources into electrochemical gradients

Structure/Assembly of Type IV Collagen

Sheet-forming Type IV collagen is a major structural component of the basal lamina 400 nm long molecule with small lobular N-terminus and large globular C-terminus Collagenous triple helix interrupted by non-helical segments that introduce flexible kinks into the molecule Formation of dimers, tetramers, and higher-order sheet-like networks: -lateral interactions between triple-helical segments -head-to-head and tail-to-tail interactions between globular domains -multiple unusual sulfilimine or thiether bonds between hydroxylysine/lysine and methionine residues covalently cross-link some adjacent C-terminal domains and contribute to stability of network

What are viroids?

Short circular strands of RNA without capsid protein capable of self-replication through hijacking cells Typically affect plants and cause lesions, developmental problems, infertility, etc.

What are Okazaki fragments?

Short lengths of single-stranded DNA made on the lagging strand.

What are RNA primers?

Short strand of RNA recruited by primase to serve as starting point for DNA synthesis

What are the two classes of actin filament-binding proteins?

Side-binding proteins (high concentration) - i.e. tropomyosin, which elongates proteins that interact with 6-7 monomers simultaneously, stabilizing, stiffening, and preventing interaction with the filament Capping Proteins (low concentration) - prevent depolymerization by holding either the plus or minus end together

What are the two parts of surface receptors for epinephrine?

Signal Binding Site - polar outside part Cytoplasmic End - nonpolar inside portion

How are ribosomes directed to the ER membrane?

Signal Recognition Peptides (SRPs) bind the signal sequences emerging from the ribosomes and pause translation SRP Receptor then binds SRP-ribosome complex and guides it to a protein translocator The SRP and its receptor then split off and dissociate while the Ribosome remains attached the the translocator for co-translocation

What are the roles of signaling molecules, effector proteins, intracellular proteins, and receptor proteins in the biosignaling pathway?

Signaling Molecule - extracellular source of info for cell Receptor Protein - Interacts with signaling molecule that undergoes change upon binding to pass info into cell, translating extracellular signal to intracellular signal Intracellular Signaling Proteins - amplify, translate, transmit receptor protein info throughout cell Effector Proteins - Functional end of signaling chain that is ultimately responsible for changes in activity/function

Which type of proteins typically use lipid anchors?

Signaling proteins

What is the difference between signs and symptoms of disease?

Signs - Objective and measurable evidence of disease Symptoms - Subjective feelings that can't be measured objectively

Silent, Missense, Nonsense, Frameshift Mutations

Silent - change in nucleotide that doesn't affect amino acids or structure (degeneracy) Missense - base substitution in which amino acid change does occur Nonsense - early stop codon Frameshift - shift of reading frame

What are the differences in eukaryotic translation initiation?

Similar except methionine initiator tRNA used instead of bacterial initiator tRNA with covalently modified N-formylmethionine Also additional factors required called eIFs (eukaryotic Initiation Factors)

Compare and contrast the human and nematode pathways for apoptosis.

Similar proteins play corresponding roles; both have BH3 only (EGL-1 in nematodes, many in mammals) Nematodes have a more linear and simplar process with CED proteins while mammals have more players and invovled CED-9 promotes survival by binding CED-4 to prevent activation like Bcl-2 binds Bak/Bax EGL-1 binds CED-9 to release it from CED-4 and allow free CED-4 to activate CED-3 initiator caspase

Role of Mast Cells

Similar to basophils Leave blood and are found in other tissues though

What are the two types of staining?

Simple Staining - stain all of organisms same color to emphasize specific structures Differential Staining - use multiple stains/agents and stain diff organisms different colors

What are the repair methods for chromosome breakage?

Single Stranded Annealing (SSA) - extensive resection utilizing adjacent homology with loss of intervening material Homologous Recombination (HR) - use complementary chromosome Non-homologous End Joining (NHEJ) - last ditch effort linking of two blunt ends with no homology required, often mutagenic

What happens in anaphase?

Sister chromatids are separated by shortening of the spindle fibers

3 Types of population changes

Size Location Genetic Composition

What is a plasmid?

Small circular sections of additional bacterial DNA with genes usually interrelated in function

What types of sex chromosome mutations are survivable vs. not?

Smaller the chromosome with the mutation, more survivable

What is the difference between the smooth ER and rough ER?

Smooth er has no ribosomes

What is the purpose of biofilms?

Social interaction and coexistence

Why can't Na+ get through the solvation shell for potassium? How is K+ pushed through?

Sodium ions are only large enough to bond with two of the 4 carbonyl's, making making it more favorably still connected to its solvation shell so that it cannot progress and is bumped out by K+ K+ bonds favorably, then is pushed through to next bonding site by incoming K+ ions

What types of bonds are made/formed from cytoskeletal monomeric subunits?

Soluble, rapidly connecting and disconnecting subunits interact noncovalently and derive strength of structures through multiple monomers reacting with multiple others

Hypertonic

Solute concentration greater outside than in -> cell loses water

Hypotonic

Solute concentration less than that inside cell -> water moves into cell

What are the updates and limitations to the one gene-one enzyme hypothesis? (name 3)

Some proteins are composed of two or more different polypeptides, so really it is one gene one polypeptide Many genes do not encode polypeptides (tRNA, rRNA, etc.) One gene can encode multiple polypeptides through alternative splicing

What is a carrier?

Someone who has a recessive allele that is not expressed (usually for a disease), but therefore can pass this as his/her only allele down to their offspring with 50% chance

What is attenuation?

Something that can occur in bacteria only due to coupling of transcription and translation Transcription begins but is terminated before entire mRNA is made Segment of DNA called Attenuator facilitates this termination

Inheritance of TNRE disorders

Sometimes progressively worsens in generations Often worse if inherited from certain parent (Huntington's worse from father, myotonic muscular dystrophy worse from mother) Suggets TNRE can occur more frequently during oogenesis or spermatogenesis depending on gene involved

Calvin Cycle Breakdown (inputs, outputs, cycles, enzymes, etc.)

Sort of like reverse glycolysis Part I - Carboxylation - 3 CO2 brought in and along with 3 recycled ribulose 1,5-BPs to make six 3-phosphoglycerate molecules. Part II - Reduction - 6 ATP used to phosphorylate six 3Ps to 1,3-PGs, then 6 NADPH used to reduce them to 6 glyceraldehyde 3 phosphates Part III - Regeneration - 1 molecule of glyceraldehyde 3 phosphate set aside to be used for sugars/fat/amino acids, and other 5 recycled, using ATP to regenerate ribulose 1,5-BPs for next cycle

What are stroma?

Space around thylakoids

What is a body pattern?

Spatial arrangement of different body regions At cellular level, result of arrangement of cells and their specialization

What happens after the special pair receives the excited electrons?

Special pair passes electron on to electron carrier attached to PSII, creating a charge separation that holds it in place Positively charged special pair chlorophyll molecules are incredibly strong oxidants that are able to pull electrons from H2O to split it into O2 Only when water is split, replacing the electrons of the special pair, does the electron carrier dissociate and pass on to the ETC

What is the glycosidic bond?

Special type of covalent bond in carbohydrates that uses oxygen as a bridge

Defining characteristics of specific adaptive immunity (2)

Specificity to individual pathogens Memory for future infections

How is a wet mount prepared?

Specimen placed in drop of liquid on glass slide and cover slip placed over specimen

What is preformation?

Spermists - Dad and sperm is everything, mom is just an incubation chamber Also Ovists - mom has little people that dad wakes up during sex

Most common type of sphingolipid

Sphingomyelin

What do the H and N numbers refer to in influenza classifications?

Spike Types I.e. H1N1 influenza virus has H1 spikes and N1 spikes

What happens in metaphase?

Spindle lines up chromosome on midline -> metaphase plate Karyotype

What is self-splicing?

Splicing that does not require aid of enzymes and instead RNA itself functions as its own ribozyme

What is the difference between spontaneous and nonspontaneous reactions?

Spontaneous - negative Gibbs free energy, will occur without any input (but at any rate, could be extremely slowly) Non-Spontaneous - positive change in Gibbs free energy, requires energy input to occur

What are some causes of mutations?

Spontaneous Mistakes Mutagens (chemicals) Radiation (especially ionizing radiation with high-energy particles causing breakage)

What is a centromere?

Spot where new DNA strand attached to digital strand (Connection between sister chromatids)

Describe propagated spread infections

Spread via person-to-person contact, direct or indirect, usually with multiple sources an lasting extended periods of time

Standard Deviation Calculation

Square root of the variance

What is a start codon? What is the start codon and associated amino acid?

Start codons initiate translation by binding the initiation complex AUG - Methionine

Define morbidity

State of being diseased Given as absolute number of diseased individuals or number of diseased individuals per some portion of population (morbidity rate)

What is a cellular cyst?

State similar to an endospore in which cell is dormant in harsh conditions

What is the purpose of the Chi Square Test?

Statistical method used to determine "goodness of fit" or how close observed data are to those predicted from hypothesis

Biosynthesis of Fibrillar Collagens

Step 1 - Procollagen alpha chains synthesized on ribosomes associated with rER and asparagine-linked oligosaccharides added to C-terminal in ER Step 2 - Propeptides associate to form disulfide-linked trimers; G-X-Y triple repeats covalently modified and certain prolines and lysines hydroxylated (changing proline residues from cis to trans); galactose or galactose-glucose attached to some hydroxylysines Step 3 - Modifications facilitate zipper-like stabilization of triple helices; Hsp47 chaperone protein binds to stabilize helices and prevent premature aggregation into trimers Steps 4/5 - Folded procollagens transported to and through Golgi - some lateral association into small bundles Step 6 - procollagen bundles secreted Step 7 - N and C-terminal propeptides removed Step 8 - trimers assemble into covalently cross-linked fibrils; 67-nm staggering of trimers and striated appearance of fibrils Step 9 - fibrils can assemble into larger bundles - some form tendons that attach muscle to bone

Describe the process of leukocyte binding to the endothelium.

Step 1 - absence of inflammation/infections - leukocytes and endothelial cells lining blood/vessels in resting states Step 2 - inflammatory signals activate resting endothelial cells: -vesicle-sequestered selectins inserted into endothelial cell surface -exposed selectins interact with leukocyte carbohydrate ligands to mediate weak binding of leukocytes -blood flow forces loosely bound leukocytes to roll along endothelial surface of blood vessels -activated endothelial cells synthesize and express platelet-activating factor (PAF) and ICAM-1 on endothelial cell surface Step 3 - PAF and secreted activators including chemokines induce changes in leukocyte shape and activate leukocyte integrins Step 4 - tight binding between leukocyte activated integrins and endothelial cell CAMs adhere leukocyte to endothelial cells Step 5 - Leukcyote extravasates into underlying tissue

What is a stop codon and what are the stop codons?

Stop codons are nonsense codons that signify the end of a polypeptide chain UAA, UAG, and UGA

What is the mechanism of integral membrane protein transport into the ER membrane?

Stop-Transfer Sequences N-Terminal signal sequences act as start-transfer while integral act as stop-transfer

How do recycling vesicles assist cellular responses?

Storage of PM proteins in recycling vesicles allows for rapid response by responding quickly to dump necessary proteins into PM

What is the purpose of the sER?

Store ions, synthesize phospholipids

What are the purposes of the cytoskeleton?

Strength Morphology Transport scaffolding Motility structures Grow/shrink by removal/addition of monomers Highway system within cell

What are the types of aerobes and anaerobes?

Strict aerobe - requires oxygen, only does oxidative phosphorylation (e.g. brain cells) Strict Anaerobe - only fermentation, e.g. some bacterial toxins like tetanus Facultative Anaerobe - switch between the two e.g. E. Coli, yeast, muscle cells

Describe the structure of integrin proteins. What are the common features? How is integrin binding regulated? What are the roles of the domains of integrin?

Structure includes two non-covalently associated glycoproteins, one alpha and one beta subunit, both with intracellular and extracellular domains Integrins can communicate in both directions (outside cell to inside and vice versa) -Binding of matrix components can communicate message to interior -activation of integrins can communicate intracellular conditions -tension applied can result in tightening of grip on ECM -loss of tension can result in dissociation from ECM 24 diff types generated from 8 beta chains and 18 alpha chains - all but one integrin interacts with actin on intracellular surface of membrae

Nucleolus

Structure within nucleus that surrounds DNA that becomes rRNA

What are nanodiscs? How are they particularly useful?

Structures of HDL proteins used to create betls to contain portions of a membrane, allowing for structural determination of membrane-bound proteins via electron microscopy without need for crystallization

Define epidemiology

Study and tracking of geographical distribution and timing of infectious disease occurrences including: -How they are caused -How they are transmitted -How they persist

Define virulence factor

Substances made by pathogens that allow them to cause disease and determine the severity and extend of disease

What are chromosomal aberrations?

Substantial changes in chromosome structure or number

What is a strain?

Subtypes within a species that are different but more similar than different

Define infection

Successful colonization of a host by a microorganism often leading to disease

What is a poly-A-tail?

Successive adenine nucleotides added at the 3' end that protect the mRNA from degradation and also has role in transporting to cytoplasm and binding initiation complex as well

What chemical indicator test identifies lipids?

Sudan III Solution Positive - layer/clump Negative - no layer/clump

What happens in microtubules when GTP hydrolysis catches up to addition and the GTP cap is lost?

Sudden change from T-form to D-form can change microtubule from growth phase to shrinkage phase called Catastrophe Catastrophe can be stopped by the reverse conversion of shrinkage to growth, called Rescue

What are synergistic and antagonistic interactions?

Synergistic - combined effect of drugs greater than individually Antagonistic - increase in patient harm or decrease in drug effectiveness due to presence of other drug

What is the function of the sER?

Synthesis of lipids and carbohydrates Detoxification

Difference between synthetic, natural, semisynthetic drugs?

Synthetic - chemical not found in nature Natural - isolated from natural world Semisynthetic - chemically-modified natural substance

What is a Type IV Immune Hypersensitivity?

T-cell-mediated reactions that can lead to activation of macrophages and cytotoxic T cells i.e. poison ivy, chronic asthmas, Rhinitis (hay fever)

How are proteins confined to certain regions of the cell membrane in terms of epithelial cells?

TIght junctions between epithelial cells prevent transfer between apical and basal lamina

What are trinucleotide repeat expansions?

TNREs are unusual forms of mutations in trinucleotide repeat regions (normally exist) are increased above critical size and cause several genetic diseases

What are TOM, TIM, SAM, and OXA complexes and their individual roles?

TOM Complex - Translocator of Outer Membrane TIM Complex - Translocator of Inner Membrane SAM Complex - Sorting and Assembly Machinery (in outer membrane, receives from TOM to place in outer membrane) OXA Complex - cytochrome OXidase Activity (places in inner membrane)

What is the use-dilution test method of testing effectiveness of antiseptics and disinfectants?

Take sterile rod, dip into bacteria and dry Take that rod and dip it into solutions of antiseptic/disinfectant at varied concentrations Transfer rod back to sterile nutrient growth medium and check for turbidity to see evidence of bacterial survival Must be successful 59/60 times for disinfectant to be considered effective against particular organism

What is Taxol and its mechanism some of its effects?

Taxol is chemotherapy drug related to taxines from natural tree Disrupts cell division by affecting MT ability to shorten between metaphase and anaphase and pull chromosomes apart, leading to marking and apoptosis Side Effects: • GI Tract affects - ulcers, nausea, vomiting, diarrhea, loss of appetite • Bone Marrow - suppressed immune system (WBC), anemia (RBC) • Skin: easily damaged, wounds hard to heal Hair follicles: los of hair, skin, eyelashes, eyebrows, and heated follicles

What is the name for the classification, description, identification, and naming of living organisms?

Taxonomy

Which type of membrane transport methods utilize energy?

Technically all of them, whether its ATP or using the electrochemical gradient as energy in favorable conditions

What is telomerase and its significance?

Telomerase is an enzyme that creates the telomeres, active in early embryonic and germline cells. Key in early development to develop these, but stops after, leading to aging If could develop synthetic telomerase, age stopper?

What are the names and roles of the two DNA strands?

Template/Antisense/Non-coding/Minus Strand - complementary to mRNA transcript Non-template/Sense/Coding/Plus Strand - identical to RNA transcript except for uracil

Mechanism of Tautomerization Part I

Temporary change in base structure between forms Stable form = keto form, but rarely T and G convert to enol form Stable amino forms of A and C can also convert to imino form Rare forms promote AC and GT base

Structures of Beta Sheet Membrane Proteins

Tend to form large barrel-like structures that often serve as pores, transporters, channels

What are the two models for eukaryotic transcriptional termination and where does it terminate?

Terminates 500-200 nucleotides downstream from polyA signal Allosteric Model and Torpedo Model

How does prokaryotic DNA replication terminate?

Terminates sequences called ter sequences on the opposite end of the chromosome designated T1 and T2 (may be more) Termination Utilization Substance (tus) binds to the terrible sequences and stops replication forks T1 prevents clockwise fork advancement, T2 counterclockwise fork advancement

How does the cortical cytoskeleton give membranes mechanical strength and restrict membrane protein diffusion?

Tethering to macromolecular assemblies by anchoring fibrous proteins like Ankyrin to provide intracellular stabilization

How are ER resident proteins prevented from entering the Golgi? How is this facilitated by its environment?

The COPI vesicles formed in the vesicular tubular clusters have specific recognition proteins that recognize the retrieval sequences (KDEL) and bring ER resident proteins back Binding to KDEL receptors is a pH dependent process that mainly occurs in the lower pH of the Golgi

What strand are promoters located on?

The SENSE strand!

How is supercoiling prevented in DNA replication?

The Topoisomerase enzyme breaks covalent bonds, twists the structure, and forms new covalent bonds

Describe the dual roles of cadherins in the formation of the neural tube.

The adhesion belts attached to the cadherins contract causing the epithelial cells to narrow at their apex and invaginate to form the initial loop Different cells produce different types of cadherin that facilitate homophilic interactions that separate different cell types into regions and facilitate the closing of the neural tube

What is a centrosome?

The centrosome is the region of the cell that contains the centrioles and the microtubules organizing center (MTOC)

How do PIs mark organelles and membrane domains?

The different phosphorylations of them are highly compartmentalized intracellularly and signify different intentions Different organelles with various transport pathways have different PI and PIP Kinases and Phosphatases This creates a unique PIP distribution for each organelle that allows identification and drive transport

What is a gene locus?

The location of a gene on a chromosome

Which formula provides the frequency of single crossovers for asci?

The lower number provides the frequency of single crossovers (NDP+1/2T)/Total and the formula yielding the higher number takes double crossovers into account (.5(T+6NPD))/Total

What is a reading frame?

The order in which amino acids are read that is unseparated by commas or anything so must be established accurately or entire protein is messed up

turgor pressure

The pressure inside of a cell as a cell pushes itself against the cell wall in hypotonic solutions

What is gene expression?

The process by which DNA directs the synthesis of proteins and enzymes to only produce what we need

What is a lac repressor?

The protein coded by the lac I gene that when needed, creates proteins that bind to and inactivate operator

What are nucleosomes? By the numbers?

The repeating structural unit within eukaryotic chromatin composed of double-stranded segments of DNA wrapped around octamers of histone proteins 146 bp of DNA make 1.65 negative superhelical turns around an octamer

Extracellular Matrix

The substance in which animal tissue cells are embedded, consisting of protein and polysaccharides.

How are histone tails typically modified and what is the effect?

The tails of amino acids on histones are commonly methylated, phosphorylated, and acetylated and cause a variety of effects This happens by way of over 50 enzymes that have been found in animals

What is a 3' UTR?

The untranslated region at the 3' end of the mRNA

What is a 5' UTR?

The untranslated region at the 5' end of the mRNA

What is the difference between empirical and theoretical?

Theoretical - expectation Empirical - actual results and real life data

What are thermal death point and thermal death time?

Thermal Death Point - lowest temp at which all microbes are killed in 10 minutes Thermal Death Time - amount of time needed to kill microbes at a given temp

What is the purpose of modular protein domains?

They allow addition of functionality to proteins without disrupting core functions (NEED MORE ON THIS)

How are misfolded proteins exported for degradation?

They are bound by lectins (proteins that selectively bind to sugars) and chaperon proteins, unfolded, and exported to cytosol and into proteasomes

Where are proteins destined for the mitochondria made?

They are made in the cytosol on free ribosomes and then transported in to the mitochondria

How are single stranded DNA strands stabilized?

They are maintained by single stranded binding proteins (SSBP)

How are hydrolases modified in the Golgi?

They are recognized by GIcNAc phosphotransferase through a signal patch and bound at their recognition site The GIcNAc also binds UDP-GIcNAc and high-mannose oligosaccharides at its catalytic site The GIcNAc then connects them and releases the combined lysosomal hydrolase and M6P This may happen many times to individual hydrolases if they have multiple signal patches, and these provide a high-affinity signal for M6P receptors

What are the four postulates of Koch and their purpose for existing?

They are the requirements for a pathogenic organism to be positively correlated with a disease (to ID them): 1. Pathogen must be found in EVERY case of the disease and not in healthy individuals 2. Pathogen must be able to be isolated and cultivated in pure culture 3. Healthy subjects infected with pathogen must develop disease signs and symptoms identified in postulate 1 4. Pathogen must be re-isolatable from new host and be identically to original pathogen

What are the key characteristics of glycosaminoglycans (structure, properties, prevalence in connective tissue)? 4 main groups?

They are unbranched polysaccharide chains composed of repeating disaccharide units One sugar is always an amino sugar (N-acetylglucosamine or N-acetylgalactosamine) and second sugar is often uronic acid Differ in sugars and linkage types Negative charges recruit positive ions (mostly Na+) creating osmotic imbalance that recruits even more water on top of them being hydrophilic 10% of connective tissue by weight but occupy majority of the space

How are lipids metabolized without the mitochondria?

They aren't mitochondria are essential to metabolize fats in any way

How do accessory proteins affect the dynamic nature of cytoskeleton filaments?

They bind to cytoskeletal protein subunits and modify their affinity for the polymer to regulate assembly and disassembly They can also provide additional linkages between adjacent monomers or between filaments

How do antibodies help phagocytes recognize pathogens?

They bind to their antigens and present on their surfaces or use other methods of ID

Does positive or negative supercoiling cause compaction? Which one causes transcriptional activity?

They both cause compaction, but negative supercoiling is just the method of compaction utilized in DNA. Negative Supercoiling increases transcriptional activity though, so a molecule with negative supercoiling will be more transcriptionally active than a molecule with the same amount of positive supercoiling

How can bacteria take advantage of actin? Specific example?

They can essentially take the plus ends for a ride Listeria Monocytogenes - rare form of food poisoning that hijacks Arp2/Arp3 complex to move within cell, recuriting complex to its surface and using the force of newly polymerized actin to propel itself at 1um/sec leaving the comet tail shown

What is the structure of histone proteins and their related function?

They contain large amounts of lysine and arginine to maintain their positive charge to bind to phosphates along DNA backbone Core Histones - H2A, H2B, H3, and H4 Linker Histone - H1 - less tightly bound to DNA and may help compact adjacent nucleosomes - useful for epigenetic marking

How do Rab proteins on target membranes guide transport vesicles to their location?

They create cytosolic Rab membrane domains In the case shown, Rab5GEF phosphorylates GDP to GTP, releasing GDI and binding the Rab5 to the membrane while exposing its amphiphilic helix This activated Rab5 then activates PI 3-Kinase to recruit more Rab5 and additional tethering proteins into a complex that is ready to receive clathrin-coated vesicles

What do double bonds do to the structure of lipids?

They create kinks like one of the kinked tails of a phospholipid

What were the results of function determination based off ts mutants?

They discovered various proteins involved shown and named them DNA followed by a letter as shown. Rapid-Stop Mutants - ones that showed rapid arrest of DNA synthesis at non permissive temperature, thus having mutant genes encoding enzymes needed for DNA replication Slow-Stop Mutants - Completed their current round of replication but could not start another - encoded genes needed for initiation of replication

Why can't archaea be gram-stained?

They have no peptidoglycan at all (though some have pseudo peptidoglycan with slightly different structure) Some have no cell wall at all

How do small molecule activators/inhibitors work together with transcriptional activators/inhibitors

They have to both be considered in terms of overall effect and can cancel each other out or be redundant depending

What were Jacob and Monad's the method, hypothesis, experiment, and results?

They identified F factors that carried portions of the lac operon to create merozygotes for the lacI- gene with one lacI+ and one lacI- Hypothesis: lacI- mutation either results in synthesis of internal inducer or eliminates function of lac repressor that can diffuse throughout cell Experiment: -grow mutant and merozygote strain, divide into two tubes -add lactose to one of tubes and incubate both -lyse cells to allow Beta-glactosidase to escape -Add compound to measure amount of beta-galactosidase present Results - See picture

How and why did researchers work so hard to isolate polymerase mutants?

They isolated conditional mutants (such as temperature-sensitive (ts) mutants) by methods like the one shown in the picture in a "brute force" method to identify various polymerases and other enzymes involved in DNA synthesis

What is the role of the USA Centers for Disease Control and Prevention in tracking and managing infectious diseases

They keep track of epidemics by mandating that all cases of certain diseases be reported to them, to which health care practitioners are legally bound Generate reports on threats to public health

How do enzymes affect Ea, reaction rate, spontaneity, and change in free energy?

They lower Ea (activation energy), speed up reaction rate, and do NOT affect change in free energy or spontaneity

How can Enzyme activity be viewed on a free energy diagram?

They lower the hill between reactants and product, meaning they lower the energy of the transition state, allowing less energy to start the reaction

How do phospholipid translocators balance the lipid composition of the ER?

They manage this as energetically efficiently as possible At first, all the synthesized lipids are in the cytosolic half of the bilayer, overfilling that layer Scramblase then facilitates the energy-free movement of lipids down their gradients to create symmetric halves In the PM, Flippases/Floppases are used

How is the dynamic nature of the cytoskeleton important to the role of neutrophils?

They need to are used to dynamically reorganize their structure and give them the ability to move in response to stimuli and pursue bacteria

What is the role of protein kinases?

They phosphorylate other proteins

How did Wollman and Jacob kill of the Hfr cells to not interfere?

They plated them first on streptomycin mediums, an antibiotic that the Hfr were sensitive to but F- were resistant to

How are the laws of thermodynamics relevant to understanding biological reactions?

They play into the Gibbs Free Energy Equation (Change in Gibbs Free Energy = Change in Enthalpy - (Absolute Temperature)X(Change in Entropy) or ΔG = ΔH - TΔS

What is the environmental significance of Lichens?

They produce more oxygen than plants for our atmosphere

What is the role of Ran proteins in nuclear transport and which types serve which functions?

They provide directionality of transport Import - Protein with NLS binds nuclear import receptor that brings the protein into the nucleus, Ran-GEF brings in Ran-GTP to release protein into nucleus, Ran-GTP then facilitates export of import receptor back to cytosol where Ran-GAP hydrolyzes and removes Ran-GDP to allow binding of more cargo Export - Ran-GEF facilitates binding of export receptor to GTP, allowing binding of export cargo protein with it, they are exported, then Ran-GAP hydrolyzes GTP to release Ran-GDP and deliver cargo to cytosol

How do cytotoxic T cells help kill invaded pathogens and the cells they have invaded?

They release chemicals toxic chemicals into them so they can undergo apoptosis

Why can't organelles be synthesized de novo?

They require information stored in the membranes themselves, not the DNA, so some membrane must be present to produce more of itself

What is the role of single stranded binding proteins?

They stabilize the single stranded DNA after unwinding

Role of profilin, Arp2/3 complexes, and formins in the plasma membrane

They tend to associate with the PM to catalyze growth of filamentous appendages

How do motor proteins interact with cytoskeletal filaments?

They use them as roads and guides to assist in the movement of cellular components

Microtubules

Thick hollow tubes that make up the cilia, flagella, and spindle fibers.

Differences of lipid raft regions

Thicker/thinner than surrounding structures Enriched in cholesterol liquid-ordered (vs. liquid disordered)

What type of functional group is acetyl-CoA?

Thioester

Where is the energy in ATP?

Third phosphate bond, very unstable to pack that many negative charges on

What were the results and significance of the cotransduction experiment?

This 42% is the cotransduction frequency which can be used to calculate the distance apart in minutes

What is unique about helicobacter pylori's environmental preferences?

This leading causative agent of peptic ulcers thrives in the acidic stomach despite being a neutrophile by secreting urease that turns into ammonium and carbon dioxide to raise the pH in its surrounding area, creating its own optimal environment!

What is the importance of the tertiary structure of proteins? What organelle folds them?

This tertiary structure is the folding that makes the proteins functionally active; Golgi body folds them in ways to have them perform specific functions

What types of insertions/deletions cause frameshift mutations?

Those are not of nucleotides in multiples of three

What is the history of fungi?

Thought to be weird plants until 1970s when mycology took off

intermediate filaments

Threadlike proteins in the cell's cytoskeleton that are roughly twice as thick as microfilaments

Which type of response are positive feedback loops effective at producing?

Threshold Responses

Describe integrin activation as a result of thrombin signaling.

Thrombin binds to extracellular GPCR releasing Rap1 Rap 1 exchanges GDP for GTP and binds RIAM protein RIAM recruits and activates talin and kindlin proteins Complex interacts with inactive integrin protein resulting in conformational change from inactive to active conformation Active integrin binds extracellular ligand Binding causes dissociation of Rap1 complex and association of vinculin and actin filament Blood clot crosslinkage

How have humans accelerated microbial evolution

Through irresponsible use of antibiotics (overuse, misuse, incomplete use by patient noncompliance)

How do cells of the body receive positional information signals?

Through morphogens, molecules that convey positional info and promote associated developmental changes

How can mitochondrial import selectively add to intermembrane space, inner/outer membranes, etc?

Through use of start and stop sequences, OXA and SAM complex, Mia40 oxidation of proteins, etc.

What is the difference between thymine and uracil structurally?

Thymine = methylated uracil

Roles of Profilin and Thymosin. Where do they act and why?

Thymosin-bound actin is sterically prevented from binding to and elongating plus end of actin filament Profilin has opposite effect, driving polymerization at plus end and increasing the rate They are both specific to the plus end because that's where the majority of the polymerization occurs

What is the function of tight junctions? How is tight junction formation related to the compartmentalization of body cavities?

Tight junctions form to seal off body cavities and restrict diffusion of membrane components between apical and basolateral membrane portions to nothing or almost nothing (water and ions)

What is the role of monomeric GTPases in coat assembly?

Timing is crucial The GTPases essentially hydrolyze GTP to release the coating proteins at a fixed rate Rate of association must surpass rate of dissociation and then enough are held there for spontaneous vesicle formation, and this is regulated by recruitment of coat protein through PIP, Adaptor Protein Coincidence Detectors, Cargo, etc. (all related)

How do endothelia establish physical barriers to pathogens? Where are they found?

Tissues tightly packed and strongly adhered to one another to prevent invasion Found lining urogenital tract, blood vessels, lymphatic vessels, and more

Mechanism of Tautomerization Part II

To cause mutation, tautomeric shift must occur immediately prior to replication

What is the other term for DNA Gyrase?

Topoisomerase II

What is a dimer?

Tow identical molecules linked together that when activated come together

What is a quantitative trait?

Trait that varies measurably in a given species

What are discontinuous traits?

Traits that fall into two or more discrete categories like colors

What are the resulting Trans-Effect and Cis-effect/Cis-Acting Element conclusions from Jacob and Monad?

Trans-effect - genetic regulation can occur even though DNA segments not physically adjacent; mediated by genes that encode regulatory proteins Cis-Effect / Cis-Acting Element - DNA sequence that must be adjacent to genes it regulates A mutation in a trans-effect factor is complemented by the introduction of a second gene with normal function A mutation in a cis-acting element is not affected by the introduction of another normal cis-acting element

How do structural motifs allow for reading of DNA without strand separation?

Transcription factors are other proteins are able to recognize the bonding in major grooves by the variation in size and hydrogen bonds available to them without reading them

How are prokaryotic and eukaryotic translation/transcription different? Replication?

Transcription: Prokaryotic occurs in cytoplasm, eukaryotic in nucleus Prokaryotic termination by sequence, eukaryotic polyadenylation sequence is transcribed into RNA and proteins cleave RNA at this point Eukaryotic has additional modifications step that prokaryotes don't have including splicing (introns and exons, conversion to mRNA from premRNA) and add-one of poly-A tail, 5' cap, and UTRs Also humans have 98% non-coding DNA, while bacteria have only 2% non coding DNA because of the many other options along the way humans have

Which type of gene expression is the most common in bacteria?

Transcriptional

What is transduction and the two subtypes?

Transduction - bacteriophage transfers some of host's DNA from one bacterium to another Generalized - random pieces of host's DNA replicated during lytic cycle Specialized - regions of DNA next to prophase excised with phage DNA

What is a tRNA?

Transfer RNA that brings in its associated amino acid and matches its anticodon with the codon on the mRNA strand

What is gene flow?

Transfer of alleles from donor population to recipient population changing its gene pool

What is transacetylase?

Transfers acetyl group, biological role unclear

Which type of genetic transmission requires no physical contact between donor and recipient cells?

Transformation

What are the 3 basic ways prokaryotes achieve genetic diversity?

Transformation - genetic particle uptake Transduction - Viral vectors Conjugation - F+/F- sex pili and direct transfers

Transition vs. Transversion Mutations? Which is more common?

Transition - change of Py to Py or Pu to Pu Transversion - change of Py to Pu or Pu to Py Transitions are more common than transversions

What are the categories of molecules commonly found in biological systems that act as electron carriers? What are they generated from?

Transition Metals and Quinones Transition metals like Cu, Fe, Ni, and Mn can stably exist in multiple oxidation states Quinones like CoQ and Plastoquinone are organic molecules that contain a ring system capable of accepting electrons and their associated hydrogens into stable intermediates Both are generated from vitamins/minerals consumed in the diet

What are the two types of electron microscopy and difference between them? Limits and advantages?

Transmission Electron Microscopy (TEM) - very high magnification and resolution, similar to bright field but using electron beam instead of light, uses detector to "see" electrons and magnetic "lens" instead of glass, specimen must be very thin and imaging done in vacuum and with completely dehydrated specimen Scanning Electron Microscopy (SEM) - similar to TEM except electrons are shot at specimen and reflected electrons are detected and imaged; requires coating with heavy metals like gold to cause this reflection, but allows 3D images to be generated

What is polygenic inheritance?

Transmission of traits that are governed by two or more genes

What is the difference between transparency and opacity?

Transparency - degree to which light is transmitted through material Opacity - degree which light is absorbed by material (Inversely proportional)

Bulk Transport

Transport of large molecules across membrane Endocytosis and Exocytosis

Difference between transporter and channel proteins

Transporter Proteins - only ever open to one side at a time (or in occluded state) Channel Proteins - Either closed or open to both sides simultaneously

How do fats play into cellular respiration?

Triglycerides - major source of electrons, thus providing more energy than carbs Broken down into G3P Fatty acids consist of acetyl CoA as well

What is the structure/components of the G Protein of GPCRs?

Trimeric proteins with alpha subunit and Beta-Gamma Subunit Alpha and Gamma are anchored to cytosolic side of membrane with lipid anchors Alpha Subunit is a GTPase that is inactive when bound to GDP, active when GTP bound

Combined Mechanism of Bcl2 proteins and Roles of Bim, Bad, and Puma; Trophic Factor Presence/Absence Pathways, DNA damage pathway, lack of adhesion pathway

Trophic Receptor Present -> activates RTK -> activates PI-3 Kinase-PKB pathway -> PKB Phosphorylates Bad -> phosphorylated bad bound by 14-3-3 protein preventing Bad from inhibiting anti-apoptotic proteins, repressing apoptosis Trophic Receptor Absent -> unphosphorylated Bad can bind Bcl-2 -> Bak/Bax free to oligomerize and release cytochrome C -> Apaf1-cyt C combine to form apoptosome -> activation of caspase-9 -> activation of effetor proteases liek caspase-3 that proteolyze cell proteins DNA damage/UV irradiation -> Puma synthesis -> puma binds to Bak, bax, and Bcl-2 -> Bak/Bax form oligemeric pores to release cyt c Lack of Adhesion to Substrate in adhesion-dependent cells -> disruption of integrin signaling -> release of Bim from cytoskeleton -> Bim binds bak and bax to promote pore formation and cyt c release

Structure/Function of Troponin and Tropomyosin

Tropomyosin interacts with a groove along actin filaments to stabilize them Troponin is made up three troponin isomers: T - tropomyosin-binding I - Inhibitory C - Calcium-binding Resting state - T/I bound to actin, shifting tropomyosin to state outside of normal binding groove to prevent myosin heads from interacting with actin; myosin heads remain cocked Calcium influx -> Troponin C binds up to 4 calcium ions and displaces tropnin I -> tropomyosin shifts to standard binding position -> myosin interacts with actin

Extrinsic Apoptosis Pathway and Nomenclature/Structure of proteins involved

Tumor Necrosis Factor (TNF) family of proteins including TNF and Fas involved in initiation that are homotrimeric with the following domains: -Extracellular ligand binding domain -Single Transmembrane domain -Intracellular death domain Killer lymphocyte brings Fas ligand to bind Fas death receptor Intracellular FADD adaptor proteins with death domain and death effector domain form complex with caspase-8 (extrinsic initiator caspase), Fas ligand, and Fas death receptor to form Death-Inducing Signaling Complex (DISC) Caspase-8 activated and cleaves adjacent caspase-8 proteins resulting in activation of apoptotic cascade

What is the structure of the nuclear envelope?

Two bilayer Nuclear pore complexes

What is a chromosome?

Two chromatids that are attached by the centromere

General Integrin Activation Mechanism

Two conformations: Inactive - low-affinity, bent Active - high-affinity, extended

How many replication forks form in bacterial DNA replication?

Two forks at origin of replication

ABC Transporters Eukaryotic vs. Prokaryotic

Two hydrobphobic domains each built of 6 transmembrane alpha helices; mostly unidirectional Bacterial - make up 5% of genome and have both importing and exporting ABC transporters Eukaryotes - Preominantly exporting

What proteins are involved in tight junction formation?

Two main ones are Claudin and Occludin They are held together by scaffold proteins that organize junctional protein complexes

Intergenic Suppressor Mechanisms - Common Pathway

Two or more different proteins may function as enzymes in common pathway. Mutation that causes defect in one enzyme may be compensated for by mutation that increases function of a different enzyme in the same pathway

What are gene families? Significance?

Two or more genes that are derived from the same ancestral gene that can form as result of duplications They are vital because they provide the raw material for the addition of genes to a species

Interactions between Fibrillar Collagens and Fibril-Associated Proteins in Tendons and Cartilage

Type I/II - associate with nonfibrillar collgens to form diverse structures Tendons: -Type 1 fibrils all oriented in direction of stress applied to tendon -Type VI collagen and proteoglycans bind non-covalently to coat type I fibril surface, link together into thicker fibers Cartilage: -Type IX collagen molecules covalently bound at regular intervals along type II fibrils -Chondroitin sulfate chain covalently linked to Alpha2(IX) cain at flexible kink - projects outwards from fibril -Globular N-terminal region projects outward from fibril

How do cadherins contribute to cell organization? What are they two ways cell sorting can be accomplished?

Type of cadherin produced facilitates homophilic bonding and amount of cadherin produced facilitates the strength of those interactions, leading to cells naturally forming the strongest interactions and essentially sorting themselves

Define cohort studies

Type of epidemiological study in which one gathers info on a group within a population sharing a particular characteristic

Facilitate Diffusion

Type of passive transport in which carrier proteins are used to move particles through a membrane DOWN THE CONCENTRATION GRADIENT

How long are the hydrocarbon chains of fatty acids typically and do they have even or odd numbers of carbons?

Typically 4-36 carbons long with even number of carbons

What is the typical effect of euploidy in animals? Exception?

Typically polyploidy in animals is lethal Exceptions exist like bees (female diploid, males monoploid) and picture

What are the stop codons?

U Are Annoying U Go Away U Are Gone UAA, UGA, UAG

What was the Davis experiment?

U-Tube with filter blowing solvent movement but not bacterial movement Demonstrated need for physical contact for genetic transfer

snRNPs mechanism

U1: recognizes 5' splice site U2: recognizes internal A nucleotide U4-U5-U6 complex: recognizes 3' splice site U1/U4 released while splicing occurs wit U2/U5/U6 Lariat Structure

What are the PRIMARY purposes of the poly A tail, 5' cap, and UTRs?

UTRs - protection from degradation of the coding region 5' cap - recognized and binds the initiator complex (met tRNA GTP and small ribosomal subunit) Poly A tail - special role in eukaryotes dealing with when to stop transcribing

Assumptions required for correlation coefficient (2)

Unbiased sampling Normal distribution and linear relationship

How can mechanically gated channels respond to osmotic pressure?

Under hypotonic conditions, when water wants to rush out, physical compressing of membrane compresses aquaporin channels to close When hypertonic, reverse happens pulling open channels and allowing space for water to come in

What are the major features of yeasts?

Unicellular Fungi Bud off asexually Dimorphic, meaning can have more than one appearance in life both as yeast or mold, asexual or sexual

What are protists? Examples?

Unicellular eukaryotes that are not plain, fungi, or animals e.g. algae, protozoa

What are fungi? examples?

Unicellular or multicellular eukaryotes that resemble plants but are non-photosynthetic and have different cell walls e.g. yeast, mold

Types of transporters (uniport, symport, antiport)

Uniport - 1 type, 1 direction Symport - more commonly opposite charges, and in same direction Antiport - Opposite direction, and more commonly same charge

What is the standard structure of RNA?

Unlike DNA's usual double helix, RNA exists in a plethora of conformations

What is the role of helicase?

Unwinding the DNA

Types of mutations in core promoters

Up promoter - mutations increase expression Down Promoter - mutations decrease expression

What is the effect of lactose?

Upregulation of expression of lac genes

What do light dependent reactions use and produce?

Use ETC and Chemiosmosis, light, and water to produce ATP and NADPH

Base Excision Repair Mechanism Step I

Use of DNA N-glycosylases to recognize abnormal base and cleave bond between ti and sugar in DNA

What is the purpose of enzyme immunoassays?

Use of antibodies to detect presence of antigens conducted in micrometer plates or in vivo 1. Antibody's constant region binds enzyme, leaving variable region free to bind its specific antigen 2. Addition of substrate for enzyme allows antigen to be visualized or quantified

What is diauxic growth?

Use of two different energy sources (bacteria using lactose and glucose)

How do multiple types of transporters work in concert to maintain conditions within a cell?

Use of various transporters to balance out conditions enough to produce desired effect

How do plants use light energy?

Use photosystems (PS) that contain pigment molecules. Pigments absorbs light and are reduced -> they pass these electrons on to ETC and are oxidized

What is a test cross?

Used to identify genotype of dominant phenotype by crossing dominant with recessive

Active transport

Uses energy to move solutes against gradient

What type of signal sequences are used to direct cellular transport? Where are they usually placed?

Usually involves certain types of amino acids (i.e. polar, nonpolar, +/- charged) in certain pattern Predominantly found in N-terminal region but can be found internally or C-terminal as well Note that the signals tend to be complementary/attracted to destined compartments i.e. positively charged nuclear and mitochondrial import sequences to interact with negative internal leaflets of those internal membranes

What is the phenotypic effect of duplications (generally)? Compared to deletions?

Usually less harmful than deletions of comparable size and not a major causative agent of many well-defined syndromes

What percentage of the total membrane in a typical eukaryotic cell is the ER?

Usually over 50% (although actual volume of lumen is about 10% of total cell)

Mechanism of Deamination

Usually removal of amino group from cytosine base to form uracil DNA repair enzymes can recognize uracil as inappropriate and remove it, but if repair fails, C-G to A-T mutation will result during subsequent rounds of DNA replication As for the thymine piece, not recognizable like uracil, so repair enzymes cannot determine which of two bases on two DNA strands is incorrect base -> methylated cytosine bases tend to create hot spots for mutation

Benefits of membrane lipid diversity

Varied diversity allows for varied raftophilicity of proteins to spontaneously aggregate in formation of lipid rafts to have specialized portions of membrane to form specialized roles

What is the difference between gram positive and gram negative?

Varied results of differential staining Gram Positive - many layers of peptidoglycan and teicoic acid - purple result Gram Negative - thin layer of peptidoglycan and more complex outer layers including outer phospholipid membrane and Lipopolysaccharide (LPS) - pink result

Microbodies

Variety of enzyme-bearing, membrane-enclosed vesicles

How is inflammation activated?

Vasodilation and increased vascular permeability allows plasma to leak in from blood vessels to the area

What is germination?

Vegetative state when endospores rediscover favorable conditions allowing cell growth and metabolism

What are alleles?

Versions of a gene

What are cancer vaccines?

Very active area of research involving experimental and therapeutic immune system stimulating vaccine that induce immune responses to prevent or treat cancers

How does Dinitrophenol (DNP) act?

Very effective diet drug that makes mitochondrial intermembrane leaky to protons, making cellular respiration less efficient and thus requiring more breakdown of food ingested to receive sufficient energy Side effect - as protons leak across, creates excess heat that eventually can be lethal as develop inability to regulate heat

Mechanism of ER protein export

Vesicles form at specific ribosome-free sites in the ER membrane called Exit Sites through cytosolic COPII coats Only properly folded proteins are incorporated into these budding vesicles Unfolded proteins are detected through many mechanisms involving hsp and chaperone proteins

What are immature secretory vesicles? What might they contain that needs to be modified?

Vesicles that are budded off resembling diluted TGN They become concentrated and develop into mature secretory vesicles as they fuse with one another and clathrin recycles extra membrane back to the TGN They may also contain precursor proteins with sections such as N-terminal pro-peptides that must be cleaved off to yield the mature proteins. This and other proteolytic modifications allow proteins to get to this stage before being active

What is the difference between virulent and temperate phage life cycles?

Virulent - lytic cycle leading to death of host cell Temperate - lysogenic phage where viral genome integrates into host's genome and is dormant

What is a Hemagglutination Assay

Virus causes clumping of red blood cells Introduction of varying antibodies can be done until successful inhibition of virus and negative microtiter results (no clumping) showing that that antibody is the correct match to virus

What are virions?

Virus particles

What are enveloped viruses? What do we call non-enveloped viruses?

Viruses enclosed in phospholipid bilayer membrane taken from host cell in endocytosis Non-enveloped = naked

What is the mechanism of antiviral antibodies?

Viruses must bind to receptors on host cells to cause infectino Antiviral antibodies neutralize this process by coating the visions and thus blocking the binding and forming large antibody-virus complexes that are readily removed by phagocytosis

What are some ways that we detect viruses with light microscopy even though they are too small to directly see?

Visual Cytopathic Effects (CPE's) including: Loss of adhesion to culture vessel Shrinkage of nucleus or other cell component Inclusion bodies Cell Lysis

3 Gating mechanisms of channels

Voltage-Gated Ligand-Gated Mechanically-Gated

Who is DNA structure attributed to? Who else played a role and what was it?

Watson and Crick in the 1950s Roselyn Franklin later used crystallography to determine the double helix structure

What is G-banding?

Way to distinguish similar chromosomes by exposing them to dye Giesma Dark bands bind the dye heavily (generally thought to be more dense) Light bands bind the dye less i.e. 300 G bands seen in human metaphase while 800 G bands seen in prometaphase (more comact)

How have we determined proteins are not static in the membrane?

We bleach out fluorescent molecules in a small area with a laser beam, bleached molecules diffuse away, and we can measure the movement graphically from the rate of recovery Greater diffusion coefficient = faster recovery

What is treadmilling and what is required for it to occur?

When [D-actin] > Cc(D) and [T-actin] > Cc(T), treadmilling occurs, a phenomenon in which the ATP-cap plus end is growing while the ADP-cap minus end is shrinking

When do actin filaments stop growing in length? What determines k(on) and k(off)

When concentration of G-actin is decreased to point where rate of addition of G-actin is equal to rate of spontaneous depolymerization of F-actin - Steady-State, equilibrium k(on) determined by [G-actin] k(off) relatively constant for the protein

What is alternative splicing? Rules?

When different polypeptide sequences made from same gene due to variation in splicing May skip over some exons, however still always have to be sequential (can't splice 1-5-3)

Genotype-Environment Interaction

When environmental effects of phenotype differ according to genotype

What is a hypersensitivity reaction?

When immune system has cellular or humoral reaction that is undesirable

Process of activation of B-Cell Lymphocytes

When it binds to an antigen it has antibodies for, it clones itself like crazy

What is polygenic?

When pattern of inheritance occurs on continuous distribution E.g. height, weight, skin color Often a result of genes + environment

What is photorespiration?

When rubisco binds oxygen instead of carbon, producing phosphoglycolate (toxic to plant) and releasing carbon dioxide

When is photorespiration and problem and why?

When the environment is hot and dry Leads to water loss when stomata opening for gas exchange, so plant keeps stomata closed to prevent water loss -> leads to buildup of oxygen from light depenent reactions since it cannot be released

Why is the nuclear import signal not removed following import like the others?

When the nucleus breaks down and reforms during mitosis, they must be able to get back in again to not have to recreate them every time Also there are many proteins that diffuse in and out of the nucleus regularly

When is the sum rule used?

When two events, A and B, are mutually exclusive, the probability that A OR B will occur is the sum of the probability of each event

What are Zoonoses?

When virus which infects one species can also infect humans I.e. avian flu, swine flu

Expression of HoxC-6 gene in different species of vertebrates

Where its expressed determines the number/ratio of neck vertebrae

What are the visible morphological changes in necrosis?

Wildly different than apoptosis including swelling and bursting, releasing intracellular contents that can damage surrounding cells and cause inflammation

How are V-Type pumps affected by the presence/absence of an ion channel like a chloride channel?

Without Channel - effect on pH change insignificant because ATP pump's max energy is met quickly by electric gradient -> main goal is to establish electric gradient With Channel - Chloride being pumped in balances out electric gradient as protons are pumped in, allowing energetically favorable pumping of more and more H+ into membrane to have major effect on pH

What is X-inactivation?

Women can only use one of their X chromosomes, other inactivates (but they would have awesome benefits if could use both) One that activates is healthier one, an option men don't have to avoid certain C-chromosomes mutations

How does gel electrophoresis work? How does it separate DNA and based on what properties?

Works by separating materials based on charge and size. Accomplishes this by putting material in porous gel (how porous can be controlled by percent agarose) one one end and applying electric current across gel to pull negative DNA across gel to positive side Loading dye is used to weight the material down and to make it visible later to see the bands of how far everything travelled

4 Types of Physical Mutagens

X-rays, gamma rays, ionization radiation, UV light

What are the other possible sex chromosomes combinations one can end up with?

XYY, XXY, XO, XXX

What is the difference between X and Y gene and possible effects?

Y has significantly less genes than X and may account for certain male/female differences and male challenges (theory)

What bacteria species causes the Black Plague?

Yersinia pestis

Are all prokaryotes single-celled?

Yes

Are intracellular proteins also subject to combinatorial regulation?

Yes

Can fevers damage host's cells in process of defending against foreign invading cells?

Yes

Can all eukaryotes perform cellular respiration?

Yes!

Was Bob's DNA affected with HNPCC?

Yes, Bob was heterozygous for it meaning he inherited one mutated MSH-2 allele, so one more mutation and he can have it. This increased his risk from 5 to 80% chance

Can exons be rearranged in splicing?

Yes, apparently

Do nonstructural genes have promoters and terminators?

Yes, as these are present in the DNA sequence

Does the DNA Pol III always move toward the replication fork?

Yes, even in lagging strand it loops around so that it can still move that way and synthesize 5'->3'

Do nonstructural genes create RNA?

Yes, just not proteins. They encode things like rRNA, tRNA, etc.

Do enzymes require a specific environment?

Yes, they have optimal pHs and temperatures and can become denatured when they fall too far outside them. Temperature - permanently, pH - non-permanently. Different enzymes have different optimal environments

What is a proband?

a person serving as the starting point for the genetic study of a family, often the first known infected individual

What is a transcription unit?

a region of DNA that is transcribed into an RNA molecule that includes the lac Z, Y, and A genes in the lac operon

What is an Auxotroph?

a strain that cannot synthesize particular nutrient and needs that nutrient to be supplemented in a growth medium

Methods of antibodies assisting in defending against pathogens

agglutination, opsonization, neutralization

Which ploidy variation is more dangerous, aneuploidy or euploidy?

aneuploidy - usually detrimental, causing about 50% of spontaneous abortions

What are bilaterians?

animals with bilateral (left-right) symmetry

What is an autosome?

any chromosome that is not a sex chromosome

What are the structures of the 5 nitrogenous bases?

awkward adenine is the only without a carbonyl group Thymine and Uracil are the only ones with two carbonyl's ThyMine has that That extra Methyl group

Enzymatic Role of actin

catalyze hydrolysis of ATP to ADP

Why do leaves turn red in fall?

chlorophyll used to max makes all red and blue absorbed and green released making leaves green, but when there's less light and days get shorter in fall, cell stops making so much chlorophyll since its energy costly to the cell to make it, and as cell switches over to carotenoid, leaves turn red, yellow, etc.

What are degrees of freedom in chi squared tests?

df is a measure of the number of categories that are independent of each other df = n - 1 where n = total number of categories

What is nosocomial disease?

disease acquired in a clinical/hospital setting

Define infectious disease?

disease caused by direct effect of a pathogen

What is iatrogenic disease?

disease resulting from a medical procedure

What is co-dominance?

each genotype has its own distinct phenotype I.e. A and B blood producing AB blood

What is genetic complementation?

example of epistasis when two separate genes have the ability to affect the same phenotype because they are both required for something

Structure of actin and basic roles

flexible structures with 8nm diameter made up from a series of actin monomers arranged in a staggered conformation forming a helical filament Dynamic formation/degradation drives directional movement of cell and contents within it

What is budding?

forming of smaller extension of cell at one end that breaks off into new individual (yeast)

Vacuoles

found in plant cells; are kind of like lysosomes; plant vacuoles store, recycle and provide turgor

4 Inflammation-Eliciting Mediators

from Low to High BP Leukotrienes Histamines Bradykinin Prostaglandins

What is fragmentation?

growth of multiple nuclei regions cell elongation breakage into multiple pieces, each with nucleoid Method used by some cyanobacteria

What is Hfr?

high frequency of recombination exhibited when E. coli efficiently transferred chromosomal genes to F- strains

Watch

https://www.youtube.com/watch?v=YgmoHtLGb5c

What are Xenobiotic Pollutants?

human-made compounds in high levels which cause environmental imbalances

What is genetic redundancy?

identical genes on different chromosomes and different loci that make gene knockout not 100% effective

What is the key difference between lysogenic and lytic cycles?

lysogenic allows cell to still be viable and pass phage genetic info to progeny

What happens in the small and large ribosomal subunits?

mRNA-tRNA recognition and binding of IFs - small subunit APE sites action - large subunit

What is a turbidity test? Tools?

measure of amount of cloudiness organisms crate in growth medium measured using spectrophotometer?

What effect did genetics have on taxonomy?

modern taxonomy compares genetic material and proteins to determine evolutionary relationships

What is an element?

pure substance that consists entirely of one type of atom

What is the role of transcription factors?

recognize promoter and regulatory sequences to control transcription

What is the law of independent assortment?

the alleles of different genes separate independently of one another during gamete formation (meiosis II)

What is the law of independent segregation?

two copies/alleles carried by each parent segregate from one another such that each gamete only has one copy (meiosis I)

Why is ATP a good choice for energy currency of cells?

-Instability of negatively-charged phosphate groups -Mid-level free energy change allowing for efficient energy storage but not waste when powering smaller reactions

Mutation Rate

-Likelihood that gene will be altered by new mutation -Commonly expressed as number of new mutations in a given gene per cell generation i.e. hHumans - 100-200 mutations/generation (30yrs)

Structure/Mechanism/Selectivity of K+ leak channels

(B) All alpha helices have innate helix dipole that forms with N positive side and C negative side (as would expect at physiological pH) that draws all positive ions into the selectivity filter Inside filter, specifically placed Selectively Loops select for potassium through specific distancing that only favors breaking of K+ solvation shell and no other solvation shells of smaller ions (larger ions can't even fit in)

What was the Genetic Mapping Experiment by Elie Wollman and Francois Jacob in the 1950s?

-Mixing of Hfr cells positive for many proteins and F- cells negative for them -Blended cells together in a blender and removed at different times, interrupting conjugation and plating to see how many positive genes were picked up -Able to detect phenotypes based on ability to survive -Mapped based on time for cells to demonstrate phenotypes

Why can't we get map units above 50%?

-Multiple crossover events set a limit on the relationship between map distance and crossover rate -Test crosses of two genes more than 50mu apart results in no more than 50% recombination

How do aquaporins selectively allow water through, but no OH-, H+, or H3O+?

-Narrow channels allow single file water molecules that H-bond with carbonyl O's -Hydrophobic amino acids like other side, preventing any other ions from crossing -two strategically placed Asparagine residues in center of line impose bipolarity of entire line, preventing the usual passing of H+ down the line (C) as they can't make it past the N residues

What is Phenylketonuria (PKU) and what happens when we have defunct versions of it?

-PKU is a gene encoding phenylalanine hydroxylase, an enzyme that converts phenylalanine to tyrosine -With two defective alleles, phenylalanine builds up causing detrimental effects like mental impairment

What is the role of Ran-GEF proteins in mitosis? What is the status of Ran proteins? What is the role of NPCs in all of this?

-Ran-GEF (guanine exchange factor) stays associated with the chromatin during mitosis -Ran proteins adjacent to the chromatin is predominantly in the GTP bound state and is released from the NPCs -Free NPCs bind to chromatin and help to re-establish the nuclear envelope

Effect of bidirectional migration (2)

-Reduces allele frequency differences between populations -Enhances genetic diversity within a population

What are simple translocations? Another name?

-Transfer of genetic material in only one direction -AKA unbalanced translocations -usually associated with phenotypic abnormalities or even lethality

What were the Hershey and Chase experiments?

-Used radioactive-labeled phages, labeling phosphorous (DNA) in one group and sulfur (protein) in the other -result was further evidence the DNA is genetic material

What is the CREB Protein and its mechanism?

-cAMP Response Element-Binding -Regulatory TF -GCPR activation -> cAMP formation -> cAMP binds protein kinase A which travels into nucleus and phosphorylates CREB protein -> protein binds to CRE to activate transcription

Why are pea plants such a good model system to study genetics and inheritance?

-contained many clear binary phenotypes that could be bread to be pure -naturally self-fertilizing but could be manipulated -large number of offspring with short generation time

How did Robert Koch contribute to microbiology?

-established a connection between single, isolated microbes and certain diseases (anthrax, cholera, tuberculosis) IOW, linked microbes with specific diseases definitively

How did Louis Pasteur contribute to microbiology? (3 ways)

-established that individual microbe strains had unique properties -demonstrated fermentation -developed a process to reduce spoilage of food by heating and advocated that it killed microorganisms (pasteurization)

What is incomplete dominance? (Impact and molecular mechanism)

-intermediate production of a gene that is not fully recessive or dominant but somewhere in betwen -may appear phenotypically dominant

What is a biofilm?

-mini-ecosystem of multiple species of microorganisms co-inhabiting a surface under favorable growth conditions and nutrients

What is overdominance? example?

-when the heterozygote has better survival advantage than either homozygotes -i.e. sickle cell where HTs have functionality and malarial resistance

How many nucleotides are added at a time by DNA and RNA Polymerases?

1

How many cells originate a CFU?

1 cell

What is the degree of fidelity of DNA polymerase III? How does it accomplish this?

1 mistake per million base pairs -stability of base pairing -structure of DNA polymerase active site (mismatches cause distortion that does not fit properly in site) -proofreading function (proofreading domain that it sends to if miscorrect match made, see picture)

Myofibril Structure/Function

1-2 um-diameter tubes of sarcomeres attached end to end that span length of muscle cells and anchor into tendons at attachments Demonstrate incredible evenly-spaced arrays of organizations in real cells

What is the process of transcription initiation and elongation with histones?

1. Activator binds enhancer in NFR region 2. Chromatin remodeling complexes and histone modifying enzymes recruited to allow formation of pre-initiation complex in process that may include histone acetylation and eviction 3. Elongation occurs as histones are acetylated and evicted as necessary, and behind open complex histones are de-acetylated and become tightly bound again to DNA

What is a test cross? Reciprocal cross? Purposes?

-A test cross is a crossing of a recessive (genotype known) individual with a dominant phenotype (genotype unknown) to determine genotype -A reciprocal cross is the flipping of which parent is which genotype to determine if the same results are still reached

What were the Avery, MacLeod, and McCarthy (AMM) experiments?

-Built on Griffith experiments, hypothesizing that the transforming particle was DNA -combined type R cells, type S DNA, and various experimental additions including RNAase, DNAase, and proteases and saw which were successful transformations. -results of DNAase halting transformation was strong support for DNA as genetic material

What is the G-protein coupled receptor process?

1. First messenger ligand binds receptor and activates it, phosphorylating GDP to GTP 2. G-protein + GTP leave receptor 3. G-protein + GTP bind to Effector and activate it by phosphorylation 4. Effector "makes" a Second Messenger 5. Second Messenger turns on protein kinase cascade 6. Target Protein phosphorylated -> RESPONSE MOTHA ****AAAA

What are the three possible ways for excited electrons to relax when chlorophyll electrons are excited? Which is most common?

1. Fluoresce - release extra energy to heat or longer (lower energy) wavelength 2. Resonance - transfer energy (NOT the electron itself) to neighboring chlorophylls very efficiently 3. Transfer energy AND electron to adjacent electron acceptor resulting in positively charged chlorophyll molecule Commonly chlorophyll-protein complexes relax via pathway 2 until they can find a special pair for path 3

What are the 3 paths of radiant energy when it reacts with photons?

1. Fluorescence/Heat - light bumps electron to excited state and then heat/fluorescence given off when it falls back 2. Reduction - excited electron goes to primary acceptor 3. Resonance - excited electron goes back to ground state but energy toes to another pigment molecule (very efficient)

Approximate Lipid Compositions of Different Cell Membranes Chart (what are the three most abundant?)

1. Glycerophospholipids 2. Sphingolipids 3. Cholesterol

What was Experiment 8A? (CGH)

-Comparative genomic hybridization to detect deletions and duplications 1. Isolate DNA from human breast cancer and normal blood cells 2. Label breast cancer DNA with green fluorescent molecule and normal DNA with red fluorescent molecule 3. DNA strands denatured and mixed together in equal proportion 4. Allow them to hybridize to metaphase chromosomes 5. Visualize chromosomes with fluorescent microscope and analyze amount of green and red along each chromosome with computer Ratio gives evidence of numbers of duplications (ratio of 2) and deletions (0.5) on chromosomes

Describe the three main types of proteins that make up the extracellular matrix. What are they made of and what are their general physical characteristics?

1. Glycoaminoglycans - highly charged polysaccharides that are often covalently linked to proteins in the form of proteoglycans 2. Fibrous Proteins, primarily collagen family members 3. Non-collagen glycoproteins carrying Asp-linked oligosaccharides

Methods of post-translational regulation?

-Covalent modification of protein by phosphorylation, methylation, attachment of additional groups, acetylation, etc. to change activity reversibly or irreversibly -Feedback inhibition through allosteric inhibition

What are the two transcriptional regulatory options of the lac operon? Describe the first

1. Lac Repressor - inducible, negative control mechanism in which allolactose is inducer that binds to repressor and inactivates 2. Activator Protein

What are the 3 pathways of protein sorting from the Golgi?

1. M6P marker -> clathrin-coated vesicles -> lysosomes 2. Specialized secretory cells recognize secretory cell sequence 3. Unspecific, unregulated secretion to PM

Steps of phagocytosis

1. Macrophage locates bacteria 2. Eat bacteria and form Phagosomes (vesicles containing foreign particles) 3. Phagosomes fuse with lysosomes to become Phagolyososmes 4. Phagolysosome with remaining debris exocytosed

How do mammals obtain cholesterol?

-Diet (though current research indicates cholesterol from food has minimal impact on circulating cholesterol levels) -Synthesized de novo in liver

How are mitochondria and their various layers and membranes purified for study?

1. Mitochondria placed in medium of low osmolarity, allowing influx of water and swelling of matrix. OMM ruptures, releasing content of IMS while IMM remains intact 2. Centrifugation to isolate content of IMS 3. Transfer to high-osmolarity medium to shrink matrix 4. Density-gradient centrifugation separates, inner membrane, outer membrane, and matrix

How is a cotransduction experiment designed?

-Donor cell positive for two genes of mapping interest but sensitive for an antibiotic, recipient cell negative for two genes but resistant to antibiotic -Donor infected with lytic bacteriophage -Lysate from that mixed with recipient cells -Recipient cells then plated on medium testing for one phenotype and antibiotic resistance -These cells are then re-plated to test for both phenotypes

What is dosage compensation and why do we need it? Mechanisms in different species?

-Dosage compensation regulates expressions of genes on the sex chromosomes so that gene is same in product of both sexes -Necessary to ensure genetic equality between the sexes -highly condensed somatic cells forming Barr Bodies in nuclei of female cats and eye color in flies

What are the three phases of actin filament development? What is the rate-determining step? Which part is unique to in vitro?

1. Nucleation (lag phase) - actin subunits to oligomers 2. Elongation (growth phase) oligomers to growing filament 3. Steady State (equilibrium phase) simultaneous growth and removal After nucleation, elongation is rapid Instabilitiy of smaller aggregates provides a kinetic barrier to nucleation resulting in a lag phase in vitro

What are the three functions of DnaA protein?

1. Recognition of origin of replication 2. Binding to DnaA box to split AT-rich region 3. Recruiting of DNA helicase (with DnaC)

What are the goals of meiosis?

1. Reduce number of chromosomes to haploid (half) 2. Genetic diversity as raw material for evolution

What are the 3 possible fates for transmembrane receptor proteins that have been endocytosed?

1. Returned to same PM domain from which they came 2. Recycled to different part of PM 3. Degraded in lysosomes

What are the key differences between internal steroid/hormone receptors and others?

1. They are inside the cell, not on the surface 2. They affect protein creation instead of just activating already existing proteins

What are the steps in DNA replication?

1. Unwind the DNA starting at the ori 2. DNA Polymerase adds nucleotides to the existing chain on the leading and lagging strands 3. Clean-Up by combining Okazaki fragments and correcting mistakes

What is the process of receptor tyrosine kinase activation?

1. When each dimer binds a ligand, receptor is activated 2. Activated dimer cross-phosphorylate each tyrosine 3. Tyrosine phosphorylation -> PK cascade 4. Can have two responses (activate two target proteins)

Eukaryotic translation initiation breakdown

1. eIF4 binds capped mRNA 2. 40S subunit binds eIF1, eIF3, eIF5, and initiator tRNA into complex 3. eIF4 receipts mRNA to complex 4. Initiation factors dissociate 5. 60S subunit joins forming 80S complex 6. Ribosome scans to find start codon

What was the method Mendel used in his crosses?

1. mated true breeding parents 2. observed F1 phenotype - always pure dominant 3. "selfed" F1 to examine F2 generation - always 3:1 return ratio of recessive

Frequency of DS breaks in humans

10-100 breaks occur each day in typical human cell

Which chromosomes are the sex chromosomes?

23rd pair

How many types of myosin are encoded in human cells, and what are some of their alternative functions? Myosin V Role?

40 different myosin proteins (many of which we don't know their function) All but one moves towards + end of actin (Myosin VI) 9 Exclusive to the ear Myosin V - cargo transport along actin filaments

What is the approximate wavelength range of the visible spectrum?

400-700 nm

What did we believe before Mendel?

530 B.C. - Pythagoras - semen is everything woman is vessel Pluto - something similar Aristotle - first to credit women with any part in likeness 1520s - Preformation - little teeny humans in sperm grow up 1700s - Casper Wolf in Berlin determines that a code must exist

What is the significance of Otzi the Iceman?

5300 year old body found that showed evidence of prehistoric treatments of illness and infection since he had abdominal illness and lyme disease and had incisions with herbs of antibiotic and laxative properties burned into them

How many turns of the Calvin cycle are needed to make 6 G3P molecules? Glucose? RuBP?

6 G3P molecules - 3 turns RuBP - 3 turns (but 5 carbons) Glucose - 6 turns (each 3 creates an RuBP and half a glucose essentially)

What is the structure of RNA polymerase?

6 polypeptide units (quaternary structure) 5 of perform polymerizing functions 1 (the alpha subunit) binds to the promoter to initiate transcription

What is the ORC?

6-subunit complex that acts as first initiator of eukaryotic DNA replication

What is epistasis?

A phenomenon when the genotype of one gene can mask the effects of a separate gene or overwrite it such as stripes

What is Inclusion Cell (I-Cell) Disease?

A rare, inherited lysosomal storage disease in which GIcNAc phosphotransferase is inactive or missing and thus most of the hydrolytic enzymes are missing from lysosomes of many cell types, allowing large undigested substrates to aggregate in lysosomes forming large inclusions This has many effects and prevents individuals from living usually beyond 6-7 years

What is a syndrome?

A set of signs and symptoms that is characteristic of a particular disease

What is copy number variation?

A variation between members of species in which members have different numbers of a particular segment of DNA (some my have 1 copy of the gene while others may have multiple copies) -can be related to disease or entirely benign

What is an allele?

A version of a gene

How is the G-C connection different than the A-T connection?

A-T has 2 H-bonds because you have 2 T's and 2 cheeks on your A G-C has 3 H-bonds because G Can have extra

How can membrane-bending proteins shape membranes? (3 ways)

A. Control B. Hydrophobic Region of the Protein inserts as wedge, curving membrane C. Curved surface of protein binds to lipid head groups D. Protein binds to and clusters lipids that have large head groups, bending protein

Why is adjacent-2-segregation less common than adjacent-1-segregation and alternate segregation?

A1 and Alt involve centromeres going to opposite sides cell, typical in meiosis as these are points of attachment. Adjacent 2 segregation is less likely because it is the type of separation in which adjacent centromeres move to the same pole

Which type of protein if defective causes pathology in CF?

ABC Protein CFTR that is a chloride CHANNEL (not a pump)

Name of process that helps kill pathogens too large for phagocytosis?

ADCC - antibody-dependent cell-mediated cytotoxicity helps kills pathogens too large for phagocytosis

What is the wavelength of an electron?

About 0.005 nm

What percent of the human population carries inversions in their DNA?

About 2%, though most phenotypically normal

How do G-Proteins inactivate and activate?

Activate when holding G-triphosphate nucleotide like GTP and then inactivate when GTP is hydrolyzed to GDP

What are mutagens?

Agents that alter structure of DNA and cause mutations

Process of agglutiantion

Aggregation or cross-linking of pathogens to create pathogen/antibody clumps

Which methods of co-translational and post-translational translocation are utilized by eukaryotes and prokaryotes?

All (including archaea) use co-translational Post-translational difference is how energy is utilized: eukaryotes pull from inside after feeding through while prokaryotes push in from outside

What are PQ, PC Ferredoxin, etc.?

All just electron shuttlers

Cell Theory

All living things are composed of cells All cells arise from other pre existing cells Cell is basic structural and functional unit of all living organisms

Which amino acids can be acylated on their N-terminus? Which on their amides?

All on the N-terminus K, H, and R on their amides (Lysine, Histidine, and Arginine, the bases)

What are lethal alleles? (Types, impact and mechanism)

Alleles that result in death of homozygous offspring -Constitutive Lethal - HM always dies -Conditional Lethal - only dies under certain conditions -may be pleiotropic where allele may be responsible for multiple phenotypes

What is an ascus?

An ascus is a reproductive structure that contains spores

What is reverse transcriptase and a famous example of it?

An enzyme that converts RNA into DNA HIV uses this method of infection, integrating into host genome as a provirus and creating DNA to produce more of it

What is a zymogen?

An inactive enzyme precursor

What is the difference between anabolic and catabolic?

Anabolic - endergonic, from monomers to polymers for energy storage Catabolic - exergonic, from polymers to monomers for energy use

What is the difference between anaerobic respiration and fermentation?

Anaerobic - alternative inorganic terminal electron acceptors like CO2, iron, sulfate, nitrate Fermentation - uses organic molecules, usually pyruvate with yield of 2 ATP per glucose

How are proteins targeted to the lysosome?

Animal cells label their lysosomal hydrolyases with mannose-6-phosphate M6P groups M6P marks recognied by M6P receptor proteins in TGN (trans golgi network) M6P are transported to early endosomes by vesicles, detached by the low pH, and then dephosphorylated to prevent their escape pH dependent changes in receptor conformation dictate the loading and unloading of M6P modified proteins

What were the initial 3 kingdoms of Linneaean Taxonomy?

Animal, Plant, Mineral Divided into classes, orders, families, genus, and species

What is cotransport?

Another term for secondary active transport Uses protein and favorable gradient of another molecules transfer i.e. glucose/Na symporter across small intestine Includes Symport/Antiport

Where are light harvesting pigments located?

Antenna Complex

What are aseptic techniques?

Any healthcare procedure in which added precautions (gloves, disinfectants) are used to prevent contamination of person, object, area Used in our micro lab

What is the spontaneous generation theory and why was it disproven?

Aristotle's theory the life can arise from non-living matter; it was disproven because scientists like Pasteur (swan neck flask exp) and Koch proved that was actually going on was the presence of microbes

Secondary role of Arps

Arp2/Arp3 complexes can also be attached to growing actin polymers to create branched structures as shown

What does pus tell us about neutrophil activity?

As neutrophils work, they are usually destroyed after attacking invaders and the resultant cellular debris and bacteria create the buildup of pus

What are ARS elements?

Autonomously Replicating Sequences in Saccharomyces Cervevisiae (eukaryotes) that are about 50 bp in length, have high percentage of A and T, and have ARS Consensus Sequences (ACS)

What is an autotroph? Heterotroph?

Autotroph - can convert inorganic CO2 into organic compounds (plants, cyanobacteria) Heterotroph - need more complex organic carbon compounds for energy

What is the process of Lagging Strand Synthesis?

Away from replication fork, multiple RNA primers added, each being built on by DNA pol III (1000-2000 nucleotide Okazaki fragments in bacteria, 100-200 in eukaryotes), then DNA pol I removes RNA primers (unique 5'->3' exonuclease activity) and replaces with DNA. Finally, ligase catalyzes PD bonds to connect fragments

Which type of cells (T or B) associated with humoral and cellular immunity?

B Cells - Humoral T cells - Cellular

What are the essential requirements and purposes of the various Biological Safety Levels (BSLs)?

BSL-1 - Common in genetics labs, microbes not known to cause disease in healthy humans, minimal restrictions (E. coli) BSL-2 - Microbes of varying pathogenicity pose moderate risk to workers and environment; Closed environment, ventilation, eye pro (Staphylococcus Aureus) BSL-3 - Microbes present potentially lethally diseases through aerobic transmission; medical surveillance and immunizations; negative pressure systems (Myobacterium tuberculosis) BSL-4 - Dangerous, exotic, high risk of aerosol-transmission infections that are frequently fatal; rare (ebola)

Sources of membrane fatty acid diversity?

Backbone modification Changing Fatty Acids Modifying Head Group

Difference in RFs between Bacteria and Eukaryotes?

Bacteria: RF1 recognizes UAA and UAG RF2 recognizes UAA and UGA RF3 does not recognize either but required for termination process Eukaryotes: eRF1 - recognizes all three stop codons eRF3 - required for termination process

Bactericides, Viricides, Fungicides, Bacteriostatic, Fungistatic

Bactericides - kill bacteria Viricides - inactive viruses Fungicides - kill fungi Bacteriostatic - prevent bacterial growth Fungistatic - inhibit fungal growth

Why is the citric acid cycle considered aerobic when it does not involve consumption of any oxygen?

Because it is directly coupled with the ETC

What is the reference for looking up prokaryote classification and identification?

Bergey's Manuals

How do enzymes lower Ea? (List multiple ways)

Bring reactants together Allow induced fit -> conformational change Can expose reactants to altered or charged environment as well. Change shape of substrate making it more unstable

Pros of inflammation (3)

Brings in cellular defenses Washes away debris and toxins Brings in repair factors

Broad vs. Narrow Sense Heritability

Broad Sense - takes into account different types of genetic variation that may affect phenotype Narrow Sense - heritability of a trait due to additive effects of alleles

What is incorrect about the myth of hydrogen peroxide working/not working?

Bubbling actually means it is NOT working because bacteria are breaking down the hydrogen peroxide into water and oxygen by way of catalase (catalase positive bacteria)

What is the significance of the "c" and "o" at the end of rubisco?

C refers to carboylase O refers to oxygenase

Structure of ATP Synthase

C-unit, also referred to as F0 section (shown in light blue) receives protons from matrix to fuel nanoturbine Gamma shaft uses knob shown to shift conformations of beta units and kick out ATPs Alpha/Beta units are the catalytic, F1 portion

Why is C. elegans so useful to study?

C. elegans is transparent and has relatively few cells that can each individually be followed through cell lineage by researchers Also, the timing of the mutations can be tracked to show which mutations at various times have which effects

ATP Synthase Rotation

C10 ring has 10 spots for protons, and they flow down their concentration gradient through it, completing one full spin through the nanoturbine before being pumped out 10 Spots and 10 H+ used per full rotation = per production of 3 ATP This 10 subunits per ring is specific to mammalian cells, and can be adjusted to adjust the efficiency of the cell. Less subunits = more efficient but requires higher energy input

Formula for energetics of membrane transport

C2 = where it going TO!

How do C4 plants and CAM plants get around photorespiration?

C4 plants shift day/night cycle to prevent photorespiration CAM plants have alternative ways to make ATP

What is the equation for glycolysis?

C6H12O6 + 2 ATP + 2 NAD+ > 2 Pyruvate + 4 ATP + 2NADH

What is a caspase? How does a caspase function? What are the two domains of a caspase? How are they regulated? What are the two types of caspases relevant to apoptosis? What does each type of caspase target?

CASPASES are Cysteine catalytic ASPartic acid targeting proteASES Predominant proteases for apoptosis Types: -Initiator - activated by external or internal signals to initiate apoptosis by activating executioner caspases -Executioner - main acting caspases that conduct cleaving that leads to apoptosis targeting thousands of additional proteins like nuclear lamins and endonuclease inhibitory proteins Have adaptor-binding domains and protease domains

What is the formula for carbohydrates?

CH2O

What is critical micelle concentration?

CMC (property specific to individual compounds under specific conditions) is a concentration above which detergents aggregate to form micelles and rapidly diffuse in and out of micelles, keeping concentration of monomer in solution constant no matter how many micelles are present

What was disease and treatment of the case study discussed in class?

CML - chronic myeloid leukemia - translation of ABL and BCR genes -> mutated tyrosine kinase that binds ATP and substrate leading to overproduction of WBC Treatment - Imatinib (Gleevec) at least for first mutation, inhibits only the mutated tyrosine kinase

Describe cadherins. What are the common features of all cadherins? What are the function of cadherins? What do they bind? Compare and contrast classical cadherins and non-classical cadherins.

Cadherins are calcium-dependent adhesion proteins that facilitate a large family of over 180 members of cell-cell interactions and are found in genomes of all multicellular animals (but not fungi/plants) Classical Cadherins - include E-cadherin, P-cadherin, N-cadherin - highly structurally and functionally related and contain 5 extracellular cadherin domains Non-Classical - democollins, desmogleins, protocadherins - vary greatly in number and organization of extracellular domain

What is the role of calcium in heat-shock transformation?

Calcium cations bind to negative LPS layer, creating calcium bridge to bond to and bring bacteria in contact with negatively charged DNA molecules

What are the big four elements and how much of living organisms do they make up?

Carbon, nitrogen, oxygen, hydrogen; 96%

What happens in cytokinesis? Difference between animals and plants?

Cell splitting Animals: cleavage furrow Plants: cell plate

What roles do cell survival pathways play in regulating apoptosis? Explain the three pathways that promote cell survival.

Cell survival often requires constant presence of survival factors, as it usually is NOT the default! 3 Pathways: -Increased Production of Anti-apoptotic Bcl2 family protein: Survival factor bound -> activates TF -> upregulate Bcl2 protein production -Inactivation of Pro-Apoptotic BH3-only protein: Survival factor bound -> Phopshorylates/Activates Akt Kinase -> phosphorylates Bad to inactivate and free Bcl-2 -Inactivation of Anti-IAPs: Survival factor bound -> MAP kinase activated -> phosphorylation of Hid -> stops inhibition of IAPs, allowing them to inhibit apoptosis

What is direct signaling? Examples?

Cell to cell recognition Channels, immune system, plasmodesmata

What happens in prophase?

Chromosome condense Spindle (MT) beings to form between centromeres

What is the structure of tRNA?

Cloverleaf pattern with three stem-loops structures and only a few variable sites (in blue in this diagram) Acceptor stem has 3' single strand region that binds amino acid Commonly contain 80+ modified nucleotides

Difference between Co-Translational Translocation and Post-Translational Translocation by the ER?

Co-Translational - Synthesized directly into lumen Post-Translational - Synthesized by free ribosome and transported to ER

Define opsonization as it pertains to complement system

Coating of pathogens in chemicals to identify invader

What are sense codons?

Codons that code for amino acid; there are 61 of them

what is a progeny?

Collection of descendents

What are the 5 GTFs?

D - TATA-binding protein B - TFIID &TFIIF creating a bridge F - Binds RNA Pol II, helps associate TFIIE and TFIIH E - maintains open complex, regulates TFIIH H - Helices, phosphorylates c-terminal domain of RNA Pol II

Roles of D-Tubulin and T-Tubulin in Polymerization

D-Tubulin releases more energy when depolymerized Cc(D) > Cc(T) GTP cap forms on plus end, GDP cap on minus end Very similar to Actin

What are examples of second messengers?

DAG, IP3, and cAMP

4 Events that may happen to cells in during course of development

DAMD Division Migration Apoptosis Differentiation

What are the monomers of DNA and RNA?

DNA - deoxyribonucleotides RNA - ribonucleotides

What defines the beginning and end of a gene and regulates the level of RNA synthesis?

DNA Base Sequences

What are mechanisms of genetic imprinting?

DNA Methylation (inhibits gene) or other epigenetic markings that are recognized throughout the life of the organism, causing monoallelic expression and non-Mendelian patterns of inheritance

What occurs when the end of the DNA molecule is reached? (3 things)

DNA Polymerases unbind SSBPs removed Hydrogen bonds between strands re-established

What are the two toposiomerases?

DNA Topoisomerase I - relaxes negative supercoils; can NOT introduce positive from no strain tough DNA Topoisomerase II AKA DNA Gyrase - introduces negative supercoils using energy from ATP and relaxes positive supercoils where they occur; can untangle intertwined DNA molecules

What is the difference between positive and negative supercoiling? Which one is E. coli kept in and why?

DNA given a turn that unwinds the helix can cause fewer turns OR a negative supercoil and vice versa E. coli is maintained in a negative supercoiled stated to compact or shrink the genome

What is Transcription and its features?

DNA info coded into RNA One strand used as template Thymine replaced with uracil Deoxyribose replaced with ribose

What is chromatin?

DNA molecules that are tightly coiled around proteins call histones.

Which has greater processivity, DNA polymerase or RNA polymerase?

DNA polymerase

What is the role of proteoglycans (decorin, aggrecan, and syndecan) within the ECM?

Decorin - small proteoglycan containing single GAG chain that binds collagen fibrils and regulates fibril association and diameter Aggrecan - massive proteoglycan with over 100 GAG chains of two different types; major proteoglycan component of cartilage; assembles onto hyluronan chains to create protein meshworks Syndecan - anchored to cell membrane through an integral membrane core protein; interacts wih actin cytoskeleton and with signaling molecules

How does the reducing environment of the cytosol affect protein structure?

Decreases likelihood intrachain or interchain disulfide bonds will form on the cytosolic side, while they do form on noncytosolic side

What is virulence?

Degree to which organism is pathogenic Continuum from non-harmful (avirulent) to highly virulent

How does desiccation control microbes?

Dehydration, evaporation, freeze-drying

How does phenol control microbes?

Denature proteins Disrupts membranes In some mouthwashes

What are the processes involved in changing the number of surface receptors?

Desensitization - lessening of receptors - downregulation Sensitization - increase in receptors - upregulation

What proteins are involved in desmosome formation?

Desmoglein and Desmocollin - specialized cadherins They are unique in that their cytosolic domains are distinct from those in classical cadherins and bind adapter proteins (plakoglobin, desmoplakins, plakophilins) that attach to sides of intermediate filaments

General DNA repair steps

Detect irregularity Remove abnormal DNA Synthesize normal DNA

Osmosis

Diffusion of water

What is a noncommunicable disease?

Disease NOT spread between hosts

What is unique about sex chromosome aneuploidy?

Due to X inactivation, individual with more than one X chromosome can convert all additional X chromosomes into Barr bodies

How is cadherin production associated with epithelial to mesenchymal transition, and cancer? What is the shared phenotype?

E-cadherin activity is lost during the epithelial-to-mesenchymal transition (EMT) and during cancer progression, allowing cancer to detach and spread EMT: -Snail Protein suppresses E-cadherin expression -Associated with conversion of epithelial cells into malignant carcinoma cells Images: a. Normal epithelial MDCK cells grown in culture form sheet of cadherin-connected cells b. MDCK cells expressing Snail gene undergo EMT and dissociate c. E-cadherin distribution in tissue from a patient with hereditary diffuse gastric cancer

What is the intermediate that forms between ER export and Golgi retrieval of vesicles?

ER budded vesicles contain both vSNAREs and tSNAREs that untangle through NSF and then undergo Homotypic Fusion (fusion of compartments of the same type) into vesicular tubular clusters

How do mitochondria interact with the ER?

ER contact helps facilitate mitochondrial division as well as transfer of lipids to the mitochondria

How are oligosaccharide chains processed in the Golgi? What is the difference between oligosaccharide modification in ER vs. Golgi?

ER is full of soluble lumenal resident proteins/enzymes, but resident proteins of Golgi are entirely found in membrane As proteins transit the Golgi, they are modified with specific sugars for functionality, protein folding, prevention of aggregation, and limiting accessibility (evolutionary advantage after losing cell wall) Steps shown are very ordered: 1. ER immediately attaches N-linked glycosides on Asn residues, then glucosidases remove glucoses and finally mannosidase removes a very specific mannose 2. Golgi Mannosidase removes 3 more mannose 3. Addition of N-acetyl glucosamine 4. Mannose II removes two more mannose and makes resistant to endo-glycosidase 5. Final processing and addition of N-acetyl glucosamines and sialic acids Tightly held sugars are more likely to be held in High mannose form, but those that are accessible by enzymes of Golgi tend to be converted to complex

What is the purpose of Protein Disulfide Isomerase in the ER?

ER is oxidizing like the outside of the cell, and thus folds correctly for proteins destined for the extracellular environment Protein Disulfide Isomerase creates disulfide bonds in proteins contained in the ER lumen

How does the ER lumen relate to the cytosol in terms of pH and charge?

ER is slightly more acidic and positively charged (calcium ions)

What are the four pathways that deliver material to lysosomes?

Endocytosis (by way of endosomes) Phagocytosis (by way of phagosomes) Macropinocytosis (also by way of endocytosis) Autophagy - by way of autophagosome

What is Rubisco and its significance?

Enzyme that is most abundant on planet 50% of total protein in leaves Fixes 100 billion tons of carbon dioxide Takes carbon from carbon dioxide and RuBP to make 6-carbon molecule

What bond is unique to lipids?

Ester bond

Do all species have membrane bilayers?

Exception of archaebacteria - monolayer of bifunctional lipids with polar heads on each side of tails

What happens to nucleic acids in the cell during apoptosis? How is this process regulated?

Executioner caspase targets CAD inhibitory protein, iCAD, cleaving it to activate CAD CAD fragments DNA

What do exonuclease and endonuclease cleave?

Exonuclease - cleave covalent bond between two nucleotides at one end of strand Endonuclease - cleave within strand

What is the difference between exothermic and endothermic?

Exothermic - releases energy (heat) Endothermic - absorbs energy

What's a common use of ABC transporters in humans?

Export a wide variety of drugs and toxins from the cell

What does dominant refer to in genetics?

Expressed over other alleles

What is a phenotype? How is it determined?

Expression or appearance of genes and alleles, determined by observation

What type of diffusion do aquaporins and ion channels fall into?

Facilitate diffusion

What is collagen? What is its structure/role within the ECM?

Family of fibrous proteins found in all multicellular animals Secreted in large quantities by connective tissue cells Major component of skin and bone and most abundant fibrous protein in connective tissue Single chains with G-X-Y repeating motif (where X and Y are variable but frequently proline) that allow for formation of unusual left-handed helix Three of these chains organize into elongated and stiff 3D structure that provides significant tensile strength greater than that of steel wire of equal diameter These chains are then bundled into higher level structures through covalent cross-linking of lysine side chains

What are disinfectants?

Fast-acting, stable, inexpensive and easy to use antimicrobial agents capable of inactivation of most microbes

What are examples of lipids?

Fats, oils, phospholipids, waxes, sterols

What is Disruptive/Diversifying Selection?

Favors survival of 2+ difference phenotypes adapted to variable environments

What is Stabilizing Selection?

Favors survival of individuals with intermediate phenotypes Eliminates extreme phenotypes Tends to decrease genetic diversity

What is Directional Selection? Means for calculation?

Favors survival of one extreme phenotype that is better adapted to environmental condition i.e. peppered moth Calculate mean fitness and use fitness values to predict next generation

What is the difference between fermentation and anaerobic respiration?

Fermentation - way to continue to make ATP and store electrons until oxygen available Anaerobic Respiration - electrons transferred through ETC to different final acceptor (e.g. sulfate) instead of stored

How did we use microbes before knowing of their existence?

Fermented foods and beverages

Role of Fibril-associated Collagens

Fibril-associated collagens organize the collagen fibrils Different organization -> different properties of collagen matrix -Linear/Parallel -> incredible tensile strength along direction of fibers -Perpendicularly -> reduce tensile resistance in any one direction but overall increase in resistanace Type IX is specific to mesh-like networks

What is fibronectin and what is its role? What is the function of the RGD domain and synergy domain in fibronectin?

Fibronectins connect cells and ECM and influence the shape, differentiation, and movement of cells Have integrin-binding domains with RGD (AAs) motif in loop to protect from type III domain Interactions with integrins help place cell in context of its environment - integrins unfold upon interaction and tension between the cell and the ECM helping to nucleate further integrin fibril formation

What is cytogenetics? 3 Main features they use?

Field of genetics that involves microscopic examination of chromosomes to identify and classify chromosomes using: 1. Location of centromere 2. Size 3. Banding patterns

What are the rules of binomial nomenclature?

First Genus, then species genus capitalized, species lower case italics when typing, underline when written can abbreviate the genus with first letter

What type of messenger is epinephrine?

First messenger

How are RNA primers removed in eukaryotic DNA?

Flap Endonuclease

Intercalating Agents Mechanism

Flat planar structures intercalate themselves into double helix leading to mutations i.e. proflavin, acridine dyes (ethidium bromide)

What are Platyhelminths and their major features?

Flatworms Have oral sucker Infect intestines, lungs, liver, and blood vessels and can even block up those vessels in some cases Potentially lethal

Cholesterol and Temperature

Fluid at low temps and less fluid at high temps - thus key for cell communication in cold conditions; amount in membrane can be adjusted accordingly

What are molecules that possess fluorescent properties called?

Fluorochromes

Define cross-sectional studies

Focuses on studying individuals with/without disease at particular moment in time Useful in simplifying long-lasting outbreaks

What is the function of the rER?

Folds and packages proteins

Experiment 26A Results

For heterochronic mutations, timing of fates of particular cell lineages is not synchronized with development of the rest of the organism

4 overlapping stages of bilateralian development

Formation of Body Axes Segmentation of Body Determination of Structures within Segments Cell Differentiation

How are TRNEs formed?

Formation of hairpin since they always contain at least one C and G During replication, hairpin leads to increase or decrease in length of DNA Polymerase slips off DNA Hairpin forms and pulls strand back DNA polymerase hops back on and begins synthesis from new location Occurs during gamete formation, but can also happen in somatic cells

MHC II features/location?

Found on macrophages, dendritic and B cells Bind antigens for "presentation" specifically to T cells for destruction in cellular immunity

Where are nucleotides found and in what format to make new DNA molecules?

Free-floating nucleotide triphosphate (ATP, GTP, CTP, TTP) in cytoplasm/nucleus

Where do electrons come from and to in the Calvin cycle?

From NADPH to G3P

Mechanisms of Adaptation to Stimuli

From fastest to slowest: Receptor Sequestration Receptor Downregulation Receptor Inactivation Inactivation of Signaling Protein Production of inhibitory protein

What is FtsZ, MreB, MbI, and ParM?

FtsZ - prokaryotic and archaeal homolog of tubulin MreB and MbI - homologs of actin serving as scaffolding for formation of peptidoglycan structures of the cell wall in rod-shaped bacteria ParM - structurally related to actin and tubulin - encoded by many bacterial plasmids as tool to form microtubule like structures to segregate plasmid copies and ensure they go into separate daughter cells

What is the role of Glucocorticoid Response Elements (GREs)?

Function as enhancers, allowing steroid hormones to activate many genes

Eukaryotic Pathogen Virulence Factors

Fungi - Capsule Production and Mycotoxins Helminths - similar to bacteria and fungi

How do gene separation on chromosome and crossover relate?

Further apart the genes -> more likely the crossover -> higher the frequency of crossover

Type of Actin (G, F, T, D, Alpha. Beta, Gamma)

G-Actin - Globular, soluble monomer that can be ATP or ADP bound - 375 AAs F-Actin - Filamentous Polymer that can be ATP or ADP bound T-Actin - Filamentous ATP-bound actin D-Actin - Filamentous ADP-bound actin Alpha-Actin - isoform found in muscle Beta- and Gamma-Actin - expressed in almost all non-muscle cells

What phase are most cells waiting in?

G0 - holding period

What are the checkpoints of mitosis that we reviewed?

G1/S - divide or not? Check for environmental factors (radiation, chemicals, nutritional balance) G2/M - commit to mitosis? Check for damaged DNA and mutation

Relationship to Allele and Genotype Frequencies (graphically)

GG dominates when g is low Gg dominates when both allele frequencies are intermediate gg dominates when g is high

How are GPCRs downregulated in adaptation?

GPCRs can activate many G Proteins as they keep receiving signal After GPCR receptor activated for long time, GPCR Kinases (GRKs) make their way over to newly freed site of GPCRs and phosphorylate them If they stay activated long enough to be phosphorylated 3 times, Arrestin will come bind to them to deactivate or desensitize the GPCR and prevent it from activating any more G proteins

Hardy-Weinberg Assumptions for population to be in equilibrium

GRaMNN No Genetic drift Random mating No Migration No New mutation No Natural selection

What is the role of TFIID?

GTF that binds to TATA box to recruit RNA Polymerase II

General Transcription Factors vs. Regulatory Transcription Factors

GTFs - required for binding of RNA polymerase to core promoter and progression to elongation stage RTFs - regulate rate of transcription of large genes and influence ability of RNA pol to begin transcription of gene

Between GTP and GDP, which is present in higher concentration in the cytosol?

GTP present in much higher concentration

What type of cells undergo meiosis?

Gametes, sex cells, gonads

What types of cells undergo mitosis?

Gametes, sex cells, gonads AND somatic, germline

Effects of mutations in segmentation genes

Gap - entire chunks gone Pair-Rule - Every other segment, whole segments taken out Segment-Polarity - chunks between the red segments shown are removed

Gated Transport vs. Protein Translocation vs. Vesicular Transport

Gated Transport - protein transport between nucleus and cytosol via NPC i.e. RNA transport Protein Translocation - Transport between cytosol and ER or mitochondria between topologically distinct spaces (thus require protein changes in folding status usually to pass through integral membrane proteins) Vesicular Transport - Transport between topologically similar organelles in membrane-enclosed transport intermediates or loaded cargo vesicles using targeting i.e. budding between golgi and ER

Roles of Gelosin Superfamily proteins and Cofilin

Gelosin Superfamily - activated by high [Ca2+] - binds two spots (one along side and one at interface of adjacent subunits) on actin to catalyze breakage; doesn't actually split them, as thermal fluctuations after breakage destabilize and actually end up breaking Cofilin - AKA Actin Depolymerizing Factors - binds to the sides of filaments (preferentially D-actin) to twist adjacent subunits, destabilizing interactions holding subunits together by super coiling the filament

What are the types of gene expression regulation?

Gene (Transcription) mRNA (Translation) Protein (Posttranslation)

What is the bicoid gene? Origin of Name?

Gene actively transcribed in nurse cells Bicoid mRNA enters anterior end of oocyte and is trapped there Name comes from fact that larva whose mother is defective in this gene develops with two posterior ends

What is the duplication method of developing gene families?

Gene duplicates Over time, duplicated genes become different due to gradual mutations

What is horizontal gene transfer?

General category of bacteria transfer between species DNA does not have to be homologous, but small stretches can match 20% of E. Coli genome comes from horizontal gene transfer

What is an Effector?

General term referring to an enzyme in this case, but its what catalyzes or activates the second messengers

Why glucose, CO2, oxygen, and the high potential energy carriers?

Glucose - high potential energy in bonds Carbon dioxide - waste (Carbon) exceptor Oxygen - high affinity for electrons High potential energy carriers - good in betweens as they are higher affinity than glucose but less than final acceptor, oxygen

What are the ultimate effects of epinephrine release?

Glucose surges to heart, lungs, muscles, etc. causing fight or flight response

What are the "monomers" of phospholipids?

Glycerol and fatty acid

What is the makeup of a phospholipid?

Glycerol, 2 fatty acids, and a phosphate

What are the primary constituents of cell membranes and their structure?

Glycerophospholipids Two fatty acids esterified to L-glycerol-3-phosphate Charged head group Often C1FA saturated, C2FA unsaturated

What are the four steps of aerobic cellular respiration?

Glycolysis Pyruvate Oxidation Krebs or Citric Acid Cycle Oxidative Phosphorylation (ETC and Chemiosmosis)

What proteins do B-cells have on their surface that make them able to recognize foreign antigens?

Glycoprotein Antibodies/Immunoglobins

Type of biomolecule antibodies are made of

Glycoproteins

What is peptidoglycan?

Glycoproteins found only in bacteria that creates strong defensive fabric-like mesh

Cell Adhesion Molecules (CAMs)

Glycoproteins in plasma membrane that bind to specific molecules on other cells Only in animal cells

What types of linkages do forms between carbs and proteins?

Glycosidic Linkages O linkage to T, S, Y (hydroxyls) N linkage to Q, N, K, R (amines)

What is the primary goal of the Krebs Cycle? Secondary goals?

Goal - NADH and FADH2 creation (6 and 2 per glucose) Secondaries - produce 2 ATP and get rid of remaining carbon atoms as CO2

What does gram staining tell us?

Gram Positive (purple) - thick cell wall of peptidoglycan layers Gram Negative (counterstain, usually pink) - thinner layer of peptidoglycan

What is streptococcus pyogenes?

Gram positive, aerobic, hemolytic, catalase-negative, non-endospores-producing bacteria found on skin that can be pathogenic and cause strep throat, impetigo, scarlet fever, glomerulonephritis, and necrotizing fasciitis

Essential Features of Neutrophils

Granulocytes (with granules of defense's and hydrolytic enzymes) that eliminate and destroy extracellular bacteria by phagocytosis Form NETs (neutrophil extracellular traps) that are strands of DNA with toxic proteins that kill many bacteria and some host cells

Three splicing mechanisms? Which ones are self-splicing?

Group I Intron Splicing (self) Group II Intron Splicing (self) Spliceosome (not self-splicing)

What is a meristem?

Group of actively dividing cells in plants

Define populaiton

Group of individuals at risk of contracting a particular disease often defined by geography ONLY includes those susceptible to disease

What is the common strategy for virus replication and isolation? Types?

Grow/culture suitable host cells and infect them Filter out host cells to isolate virus In Vitro - outside of living organism - Lawn of host cells and Plaques where viruses successfully replicate In Vivo - inside living organism - embryonic tissues such as eggs or inject into mouse, rat etc.

What are the purposes of mitosis?

Growth of zygote, repair, after injury

What does GDI stand for? GlcNAc?

Guanine Dissociation Factor (holds the Ran-GDPs inactive and soluble in solution) N-Acetyl Glucosamines

What is HNPCC? What did we learn about Bob's DNA sample?

HNPCC (hereditary nonpolyposis colorectal cancer, AKA Lynch syndrome) is a type of colorectal cancer resulting in polyps in the colon that become cancerous. Inheriting the mutated allele of the MSH2 caretaker gene or three other caretaker genes takes the risk up from 3-5% to 80%

tRNA structure

Hairpin structure

What bacterial species causes flamingos to appear red even though their feathers are white?

Halobacterium salinarium due to photosynthetic red pigments

Are bacteria generally haploid or diploid?

Haploid

ATP Synthesis/Catalysis

Happens in the F0 portion, with the rotating shaft causing the conformational changes that bring ADP and Pi in, synthesize it, then kick it out, each in their own Beta section.

Asymmetric Ribbon Structure of Actin

Has plus and minus ends with different roles

Structure of individual histones?

Have globular domain and flexible, charged amino terminus or "tail"

What were the Chargaff experiments?

He isolated DNA, removed proteins via protease, broke down to bases by acid catalysis, used paper chromatography to separate them, and then determined Chargaff's Rule: [A]=[T] [G]=[C]

How and when is pasteurization used to control microbes?

Heat at low temps for long periods of time when complete sterilization isn't appropriate like in some food prep like milk

What are some common structural forms of viruses?

Helical with genome mixed into center (very tough) Polyhedral Viruses with various shapes Bacteriophages

What bacteria is the leading cause of ulcers?

Helicobacter pylori

Why are helminths and fungi studied as part of microbiology?

Helminths - Their eggs/larvae are microscopic Fungi - microscopic spores

What is the role of the microbiome in nonspecific host defense?

Help absorb nutrients and digest food, competing with pathogens for nutrients and attachment to epithelial cells of intestines

What is the purpose of prokaryotic cell walls?

Help maintain morphology, minimize damage to cell by osmotic pressure, and provide protection

What is the role of HDL proteins in the blood stream?

Helps keep lipids soluble in the bloodstream

What are homizygous and holandric genes?

Hemizygous - X-linked traits are homizygous in males Holandric - Y-linked genes

Define mutation

Heritable change in the genetic material

Heterochromatin vs. Euchromatin

Heterochromatin - tightly compacted regions of chromosome that are generally transcriptionally inactive with radial loop domains compacted even further Euchromatin - less condensed regions of chromosomes that are transcriptionally active

Structure of intermediate filaments and basic roles

Heterogenous family of filament proteins that form mesh structures and form into twisted, strong cables that are more long-lasting, static, and structural than the other types Support epithelial cell structure, provide structure to elongated nerve axons, form tough appendages of hair and nails

How is cholesterol synthesis regulated by the presence/absence of cholesterol in the membrane?

High Cholesterol in ER - SCAP (SREBP Cleavage Activation Protein) binds cholesterol and anchors SREBP (sterol response element binding protein, a cholesterol synthesis activator) to membrane in response to binding cholesterol in membrane Low Cholesterol in ER - Cholesterol is not bound to SCAP to activate it since the concentration is low, so SCAP changes shape to allow it and SREBP to package together into vesicle and travel to Golgi membrane, where Golgi-proteases cleave cytosolic domain of SREBP to travel to nucleus and upregulate cholesterol biosynthesis

How does the rate of ATP hydrolysis compare in G-actin vs. F-actin?

Higher in F-actin, as G-actin remains relatively high in ATP-bound conformation and then usually hydrolyzes after polymerization onto the polymer

How can enzymatic activity be altered? (And thus Rx rate)

Higher substrate concentration - faster reaction Higher temp (to a certain point) - faster reaction pH out of range - slows reaction Inhibitor - slows reaction

What do renaturation experiments tell us about genome sequence complexity?

Highly repetitive sequences renature fast and reanneal rapidly. These sequences are less likely to encode for genes

What are variant histones?

Histones other than the standard ones that can be incorporated to create specialized chromatin (over 70 histone genes in human genome) Variants exist for H1, H2A, H2B, and H3 but not H4

What is Interkinesis?

Holding phase with no DNA replication between Meiosis I and II

Homeobox and Homeodomain

Homeobox - 180 bp consensus sequence within homeotic gene Homeodomain - protein encoded by homeobox that is transcription factor that can activate/repress multiple genes associated with development

Define etiology

How diseases are caused

What is response timing in biosignaling?

How quickly a system can respond to the introduction/removal of a signal Milliseconds to seconds - synaptic signaling, phosphorylation events, second messenger production Minutes to hours - transcriptional regulation, protein production/degradation Hours to days - Differentiation, Apoptosis

How do sex chromosomes differ in humans vs. insects vs. birds?

Humans: Male XY, Female XX Insects: Male X, Female XX Birds: Male ZZ, Female ZW

What is ameboid movement?

Hw amoebas move by forming dynamics shapes and extending their pseudopods (false feet)

What is the hydration layer?

Hydration layers reduce attraction between molecules or ions promote their entry into a solution by dissolving the ion lattice and shifting everything over to cause repulsion and subsequent bonding/surrounding by polar water molecules to maintain them in solution

What is osmotic pressure in terms of membrane transport?

Hydrostatic pressure required to prevent net water flow across membrane separating solutions of different water concentrations

4 Main groups of Glycosaminoglycans

Hyluronan Chondroitin Sulfate/Dermatan Sulfate Heparan Suflate Keratan Sulfate

What is hyluronan? What is it made of? What is its function within the ECM? How is it synthesized?

Hyluronan AKA Hyaluronic Acid AKA Hyluronate Simplest of GAGs and unique in method of production and composition No protein attachment, no sulfate groups, idnetical repeating subunits through length of molecule (shown) Common in joints with role in resisting compressive forces Synthesized directly on cell surface, effectively spun; synthesis can drive separation between cells allowing for cell migration

What are varied response types to signals in biosignaling?

Hyperbolic Response - as concentration of signal molecule changes it generates a proportional response Sigmoidal Response - Minimal response at low/high concentrations, but intermediate range small concentration differences result in large changes Treshhold Response - All or none

What is the first sign of aspirin poisoning? Treatment?

Hyperventilation (Because body rid itself of carbon dioxide produced by addition of acid (aspirin) to blood, lowering pH and shifting carbonic acid bicarbonate buffer to the left Treatment - bicarbonate toe drive back down carbon dioxide

How does TNREs in noncoding regions affect the individual?

Hypothesized to cause abnormal changes in RNA structure May produce methylated CpG islands which may silence gene

What is the formula for interference?

I = 1 - C

What are the protein complexes in the ETC and where are they? Primary purpose?

I, III, and IV - integral membrane proteins II - in matrix Purpose - pump protons from matrix into IMC (inner mitochondrial compartment, basically the space between mitochondrial membranes)

What is the goal of epidemiology?

ID and control outbreaks of diseases

What is the average number of hydrogen bonds per water molecule in an ice lattice? Water lattice?

Ice lattice - 4.0 hydrogen bonds per water molecule Watter lattice - 3.4 Thus water lattice more dense and less rigid

What can't eukaryotes use mitosis for both like bacterial cells?

If our diploid combined with another diploid we'd be 4n, then 8n, then 16n, etc. cells would explode

What is a Type I Immune Hypersensitivity?

IgE antibodies generated against a soluble antigen, recruiting a mast cell response Immune System response to allergen exposure (first exposure sensitizes, subsequent exposures lead to hypersensitivity reactions) Localized or systemic reactions (hives, fever, asthma, anaphylactic shock)

What is a Type II Immune Hypersensitivity?

IgG and IgM antibodies recognize cellular-bound antigens (foreign or self) invoking immune response Causes complement activation, inflammation, lysis, or cytotoxic T cell activation i.e. blood type mismatching

Where does glycolysis occur?

In the cytoplasm

Define Horizontal Gene Transfer

Incorporation of genetic material form another organism without being the offspring of that organism, often between different species, accounting for 20-30% of variation in genetic composition of modern prokaryotes

Fever Process

Increased body temp Vasoconstriction to keep blood central and minimize heat loss Shivering to generate additional body heat through muscles Lack of Sweating Crisis Phase - fever "Breaks" and temp decreases, sweating and vasodilation occur

What is the molecule added

Incredibly fast activation of target protein by protein kinases activating other protein kinases and amplifying the signal

What are the requirements for using the product rule of probability?

Independent events with no effect on one another occurring in succession (not simultaneously)

What is a carrier? Passive vs. active?

Individual that can transmit pathogen without displaying symptoms Passive - contaminated with pathogen NOT infected Active - infected and either symptomatic or asymptomatic

What is autopolyploidy?

Individual with additional sets of chromosomes resulting from some nondisjunction issue

What is a genetic mosaic?

Individual with somatic regions that are genotypical different from one another

What are inversion heterozygotes?

Individuals with one copy of a normal chromosome and one copy of an inverted one -can be phenotypically normal -danger lies in meiosis I when normal and inversion chromosome form Inversion Loop to synapse properly, and if crossover occurs within inversion loop, highly abnormal chromosomes result

What are inducible and repressible genes?

Inducible - regulated by inducers Repressible - regulated by corepressors (not necessarily repressors!)

What is induction?

Induction - process by which cell or group of cells governs developmental fate of neighboring cells

4 Major functions of T lymphocytes

Inflammation Recruitment of more T Cells Activation of Macrophages Regulate Immune Response (Helper T cells)

Role of transcription factors?

Influence ability of RNA polymerase to transcribe given gene

What is de novo methylation?

Infrequent, highly-regulated methylation of DNA that was previously unmethylated Phenomenon occurs in replication in which newly created complementary segment contains unmethylated cytosines, creating hemimethylated replicated DNA, but then that new DNA is fully methylated by DNA Methyltransferase through Maintenance Methylation process to preserve methylation in future cells

Define immunodeficiency

Inherited or acquired disorders where the host immune defenses are defective or absent

How does carbon monoxide act?

Inhibits protein complex IV

Three stages of translation

Initiation Elongation Termination

What are the steps of translation?

Initiation - met-TRNA-anticodon-GTP-small-ribosome complex binds to 5' cap of mRNA; complex scans mRNA until reaches AUG in P site, establishes reading frame, then large ribosomal subunit binds, GTP hydrolyzed, and it gets moving Elongation - tRNAs with matching anticodons bring amino acids to the growing polypeptide chain Termination - in A site, comes to stop codon and polypeptide release, ribosomal complex falls off, protein moves on for final modifications

Overview of 3 stages of prokaryotic transcription

Initiation - promoter = recognition site for Tis, Tis enable RNA polymerase to bind to promoter and DNA is denatured into a bubble known as open complex Elongation - RNA polymerase slides along DNA in open complex to synthesize RNA Termination - terminator is reached that causes RNA polymerase and RNA transcript to dissociate

What are the two distinct membranes of the nuclear envelope, their differences, the space between them, and the method of transport across them?

Inner Nuclear Membrane - laminar proteins bound to chromosome and nucleus and anchoring to cytoskeleton Outer Nuclear Membrane - contiguous with ER and engaged in protein synthesis Perinuclear Space - region between these two membranes tat is continuous with ER lumen NPCs perforate both the membranes allowing selective bidirectional flow

What makes up the 3 distinct sub-cellular regions? (inside, outside, prokaryotic) What characteristics define them?

Inside - nucleus and cytosol - functionally contiguous, topologically distinct Outside (similar to ECF) - ER, vacuoles, Golgi - Internal leaflets of their membranes share composition with external leaflets of plasma membrane and vice versa Prokaryotic - Plastids and Mitochondria - membrane composition similar to prokaryotes (double membranes), contain own genomes, synthesize most of their own proteins

How does the ETC relate to the movement of sperm/bacteria?

Instead of being coupled with ATP synthase, the protons are pumped through a motor with no catalytic region. Instead, the same nanoturbine as ATP synthase is utilized to spin a flagellum and create propulsion

What is a molecule?

Joining of two or more elements/atoms by a chemical bond

Define antibody affinity

Likelihood/desire of bond between antibody and antigen

What are Quantitative Trait Loci (QTLs)?

Locations on chromosomes that affect outcome of quantitive traits

What is a compound?

Molecule with two or more different elements

Is metabolism ever at equilibrium?

No, that would be death

What is the disease-causing strain of E. coli?

O157:H7

What is chromosomal deficiency? Consequences?

Occurs when chromosome breaks and a fragment is lost Consequences can occur phenotypically when the size of the deletion is sufficient, and phenotype consequences are usually detrimental

How can Rab cascades have an effect on the identity of organelles?

Organelles like endosomes change their function over time Rab cascades (recruitment of Rab effector proteins) can change which Rab proteins are associated with the organelle membrane, which can result in displacement of initial Rab protein and Rab effectors for new ones

How are glycoproteins organized and what are their roles in the ECM?

Organized into multidomain (MD) proteins that serve to interact with multiple components of the ECM providing site for organization Each domain folds independently resulting in a beads on a string type morphology for MD proteins

Why is chromatin coiled around histones?

Otherwise wouldn't fit in nucleus

What is the structure of the mitochondria?

Outer membrane, inner membrane, and matrix

What macromolecule are enzymes?

Proteins

What is more stable, DNA or RNA?

RNA is usually unstable while DNA is generally stable

Where does H2O splitting send its electrons?

Reaction center

What are the two types of light transmission in an objet?

Refraction and Scattering

What is GTPase Activating Protein (GAP)?

Required helper protein for some G-proteins to hydrolyze the GTPs into GDPs

How are morphogen gradients established?

Secretion and transport to neighboring cells

How effective are enzymes?

Speed up Rx's 100X-1,000,000X/sec faster

Cholesterol belongs to family of...

Sterols

What is the process of translation termination?

Stop Codon / Nonsense Codon reached These codons recognized by Release Factors instead of tRNAs (RFs similar structure to tRNAs)

What determines cell size?

Surface area to volume ratio

What is the most common mechanism for activation upon signal binding for RTKs?

Symmetric Dimerization, trans-autophosphorylation, production of phosphorylated binding sites for proteins

What are some other common prokaryotic cell arrangements?

Take pic and add here

What is neuroplasticity?

The brain's ability to change structure or function due to learning, illness, or brain damage.

What is a proteome?

The full range of proteins that a cell makes at a given time

What is the replisome?

The helicase-primase primosome combined with the polymerase enzymes

What is the key difference between the water and ice lattices?

The ice lattice is packed less densely than the water lattice, making water expand when frozen

What is deoxyribonucleoside?

The individual nucleotides dATP, dGTP, dCTP, and dTTPs that are added by DNA polymerase III with a P.D. Bond to the growing replication chain

How are the Vesicular Tubular Clusters transported to the Golgi and which part of the Golgi?

They are carried on microtubules through interactions with motor proteins to the cis Golgi network

What is a translocation cross?

Unusual structure created by balanced translocations during meiosis containing 4 pairs of sister chromatids

What is released at the end of the CR ETC?

Water is released

What is the role of cytokine receptors on host cells?

Water-Soluble Cellular Chemical Messenger Molecules Used to turn on/off pathways in body dealing with nonspecific defenses

What is unique about mitochondrial DNA?

We all inherit our mitochondrial DNA from only our mothers

What is pleiotropy?

When 1 gene has more than 1 effect on an individuals phenotype

How can the relationship between the concentration of actin and critical concentration be used to determine spontaneity of the process? How can a spontaneous situation be utilized?

When [actin]> Cc: Delta G negative (spontaneous) When [actin] < Cc: Delta G positive (nonspontaneous) Negative Delta G can be used to power other processes like movement of attached proteins/cargo or pushing of the membrane

What is cross-resistance?

When a resistance mechanisms gives resistance to multiple drugs

What is complete nondisjunction?

When all chromosomes undergo nondisjunction and migrate to one daughter cell together resulting in one diploid cell and one without chromosomes Diploid gamete can then participate in fertilization to yield triploid individual

What is fluorescence?

When materials absorb one wavelength of light and give off or emit a different wavelength at a lower energy

Define herd immunity

When most people vaccinated and thus immune, those who can't be are protected because no one around them can contract and spread the pathogen

What is codominance? example?

When multiple alleles can be simultaneously expressed i.e. blood type where blood group genes code for proteins that transfer sugar groups to the surface of RBCs

What does it mean to be parafocal?

When multiple lenses, such as objective lenses on a microscope, when switched through do not require any refocusing because their focal points are in sync

Result of loss-of-function homeotic genes?

When particular homeotic gene defective, its protein function is either degraded or lost and its function is replaced by gene that acts in adjacent anterior region (it defaults to the next strongest gradients essentially)

Which end of actin has a higher critical concentration

While the plus end grows faster, both ends have the same critical concentration because they have the same ratio of koff/kon on each end. While kon is faster at the plus end, off is faster as well to keep the ratio koff/kon=Cc constant

What are wild type and mutant alleles in terms of gains/losses of function?

Wild Type - prevalent allele in population; makes protein in proper amount with normal function Mutant - result of mutation, less prevalent, defective protein production

What is a gamete?

a mature haploid male or female germ cell that is able to unite with another of the opposite sex in sexual reproduction to form a zygote

What are homeotic genes?

a set of master control genes that regulates organs that develop in specific parts of the body

What is germ plasm?

beginning of understanding that mom and dad both contribute genetic material, though it was wrong in the mechanism, thinking it was a blending of characteristics

carrier proteins

bind to molecules and change shape to shuttle them across the membrane - facilitate diffusion

Group I Splicing

binding of free guanosine to site within intron leading to cleavage at 3' end of exon 1

What are recombinant cells?

cell that contain new allelic combinations

What's the difference between cytosol and cytoplasm?

cytosol - water party of cytoplasm, cell fluid cytoplasm - cytosol and all the organelles

What is the gene modifier effect? (impact and mechanism)

example of epistasis in which two phenotypes exhibit semi-independence

Intergenic Suppressor Mechanisms - Redundant Function

first mutation inhibits function of a protein, second alters different protein to carry out that function (rare)

Flippase vs. Floppase vs. Scramblase

flIppase flipds it INside flOppase flips it OUTside

Apoptosis etymology

from Greek for "falling off"

What stages and membrane fusions do lysosomes undergo in their life cycles?

fuse with pre-existing lysosomes or pre-existing endolysosomes Also fuse with phagosomes

What are formites?

inanimate objects capable of spreading infectious agents such as pens, pencils, doorknobs, etc.

How can the individual rates of T and D-actin polymerization be used to calculate Cc.

k(D) on and k(T) off are both small since T usually adds on and D usually comes off, so they can be ignored

What are the structural genes of the lac operon? Their products and functions?

lacZ - encodes B-galactosidase - enzymatically cleaves lactose and lactose analogues and converts lactose to allolactose (isomer) lacY - Encodes lactose permease - membrane protein required for transport of lactose and analogues lacA - Encodes galactoside transacetylase - covalently modifies lactose and analogues, functional necessity unclear

What is the process of conjugation?

linkage of bacterial cells via sex pilus requiring F factor to generate proteins involved in sex pili formation

What are transmission profiles of epigenetic signals?

methods for which to alter gene expression by modifying a gene such as X-chromosome inactivation or genomic imprinting,

What are Helminths?

multicellular parasitic worms visible to human eye

Somatic Mutations

mutations that occur directly in a body cell or in one of its precursor cells Patches of affected area found are these, size of patch dependent on timing of mutation (earlier = larger)

What is a chromosome?

nucleoprotein complex of DNA and histones (eukaryotes)

What is the formula for coefficient of coincidence?

observed double crossovers/expected double crossovers

How any antigens does a given B-cell recognize?

one

What is an Ori-T?

origin of transfer

What is the germ theory of disease?

pathogenic microbes cause infectious disease by invading humans, animals and other hosts and being transferred between them

How do GTP and ATP carry so much energy?

phosphate groups all carry charges of -2, so bringing three so closely together in GTP and ATP molecules builds up energy of repulsion between phosphate groups

What is the mutation rate?

probabilty a gene will be altered by a new mutation

What is bioremediation? types?

process by which microbial metabolism removes pollutants from environment In situ - on site, microbes released into environment Ex Situ - contaminated materials removed from environment and treated somewhere else

Phagocytosis

process in which phagocytes engulf and digest microorganisms and cellular debris

What is necroptosis?

programmed version of necrosis not well understood

anchoring junctions

protein attachments between adjacent animal cells

Define endotoxin

proteins found on outer membrane of Gram-negative bacteria such as LPS

What is pseudo-autosomal inheritance?

refers to few genes found on both X and Y chromosomes

What is a wild-type allele?

refers to the phenotype of the most common form of a species as it occurs in nature

endomembrane system

regulates protein traffic and performs metabolic functions in the cell

What are the functions of non-coding DNA discussed in class?

regulation of gene expression chromsome stability

What is an operon?

regulatory unit consisting of a few structural genes under control of one promoter Contains promoter, terminator, structural genes, and operator

What are map units and centiMorgan?

same thing, relative unit of distance between to genes as % of gene length 1cM = 1mu = 1% recombinant offspring in testcross

What is nondisjunction?

separation failure in meiosis Usually in anaphase I, but can happen in anaphase II Can cause trisomy disorders

What is the situation that results in an ascus?

sexual reproduction in certain haploid species in which formation of a diploid cell followed by meiosis generates haploid spores that associate in an ascus

What are the abbreviations for the different size arms of a chromosome? How are they drawn?

short arm - p (petite) long arm - q short arm is always drawn on top

Group II Splicing

similar to Group I except 2' OH group in adenosine begins catalytic process

What types of genetic material can viruses contain?

single and double stranded RNA and DNA

Composition of mucus

sticky, moist substances made of protein, carbohydrates, and water

What is a 5' cap?

successive Guanine's that are used to bind the initiation complex in translation and protect it from degradation (usually 7 of them)

What was Francis Crick's Adaptor Hypothesis in the 1950s?

tRNAs play direct role in recognition of codons in the mRNA tRNA has two functions: 1. Recognizing 3-base codon in mRNA 2. Carrying amino acid that is specific for that codon

What are isoacceptor tRNAs?

tRNAs that are able to recognize the same codon

Germ-line mutations

those that occur directly in sperm or egg cell, or in one of their precursor cells Passed to half of the gametes in the next generation

What is prokaryotic generation time?

time for population to double

What is eukaryotic generation time?

time to go form one point in life cycle to same point in next generation

Which trp genes are involved in biosynthesis of tryptophan and which in regulation?

trpA, B, C, D, E - biosynthesis trpR, trpL - regulation trpR - encodes trp repressor protein, functions in repression trpL - encodes short peptide called Leader peptide, functions in attenuation

How do actin isoforms differ?

vary only slightly in their AA composition within species

How did Mendel come to the conclusions of his laws? Discuss data and reasoning.

walk through and explain each of these

What is a chromosomal translocation?

when a segment of one chromosome becomes attached to another

What is heteroplasmy?

when cell contains extranuclear DNA that differs in traits

What is epistasis?

when certain genes have affects on other genes' expression think assembly line

What is a prophage?

when phage genome is dormant and integrated into host's genome