MCAT 2020

post-translational modification

Changes to the new protein that may be critical to its final function, like folding, phosphorylating glycosylating, or lipidating

Pyrimidines

Cytosine (C) Thymine (T) Uracil (U) in RNA

right thoracic duct

Drains lymph from the upper right quadrant onto the right subclavian vein

Deleterious mutation

Genetic changes that are harmful to an organism. Sickle cell disease leads to early death.

advantageous mutation

Genetic changes that improve their carriers' chances of survival or reproduction. Ex. point mutation for the gene for hemoglobin that leads to sickle cell disease, protective against malaria.

repetitive DNA

Nucleotide sequences, usually noncoding, that are present in many copies in a eukaryotic genome. The repeated units may be short and arranged tandemly (in series) or long and dispersed in the genome. (Junk)

Glycine (Fly, G)

Nonpolar small found in beta turns, not found in alpha helices (destabilize it) ambivalent (found outside and inside molecule)

Random mutation

Random mutations are the random changes in the genes of individuals, which allows for genetic variability and evolution to occur. Usually occurs as an error of replication or damage by external factors.

Excision repair

a DNA-repair process where enzymes remove a damaged portion of DNA, synthesize a replacement section in place, and attach it to the neighboring DNA segments

retinal disparity

a binocular cue for perceiving depth by comparing images from the retinas in the two eyes, the brain computes distance—the greater the disparity (difference) between the two images, the closer the object.

Silent mutations

a change in the nucleotide sequence that ends up encoding for the same amino acids, potentially relying on wobble pairing.

phosphodiester bond

a chemical bond of the kind joining successive sugar molecules in a polynucleotide.

endothermic reaction

a chemical reaction that requires heat. Delta H is positive.

Sucrose (glu-a-1,2,-fru)

a disaccharide composed of a-glucose and B-fructose. table sugar.

operon model

a group of genes is regulated and expressed together as a unit

Chromosomal proteins

a histone and nonhistone protein associated with DNA in a eukaryotic nuclear chromosome

Relative size

a monocular cue for perceiving depth; the smaller retinal image is farther away

cooperativity

a phenomenon in which the shape of one subunit of an enzyme consisting of several subunits is altered by the substrate so as the change the shape of a neighboring subunit

Missense mutatution

a point mutation in which a single nucleotide change changes one amino acid.

cytoplasmic/extranuclear inheritance

- inheritance of things other than genomic DNA. - All cellular organelles, such as mitochondria, is inherited from the mother

convergence

A binocular cue for perceiving depth; the extent to which the eyes converge inward when looking at an object. -Things far away: eyes are relaxes -Things close to us: eyes contract

Plasmids

-double stranded DNA -can exist and replicate independently of the genomic DNA, or can be integrated into it -Plasmids are inherited -not essential for growth and reproduction in the wild

Starch

-glucose molecules joined by a alpha 1-4 linkage -amylose =unbranched -amylopectin =branched -stored form of sugars in plants, plants able to synthesize glucose using light energy gathered in photosynthesis, and excess glucose, beyond the plant's immediate energy needs, is stores as starch in different plant parts.

Triaglycerides

3 fatty acids esterified to glycerol. Non polar tails used for energy storage. Digested by lipase. With low food intake, broken down by liver to form ketone bodies.

Centrioles

Cell organelle that aids in cell division in animal cells only -located in center of centrosomes, move to opposite ends of cell

Induced-fit Model

Change in the shape of an enzyme's active site that enhances the fit between the active site and its substrate(s)

Membrane dynamics

everything in the cell moves around, many ways to move phospholipids

Polysaccharides

ex. starch, glycogen, cellulose, chitin -> polymers of glucose Cellulose = unbranched chain (useful for rigid plant cells walls) with a B-1,4 linkage

point mutation

gene mutation in which a single base pair in DNA has been changed

Parental Generation = P

generation of the parent

structural genes of operon

genes that code for proteins

Adaption

genetic change in a population caused by natural selection

Genotype

genetic makeup of an organism

Insulin

helps cells absorb glucose, reducing blood sugar and providing cells with glucose for energy.

Chair structure of carbohydrates

hexoses from six-membered structures that adopt more conformationally favorable chair structure that reduces steric hindrance. Axial groups project straight up or down, equatorial groups project out from the ring.

Solvation layer (entropy)

interactions between water and hydrophobic aa is highly structure (Clathrate cages high entropy), thus hydrophobic aa found inside (less entropy)

Role of proline

introduces kinks in protein chain, doesn't make bonds really

Smooth endoplasmic reticulum

involved in gluconeogenesis and fat storage (in liver), detoxification of alcohol, cholesterol formation, Function depends on cell type.

Determination

irreversible commitment to become a certain cell type

Primase

lays down RNA primers

Endocrine gland

main structure responsible for hormonal secretion in the endocrine system

Steroids

maintains membrane fluidity and stability (cholesterol), can bind to steroid hormone receptors

Hardy-Weinberg Principle

principle that allele frequencies in a population will remain constant unless one or more factors cause the frequencies to change. P + q = 1 1= P^2+2pq+q^2 5 factors: 1. infinitely large population 2. no migration 3. no mutation 4. random mating (no sexual selection) 5. no natural selection.

Cell migration

process by which neural crest cells travel to various locations in body (remember the peripheral nervous system, its everywhere!)

Biosignaling

process in which cells receive & act on signals

Transformation

process in which one strain of bacteria is changed by a gene or genes from another strain of bacteria. -bacteria take in plasmids and DNA fragments and integrates them into the genome *when bacterium dies, it lyses and spill DNA into environment *If DNA fragments contained antibiotic resistant gene, then the transformation just made the bacteria antibiotic resistant

Implantation

process in which the blastocyst attaches to the wall of the uterus 1. zygote 2. Morula (solid ball) 3. Blastula or blastocyst (mammals) 3. implants in endometrium

Birth

oxygen from mom to breathing nutrients from mom to suckling fetal circulation which bypasses lungs and liver to normal circulation by closing off ducts and openings

Isoelectric point (pI)

pH where net charge on protein is zero. Average of two pKas where charge is 0.

Lipoprotein

packages triglycerides + other hydrophobic substances to compactly send to various tissues. Name of particular lipoprotein produced within intestinal cell from absorbed fats. = chylomicron

Programmed cell death

regulated by protein activity

Primary (1) Structure

peptide chain of amino acids

Cysteine (Cys, C)

polar, -SH

Threonine (Thr, T)

polar, alcohol branched

Serine (Ser, S)

polar, alcohol group

Asparagine (Asn, N)

polar, amide group

Glutamine (Gln, Q)

polar, amide group, 3 carbons

Tyrosine (Tyr, T)

polar, aromatic with alcohol

S

preparing cell for mitosis, lot of DNA replication

myosin

primary motor protein in sliding filament model. Act with actin.

Role of cystine

staples protein together in tertiary + Quaternary structure, covalent bonds

Pluripotency: Stem cells

stems cells in blastocyst are pluripotent, can become most cells, depends on location

Recombination

the crossing over or trading of allele between two homologous chromosomes that takes place during Meiosis I

Polymorphism

the existence of two or more forms of individuals within the same animal species (independent of sex differences).

Speciation

the formation of new species as a result of evolution

Y chromosome

the sex chromosome found only in males. Shorter compared to X chromosome and has less genes. Its allele are present as the only copy for each of its genes.

Membrane channels

to help ions cross the membrane

Q > K

too many products, system will shift to left (to reactants)

Q < K

too many reactants, system will shift to right (to products)

Increase pressure of system

towards fewer moles of gas

decrease pressure of system

towards more moles of gas

multiple allele trait

trait controlled by one gene with more than two alleles

Uncatalyzed movement

trans-bilayer diffusion. Phospholipid on the outer leaflet (extracellular part of membrane) moves into the inner leaflet and vice versa. Very slow movement = no catalyst

complete dominance

a relationship in which one allele is completely dominant over another

Translocation error

a sequence of nucleotides is moved from one place in the genome to another

Deletion mutation

a sequence of nucleotides is removed

Base substituion Mutation

a single change in a nucleotide along the DNA sequence

Aspartic Acid (Asp, D)

acidic, pH = 3.9

Glutamic Acid (Glu, E)

acidic, pH = 4.2

nonoxidative phase of PPP

after oxidative phase. Converts Ribulose-5-Phophate into Ribose -5-phophate, sugar used to make DNA and RNA.

Fermentation

anaerobic glycolysis Key enzyme: Lactate dehydrogenase Alcohol fermentation = pyruvate reduced to ethanol Lactic acid fermentation = pyruvate reduced to lactate Purpose: to regenerate NAD+ for glycolysis

Water-soluble vitamins

anything that's not fat soluble. Less toxic as it can be peed out. Ex. B1, B12, Folate, Vitamin C

Leakage

applies to the introduction of new alleles from an outside source, such as a different species or cases like paternal mitochondrial DNA being passed to offspring.

D/L absolute configuration

assigned based on chirality of the carbon atom furthest from the carbonyl group D = to right, L = to left.

Transferases

atom/group transfer

Parasitic

bacteria benefits at the expense of the host. ex. Disease causing

Conjugation

bacteria transfer DNA between one another through the sex pillus *A bacterium able to made the pillus (F+) has a plasmid that contains the pillus genes -F+ can transfer plasmid to F- bacteria -conjugation can also transfer some genomic DNA (because F+ plasmid can integrate into the chromosome)

Transduction

bacteriophages (virus) undergoing lysogenic life cycle incorporate the viral DNA into the bacterial genome 1. Virus infects cell, host DNA degraded into fragments, viral DNA takes over control 2. Host DNA fragment gets packed into virus progeny by accident 3. Virus progeny infects another cell, injects previous host's DNA fragment 3. fragment enters cell, finds its homologous counterpart and crossover

Lysine (Lys, K)

basic, pH = 10.5 (4 carbons, amino)

Arginine (Arg, R)

basic, pH = 12.5 (3carbons, 3 Nitrogens)

Histidine (His, H)

basic, pH = 6

Tetrad

because each of the homologous chromosomes coming together during recombination consists of two sister chromatids, the pair of homologous complexes a total of four chromatids, a tetrad, in meiosis I

Differentiation

becoming a cell type and adopting its specialized functions

single allele traits

controlled by a single allele of a gene

Glycolysis (aerobic + anaerobic)

converts glucose to 2 molecules of pyruvate in the cytosol Key enzymes: Hexokinase, Phosphofructokinase (PFK-1: rate limiting enzyme), Pyruvate kinase. Inhibited by ATP

Aerobic decarboxylation

converts pyruvate (3 carbons) to acetyl group (2 carbons) Key enzyme: Pyruvate dehydrogenase only occurs in the presence of oxygen. Acetyl group attached to coenzyme A to make acetyl CoA. Feeder pathways: glycogen, starch metabolism

Reduction half reaction

describes species that gains electrons

Oxidation half reaction

describes species that loves electrons

Fluid mosaic model

describes the membrane as protein boats floating in a sea of lipids

Obligate anaerobe

dies when oxygen is present

Hydrolysis of the glycoside linkage

different glycosidic linkages require specific enzymes for hydrolysis to break the bond. Presence of appropriate enzymes will determine whether an organism is able to metabolize certain carbohydrates. Glycoside + H20 + catalyst -> hydrolysis ex of catalysis: amylase for starch and glycosylase for nucleotide

Endoderm

digestive tract, respiratory tracts, liver, pancreas, thymus, thyroid

Lactose (gal-B-1,4,-glu)

disaccharide made from B-galactose and glucose by 1-4 linkage

Denaturation of proteins

disruption of secondary, tertiary, and secondary structures

left thoracic duct

drains most of body's lymph into veins on left side of body. Chlymicrons in lymph reach arteries which drain into capillary beds, which is the site of absorption of fats by other tissues in the body.

Fasting

during fasting, when the body needs to maintain blood glucose levels for the brain and RBCs, they cannot use these fatty acids. The process of gluconeogenesis, which occurs largely in the liver, requires a lot of ATP. So, the liver takes a lot of these fats and breaks them down to produce the ATP necessary to produce gluconeogenesis. Process of converting glucose into fatty acids is also halted when levels of insulin fall.

Adenine with Thymine

2 hydrogen bonds

delta G naught < 0 (negative)

spontaneous

Osmotic pressure

"Pulling" pressure generated by concentration gradient encouraging osmosis. Force that moves water down the concentration gradient. Greater the difference in tonicity across the semi-permeable membrane, the greater the osmotic pressure. In capillaries, osmotic pressure encourages flow of blood from tissues into capillaries. Hydrostatic pressure (pressure by slow movement of blood) counteracts osmotic pressure and encourages flow from capillaries into tissue.

Electron transport chain

(Oxidative phosphylation) in cristae (inner membrane of mitochondria) Input: NADH and FADH2 Output: NAD+ and FADH O2 reduced to H2O Energy released from these reactions generates a proton gradient, which drives ATP synthase to make ATP. H+ can only migrate down the proton gradient through ATP synthase. Like a water mill, ATP synthase harnesses the energy of the falling protons to concert ADP to ATP. ETC is inhibited by certain antibiotics, by cyanide, azide, and carbon monoxide

Transposons

*also present in eukaryotes -heterogeneous class of genetic elements that can insert at new locations on chromosomes. 3 major groups 1. Retrotransposons 2. DNA transposons 3. miniature inverted-repeat transposable elemtents -translocate via a cut and paste mechanism -cause significanct changes in genome organization and gene sequence. They can give insertion/deletion mutant and chromosomal inversion mutant. -used as tools in gene delivery or targeted mutations

mRNA processing

- 5' guanine cap - 3' poly-A tail - RNA splicing of exons = remove introns + "splice" together exons -transported to cytoplasm where they are translated to ribosomes

ATP group transfers

- ATP can be hydrolyzed at different positions, producing different options for group transfers - play roles in reaction mechanisms to improve thermodynamic favorability beyond just coupling with the -ΔG of ATP hydrolysis. - Depending on nucleophilic attack on the α, β, or γ phosphate, either transfer of a single phosphoryl group, a pyrophosphoryl group, or adenylyl group (the AMP portion with inorganic pyrophosphate released) will take place, respectively.

Meiosis vs Mitosis

- meiosis has 2 cell divisions, mitosis only one - in meiosis homologous chromosomes pair up on cell's equator, in mitosis homologous chromosomes never pair up - in anaphase 1 of meiosis sister chromatids are still paired, in anaphase in mitosis, sister chromatids are separated - meiosis results in a haploid cell, mitosis results in a diploid - meiosis has two cell divisions, mitosis only one

DNA denaturation

-Double helix can be denatured by conditions that disrupt H bonding & base-pairing -results in separation of double helix into 2 single strands -heat, alkaline pH, and chemicals like formaldehyde & urea are used to denature DNA -the higher the G-C content, the higher the temperature required to denature DNA -denatured, single stranded DNA can be reannealed (brought back together) if the denaturing condition is slowly removed

Replicating the ends of DNA molecules

-Limitations of DNA polymerase create problems for the linear DNA of eukaryotic chromosomes -The usual replication machinery provides no way to complete the 5' ends, so repeated rounds of replication produce shorter DNA molecules

Acetal formation

-OH attack on carbonyl group = produces polysaccharides if the -OH is from another monosaccharide

Hemiacetal formation

-OH attacks carbonyl group, produces ring form

Functional and evolutionary importance of introns

-Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during RNA splicing -Such variations are called alternative RNA splicing -Because of alternative splicing, the number of different proteins an organism can produce is much greater than its number of genes. Efficient way to generate a wide variety of proteins through use of mRNA compared to modifying preexisting proteins.

Bacteria

-all have cell membrane and cytoplasm -some have flagella and fimbriae (similar to cilia). -flagella is made of flagellin, mechanism is rotation powered by a proton or sodium gradient *eukaryotic flagella is made of mictrotubules -bacterial flagella and eukaryotic flagella distance enough that scientists are able to develop antibacterial vaccines that specifically target bacterial flagella. -also, many antibiotics target the bacterial ribosome, which is significantly smaller than the eukaryotic ribosome. -no membrane-enclosed nucleus. genetic material is located in an irregular region called the nucleoid. Prokaryotic cytoskeleton pulls replicated DNA apart. -don't have Golgi, ER, mitochondria, Chloroplasts -Bacterial cell wall is made of peptidoglycan, a polysaccharide-protein molecule. plant cell wall is made of cellulose and fungi cell wall is made of chitin

Virus life cycle

-cannot replicated by themselves, depend on host organelles to replicate (ribosomes) *retroviruses contain their own reverse polymerase to convert RNA to DNA before the host's polymerases take over 1. attachment to host, penetration, entry of viral genetic material 2. use of host to replicate genetic info (ribosomes synthesize necessary enzymes, host's ATP provides necessary energy, host also provides raw materials, such as amino acids) 3. self assembly and release of new viral particles, the coat proteins and viral genetic material will assemble into viral particles by themselves.

Cancer cells

-continue to grow and divide in situations normal cells would not -fail to respond to cellular controls to halt growth -avoid apoptosis even with extensive DNA damage -stimulate angiogenesis (cause new blood vessels to grow to nourish the cancer cell) -immortal, don't die after a number of divisions -can metastasize -break off and then grow in another location

structure of ribosomes

-made of RNA -looks like an upside down snowman -made of 2 parts called large and small sub unit

Gene regulation in development

-modification of DNA methylation can shut off or turn on genes -modification of histones too (acetylation of histone proteins decreases positive charge on lysine residues and weakens interaction of DNA with histone, open DNA = easier transcription)

Virus structure

-protein coat covers nucleic cid -some virus have an envelope derived from host cells membrane, while other lack is (non enveloped) *enveloped viruses bud off the host's membrane *non-enveloped viruses cause the host to burst to release viral particles -lack organelles + nucleus, genetic material simply packed in proton coat -can contain either RNA or DNA as genomic content. *Those that convert their genome into DNA inside their host are known as retroviruses e.g. HIV -roughply 100 times smaller than bacteria and eukaryotes

Archaea

-single celled organisms -look like bacteria but contain genes + metabolic pathways more similar to eukaryotes -extremophiles = most commonly found in harsh environments with high temperatures, high salinity, no light, etc. -some photosynthetic, most chemosynthetic = generate energy from inorganic compounds, including sulfur and nitrogen (e.g. ammonia) -eukaryotes and domain Archaea share common origin due to similarities. *both start translation with methionine, contain similar RNA polymerase, associate DNA with histones. *However, Archaea contain a single circular chromosome, divided by binary fission or budding, and overall share similar structure to bacteria -resistant to many antibiotics

Mechanism of transcription

1) Helicase and topoisomerase unwind the dsDNA. 2) RNA polymerase II binds to TATA box within the promoter region of the gene (25 base pairs upstream) 3) hnRNA is synthesized from the DNA template (antisense) strand and stopped once termination signal. *Post-translational modifications* 4) A 7-methylguanylate triphosphate cap added to 5' end. 5) Poly-A tail added to 3' end 6) Splicing done by snRNA and snRNPs in the spliceosome. Process removes introns. 7) Alternative splicing (combining of exons) allows more variability of gene products 8) Leave nucleus and into cytosol.

Unsaturated fatty acids

1+ double bonds, bent or kinked structure, liquids at room temperature (lower melting point)

In order to be classified as a carbohydrate, a molecule must have...

1. At least a 3-carbon backbone 2. An aldehyde of ketone group 3. At least 2 hydroxyl groups

Development

1. Zygote 2. Blastocyst 3. Implantation 4. Gastrulation 5. Organogenesis

Retrovirus life cycle

1. enters host 2. viral reverse transcriptase converts viral RNA genome into double-stranded DNA 3. Virally encoded enzyme, called integrate, adds in viral DNA into the host's genome at a random place 4. When the host replicates, the viral DNA gets replicated also.

Cytosine with Guanine

3 hydrogen bonds

Net results of electron transport chain

34 ATP per glucose molecule, never achieved because leaky mitochondrial membranes so actual yield of ~32 ATPs made. 6 H20 formed when electrons unite with O2 at the end of ETcC.

Enhancers

A DNA sequence that recognizes certain transcription factors that can stimulate transcription of nearby genes.

Neural crest

A band of cells along the border where the neural tube pinches off from the ectoderm; the cells migrate to various parts of the embryo and form the pigment cells in the skin, bones of the skull, the teeth, the adrenal glands, and parts of the peripheral nervous system.

Bottleneck

A change in allele frequency following a dramatic reduction in the size of a population

Codon, Anticodon

A codon is a three-base sequence (three nitrogen bases in a row) on mRNA. It calls for a specific amino acid to be brought to the growing polypeptide. An anticodon is a three-base sequence on tRNA. It matches the codon and brings an amino acid (releasing it to form chain).

Glycosidic linkage

A covalent bond formed between two monosaccharides by a dehydration reaction. -acetal linkage = involved hydroxyl group of the anomeric carbon. -can also mean linkage between sugar and base in nucleotides

deoxyribonucleic acid (DNA), Watson-Crick model

A double-stranded, helical nucleic acid molecule capable of replicating and determining the inherited structure of a cell's proteins.

Inversion mutation

A genetic mutation in which the order of a segment of genetic material is reversed. This type of mutation can involve a small number of nucleotides as well as larger sections of a chromosome containing more than one gene. A portion of the DNA sequence is inverted.

Mispairing mutation

A not pairing with T, or G not pairing with C.

nonsense mutation

A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.

incomplete dominance

A pattern of inheritance in which two alleles, inherited from the parents, are neither dominant nor recessive. The resulting offspring have a phenotype that is a blending of the parental traits.

DNA annealing

A process by which DNA is first temporatily denatured at temps just below boiling. The heat breaks the H-bonds and seperates the strands of the DNA double helix. As the denatured DNA is cooled, a complementary strand or small piece of a c. strand is chosen, the engineer will hybridize (anneal) to the orginal strand allowing the engineer to test/manipulate the DNA in a vast variety of ways

Natural Selection

A process in which individuals that have certain inherited traits tend to survive and reproduce at higher rates than other individuals because of those traits.

TATA box

A promoter DNA sequence crucial in forming the transcription initiation complex.

exothermic reaction

A reaction that releases energy in the form of heat. delta H is negative.

Gene

A segment of DNA on a chromosome that codes for a specific trait

triplet code

A set of three-nucleotide-long words that specify the amino acids for polypeptide chains.

Epimers

A subtype of diastereomers that differ in absolute configuration at exactly one chiral carbon

Bacteriophage

A virus that infects bacteria -head stores genetic material -sheath provides a passageway for genetic material to be injected into the host bacteria -tail fibers attach to the host bacteria

synaptonemal complex

A zipper-like protein structure that causes replicated homologs to become physically connected during prophase of meiosis I; sets the stage for crossing over.

initiation codon

AUG (methionine)

Purines

Adenine (A) and Guanine (G)

Repair after replication

After replication (1st level of repair): 3'-5' exonuclease activity of DNA Pol removes mismatched nucleotide.

Allosteric enzymes

Allosteric site present, molecule binds it, can either upregulate or donwregulate the enzyme function

Active Site model

Also called the "lock and key" model, this states that the active site of an enzyme and its substrate are perfectly complementary.

Recessive

An allele that is masked when a dominant allele is present

Immune system proteins

Antibodies (immunoglobulins) target a specific antigen, which may be a protein on the surface of a pathogen or toxin

Phenotype

An organism's physical appearance, or visible traits.

Passive transport

Any thermodynamically favorable movement of a solute across a membrane (down the gradient). Simple diffusion: solute diffuses through membrane without any help from a protein Facilitated diffusion: w/ protein e.g. steroid hormones

Zwitterion

At a neutral pH or pI, aa exist as a dipolar ion.

Bacteria exponential growth

Bacterial growth starts off being exponential because of the nature of binary fission. Later, when food becomes short, and it gets crowded, growth slows and eventually plateaus

Function in transmission of genetic information

Because of the complementary nature of base pairing, DNA can transmit genetic information through replication.

Loss of Cell Cycle Controls in Cancer Cells

Cancer cells do not respond normally to the body's control mechanisms Cancer cells may not need growth factors to grow and divide They may make their own growth factor They may convey a growth factor's signal without the presence of the growth factor They may have an abnormal cell cycle control system. two types of mutations than can cause cancer -deactivation of checkpoint proteins (tumor repressor) -activation of gene causing proliferation of cell (oncogene)

Allele

Different forms of a gene

Prophase

Chromosomes become visable (condensation of chromatin into chromosomes), nuclear envelop dissolves, spindle forms, centrioles move to opposite poles of cell

Exons

Coding segments of eukaryotic DNA.

transcription factors

Collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription.

Osmosis

Colligative properties: properties based on NUMBER of particles present, rather than type. Water diffuses freely across the membrane, but not ions Spontaneous net movement of solute molecules through a semi-permeable membrane in the direction that tends to equalize the solute concentrations on the two sides.

Gene pool

Combined genetic information (all alleles for a gene) of all the members of a particular population. Description of genetic variation. Higher = more fitness

Composition and function of cilia and flagella

Composition: 9 pairs (18) of microtubules form a circle around 2 lone microtubules (9+2 arrangement) Function: move fluid to cause cell or nearby substances to move

Repair of Mutations

DNA polymerase proofreads the new strand against the old strand. If errors occur in sex cells - mutation may be passed onto offspring. If errors occur in body cells- cancer may result

Light repair (w/ photolyase)

DNA repair enzymes that repair damage caused by exposure to ultraviolet light. Require visible light for their own activation and for the actual DNA repair

ATP hydrolysis

Delta G <<0 -Adenosine 5' -triphosphate (ATP) serves as main source of free energy in living cells. -Energy stored by ATP can be liberated through direct hydrolysis or group transfer. -Direct hydrolysis of ATP consists of nucleophilic attack by H20 at y phosphate position of ATP and cleavage of the y-B phophoanhydride bond. ATP + H20 = ADP + Pi Delta G naught = -30.5kJ/mol

Increase temperature

Endothermic reaction is favored

Heterochromatin

Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed.

Hormones influencing sperm production

FSF and LSH

Regulation of glycolysis and gluconeogenesis

Fast-acting forms of regulation: Large influx of glucose promotes glycolysis. Large influx of oxaloacetate promotes gluconerogenesis. Lots of ATP = gluconeogenesis favored Slow-acting forms of regulation: often take advantage of transcriptional changes within the cell. Imagine an organism is in a long-term fasting state. It will want to up-regulate the transcription of enzymes that promote things like gluconeogenesis to dump glucose into the blood. It's implied that the process of going from DNA to mRNA to enzymes will take much longer than simple Le Châtlier or allosteric regulation. This is more of an adaptive process that allows the organism to adapt to more long-term changes that it experiences in its environment.

F1 Generation

Filial 1 = children of P

F2 Generation

Filial 2 = grandchildren of P

Free Energy

For non-standard conditions. The energy that is available to do work - the difference between the change in enthalpy and the product of the entropy change and the absolute temperature. Delta G = 0 at equilibrium. Delta G = Delta G naught + RTln(Q) Delta G naught = -RTln(Q) at equilibrium

directional selection

Form of natural selection in which the entire curve moves; occurs when individuals at one end of a distribution curve have higher fitness than individuals in the middle or at the other end of the curve. Selects for a trait of one extreme.

Spermatogenesis

Formation of sperm 1. Spermatogonia in testes undergo mitosis, produce two diploid copies, one called primary spermatoctye 2. primary spermatocyte under meiosis I to produce two haploid secondary spermatocytes 3. secondary spermatocytes undergo meiosis II to make spermatids 4. spermatids mature, lose cytoplasm, gain tail to become mature 5. ejaculation sends them through vans defers, into urethra, and then out of the penis *sperm production occurs in the seminiferous tubules

Louis Pasteur

French scientist -did famous experiment known as the Swan-Neck Bottle experiment while proved that all cells come from preexisting cells

Penetrance

Frequency. that a genotype will result in a phenotype. 100% penetrance means that if you have the genes for being smart, your will 100% be smart.

Evolutionary time as measured by. gradual random changes in genome.

Genetic drift and other random factors will produce changes over time that are not selected for. By measuring the amount of random change or mutation rates in a genome, it is theorized to be able to estimate the amount of time that passed since the diverging of different species using this so-called molecular evolutionary clock. "molecular clock"

Matthias Schneiden

German botanist that looked at all sorts of plants under a microscope and noticed all had the same microscopic structure.

Rudolph Virchow

German physician and pathologist, observed bacteria that divided and formed two bacteria that were identical = binary fission

Theodor Schwann

German scientist looked at nervous system of different animals and noticed all had similar structure that were these cells

denaturing agents

Heat, strong acid and base (breaks covalent bonds, H-bonds), reducing agents (breaks disulfide bonds), detergents, heavy metal ions, etc.

Effects of local conditions on enzyme activity

Heat: first increases, but get denatures at high heats. changes in pH can denature. Human blood = 7.4 Increasing levels of salt can disrupts hydrogen and ionic bonds.

G1 checkpoint

If conditions are not appropriate or if the cell is generically programmed not to divide, the cell proceeds no further through the cell cycle. Remains in an extended G1 phase or G0 phase Ex. nerve and muscle cells Favorable conditions based on cell side (large = ready)

Multiple origins of replication

In Eukaryotes, because eukaryotic chromosomes are much larger, so multiple origins are needed to replicate the entire chromosome in a short amount of time

Central Dogma

Information flows from DNA -> RNA -> Protein

Obesity and regulation of body mass

Insulin, leptin, and gherkin help regulate whether the energy or food that we've consumes is stored or if we let is pass through and become waste. The things we do to get rid of energy or consume energy include basal metabolic rate or amount of energy we burn at rest. Leptin: hormone that lives in our fat tissue, and goes to hypothalamus, part of the brain that tells us we're not hungry Highlights importance of having correct hormones flowing through bloodstream to talk to the brain based on the nutrients or diet you have to regulate your body mass.

Beta sheets

Intermolecular forces, can be parallel or antiparallel

Desmosomes

Join two cells at a single point, present in cells that experience stress due to sliding (skin, intestinal epithelium) =gives strength to tissues

Catalytic Efficiency

Kcat/Km, Enzyme's Turnover number

Centromeres

Located in the center of the "X", they hold the chromatids together in a chromosome. They also help the chromosomes attach to the spindle fibers.

locus

Location of a gene on a chromosome

Asters

Microtubules and fibers that radiate out from the centrioles.

Absolute configuration at the alpha position

Most S except Cysteine. All chiral except Glycine.

Lateral Diffusion

Movement of phospholipid from side to side, fast type of movement

NADH, NADPH

NADH utilized in cellular respiration. Produced in catabolic reactions and later used in ETC to obtain energy by converting NADH back to NAD+. NADPH primarily produced in oxidative part of the Pentose phosphate pathway. used in 1) anabolic synthesis to produce cholesterol, fatty acid, transmitter substance and nucleotides 2) detoxifying processes as an antioxidant NADH and NADPH are both reductive agents.

stabilizing selection

Natural selection that favors intermediate variants by acting against extreme phenotypes

small nuclear RNA (snRNA)

Noncoding RNA found in eukaryotes and involved in splicing, polyadenylation, and other processes in the nucleus.

Introns

Noncoding segments of nucleic acid that lie between coding sequences.

Addition mutation

One base is added to the DNA sequence. Causes reading frame shift, including duplications or gene amplifications.

Independent assortment

One of Mendel's principles that states that genes for different traits can segregate independently during the formation of gametes

Endocytosis

Phagocytosis=ligands signal for membrane to engulf particles Pinocytosis = engulfs extraceullular fluid, takes up solute Recepor-mediated endocytosis = takes up ligands

Hybridization

Process of two complementary, single-stranded DNA or RNA combining together, producing a double-stranded molecule through base pairing. Technique is used for interbreeding between individuals of genetically distinct populations. Hybrids between species are likely to be infertile due to pairing issues between chromosomes (e.g. mule)

Apoptosis

Programmed cell death -occurs in response to to normal tissue development or in case where cell decides to die when can't save itself from disease. -clean and healthy -Afterwards, the apoptosis cell releases chemicals that attract macrophages and gets engulfed -brought upon by development or immune response (infected/cancerous cells killed by cytoxic T cells/natural killer cells)

Repair during replication

Proofreeding by DNA polymerase corrects errors during replication

Rough endoplasmic reticulum

RER Synthesis almost all proteins to be secreted out of cell, covered in ribosomes. synthesis of proteins into the lumen.

wobble pairing

Refers to flexibility in the pairing between the base at the 5' end of a tRNA anticodon and the base at the 3' end of an mRNA codon. This flexibility allows a single tRNA to read more than one mRNA codon. Third position is less positionally constrained, allowing for non-standard base pairs to form. Nucleotide codons with differences in the last position then tend to code for the same amino acid (evolutionary advantage).

DNA polymerase I

Removes RNA primers from fragments and replaces it with required nucleotides

Telomeres

Repeated DNA sequences at the ends of eukaryotic chromosomes.

Supercoiling

Repeatedly coiling DNA molecule to make chromosome shorter and wider. Because DNA is so long, supercoiling reduces the space and allows for DNA to be packaged.

Mechanism of replication

Replicating a molecule of double-stranded DNA involves unwinding its helical structure, separating its two strands, and filling in new partner strands from free nucleic acids (nucleotides)

Gluconeogenesis

Reversal of glycolysis. Converts non-carbohydrate sources (e.g. amino acids) in our liver to glucose. Rate-limiting enzymes: fructose 1,6-bisphosphatase

Bacilli

Rod shaped bacteria

G-protein coupled receptors

Secondary messenger system -binding of NT to receptor causing release of attached G proteins alpha subunit alpha subunit release in post synaptic neuron, has a variety of effects 1. Activated separate specific ion channels 2. active second messenger 3. Activate intracellular enzymes 4. Active transcription

Senescence and aging

Senescene: process by which cells stop proliferating in response to environmental stressors and are cleared away by immune cells (allows for shaping of tissue) loss of cells power of division and growth, implication in age how cells deteriorate with age

Origin of replication

Site where the replication of a DNA molecule begins, consisting of a specific sequence of nucleotides.

Active Transport

Sodium/Potassium Pump -secondary active tranport that maintains negative potential across lipid bilayer -pumps 3 sodium out, 2 potassium in -cell maintains negative resting potential -requires energy input -always involves a protein Primary: ATP hydrolysis is coupled to transport molecules Secondary: ATP is first used to create a gradient, then potential energy is used to transport the molecules (indirectly uses ATP)

Fertilization

Sperm + egg ->zygote

Le Chatelier's Principle

States that if a stress is applied to a system at equilibrium, the system shifts in the direction that relieves the stress.

Expressivity

The degree to which a penetrant gene is expressed. Constant = if gene for being to smart manages to penetrate (show up as a trait), then IQ is 120. Variable Expressivity = your IQ does not have to be 120, it could be somewhat lower or higher.

Jacob-Monod Model

The description of the structure and function of operons in prokaryotes, in which operons have structural genes, an operator site, a promoter site, and a regulator gene

fitness concept

The fittest organism is the one that can best survive to reproduce offspring. Fitness is defined as the ability to pass your genes on.

mRNA (messenger RNA)

The form of RNA which is created as a blueprint from DNA; carries instructions for making a protein

Euchromatin

The less condensed form of eukaryotic chromatin that is available for transcription.

Oogenesis

The production of mature egg cells

Evolutionary success as an increase in percent representation in the gene pool of the next generation

The products of evolution can be seen from many perspectives, from population change to the survivability of individuals to the presence of a particular gene or even its specific alleles. Alleles that produce traits that are selected for will increase in frequency in the gene pool, thereby creating another measure of evolutionary success.

Secondary (2) structure

The second level of protein structure; the regular local patterns of coils or folds of a polypeptide chain, due to hydrogen bonds.

Homozygous

The state of possessing two identical forms of a particular gene, one inherited from each parent.

termination codons

UAA, UGA, UAG When an annoying person comes up to you, you're gonna tell them: Stop, U Are Annoying, U Go Away, U Are Gone.

Biometry: Statistical methods

Use of statistical methods to understand biological data, ID genes in the population that are bad. Methods include probabilistic tools, Bayesian computations, and multivariate statistics.

Testcross

You have something with dominant phenotype (not sure of genotype). To find out, cross it with homozygous recessive. If Aa, half will express recessive phenotype.

Waxes

contributes to stability, forms barrier against water

Double crossovers

allows for the chance of a portion of the original combination of alleles along a chromosome to again segregate together, as the ends of the homologous are switched again at some point downstream of the first crossover.

a/b anomeric configuration

alpha = down beta = up anomeric carbon is the carbon derived from the carbonyl carbon (the ketone or aldehyde functional group) of the open-chain form of the carbohydrate molecule.

Fatty acid

amphipathic molecules with poler carboxylate-head group and non polar hydrocarbon tail

DNA ligase

an enzyme that eventually joins the sugar-phosphate backbones of the Okazaki fragments

General concept of mutation

error in DNA sequence

Oxidation of fatty acids

beta oxidation occurs in the matrix of the mitochondria or in peroxisomes (when chain is too long for mitochondria to handle). makes acetyl-CoA (feeds into Krebs cycle), FADH2, and NADH fats give more energy than any other food source.

Disulfide bond (covalent)

between two cysteine (oxidation) -> cystine

Binding proteins

bind a specific substrate, either to sequester it in the body or hold is concentration at a steady state

Cell adhesion molecules (CAM)

bind cells to cells or surfaces. Anchor them to ECM.

Receptor enzymes

bind neurotransmitter or hormones and triggers processes in cell. NT binding to receptor makes postsynaptic side more permeable to ions. -NTs released back into cleft after binding to receptor *wats to destroy NTs in clef afterwards 1. Destroy using enzyme 2. Reabsorb into presynaptic cleft 3. Diffused out of cleft

Uncompetitive inhibitor

binds to EIS at allosteric site, increases Km, decreases Km

Competitive inhibitors

binds to active site, increases Km, doesn't affect Vmax

Non-competitive inhibitor

binds to allosteric site w or w/o substrate, doesn't affect Km, decreases Vmax.

Mixed inhibitors

binds to allosteric site. ether bonds to ES or E, either decreases or increases Km, decreases Vmax

Mesoderm

blood cells, connective tissues, and various organs

Glucose

blood sugar and product of photosynthesis -forms pyranose when carbon 5 attacks carbonyl carbon

Connective

blood, bone, tendons, ligaments, cartilage

Regulation of metabolic pathways

body continually degraded + synthesizes proteins in order to keep organisms functioning properly at a steady state. Keeps metabolic enzymes fresh and new so there will be very few issues.

Post absorptive state

body needs to take the stored energy and use it

phosphoanhydride bond

bond that connects phosphates in an ATP molecule

Mutualistic

both bacteria and host benefits. Ex. E. coli in gut, natural flora on skin

Nervous

brain, spinal cord, nerves

Lyases

break chemical bonds NOT involving hydrolysis or oxidation

Hydrolysis

breakdown of compound via addition of water (ex. proteins)

Glycogenolysis

breakdown of stored glycogen to glucose. Rate limiting enzyme: glycogen phosphorylase. Enzyme is activated by glucagon in liver. In skeletal muscle, it is activated by AMP and epinephrine, which signal that muscle is active and requires more glucose. It is inhibited by ATP.

Covalently-modified enzymes

can either activate or deactivate an enzyme through the addition or removal or a modifier using a reversible covalent bond (e.g. phosphorylation)

Motor proteins

capable of force generation through conformational change

Peptide bond (covalent)pep

carboxylic acid (OH) + amino (H) --> H20 + peptide bond (dehydration)

Frontal lobe

carries out executive functions like planning, impulsive inhibitions

Ribozymes

catalytic RNA molecules that function as enzymes and can splice RNA, found in ribosome where they join amino acids together to form protein chains.

Isomerases

catalyze isomerization

Oxidoreductases

catalyze oxidation-reduction reactions

Enzyme function

catalyze reactions by reducing activation energy. ex. metabolism and digestion. Very specific.

Ligases

catalyze the formation of bonds

Growth arrest

cell arrests for many reasons, does not proceed through cycle -too much genomic mutation/damage causes cell to arrest in M phase -contact inhibition, normal epithelial cells stop growing when it gets crowded such that it's touching adjacent cells -lack of food

Autophagy

cell degrades its own internal structures via its stomach (lysomes), occurs before apoptosis

G1

cell growth, protein, RNA, and phospholipid synthesis active

G2

cell prepares to divide, RNA and proteins (esp tubulin) are produced

founder effect

change in allele frequencies as a result of the migration of a small subgroup of a population

Genetic drift

change in allele frequencies for genes across a population, can be caused by random fluctuations but produce dramatic changes in the genetic makeup of the population over time. Effect of genetic drift increases at the population size decreases. (e.g. founder effect (island) and bottleneck effect)

Genetic drift

change in allele frequency due to change event

Delta G and equilibrium constant

change in free energy delta G naught = -RTln(Keq)

Sex-linked characteristics

characteristics determined by genes located on the sex chromosomes (X, Y). diseases in these more prevalent in males where can't be masked by dominant.

G2 checkpoint

checks for mitosis promoting factor (MTF) high MTF levels indicate aligned chromosomes, mitosis is triggered

Metaphase

chromosomes align across equator of cell

alpha helices

clockwise coils around a central axis, intramolecular forces, more stable than beta turns

Regulator gene of operon

codes for the repressor protein

Nucleus

compartmentalization, storage of genetic information -nuclear membrane/nuclear envelope surrounds the nucleus -genetic info stored as DNA

Citric Acid Cycle (Krebs Cycle)

completes the breakdown of glucose. in mitochondria matrix. allosteric regulation. Acetyl-CoA is major substrate so less Acetyl-Coa = slower rate Net results: 2 ATP per glucose (per 2 acetyl CoA) 6 NADH and 2 FADH2 4 CO2

Nucleosides

composed of nitrogenous base and five carbon sugar

Microtubules

composition and role in support and transport. Composition: made up of 13 tubular filaments arranged in a hollow tube -support: support shape of cell -tranport: serves as platform for vesicle (dyne and kinesis) -also moves chromosomes around the cell vis spindle apparatus

Microfilaments

compositions and role in cleavage and contractility. Composition: actin filaments, globular subunits -cleave: pinches cytoplasm during cytokinesis -contractibility: interact with myosin to cause muscle contractions

Cytochromes

compounds consisting of heme bonded to a protein. They function as electron transfer agents in many metabolic pathways, especially cellular respiration. Cytochrome c transfers electrons from complex III to complex IV in ETC.

Nuclear envelope, pores

envelope = double phospholipid bilayer wrapping around the nucleus pores = large holes perforating envelope, lets RNA out but not DNA

Peptidase

enzyme that breaks down proteins into amino acids. Nitrogen in amino acid is converted to urea. Carbon in amino acid is converted to pyruvate of acetyl-coA, depending on amino acid. Carbon products from amino acid metabolism can either feed into the Krebs cycle, fatty acid synthesis, or be the starting material for gluconeogeneis.

Gyrase

enzyme that relieves buildup of torque during unwinding

Exonuclease

enzyme that removes successive nucleotides from the end of a polynucleotide molecules

lipoprotein lipase

enzymes in capillary bed that take triglycerides in chylomicron and break them up into fatty acids. Activated by insulin.

Lipases

enzymes that break down lipids into smaller pieces for the cell to absorb. Some are secreted by pancreas, others are found naturally along the border of the cells.

Helicase

enzymes that unwinds DNA double helix during replication

Ectoderm

epidermis of skin, nervous system, eyes, spinal cord

Keq = 1

equal amount of products and reactants

Phospholipids

fatty acids bound to glycerol, phosphate, and other groups. Used for cell membranes.

Cholesterol

fatty acids in ring form. ring is nonpolar and -OH head group is polar. Used for steroid hormones, bile, membrane fluidity.

Decrease temperature

favors the exothermic reaction

Gastrulation

first cell movements -formation of primary germ layers (endoderm, mesoderm, ectoderm)

Robert Hooke

first person to observe cells under microscope

Golgi apparatus

flattened, membrane bound sacs, organizes and concentrates proteins into vesicles full of proteins. Can secrete proteins out of cell or back into mitochondria or ER.

FAD

flavin adenine dinucleotide

Feedback regulation

form of allosteric regulation where final product of sequence (when accumulates), binds to first enzyme in series to inhibit its activity

binary fission

form of asexual reproduction in single-celled organisms 1. DNA replicates 2. separated by attached to cell membrane as cell elongates 2. Cytokinesis divided parent cell into two daughter cells

disruptive selection

form of natural selection in which a single curve splits into two; occurs when individuals at the upper and lower ends of a distribution curve have higher fitness than individuals near the middle

Tight junctions

form watertight seal from cell to cell, prevents fluids from moving past. Can act as a barrier to prevent fluid from seeping past cells, present in endothelial cells.

Glycogenesis

formation of glycogen from glucose Rate-limiting enzyme: glycogen synthase. Stimulated by insulin and is inhibited by epinephrine and glucagon.

Proline (Pro, P)

found in beta turns and alpha-helices to cause kink to turn. non-polar, ambivalent

delta G naught prime (standard state)

free energy change of a reaction under "standard conditions" which are defined as: All reactants and products are at an initial concentration of 1.0M, P=100kPa, 25 celsius, 298K.

Gene mapping

genetic recombination occurs between maternal and paternal sister chromatids; more likely for recombination to occur over a larger distance (can enhance genetic information anywhere along the long strength of a chromatid). Further apart that two genes are, the more likely it is that they recombine.

Neural tube

gives rise to the central nervous system

Deoxy

has a -H in place of an -OH at a certain position

Heterozygous

having different alleles at a gene locus

ATP synthase

hydrogen going through ATP synthase is considered chemiosmosis. Phosphorylation happens as the hydrogens experience chemiosmosis and go back in to turn the axle and push the ADP and phosphate groups together. Substrate phosphylation, on the other hand, is involved in glycolysis and is where you have an enzyme directly helping to peruse the ATP without any type of chemiosmosis or proton gradient.

Hydrolases

hydrolysis reactions (ex. breaking peptide bonds)

Role of hydrophobic bonding

hydrophobic aa found in interior or protein, folds in on itself

Hormonal regulation: insulin and glucagon

if blood sugar level rises, stimulates body to release hormone insulin. If blood glucose level decrease, stimulates body to release hormone glucagon. Insulin promotes glycolysis and glucagon promotes gluconeogenesis.

Sugar phosphate background

important structural component of DNA, consists of 5-carbon sugar + phosphate group. Sugars linked together by a phosphodiester bond, between carbon 4 on their chain and CH2 group attached to phosphate ion.

semi-conservative replication

in each new DNA double helix, one strand is from the original molecule, and one strand is new

Spliceosomes

in eukaryotes, a large, complex assembly of snRNPs (small nuclear ribonucleoproteins) in nucleus that catalyzes removal of introns from primary RNA transcripts

Integral membrane proteins

integrated into membrane, at least on hydrophobic region that anchors them to the hydrophobic core of the phospholipid bilayer. Those than span entire membrane are called transmembrane proteins.

Cerebellum

integrates, processes sensory, motor, vestibular input

Zymogen

inactive form of an enzyme, can be converted into an active enzyme when activated by another enzyme

Transcriptional regulation

increases or decreases the synthesis of mRNA encoding a specific enzyme. Transcription factors (protein) bind to enhancers or silencers (DNA).

Glucagon

instructs liver to release stored glucose, causing blood sugar levels to rise.

Gated ion channels

let ions from oner side of the membrane to another. Voltage gated: Na and K channels involved in action potential, speed at which they. open are different Ca2+ channels located at presynaptic side of synaptic clef. Action potential causes channels to open, Ca2+ to flow into cell. Causes efflux of NT vesicles.

Epithelial cells

line inside and outside of organs -single layer: found in alveoli, capillaries -stratified: multiple layers, found in stomach, esophagus

Kinetochore

located at centromere of joined chromatids, structure of protein and DNA that attach to microtubules *Kinetochore microtubules connect centromeres to centrosomes/centrioles. their shortening pulls sister chromatids apart.

Flavoproteins

located on matrix face of the inner mitochondria membrane and functions as a specific electron acceptor for primary dehydrogenases, transferring the electrons to the ubiquinone pool in the inner mitochondria matrix.

Lacteals

lymphatic capillaries that surround cells, have larger pores relative to blood capillary and thus allow chylomicrons to travel within them and from cells.

Oxidative phase of PPP

made of 2 irreversible steps, makes ribulose-5-phosphate. -1H20 +2NADPH +1CO2

Anabolism of Fats

makes biologically important fats like phospholipids and triglycerides. Precursor: Acetyl-CoA Rate limiting enzyme: Acetyl-CoA Carboxylase (adds carboxy group) Citrate: allosteric activator Insulin: activator Long-chain fatty acid: inhibits Glucagon: hormonal inhibitor, signals adipose cells to release fatty acids for our cells to break down.

Maltose (glu-a-1,4-glu)

malt sugar, made of two glucose molecules

Inbreeding

mating between relatives (usually true for a small population), limits genetic diversity and increases likelihood of recessive disorders within a population. Also decreases heterozygotes

Backcross

matting between the offspring and the parent =preserve parental genotype

Significance of meiosis

meiosis introduces genetic variability by genetic recombination. Genetic recombination is the product of independent assortment and crossing-over, which introduces genetic variability. Produces 4 haploid distinct cells and gametes.

Lyosomes

membrane-bound vesicles containing hydrolytic enzymes. Digests food + viral/baterial particles. Rupture during apoptosis -cells also shrinks and cascades (protease enzymes) are activated -hydrolytic enzymes are activated by low pH -pH lowered by lysosome pumping protons into its interior after binding to a food vesicle

Centrioles

microtubule organizing centers -attached to "-" end of microtubule centriole: production of flagella and cilia, form the centrosome (2 centrioles) microtubules radiate out of these barrel shaped structures, which are made of microtubules themselves

spindle microtubules

microtubules connecting the two centrioles

M

mitosis, division of nucleus

Soluble electron carriers

molecules that are capable of accepting or donating electrons (often via binding, releasing hydrogen) and can shuttle to/from other acceptors/donors to continue the redox process. NAD (NAD+ when oxidized, NADH when reduced) accepts electrons (reduced) in glycolysis and the citric acid cycle and donated them (oxidized) to the electron transport chain. FAD (FAD when oxidized, FADH2 when reduced) also accepts electrons (reduced) at the citric acid cycle and donated them (oxidized) to the electron transport chain. -Water soluble carries are free floating in cytosol, lipid-soluble embossed in membrane -Flow of electrons in the electron transport chain allows the production of energy to produce ATP.

Keq > 1

more products present at equilibrium

Keq < 1

more reactants present at equilibrium

kinesis and dyneins

motor proteins that interact with microtubules. Kinesis go away from nucleus, dynein go toward nucleus

Chemotaxis

movement of a motile cell or organism, or part of one, in a direction corresponding to a gradient of increasing or decreasing concentration of a particular substance.

Electrophoresis

movement of charge particles in a fluid/gel under the influence of an electric field

Quaternary (4) Structure

multiple polypeptide chains, same interactions as tertiary

Specialization

multiple special adaptations within a species, such that you get multiple organisms of the same species who can fulfill different roles and niches within the same ecosystem.

Obligate aerobe

must have oxygen for growth

frameshift mutation

mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide, dramatic effects.

Catalyzed movement

need a catalyst (protein), used ATP, protein is called a flippase Floppase also used ATP to bring phospholipid from inner leaflet to the outer leaflet

Saturated fatty acids

no double bonds, solid at room temperature, higher melting point, maximum hydrogens

delta G naught > 0 (positive)

non spontaneous

operator site of operon

non transcribable region of DNA capable of binding a repressor protein

G0

non-growing state, more protein production takes place here

Nucleolus

non-membrane bound area in nucleus. Transcribes rRNA and assembled ribosomal subunits.

Isoleucine (Ile, L)

non-polar

Valine (Val, V)

non-polar, aliphatic

Alanine (Ala, A)

non-polar, ambivalent

Methionine (Met, M)

non-polar, start codon (AUG) transcripts methionine

Phenylalanine (The, F)

nonpolar, aromatic

Tryptophan (Trp, W)

nonpolar, aromatic

Cofactors

nonprotein enzyme helpers, ex. Fe+ to stabilize/hold substrate, also include K+, Mg2+

Inducing reaction to more forward

note: Adding or removing solids or liquids at equilibrium doesn't do anything that will knock the system off its equilibrium. Can only alter aq.

Telophase

nuclear membrane forms, chromosomes decondense, cytokinesis continues

Nucleotides

nucleoside linked to phosphate group, basic structural unit of nucleic acids such as DNA

single copy DNA

nucleotide sequences represented by only one copy of a nucleotide sequence and are associated with regions of euchromatin (DNA prevalence tin cells that are active in transcription) that are being actively transcribed

nonhistone proteins

numerous nuclear proteins generally involved in controlling the activity of specific regions of the DNA

Commensalistic

one benefits while the other has no effect

Induction

one group of cells changing the behavior of an adjacent group of cells mechanisms: physical touching of cells or by releasing chemicals

Galactose

one of the monomers that make of lactose, less sweet than glucose (its epimer, differing at C4).

gene repression in bacteria

operans have a binding site for regulatory proteins that turn expression of the operon "up" or "down."

Peroxisomes

organelles that collect peroxides. -vesicles in cytosol involved in production + breakdown of hydrogen peroxide. -also involved in lipid + protein storage, detoxification, and regulation of oxygen concentration -essential for lipid breakdown, detoxification of drugs and chemicals in liver -prevent damage from oxygen radicals

Coenzymes

organic cofactors, loosely bound to enzyme, carriers to the enzymes. Ex. vitamins, biotin, NADH

Facultative anaerobe

organism that can survive with or without oxygen -doesn't need oxygen for growth, but grows better with oxygen

Peripheral membrane proteins

outside and and inside surfaced of membranes, attached either to integral proteins or phospholipids. Do not stick into the hydrophobic core of the membrane (more loosely attached).

Tertiary (3) Structure

overall 3D shape of a polypeptide

Cerebrum

processes and interprets sensory information. Impose higher level meaning on this information. Top down influence

Translational error mutation

produces a polypeptide with one or more incorrect amino acids

Transcription error mutation

produces an incorrect mRNA transcript which may be overcome by the volume of mRNA produced for a given round of gene expression.

group selection

proposed mechanism of evolution in which natural selection acts at the level of the group, instead of at the more conventional level of the individual. Argues on the basis of mathematical models that individuals would not altruistically sacrifice fitness for the sake of the group. Then benefit outweighs the cost, altruistic behavior is selected for.

Histones

protein molecules around which DNA is tightly coiled in chromatin

Selection by differential reproduction

refers to unequal capacities for individuals of a population to reproduce due to trait variation. individuals who produce more viable offspring are selected for. Individuals who reproduce less viable offspring are selected against.

DNA binding proteins

proteins that bind to regions of nuclear DNA near genes and directly switch these genes on or off

initiation factors

proteins that bind to ribosomal small subunit and mRNA that bring components together in the correct positions to start translation

Flavoproteins

proteins that contain a nucleic acid derivative of riboflavin: the Flavin adenine dinucleotide (FAD) or flavin mononucleotide (FMN) -involvement as a cofactor gives the molecules a regulatory role. -located on matrix face of inner mitochondrial membrane.

Cell theory impact on Biology

proved that cells were the basic structural, functional, and biological unit of life and cells come from preexisting cells

Promoter site of operon

provides a place for RNA polymerase to bind

DNA hybridization

refers to a molecular biology technique that measures the degree of genetic similarity between pools of DNA sequences. It is usually used to determine the genetic distance between two organisms

termination factor

release factor; in translation; no tRNA matches up with stop codon; everything dissociates

Sex Determiniation

relies on inheritance from a female's XX of an X chromosomes and inheritance from a male's XY genotype of either X or Y chromosome, thus making the selection of sex chromosome in the male gamete the deciding factor.

Silencers

repressor proteins that may bind to DNA sequences and inhibit the start of transcription

Outbreeding

reproduction among distantly or unrelated individuals, improves changes of genetic diversity and protects against the widespread increase in recessive disorders within a population. Increases heterozygosity.

Single crossovers

results in genetic recombination. The chromatids involved in this single crossover exchange alleles at a given locus. Results in 2/4 recombinants. Will switch out all alleles downstream from the point of crossover.

Intermediate filaments

role in support -not as flexible as microfilaments and microtubules -primarily used for structural rigidity Keratin = intermediate filament

Exocytosis

same as endocytosis but backwards

Glycogen

same as starch, but with additional alpha 1-6 linkages for branching, storage of glucose in muscles

Beta turns

secondary structure that causes changes in direction of polypeptide chain (mostly glycine and proline)

Bile

secreted by liver into the small intestine. Breaks up fat molecules into small pieces, increasing surface area for which lipase enzymes can act upon them.

Mitochondria

self-replication, have own DNA and ribosomes, different from host in both structure + sequence. replicate independently from the cell containing the mitochondria, do not share same genome with host. All serve to support the endosymbiosis theory. Inner membrane = surrounds matrix Folds of inner membrane make up the cristae.

Absorptive metabolic state

series of metabolic reactions that your body does when food is in plenty

Okazaki fragments

short sequences of DNA nucleotides that are synthesized discontinuously and later linked together by the enzyme ligase.

Monosaccharides

simple sugars (CH2O)n sugars are names according to their number of carbons 3 = trioses 5 = pentoses 6 = hexoses -Ribose is an aldopentose that forms a five member ring and is important for the synthesis of nucleic acids.

Anaphase

sister chromatids pulled apart, cytokinesis begins

Co-dominance

situation in which both alleles of a gene contribute to the phenotype of the organism

Muscle

skeletal, smooth, and cardiac muscles

epithelial tissue

skin, lining of organs

Gap junctions

small tunnels connecting cells. Action potentials, small molecules, ions can propagate through them. Present in cardiac and smooth muscle =to allow rapid spread of depolarization.

Hormone types

small, hydrophobic = cross membrane, act on transcription usually, cause the increase of membrane/target proteins in a cell Large, lipophobic = binds to receptor on cell membrane, could cause activation of second messenger which kicks off chemical cascade Same signaling molecules can have different effects depending on cell location.

small nuclear proteins (snRNP)

snRNAs combined with proteins, form a spliceosome.

Positive control in bacteria

some regulatory proteins are activators. When an activator is bound to its DNA binding site, it increases transcription of the. operon (by helping RNA polymerase bind to the promoter)

Existence of regenerative capacity in various species

some systems (skin, liver, and blood) have multipotent stem cells which can regenerate these systems as needed (since these systems are injured or lost often)

Mutagens

something that causes a mutation

Carcinogen

something that causes a mutation that cause cancer. They are almost always mutations except some direct mitogens = increase mitosis. subclass of mutagens.

Inborn errors of metabolism

specific class of inherited mutations that affect important metabolic enzymes.

Cocci

spherical bacteria

Spirilli

spiral shaped bacteria

Adipose cells

store fat, small nuclei. Biggest absorber of fatty acids. Turn them into triglycerides. Glucagon signal adipose cells to release all of their fatty acids into bloodstream. They are hydrophobic, so the body allows these free fatty acids to travel in and alongside large proteins in the blood called albumin, which are made by the liver.

Prions

sub viral particle -no genetic material, only made of proteins -tends to be beta sheet, when beta sheet comes in contact with alpha helix, it will change the alpha to beta sheet. As more and more become beta sheets, this creates protein deposits. -this happens somewhere in the brain, normal cleanup still happen. This leaves huge holes in your brain as the proteins are removed causing disease.

Viroids

sub viral particle -smaller than viruses -made only of a single strand of circular RNA -originally, found to only infect plants, but found today to infect humans too such as Hepatitis D -thought to be catalytic RNA, meaning it can make of break covalent bonds, it can self-cleave to create more viroids. Done confuse with visions which are whole viruses.

From Fischer notation to chair representations of Haworth projections

substituents on the left of the chain appear on the top of the ring, -OH group on anomeric carbon (Fischer carbonyl) can be either Up (beta) or down (alpha) -CH2OH group on carbon 5 points up for D, down for L

Anomers

subtype of epimers that differ at the anomeric carbon

Fructose

sugar in fruits, sweeter than glucose -forms furanose when carbon 5 attacks carbonyl carbon

Furanose

sugars in a 5 membered ring structure = pentagonal shape

Pyranose

sugars in a 6 membered right structure = hexagonal shape

Ketose

sugars with a ketone group

Aldose

sugars with an aldehyde group

Carbohydrates

sugars, monosaccharides, disaccharides, polysaccharides

Synapsis or crossing-over mechanism for increasing genetic diversity

synapsis and crossing over help increase genetic diversity (genes recombine and create larger diversity in number of recombinants).

DNA polymerase III

synthesizes new DNA only in the 5' to 3' direction, requires ATP

Q = K

system is at equilibrium

constancy perception

tendency to perceive an object you are familiar with as having a constant shape, size, and brightness despite the stimuli changes that occur

depth perception

the ability to see objects in three dimensions although the images that strike the retina are two-dimensional; allows us to judge distance

catalysis

the acceleration of a chemical reaction by a catalyst

Polyadenylation

the addition of multiple adenine nucleotides to the 3' end of a newly synthesized mRNA molecule, protects mRNA from enzymatic degradation in the cytoplasm and aids in transcription, termination, export of the mRNA from the nucleus, and translation.

Ketone bodies

the by-products of the incomplete breakdown of fat. Many of the tissues in our body that rely exclusively on glucose for the production of energy are more flexible during starvation (fasting). Start using different fuel source after several days called Ketones. Ketones are effective, unlike fatty acids, because they are water soluble enough to cross the blood-brain barrier and allow us to produce ATP in times of starvation. Acetyl-coA produces ketones inside liver. They then leaves, go into the bloodstream, and other tissues like the brain can take out the ketones, convert them back into Acetyl-CoA, which can enter the Krebs cycle and contribute to the production of ATP.

Wild-type

the phenotype for a character most commonly observed in natural populations

form perception

the process by which sensations are organized into meaningful shapes and patterns

motion perception

the process of inferring the speed and direction of elements in a scene based on visual, vestibular and proprioceptive inputs.

Equilibrium constant (Keq)

the ratio of product concentrations to reactant concentrations at equilibrium, with each concentration raised to a power equal to the number of moles of that substance in the balanced chemical equation

Membrane potential

the resting potential of the cell membrane is negative because of the sodium/potassium pump

Cyclization

the ring formation of carbohydrates form their straight-chain form. -formed by nucleophilic attack by one of the hydroxyls on the carbonyl carbon, which can occur on either face of the carbonyl, producing two possible outcomes (anomers)

gene linkage

the tendency of DNA sequences that are close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction

phosphoryl group transfers

the transfer of a high-energy phosphate group from ATP to another molecule. critical biological important for also creating energy currency of ATP.

Half reactions

the two parts of an oxidation-reduction reaction, one representing oxidation, the other reduction

degenerate code

there are more codons (64) than there are amino acids to be coded, so most amino acids are coded by more than one code.

Diffusion

thermodynamically spontaneous process -movement of solutes from higher concentration to Lowe concentration, creates a negative free energy change (Delta G) -Increases the entropy of a system and decreases the free energy -chemical concentration gradient and electrical gradient dictate direction of diffusion

role of ribosomes

these organelles use the sequence of codons in mRNA to assemble amino acids into polypeptide chains

Membrane receptors

transmit signals from the extracellular space into cytoplasm. Ligand=hormones and neurotransmitters that require membrane receptors to cross the plasma membrane. The binding of membrane receptors triggers production of second messengers.

Connective tissue cells

two components 1. cells 2. matrix (made out of ground substance and/or fibers) Extracellular matrix: molecular network that holds tissue cells in place. Fibroblasts secrete fibrous proteins that make the matrix Consistency, rigidity of matrix varies from cell to cell. 3 classes of molecules making up animal cell matrixes: 1. Glycosaminoglycans and proteoglycans: provide flexibility (elasticity) to matrix 2. structural proteins: provide strength 3. Adhesion: help individual cells within tissues to stick together

Chromatid

two identical copies of a chromosome, joined together by a centromere

Disaccharides

two monosaccharides linked together via dehydration (condensation) reaction. -hydroxyl group of one sugar combines with hydrogen of another, releasing molecule of water, forming covalent bond known as glycosidic linkage

tRNA (transfer RNA)

type of RNA molecule that transfers amino acids to ribosomes during protein synthesis. Matches anticodon to codon on mRNA.

rRNA (ribosomal RNA)

type of RNA that combines with proteins to form ribosomes

Centimorgen (cM)

unit of measurement we use to measure distance off a chromosome (or genetic map unit)

SDS-Page

uses charge, but based on size

Pentose phosphate pathway

uses glucose-6-phosphate (from glycolysis or other methods) to make ribose 5-phosphate, used to make DNA and RNA also makes NADPH, which help with building other molecules in cytosol Key enzyme: Glucose-6-phosphate dehydrogenase

Michaelis-Menten equation

v = (vmax [S])/(Km + [S])