BIO 181: Final Exam Review

Where are acids on the pH scale?

0-7

Parts of a triglyceride

1 glycerol (3 carbon molecule with hydrogen and hydroxyl groups) and 3 fatty acids/hydrocarbon chain (monomers)

What is the function of the EMC in animal cells?

1 provides structural support for the cell 2. Helps the cell stick together 3. Special: allows protein to protein attachments that link ECM to cells cytoskeleton

Which experiments proved that DNA was the building block of hereditary information?

1. 1928 - Griffith 2. 1940s - Avery, MacLeod, McCarty 3. 1940s - Hershey and Chase

What are are amino acid monomers made of?

1. A central carbon atom (alpha carbon) 2. Amine group (NH2) 3. Carboxylic acid group (COOH) 4. Hydrogen atom 5. Variable side chain (R group) All covalent bonds

What two things does active transport require?

1. ATP as energy 2. Protein pumps •transmembrane proteins that hydrolyze ATP and move material across the membrane

What does cell theory state?

1. All organisms are made of cells 2. All cells come from preexisting cells

What two pieces are photosystems composed of?

1. Antenna complex 2. Reaction center

What are the two important regions on tRNA?

1. Anticodon •located at the bottom of the molecule •function is to decode a codon -used complementary base pairing -tRNA complementary base pairs with mRNA (forms hydrogen bonds) -this anticodon is the three letters that are actually corresponding directly to the amino acid =decoding of this is done at the opposite side of molecule 2. Acceptor stem •an amino acid will be bound to this end •will always be a CCA sequence at the 3' end

What were the two competing hypothesis for heredity in 1800's (just name)? What did they try to explain?

1. Blending hypothesis 2. Acquired characteristics hypothesis •tried to explain exactly why offspring resembled their parents

Which of the 3 main macromolecules do cell use for metabolic pathways? (In order form most to least common)

1. Carbohydrates •readily available energy source 2. Fats •carbs lacking 3. Proteins •fat and carbs lacking

What are the two main functions of ribosomes? What is it composed of?

1. Catalyze the synthesis of polypeptide bonds between the newly synthesized amino acids 2. House the tRNA for the transcription process to take place Composed of small and large subunits

What the anatomy behind the ATP synthase (3 major parts)? Also mention function

1. F0 unit •the part that integrates itself within the membrane •allows the H+ ions to flow 2. F1 unit •called the head/knob •faces into the mitochondrial matrix •this makes the ATP 3. Stalk •connects F1 and F0 pieces

What was the background knowledge that led to Beadle and Tatums experiments and further on?

1. Gregor Mendel proved that an organism phenotype was caused by the HM passed down by its parents 2. This hereditary material was sorted into units called genes 3. Avery and Hershey found that hereditary material is DNA molecule =now need the link between DNA as the genotype and protein as the phenotype

What was the outline of Griffith's experiment? What happened at each step?

1. Griffith injected the mice with R strain bacteria •mice lived because they did not cause disease (benign) 2. Injected mice with S strain bacteria •mice died from pneumonia (virulent) =confirmed that S strain will cause disease 3. Heated the bacteria and killed the S strain cells and injected it into mice •killed the cells (rendered inactive) and the mice lived (confined that bacteria is what kills the mice) 4. Mixed R strain with heat-killed S strain and injected in mice •the mice died (but should have lived since neither killed the mice)

What are the steps of DNA replication? (Stepwise process) Use enzymes

1. Helicase (opens up the strands of the double helix) 2. Single-stranded binding proteins (keep the strands from re-zippering) 3. Topoisomerases (prevent the double helix from knotting) 4. Primase (lays down the RNA strand) 5. DNA polymerase III (build the new DNA strand off of the primer) 6. DNA polymerase I (removes the primers and adds the complementary bases) 7. DNA ligase (creates bonds to finish the strands)

What were the questions researchers needed answers to after DNA was found to be the hereditary material?

1. How does an organisms genotype (DNA) specify its phenotype 2. Is there a link between genes made of DNA as enzymes made up of protein

What are the two overall phases of mitosis? What occurs in each?

1. Karyokinesis (happens first) •the genetic material in the form of chromosomes (duplicates) separate -go to either side of the cell 2. Cytokinesis (happens second) •physical splitting of the cytoplasm and membrane •produces two separate distinct cells

What are the two subcategories of photosynthesis?

1. Light dependent reactions •directly needs sunlight 2. Light independent creations •does not occur only in night time, it just doesn't directly need sunlight

Where can ribosomes be found? Why are they found here?

1. Many are found in the cytosol (fluid part of cytoplasms) all over the cell 2. The rest are attached to the outer surface of the rough ER (outer nuclear membrane) =they are all over the cell so protein can be distribute to all parts of the cell that need it (it's that important)

What is the very first step which includes both activated carriers of the ETC?

1. NADH donates its electron to a flavin containing protein at the start of the chain (complex 1) •it directly produces H+ ion gradient 2. FADH2 donates its electron to an iron-sulfur protein (complex 2) •indirectly produces gradient by first passing electron to ubiquinone

How do the subunits of a photosystems capture light?

1. Red or blue photon strikes chlorophyll molecule in antenna complex 2. Chlorophyll absorbs photons light —-> exciting one electron 3. Chlorophyll passes energy (not electron) to nearby pigment molecule 4. Another Electron is excited in response

What are the two key differences between replication and transcription?

1. Replication synthesized entire chromosomes from the DNA templates •transcription synthesizes copies of genes (only segments) 2. Replication has two template strands •transcription only has one strand, making only one template strand

How do cells know how to stop replicating?

1. Resource limitation -would cause a lack of food -replication slows down b/c of lack of nutrition

How does the primary structure of RNA differ from DNA?

1. Ribose vs deoxyribose 2. Uracil vs Thymine

What were the three predictions created by Meselson-Stahl in their experiment?

1. Semi conservative model •generation 0 has all 15N •generation 1 has each helix made of old and new strand •generation 2 has 1/2 the helixes with low density, 1/2 with new medium density 2. Conservative model •generation 1, two helixes, one totally light one totally heavy •generation 2, 1/4 high density, 3/4 low density 3. Dispersive •generation 1, hybrids •generation 2, all intermediate densities =different distributions in the second generation was used to conclude the results

What is the process of the initiation phase of transcription?

1. Sigma opens up the DNA double helix •the template strand is threshed through the RNA pol active sight 2. Incoming NTP pairs with complementary base on the DNA template with the help of core enzyme 3. Sigma is no longer needed and dissociates from the core enzymes once initiation is completed

What are the two primary components of DNA? What are at the end?

1. Sugar-phosphate backbone (3'5' linkage) 2. Series nitrogen-consisting basis that project into the middle of the molecule •one end has exposed 3' hydroxyl group •one end has exposed 5' hydroxyl group

What are the two major differences (and points of importance) between mitosis and Meiosis I?

1. Tetrads are formed in prophase I by linking homologous chromosomes •this allows crossing over to occur 2. Metaphase •in mitosis, individual chromosomes align at the metaphase plate (single file) •in meiosis, homologous pairs align at the metaphase plate (2 by 2)

What are the first major step of the Krebs cycle?

1. The 2 carbon acetyl CoA group is bonded go a 4 carbon oxaloacetate •this creates a 6 carbon molecule called citrate (first molecule produced in Krebs cycle) =makes sense that carbon dioxide is formed each cycle because it's turning from hexose to a 4 carbon molecule

How can the structure of a eukaryotic cell be used to infer its functions?

1. The shape of organelles membranes and enzymes it contains = function •high surface area vs low surface area, proteins have specific functions 2. Type , size and # of organelles in cell =function •lots of mitochondria in muscle for energy, lots of Rough ER in pancreas to produce enzymes

What are two challenges arise from opening the double helix and exposing each strand? (2 broad)

1. The strands could easily form back together directly after the helicase pases and prevent synthesis 2. As helicase unzips the strands, the double helix side will tend to coil tightly (supercoiling) which disrupts function

Why are the chromosomes lined up in metaphase? (2)

1. To keep track of all the copies •a form of organization to keep the process error free 2. In anaphase, all sister chromatids migrate an equal distance to travel •one is not closer or farther away from the poles of the cell

Why does the cell elongate in telophase?

1. To make the cell splitting process easier •more room for the cell to pinch into two 2. To make sure both nuclei will be in two separate daughter cells and not caught inbetween (copies in every daughter cell)

What two rules did Erwin Chargraff establish for DNA?

1. Total # purines = pyrimidines 2. #'s A = T; C = G

Since the semiconservative model was correct, what are the two broad steps of DNA replication?

1. Two strands of the double helix will be separated •nitrogenous based are exposed -can function as a template 2. Following principle of complementary bases, new strand is synthesized against template •hydrogen bonding allows this to occur, phosphodiester linkages allows the new strand to form a backbone =generated two new double helixes •each is made up of one old strand and one newly synthesized strand

What two questions did researchers ask after DNA was found to be HM?

1. What mechanism allows simple primary and secondary structure of DNA hold information? •how can it tell the cell how to make proteins and what to do? 2. how is the information synthesized/copies to get passed without error from one cell/generation to the next one? •how does the hereditary particles maintain integrity (Mendel)

What do all metabolic processes depend on? How are these things created? What is the implication?

1.Enzymes 2. Enzymes are genetically encoded by the DNA in cells 3. Metabolic pathways are genetically determined features of cells •cell must be genetically predispositioned to do fermentation or CR -human cells can do both, but many organisms cannot do so

What is the path of electron transfer in the ETC?

1.First NADH donates electron to complex 1 (FMN) At the same time, FADH2 donates electrons to complex II (FeS) 2. both give their electron to ubiquinone (Q) -delivers it to complex 3 3. Complex three gives electrons to cytochrome c -who gives to complex 4 5. Complex 4 gives the electrons to oxygen which creates water molecules

How many copies of chromosomes to each multicellular eukaryote possess (in terms of somatic cells)? What is this called?

2 copies of every chromosome within the somatic cells •called diploid condition (2n)

In molecular geometry, what does each line represent?

2 electrons/electron pair

What do phospholipids consist of?

2 fatty acid chain connected to glycerol connected to a phosphate group (PO4^3-)

What insight comes from knowing NADH and FADH2 are cofactors?

2 main insights 1. They fully participate in allowing the enzyme to bind to the substrate (function) 2. Participates in the catalysis and energy exchange processes (Enzyme is Costco, shopping cart is NAD)

What comes out of glycolysis? (Broad)

2 pyruvate, 2 ATP, 2 NADH •pyruvate is a three carbon molecule (triose) •high energy molecule and 2 activated carriers

What types of grooves does DNA have?

2 types •major grooves •minor grooves Differ in size and provide access to nucleotide bases

How are individuals connected in pedigrees?

2 ways: generational and relationship lines •generational lines are vertical -used for parents to children •relationship lines are horizontal -used for siblings or mating partners (biology, not social contract like marriage)

How many amino acids found in most living organisms? How do they differ?

20 amino acids make up all the proteins •differ in the structure of side chain (R group)

How many primary checkpoints occur in the cell cycle? Which one does MPF control?

3 primary ones -G1, G2, M •MPF confirm the G2 phase checkpoint

What is the optimal temperature for enzyme activity in humans?

37*C or 98.6*F

How many steps are involved when receptors bind to hormones? What are they?

4 steps 1. Signal reception 2. Single processing 3. Signal response 4. Signal deactivation (very important)

How many leaflets on a mitochondria/chloroplast?

4 total leaflets-two total lipid bilayer membranes •inner bilayer •outer bilayer =Inter membrane space Therefore, water is in outside in cytosol, in the intermembrane space, and inside the cell

How many amino acids were predicted by Galows codons? How is this explained in a table?

64 amino acid combinations could be predicted by the triplet codon •too many, there are extras This leads to several properties of the genetic code •characteristics appear =predictive, start/stop codon, redundant, universal

What is the reaction for photosynthesis?

6CO2 + 6H2O ------> C6H12O6 + 6O2 •oxygen is a byproduct This is the exact reverse of cellular respiration

What happens a pea seed is planted? And once mature?

7-10 days it will germinate and produce a new plant (organism) •contains genetics from two parents -occurs during fertilization event Once mature it produces both sperm and egg cells •can be used to fertilize and produce new zygote (packaged in new seed) -new seed for through mitosis to become new offspring

Where are bases on the pH scale?

8-14

What is copied during transcription? (Vs what's not copied)

A DNA gene is used to make an RNA photocopy •this photocopy is called messenger RNA (mRNA) -intermediary between DNA and protein = central dogma Just copying region of chromosome •not the entire chromosome

Cis unsaturated fatty acid shape

A bent or V shape

Polar covalent bond example

A bond is formed between potassium and fluorine atoms •fluorine atom has a stronger pull on the electrons and thus has a partial negative charge •potassium has less of a pull on the electrons and thus has a partially positive charge

Ketone group

A chemical group consisting of a carbon double bonded to oxygen (must be in middle of chain) •sugar

What would occur if the chromosomes were not lined up in metaphase?

A chromosome could be found closer to one spindle fibers than the other •one sister chromatid has to travel a much longer distance than another chromatid (very short distance) -everything is timed in mitosis (constant process), chromatid may not make it the entire way across before telophase/cytokinesis begins =called non-disjunction •chromosomes are missegrageted •some daughter cells has extra copies of chromosomes while another is missing

What is cancer? What is it causes by?

A complex family of diseases that affects humans and animals •causes by cells that grow uncontrollably (these cells are damaged in some way) -invade other tissues and spread to other sites of body

What occurs in splicing?

A complex protein called the spliceosome does this action of removing introns •made of small nuclear ribonucleao-proteins (snRPs) =consist of 145 difft RNA and protein components •mature mRNA does not have any introns This is done is a type of lasso formation —> see slide for details

What does an alpha linkages (1-4) look like in a polysaccharide?

A downward V shape with oxygen bonded in the middle •on the opposite side of carbon 6

What is light? What are it's forms?

A form of energy called electromagnetic radiation •exists as both a particle and wave

What should the left side of an polypeptide possess? What is it called?

A free amine group (NH3+/NH2) •N terminus

What should the right side of the polypeptide possess? What is it called?

A free carboxylic acid group (COO-/COOH) •C terminus

What is an enzyme?

A fully folded protein which catalyzes a specific chemical reaction

What are homozygous genotypes? What happens when they go through segregation?

A genotype in which both alleles are identical •considered true breeding -only have 1 type of gamete to contribute in meiosis -all gametes will have exact same genetic information for trait

What is it called when glucose and fructose bond?

A glucose/fructose disaccharide = sucrose (table sugar)

Solution

A homogeneous mixture of two or more substances

How are individuals have are deceased represented by a pedigree?

A line is slashed through the shape

What is produced when 3 fatty acids combine with glycerol?

A lipid and 3 water molecules

How many net ATP molecules can be made out of glucose?

A maximum yield of around 30 ATP

Neils Bohr's model of an atom

A model that places an atoms electrons into a series of concentric shells surrounding the nucleus

ampipathic

A molecule that has a both a hydrophilic (polar) region and a hydrophobic (nonpolar) region

What are the two parts what theories in biology usually consist of?

A pattern and a process

How is the investment phase portrayed in an image during glycolysis? What about payoff?

A phosphate group is broken from ATP and bonds to the glucose molecule •it carries with it electrons which are energy -chemical potential energy Payoff is when phosphate is phosphate group leaving molecule and forming bond either ADP •more ATP formed then lost in beginning

How do photons effect the electron shells?

A photon can boost an electron in to a higher shell, this excited state electron is unstable and returns to its ground state by releasing a photon of light

What do most cells posses that functions as protect from extracellular environment?

A protective layer or wall

How many steps of glycolysis? What is it's environmental condition?

A series of 10 steps of chemical reaction •does not require oxygen so considered anaerobic

What is seen with pyrimidines?

A single six membered/carbon ring •based included: cytosine, uracil, and thymine (U only for RNA, T only for DNA)

Aquaporins

A transport protein (channel) in the plasma membrane of a plant or animal cell that specifically facilitates the diffusion of water across the membrane

What was George Beadles and Edward Tatums model organism? What did they study from it?

A type of bread mold called Neurospora ceases •they studied gene function by making genetic mutations in the mold -Beatle said that by breaking genes, one can determine their function (whatever function was missing in the cells) -this was the reason behind creating mutations

Phagocytosis

A type of endocytosis in which a cell engulfs large particles or whole cells

Pinocytosis

A type of endocytosis in which the cell ingests extracellular fluid and its dissolved solutes

facilitated diffusion

A type of passive transport where materials who which would not normally be able to cross the cell membrane can cross •large polar molecules and ions can't cross •with the assist of membrane proteins they can cross •movement from high to low concentration gradient, no energy needed! -decreases charge and concentration difference

What is the meaning it an ice-cream scoop tumors?

A way to describe benign tumors •surgically extract them with high success rate -can actually open a body and scoop the cells away from the other tissue (comes out easily)

Because monosaccharides can form a wide variety of structures/configuration, it perform...

A wide variety it functions •building blocks in the synthesis of other molecules •indicate cell identity •store chemical energy •provide cells with fibrous structural material

What base pairs are found in DNA?

A-T, C-G

What occurs in the A site? P site? E site?

A: Acceptor site for an aminoacyl tRNA (in other words adds in the amino acid) P: peptide bond forms after amino Acid is added E: tRNA exits ribosome after donating amino acid to the chain •holds the tRNA =during translation, all 3 sights contain tRNA bound at their anticodon to the complementary codons on the mRNA transcript •large subunit of ribosome does the catalysis of proteins to make enzymes

In glycolysis, what must be present to from ATP? (Other than glucose)

ADP needs to be present in order to accept the third phosphate molecule and become ATP (Empty shopping cart being filled up)

What is the primary activated carrier in cells? What is it's original form?

ATP (tri) •original form was ADP (di), so ATP is the "activated" form

What are the major players in feedback inhibition of glycolysis? Why this a good place to stop?

ATP molecules are used to inhibit the process of glycolysis •comes into contact with the enzyme phosphofructokinase Regulation point is critical due to the product of the enzyme only able to be used in glycolysis

Mitochondria function

ATP production •inner membrane (cristae) holds place for ATP synthesis •matrix has enzymes for metabolism

What protein regenerates ATP? How does it do this?

ATP synthase creates ATP •it acts as a facilitated carrier by allowing hydrogen ions to enter and leave the other side •this releases the potential energy built up in the gradient which is harnessed by synthase =it uses that energy to bind a phosphate group to ADP —-> ATP

What is the cycle between ATP and NAD? What is there difference?

ATP: constantly being used by the cell and needs to be recharged after being used •can be seen in the formation of ATP from ADP + Pi and vice verse NAD: not used as much by the cell and it is less common to see if being regenerated •NADH being formed from NAD+ and a hydrogen atom =importance is that both ADP and NAD+ are needed to conduct glycolysis (regeneration is a must)

Knowing how important the exact sequence of letter are, what occurs when a single base pair is changed?

According to central dogma: 1. DNA as the information storage sight has an error in the code •that error is present as a base pair change 2. RNA photocopies the mistake and transports the information to a ribosome •same mistake persists along the proceed 3. Altered RNA sequence causes a polypeptide with different amino acid sequence than intended •a difference in structure= difference in function -altered polypeptide structure will cause an altered polypeptide function

Example: how can a lung cancer be found among liver cells?

According to metastasis: •the original tumor cells can travel through the bloodstream to other areas =the lung cancer cells traveled along the stream and were deposited in the liver •lung cancer cells are now growing in the liver (creation of lung tumor on the liver)

What goes into the Krebs cycle? What comes out of it?

Acetyl CoA goes into it NADH + FADH2 comes out •comes out because goes into the next process (fuel ETC) Also: ATP and CO2

What is the last step in alcoholic fermentation? What is produced?

Acetylaldehyde is reduced/picks up electrons from NADH •NAD+ is formed •ethanol is a byproduct (alcohol)

What happens when acids interact with biological molecules (proteins and lipids)?

Acids are capable of adding hydrogen ions

How do animals, fungi and slime molds conduct cytokinesis (broad)?

Actin filaments and myosin motors are the major players •filaments form a ring in the cell and constrict the cell in half -creates a pinched structure in membrane called cleavage furrow

How does a cell know (after interphase) that it is time to enter mitosis and divide? (Specific player)

Activated protein complex called mitosis-promoting factor (MPF) •located in cytoplasm -if cells have this on cytoplasm —> undergo mitosis -it cells don't have this —-> mitosis will not happen

Beta glucose when consumed...

Acts like fiber and causes someone to have great poops

This facilitates capillary action within thin tubes between water molecules and other materials

Adhesion (when water pulls on glass to make the U shape)

To pass the G1 checkpoint, 5 different players must be present and working together? How is this beneficial for the cell? How is this disadvantageous?

Advantage: •allows for fine tuning controls of regulation (functionality) -necessary for such advanced/organized organisms Disadvantage: •if any one of the 5 players are mutated/defective, the entire checkpoint will become useless •example of misregulation of social control =causes cancer •so many regulatory complexes in G1, and also G2 and M checkpoints -so many opportunities for a mistake to cause cancer -also causes each cancer to be unique

What prevents DNA strands from reannealing to form a double helix?

After the helicase passes over, the hydrogen bonds remain broken but they could be formed again •still complementary and antiparallel to each other Single-stranded DNA binding proteins prevent this from happening •bind to exposed single stranded DNA within the bubble -keep strands from zippering back together

Where is the difference between CR and fermentation in the process of sugar breakdown? What is the major difference?

After the step of glycolysis •cellular respiration is aerobic -the electron carrier oxygen is present -extracts as much energy as possible •fermentation is anaerobic -oxygen is absent in the process -can only produce a little energy

How does crossing over occur?

After the synaptonemal complex has been formed, complex proteins will form along locations (could be many) of the synapsed homologs •this allows chromosome segments to be swapped b/w non-sister chromatids

Which cells use aerobic respiration?

All eukaryotes and some prokaryotes (others use anaerobic respiration)

How are the all DNA polymerases related? How does this pose problems?

All evolutionarily related because can only add new nucleotides to existing 3' OH groups •addition of nucleotide to free hydroxyl group on existing chain -must be available in order to add nucleotides -active site requires that structure 3' designate the end of a strand and 5' is the start •DNA synthesis always goes in 5' to 3' direction =polymerase can't begin the process of strand replication because no free hydroxyl group exists, the strand itself doesn't exist yet •needs a starting point to provide chemistry

Which component of the ETC is the lone different molecule? What is it's name?

All proteins are integral or peripheral and are embedded except one •it moves throughout the hydrophobic core of the lipid bilayer membrane -nonpolar, lip-soluble ubiquinone (Q)

What are different versions of genes for the same trait called? What is their importance?

Alleles •responsible for phenotypic variation in the traits

What is the structure of carotenoids? Examples of other accessory pigments?

Almost entirely hydrophobic Also called accessory pigments Mainly just a hydrocarbon chain attached to two "heads" on either side •xanthophylls and phycobilins

C-OH in a down orientation called...

Alpha glucose

What occurs in early prophase I?

Already know: •chromosomes condense half way •nuclear envelope begins to break down •spindles begins to develop from centrosomes New: •homologous chromosomes (duplicated sister chromatids in each) pair up -called synapsis (not just random line up)

Condensation reaction

Also known as dehydration synthesis •process of joining monomers to monomers or monomer to polymers or polymers to polymers •each reaction yields a single molecule of water (water is generated but at the same time lost)

What does the backbone of a nucleic acid consist of?

Alternating sugar and phosphate groups •nitrogenous bases jut out from the backbone

According to the energy diagrams, reactions are spontaneous... so why enzymes?

Although it may appear that way, there is an energy barrier in both the endergonic and exergonic processes •enzymes function in lowering this activation energy barrier -seen as speeding it up and more likely to happen

Knowing one half of the new strand is lagging and the other is leading, how will it appear? (In chunks?)

Although it may seem to contain Okazaki fragments, the new strand will be one continuous strand with no gaps or chunks in between (Thanks to ligase)

Why doesn't starch dissolve in water?

Although it's hydrophilic, it's a huge molecule and water cannot break the bonds

benzene ring (phenyl) (how to interpret)

Although not labeled, it is solely made up of carbon and hydrogen •Each point represents a carbon atom •each line represents a covalent bond •parallel lines are double bonds •every bonding position necessary to make carbon full is taken up by a hydrogen

What structures to bacteria form when interacting with each other? What is it?

Although unicellular, bacteria live and communicate together to create Biofilms •it is complex but not a tissue -not as organized and not same functional relevance •acquires new properties that bacteria cells alone do not possess

Macromolecule: Proteins Monomer: Function: Example:

Amino acid Enzymes, structural material, peptides Hair

How can the transition state help explain catalysis?

Amino acid side chains are present in the active site, they from bonds with the substrate •these are shirt lived covalent bonds and non covalent interactions -in the transition state, these bonds assist with the transfer of electrons/atoms for product formation

What are the monomers of proteins?

Amino acids

Which molecule caused a positive charge on an amino acid? What does this mean in terms of Ph?

Amino group (NH3) causes a positive charge (R group) •it becomes more basic/alkaline

Integral membrane proteins structure

Amphipathic (both water loving and water repelling sides) •span the entire lipid bilayer -two polar sides facing intra/extra cellular -nonpolar áreas inside the space

What is a liposome and what is it's importance?

An artificially created membrane bound vesicles •contains the lipid bilayer and mimics membranes found in cells Used in experiments to find it and how the lipid bilayer is permeable (Different from micelle; water can be on inside and outside)

Adhesion

An attraction between molecules of different substances

What does the principe of segregation say?

An individual carries to hereditary determinants (alleles) •reproductive organs will segregate the alleles (2) into different gametes (4) -diploid cell —> separate alleles (chromosomes) into haploid daughter cells •gametes then come back together to form a zygote =explains the process of meiosis (gamete formation)

Cell

An individual highly organized biological compartment •smallest unit capable of accomplishing life's functions

What does the beta linkages (1-4) look like in a polysaccharide? What does the polysaccharide of these linkages look like?

An upside down V where oxygen is on the same side of the number 6 carbon •long linear chains which are linked by hydrogen bonds=creates a lattice

What are proteins also called? Why are they called this?

Animated hydrocarbons Because they are composed carbon, hydrogen, oxygen and nitrogen (nitrogen is in amino acids)

The atom that receive an electron

Anion (add -ide to the end; negatively charged •one more electron than protons

Polysaccharide

Another name for carbohydrate •polymer of carbs (multiple monomers)

What is a trait? Was does measurable include?

Any measurable characteristics about individuals •anything that one can measure, not just what can we observe Ex: eye/hair color, height, earlobes, widows peak etc.. (observable) •non observable by just seeing: natural resistance HIV, enzyme for metabolism lactose/ethanol

What feature is shared among all cells?

Appearance of plasma/cell membrane

Examples of polyunsaturated fatty acids

Arachidonic, linoleic, linolenic

Shells closed to the nucleus...

Are lower in energy and the ones further away because they collect electrons first

Why did studying arginine synthesis help Srb and Horowitz?

Arginine is an amino acid •it is biosynthesized in a multi step metabolic process that needs multiple enzymes -knew the pathways + enzymes •in the series of enzymes, each one should be coded by one specific gene =should identify separate bread mold mutants who each could not produce one of the enzymes in the pathway •separate mutant line (each one had a mutation in a different gene) that is broken form enzyme 1 + 2 + 3 in the pathway -link between gene and enzyme (if the genes were altered through radiation, proteins should be nonfunctional as well)

What is the expanded/explained version of the central dogma formula? What are the two steps?

Arrow 1: the sequence if based in a particular stretch of DNA codes for complimentary base sequence on RNA Arrow 2: the RNA base sequence is a code for the specific amino acids found in a protein/polypeptide Steps: 1. Transcription (first arrow) •DNA transcribed to make RNA -photocopy or replica (letter for letter copy; not anything new) -product is very similar to parent (RNA vs DNA) 2. Translation (second arrow) •RNA is translated to make proteins (Very distinct) -translating languages: nucleotide code (4 NTP's) to protein amino acid sequences (20) -outcome is very different than the reactant =DNA genes code for amino acid based polypeptides

How is DNA represented in a prokaryote?

As a chromosome •one circular double stranded molecule •located in nucleoid region

How do animals store sugar?

As glycogen

Why does higher temperatures increase membrane permeability? Decrease with cold?

As molecules warm up: •thermal energy increases •increases kinetic energy •this causes molecules to hit each other with greater force and become farther apart (space) =more permeability When cold, less kinetic energy so closer together

After generating and isolating mutants, what were the results of Srb and Horowitz experiment? What did it mean?

As predicted, three distinctive types of mutants (arg 1, arg 2, and arg 3) appeared •arg 1 lacked enzyme 1; arg 2 lacked enzyme 2; arg 3 lacked make enzyme 3 -each different mutation in a gene caused a lack of a different enzyme within the three separate mutant cell lines =there is a causal relationship between genes and protein enzymes •genes contain info for making protein/enzymes

Functions of desmosomes in cells...

As seen in the epidermal cells, desmosomes are linked to one another by cytoskeleton fibers •they act as anchors for membrane of adjacent cells •also help epithelial cells anchor to other cells beneath them (which are made up of lamella like substance and collagen fibers) =big interconnected network

How do plants store carbs?

As starch

What were the findings and conclusion of Frye - Edidin experiment?

At first, the human side of cell had only human cell proteins, mouse side only had mouse cell proteins •left at room temperature for certain amount of time -later on, the fused cells has a mixture of markers distributed evenly throughout the entire cell membrane =components of membrane are dynamic/moving/floating

When do high affinity enzymes reach maximum reaction rate?

At relatively low substrate concentrations

When does the G2 checkpoint occur? What happens?

At the end of the G2 phase and right before M phase •checks if: -chromosome replication actually happened fully -new synthesized DNA has no mistakes/damage -activated MPF is present (transition into prophase)

Why does the nuclear envelope break down in prometaphase?

At this point, the chromosomes are completely condensed •no worry about them being tangled, it can safely occur The spindle fibers are in position •they cannot cross the membrane but need to make connections with the sister chromatids -allows them to connect at the kinetochore

Covalent bonds occur when...

Atoms fill their valence shells by sharing one or more pairs of electrons

Hydrophilic

Attracted to water (usually polar)

Cohesion

Attraction between molecules of the same substance

What process do lysosomes undergo to break down unneeded macromolecules or organelles?

Autophagy

What is the position of the backbone vs the nitrogenous base in DNA?

Backbone faces the exterior of DNA, base faces the interior

What are most prokaryotes?

Bacteria

What types of extra cellular material is found in bacteria? Plants? Animals?

Bacteria: Capsules and slime layers Plants, algae, fungi: Cell wall Animals: extracellular matrices (EMCs)

Where does transcription and translation take place for bacteria? For Eukaryotes? Does this have importance in terms of timing?

Bacteria: both processes are conducted in the cytosol •no nucleus •each can happen simultaneously -bacteria cells start translating mRNA before it's done being transformed Eukaryotes: transcription is in nucleus, translation is in the cytosol •separated by space and time = not at the same time •mRNA is first synthesized in the nucleus and then transported to the cytosol for ribosomal translation

What is the different in the starting points of replication for bacteria and eukaryotic cells?

Bacteria: chromosomes are circular and not as complex/long •they only possess one origin Eukaryote: chromosomes are linear and long/more complex •possess multiple of origins of locations =is the molecule is larger, more starting points need to be present to replicate it in a short time (1 replication site takes way too much time)

How are DNA polymerases different in bacterial vs eukaryotic cells?

Bacterial: 3 main types Eukaryotic: many more

Which carbon is the nitrogenous base attached to? which carbon is the phosphate group attached to?

Base= carbon 1 prime Group= carbon 5 prime

How does fecal matter relate to macromolecules?

Based off the Bristol-Stool scale •if poop is floppy and loose and sinks to bottom -getting good fiber and hydrated •if floats to the top -hydrophobic and eating too many lipids •if like a rock -not enough fiber and too much protein

Which part of the cell cycle does Cdk assist in? (Phase of mitosis)

Based on its enzymatic functions and that it begins mitosis, it assists the roles of prophase •phosphorylates chromosomal proteins •initiates nuclear envelope breakdown •activated mitotic spindle •degraded cyclin =phosphorylates all the enzymes that allow these things to occur •it is a regulator for if mitosis/prophase will begin and if the cell will eventually divide

What are the two different approaches to cell cycle defects (causes cancerous cells)?

Based on the idea of two different cell cycle regulators •some help speed up the process (cell cycle) while others help slow it down Called oncogenes and tumor suppressors respectively

Which part of the life cycle is meiosis used in?

Basis of sexual reproduction part of the life cycle

What is the function of tight junctions?

Because cells are stitched so tightly, it creates a molecular seal •molecules can't escape tissue into the environment Ex: skin has these connections so insides don't escape

Why is measuring energy so diverse? What are examples?

Because energy comes in so many different forms, there are lots of ways to measure it (different units) •joules/watts (chem/physics) •ergs (exercise science) •electron bolts (chem) •British thermal units (AC) •calories (nutrition)

What happens when a bundle of cytoskeleton fibers were stimulated in one epithelial cell?

Because it is so connected due to desmosomes, lamella, and collagen fibers = It would be felt by many of the cells around it and all through the tissue Ex: yank on skin, can feel it further from place you pull

What occurs in telophase? Why is it important?

Because the chromatids are now in opposite sides, a nuclear envelope re-forms •remember this is called compartamentilization, keeps processes separated The spindle fibers are no longer necessary and disintegrate

What is the implication behind organisms that have a common ancestry?

Because their structures will be similar, that means that their functions must also be similar •organisms with common ancestry carry out life in similar ways =successful structures are maintained and passed on

What occurs to genes in the S phase?

Because these are portions of DNA, they are replicated during this phase •DNA replication phase = gene replication phase =copies of gene 1 and 2 will be identical to each other

Why do hydrogen bonds, van der Waals forces, and electrostatic interactions not apply to the same category of bonds?

Because they are intermolecular proceses

How do large polar molecules and ions move across the cell membrane?

Because they are not freely permeable, they cannot diffuse spontaneously •proteins exist in the membrane which act as channels/conduits =provide both chemistry and physical space for those molecules to travel back and forth

Why do animals store sugar in the form of alpha glucose?

Because we possess specific enzymes to break down alpha glucose •we do not posses enzymes to break down beta linked sugars

C-OH in an upward orientation called ...

Beta glucose

What is seen with purines?

Bigger nitrogenous bases with a five membered and 6 membered ring together •bases includes: adenine and guanine

Which of the two metabolic pathways occur in animals? Occur at equal frequency?

Both anabolic and catabolic pathways exist in animals •they occur at equal rates in the body -in order for one to occur, the other must occur with it (to make those polymers, energy needs to be created through breaking down those polymers) =for an anabolic/endergonic reaction to occur, a catabolic/exergonic reaction needs to provide the energy (connected)

Could a micelle be an effective cell membrane for a living cell? Why/why not?

Both the exoplasmic and protoplasmic space contain water in a living cell •outside the cell there are water molecules being transported by the body •inside the cell, cytoplasm is 70% water =micelle cannot interact with two watery sides due to it only having a single layer —> not effective at all

Galactose function and examples (comparing to glucose)

Brain can't eat this so it has to convert it into glucose •part of milk sugar so some can't digest is lactose intolerant

What is genetics? Who are the "patients" for geneticists? Why?

Branch of bio that studied inheritance of traits •model organisms are the usual "patients" -conclusions drawn from them can be applied to many species

Chemicals role in body

Break down cells even further and they are highest organized assembles of non-living molecules

How are organic polymers synthesized?

By bonding together monomers with special types of covalent bonds

How are polymers broken down?

By breaking the covalent bonds that link the monomers

How are amino acid characteristics interpreted?

By looking at the primary, secondary, tertiary and quaternary structures

Carbonyl group

C=O Specific functional group; carbon atom double bonded to an oxygen atom

Methane + molecular geometry

CH4 Tetrahedron = very distinct shape, takes up space as well

Description of process stomata goes through...

CO2 concentrations low: •stomata open up and allow CO2 diffuse to spaces inbetween cells (into core called mesophyll) Fun facts: Stomata is open during day but closed at night

What is the major motor protein seen during anaphase? What does it do?

Called Dynein •it connects to the crown region of the kinetochore (which is attached to the centromere proteins which is a part of the chromosome) •it "walks" or pushes against the microtubule, pushing the kinetochore and chromosome closer to the centrosome -requires ATP energy

What are the spaces inbetween genes in DNA?

Called an intervening sequence •sometimes contains regulating sequences -control when the genes it borders will be expressed •not used for protein synthesis/coding sequences

What are hereditary determinants seen as today?

Called genes, they code for specific traits

What was the second generation in Mendels experiments called? How are they created?

Called hybrids •when mating two pure lines that each have a different particular phenotypes for traits Ex: green producing plant mixed with yellow producing plant = hybrids

What where the mutant bread molds called? How did they become mutated?

Called knockout mutants or null mutants •mutant bread mold cell lines with broken/altered genes -created altered phenotypes which could be studied and determine function of genes They were altered using radiation •functional genes —> mutant nonfictional genes

How do the mismatch repair enzymes tell apart the newly synthesized DNA from old DNA (need to remove incorrect base pair form new DNA)?

Called methylation state in bacteria •old DNA has methyl groups while new DNA does not -enzymes replace base pair lacking methyl = new DNA In Eukaryotes it's the recognition of nicks (single-stranded breaks)

What are different versions of traits?

Called phenotypes •hair color = trait -brown hair color= phenotype (version of trait)

What direct/physical structure for communication are present in plant cells? What are they?

Called plasmodesmata •conduits/channels through cellulose material and middle lamella

What mechanism allows cells to communicate with another to stop the growth of tumors?

Called social control •tight control mechanism •cell signaling process driven by growth factors

Which enzyme lays down the telomeres? How does it do this? How does this fix the problem?

Called telomerase •helps cells preserve the length of their chromosomes Type of polymerase that is special bc it has its own RNA template for synthesizing DNA •carries its own primer and can synthesize DNA = extends the template strand (not the new synthesized strand) -primase adds primer to the extended template and DNA pol III can synthesize a final Okazaki fragment (primer laid in the lagging strand) =fragment that is synthesized included original genetic info and some of the telomere •fragment that is overhang (after primer is removed) is the repetitive/expendable end of the telomere -preserves critical DNA and shortens the telomere (solves the problem)

What do some chromosomes have at the very end of their strands to deal with the end problem?

Called telomeres •repetitive sequences found at the end of linear chromosomes -do not possess any important genes, simply place holders -represent a strategy for dealing with the problem •if they're disintegrated, then important genes can be altered/deleted

What occurs in the light independent reaction?

Called the Calvin cycle •captured carbon dioxide and build sugar -covalently links carbon together to make sugar -anabolic process =This requires energy (endergonic) which is coming from ATP and NADPH

What comes after synthesis of DNA and before mitosis? What occurs in this phase?

Called the G2 phase •gets ready for mitosis by building necessary structures to separate chromosomes and split cell in half

What hypothesis did Mendel create to explain his results from the experiments? What were the three main conclusions within it

Called the particulate inheritance hypothesis 1. Hereditary determinants (responsible for round vs wrinkled) had to be particles •must act like matter —> can be handed down from one generation to next 2. Particles maintained "integrity" during passing •started with wrinkled, disappeared, came back F2 -wrinkled trait was the same = traits are not changed but maintained (just not expressed) 3. Each individual possesses two copies of each hereditary determinate (for given trait), this controls traits •F1 all round, but somehow produced wrinkled F2 -wrinkled trait has to be present in F1, therefore each plant must possess 2 traits (1 expressed, one masked) =adult individuals diploid (2 chromosomes copies/hereditary determinants)

What is the regulatory subunit (RNA pol) in bacterial cells? Eukaryote cells?

Called the sigma factor for prokaryotes •tells the enzyme wheee and when to start synthesizing RNA Called general transcription factor for eukaryotes

Which portion of the cell cycle creates copies of the chromosomes? Why is it important?

Called the synthesis (S) phase of interphase •also DNA synthesis or replication If not for this process, the daughter cell would not have a copy of the genetic material = one of the daughter cells wouldn't be functional

What condition appears if the nucleotide excision repair does not work?

Called xeroderma pigmentosum (XP) •genetic disorder in repair mechanisms -rare autosomal recessive disease •skin becomes prone to lesions and eczema appearance Cant correct thymine dimers caused by sunlight •skin cells can't repair damage -die and leave scars behind =must avoid sunlight or be covered completely in clothing

What happens during osmosis?

Can be thought of in two ways 1. Water spontaneously moves toward the solution with higher solute concentration (water molecules attracted to more solutes) 2. Water molecules have their own concentration gradient and move from high to low

Carriers function

Can bind to molecules and change it's shape to "carry" the material to the other side

What is the benefit with being able to do oxidative phosphorylation? (Advantage to dissociate ATP production from the activity of the enzyme = same thing)

Can do the electron transport chain which dissociates one to one method of ATP synthesis •store NADH and also stock pile hydrogen ion gradient =when food is not present, can slowly take energy from that pile •don't have to shut down systems (dormant)

How can one view condensed chromosomes?

Can see them with a light microscope •flourscent labels •they will be duplicated bc in mitotic phase

What happens when a cell loses control of its cell cycle?

Cancer

How does cancer improperly respond to social control and growth factors?

Cancer cells can divide without growth favored, leads to two possibilities 1. Cancer cells stop listening and divide uncontrollably 2. Cancer cells are too sensitive to the growth factor and divide "extra" when growth factors are their

What does the suffix -ose mean?

Carbohydrate

How can diets be manipulated to cut out fats?

Carbohydrate deficient diets that are focused on protein •fats will be metabolized for energy =does do harm to digestive system at first -not used to not getting sugar + getting lots of protein Called ketoemphasis

Which atoms make up humans mostly?

Carbon and oxygen

Why is carbon an important element for life?

Carbon has 4 electrons in its valence shell, therefore it can share a covalent bond with up to 4 other atoms (and itself) •it produced a very diverse set of covalent bonds with just a single atom •it's structure is very diverse and so is its function

The 4 main organic elements

Carbon, hydrogen, nitrogen and oxygen

Lipid

Carbon-containing biological molecules that is largely nonpolar and hydrophobic

Which molecule caused a negative charge in an amino acid? What does this mean in terms of Ph?

Carboxylic acid caused a negative charge (R group) •it becomes more acidic

Which molecule creates a pattern in the Krebs cycle?

Carboxylic acids (COOH) are oxidized •the release of electrons are picked up by activated carriers •it is created though the breaking of a carbon bond which produces carbon dioxide (reduces NADH)

What is the order that cells use macromolecules for producing energy?

Carbs, then fats, and lastly proteins

What type of metabolic pathway is associated with cellular respiration?

Catabolic pathways •the formation of monomers from glucose causes the release of energy C6H12O6 + 6O2 ——> 6CO2 + 6H2O + energy

What type of metabolism pathway is fermentation and cellular respiration?

Catabolism •the breakdown of high energy molecules to produce usable new energy Hydrolitic reaction (based on hydrolysis)

The atom that donates an electron (ionic bond)

Cation (positively charged) •one less electron than protons

What structure is just inside of the cell wall? What is it's importance?

Cell membrane •it is semipermeable meaning that it controls what goes inside and outside of the cell •distinguishes between outside of cell and inside of cell (cell wall is exoplasmic space)

What is a prokaryotes outermost feature? Why is it important?

Cell wall •it protects the cell and gives them shape and structure (Polysaccharide beta 1-4 link: peptidogycan) -it does not determine what goes in or out of the cell! •has permeability (even large molecules) but membrane has the final decision

What type of building blocks establish is the foundations of life?

Cells

Do cells communicate? Is it important?

Cells do communicate with one another and can receive signals from the environment •extremely important -listens to cues and it regulates cells in cell cycle Ex: growth factors serve as the signals/cues

What is the implication from the sea sponge experiment and selective adhesion? (How do cells interact)

Cells do not just passively make connections in a random manner •they make connections to work together and to create an overall function

How does the cell prevent supercoiling (over/under twisting) of the double helix?

Cells need to manage the coiling DNA (torsional/twisting strain) •cells become nonfunctional and will die Enzyme topoisomerase regulates the double helix and prevents torsional strain •keeps the DNA functional

What materials were used in the Frye - Edidin experiment? Why were they important?

Cells of two different organism •human cells •mouse cells Each cell is tagged with different proteins which are unique, can be used to differentiate between cells -allows to tack where those proteins reside in the cell

What does the chromosome theory of inheritance state?

Cells posses chromosomes and these structures are composed of the hereditary determinants described by Mendel •now called genes

Which cells have lots of SER?

Cells that a part of the glandular system (secrete hormones or lipids) Ex; liver cells

What occurs in active transport?

Cells transport molecules or ions against their concentration/electrochemical gradients •requires ATP as form of energy

Where can one find beta glucose molecules linked by beta-1,4- glycosidic linkages?

Cellulose •plant cell walls Chitin •fungal cells walls/insect skeleton(shell) Peptidoglycan •bacterial cell wall =surrounding cells in rigidity

Nucleus

Center of an atom; contains protons and neutrons

What structures appear in animal cells that do not appear in plant cells?

Centrioles

What occurs in anaphase?

Centrioles separate the centromeres •sister chromatids can now be moved to opposite sides of the cell

Where do the spindle fibers attach?

Centromere of each sister chromatids

What are the main players of prometaphase? What is there condition?

Centrosomes •they have completely migrated to opposite sides (finished moving) Spindle fibers •continuing to reach out towards each other (some fibers to go to the other side) Nuclear envelope •the nuclear envelope has broken down Chromosomes •completely condensed by this point •still dispersed in region of the nucleus

In late interphase, other than DNA what else has replicated?

Centrosomes •two of them -necessary for mitosis •have centrioles

What are the two integral proteins that function for facilitated diffusion?

Channels and carriers •can transport small molecules or ions

What is the importance of regulation in general?

Checks the amount of glucose being oxidized •stops this process when cell or body doesn't need more ATP •conserving energy

What are the two types of chlorophylls? What light do they absorb?

Chlorophyll a and b •absorb red and blue light (drive photosynthesis) •transmit green

What are the two classes of pigments in photosynthesis? How are they different?

Chlorophyll and carotenoids Different based on the specific wavelengths of light they absorb and reflect •this is based on their molecular structure

What structures appear in plant cells that do not appear in animal cells?

Chloroplast, cell wall, central vacuole

Where photosynthesis take place in Eukaryotic cells? How about Cyanobacteria?

Chloroplasts In the cytosol and cell membrane (precursors to chloroplast)

Which term describes copies of chromosomes in their condensed form?

Chromatid •this is one half of a duplicated chromosome Together, they are called sister chromatids

In prophase, who are the main players? What is their condition?

Chromosomes •start the process of condensed •partially there but not entirely Centrosomes •two of them (each contain pair of centrioles) •making the path to opposite sides of the cell (not there yet) Mitotic spindle •start to form from the centrosomes, not doing anything yet Actin filaments •they surround the entire cell and will be useful later

What are the players of telophase? What are their conditions?

Chromosomes •clearly separated on each side of the cell •they begin to decondense Cell proper •cell membrane elongates to get ready for cytokinesis Spindle fibers •still on opposite poles of the cell •are pushing the two poles away from each other to elongate cell -NOT spindle microtubules attached to kinetochores -others that overlap each other and push each other away (spreads cell) Nuclear envelope •begins to reform around both sets of separate chromosomes (two new membranes)

Continued: what happens to the 4 duplicated chromosomes in mitosis? (And after mitosis)

Chromosomes are formed into X structures •still considered 4 chromosomes, but again they are duplicated -two sister chromatids in each They copies in each chromosome separate in karyokinesis and cytokinesis •two daughter cells are created (parent cell disappears) -each one contains the original 4 chromosomes like parent cell -uncondensed from =these daughter cells are genetic clones of the parental cell •they all do the same function

What are photosystems?

Clusters of light gathering pigments such as chlorophyll and other accessory pigments •they are held in place by protein multi subunits in the thylakoid membrane

How is the idea of vitamins related to enzymes? Why are they now important?

Cofactors are derived from B vitamins that we acquire from our diet •they help enzymes perform their function and ultimately help cells perform their functions =if you didn't get this in your diet, your body could not do what it needs to do to stay healthy

What gives molecules of water it's strong surface tension?

Cohesion between the molecules (this is how things walk on water)

What will the cell change if it is in a cold environment? Warm environment?

Cold: •make phospholipids have unsaturated tails, less cholesterol -want the permeability to increase in response to decrease due to temp Warm: •make phospholipids have saturated tails, more cholesterol •makes less permeable due to increase seen by temp change

Which complexes (or other players) pump hydrogen ions to the intermembranous space? What is this process doing to energy?

Complex I, ubiquinone, and Complex IV •it is transferring the energy from the electron to pumping H+ ions =this creates an electrochemical gradient which is a source of potential energy (conservation of energy)

Which types of cells contain additional membrane partitions? What are these called?

Complex cells do •exoplasmic and protoplasmic spaces

Cytoskeleton structure

Complex network of protein fibers •actin filaments •intermediate filaments •microtubules Also transports materials within the cell

Are the components of a membrane static or dynamic?

Components such as lipids are in constant motion moving past each other •very dynamic Ex: Rubber duckies in a pond is a good representation

Ribosomes structure

Composed of RNA and proteins •have a large and small subunit

Isomers

Compounds with the same formula but different structures •ex: glucose v galactose

How are phospholipids made?

Condensation reaction (same as triglycerides)

What is the G0 state in cell division?

Considerad a "resting" state between the end of mitosis and the beginning of G1 Ex: Neurons

What are the sister chromatids called at the end of anaphase?

Considered individual chromosomes now

Who was Gregor Mendel? Study/work/education etc?

Considered the father of genetics •training in botany/naturalism •19th century monk, educated university of Vienna -didn't make it though college (not connect with mentors) •worked in monastery where studies biology -lots of resources found here like plants =found 3 key mentors who helped him achieve goals

What is the structure of a lipid micelle?

Consists of a single layer of amphipathic lipids •creates a sphere of phospholipids -hydrophilic heads interact with water on the outside -hydrophobic tail creates a bubble in the middle with no water present

Who is the main player in cellular respiration? What do they do in the molecular level?

Consumers/animals and decomposers •release the energy in glucose (eaten from excess in plants) by separating carbon atoms to form carbon dioxide

Acids

Contain high concentrations of H+ ions in solution

Bases

Contain low concentrations of H+ ions in solution

How did Avery perform his experiment?

Created three different preparations of heat-killed S strained cells •each preparation was treated with a different enzyme to kill of one of the options -prep 1 treated with protease—> killed protein and left RNA and DNA behind -prep 2 rnase enzyme —> killed RNA -prep 3 dnase enzyme (removed DNA) •mixed each preparation with r strained cells and infected mice =which ones capable killing mice

How are triglycerides formed?

Created through condensation reactions •carboxylic acid group (COOH) of fatty acid joins the hydroxyl groups (3; OH) of glycerol

Who took the lead in testing the triplet codon hypothesis? How did they do this? What did he find?

Crick did this •be made deletion and insertion mutations in viral DNA to run their experiment Revealed that triplet code was indeed valid for translation •first found that coding sequences have reading frames -could be destroyed by mutations and later restored if it was in multiples of three

What are the checkpoints in the cell cycle?

Critical regulation points in the cell cycle (way station) •determines if the cell is ready/appropriate to progress to the next phase -occurs due to the interaction between regulatory molecules

What is a mono hybrid cross?

Crosses that are only concerned with one trait •mating of parents that at heterozygous for one trait

Perixosome function

Crucial oxidation and reduction reactions •breakdown of fatty acids and amino acids •storage of oil in seeds •toxic oxygen detoxification in leaves

How are the rings of steroids made?

Cyclizing a special triterpenoid hydrocarbon (fatty acid) called squalene

What structural material do Eukaryotes have more than Prokaryotes?

Cytoskeleton •diverse network of cytoskeleton made out of protein fibers =helps Eukaryotes maintain organization

How does high energy light effect DNA? Specially UV light?

DNA can be broken down/altered by radiation •UV light is one example and causes thymine diners to form ( -happens when adjacent T's on a strand (single) become covalently linked through nitrogenous bases -forms structural speed bumb in double helix =alters function of DNA

What is the necessary steps to building chromosomes (broad, connect 1st unit)? Why is this important?

DNA is made up nucleotide building blocks •they have to be connected through condensation reactions (phosphodiester bonds) Chromosomes are made up of millions of building blocks (23 needs to copy; mitosis is 46) -takes time to do this, growth is a major part of the cell cycle =takes a lot of resources and time

What molecules must be transferred from cell to cell for them to function properly?

DNA is the key molecule that needs to be transferred •it provides an information source on how the cell should function =cell cycle and mitosis explains how this occurs and why it needs to occur

What is the polymer and monomer of DNA? How are they attached?

DNA is the polymer and it is made up of polymers called nucleotides •nucleotides are made up of a deoxyribose sugar, phosphate group (negatively charged), and a nitrogenous base -the phosphate group is attached to the 5' carbon in sugar ring -hydroxyl group in 3' sugar (no hydroxyl on 2 prime sugar) =hydroxide bonds to the phosphate group (3'5' linkage) •makes phosphodiester linkage

How can RNA come from DNA? (Hypothesis)

DNA molecules can be made from a DNA template •through help or DNA pol = RNA must also be made from a DNA •but is it compliments base driven/template based driven?

Which player takes out the RNA primer? Which fills in the gap?

DNA polymerase I (bacterial cells) has the function of removing the primers and filling in the gaps with commentary dNTPs of the template strand •DNA ligase then will form the final covalent/phosphodiester bonds to complete the process and form a continuous strand

Who does proofreading? What is proofreading?

DNA polymerase III does this •constantly checking for proper match negasen paired bases •occurs during DNA synthesis -most mistakes are fixed in this phase

What is the most important part of the cell cycle? Will there be a checkpoint for this?

DNA replication is the most critical part •two checkpoints make sure this process will go normally/went normally -G1 = makes sure there's enough resources (no commitment unless ready) -G2 = checks the replicated DNA for errors (don't want any mutations in the daughter cells DNA)

What is the formula of Central Dogma? What does it mean? List the research steps necessary to come to this conclusion

DNA —-> RNA —-> proteins •this is the explanation of how information flows in cells 1. Beadle and Tatum created their one gene one enzyme hypothesis 2. Srb and Horowitz proved the hypothesis, proving DNA hold info for protein synthesis 3. Crick proved DNA was code for amino acid •questioned a direct relationship between the two (thought it was indirect) 4. Jacob and Monod proved that mRNA was that intermediary =all mixed together to create central dogma

# of strands DNA v RNA

DNA: 2 RNA: 1

What does the DNA represent in terms of hereditary material? How about RNA? Finally proteins? What is the implication of this?

DNA: genotype •it is the code that will cause proteins to be made, the traits or phenotypes RNA: intermediary •almost exact copy of the DNA, simply being transported Proteins: phenotype •establishes traits (presence of enzymes), measurable characteristics Central dogma creates a relationship between genotype and phenotype

What is the hereditary material that is passed down from generation to generation?

DNA; nucleic acids •not protein

What organisms can break beta linkages?

Decomposes who help break down beta monomers into something other organisms can use (recycling resources) •termites

What is fluidity?

Degree molecular components in the membrane may be displaced (how easily components move around each other) •more movement = more spaces or channels for molecules to get thru

Nucleolus structure and function

Dense (dark) area within the nucleus •synthesis of ribosomal RNA molecules occurs here

What is the specific building blocks for DNA synthesis? (Nucleotides but more specific) why are they important?

Deoxyribonucleoside triphosphates (dNTPs) •monomeric nucleotide building blocks make up DNA Strand •N is place holder/general term) stands for any of 4 nitrogenous bases -dATP/dGTP/dTTP/dCTP =need all four types of nucleotides for DNA molecule •T part means triphosphate (3 phosphate groups) -very similar structure to ATP -holds energy within the phosphate groups=each nucleotides have energy which is necessary to create phosphodiester bonds

The way the pyruvate is used...

Determines the type of fermentation that is present or being done •can either be lactic acid fermentation or alcohol fermentation

What did Maurice Wilkins do and propose?

Devised new methods for producing and photographing crystals of DNA •proposed double stranded DNA forms a helical structure

Which mechanism drives passive transport? What is it?

Diffusion drives passive transport •it is the random movement of solutes due to kinetic energy

What occurs when cells are tightly connected to one another in terms of there communication?

Direct/physical connections •allow fast local communication networks •cells work together in a localized area

What does the phrase central dogma mean in itself?

Dogma= established, routine, default information flow (but can be manipulated) Central= fundamental aspect it biology •operates in every single organism (even viruses) •central to each organism -more evidence that all life shares a common link

Mitochondria structure

Double membrane (double lipid bilayer) forms around it •has an Inter membranous space -folds into sac like cristae •space between the cristae is mitochondrial matrix

What is a specific genetic disorder that is liked with non-disjunction?

Downs Syndrome •no metaphase plate was achieved so one chromatid did not make the journey to the other side •the cell ended up with an extra chromosome =explains extra copy of chromosome 21 (downs syndrome cause)

Which metabolic pathway is associated with photosynthesis?

Due to carbon dioxide being strung together to form glucose... -heart of anabolism on earth 6CO2 + 6H2O + energy ——-> C6H12O6 + 6H2O

Why do eukaryotic cells have membrane bound organelles?

Due to eukaryotic cells being so large, molecules can't easily diffuse across the entire cell •by separating the processes, it specializes certain regions for special jobs •structures won't interact with one another but are separate (this is called compartmentalization =increases efficiency of chemical reactions and thus efficiency of the cell

What does antiparallel mean?

Due to the base pairing rules and hydrogen bonding •two strands run in oppose directions

How do physicists and engineers use unstable isotopes?

Due to the isotope generating energy it can generate large quantities of electricity in nuclear fission reactors and can be used for studying the origins of the universe

How do carbs interact with water?

Due to the presence of oxygen/water (which is more electronegative) it causes the molecule to become polar •carbs are hydrophilic/will dissolve in water

What caused chlorophylls and carotenoids to absorb different types of light? How so in each?

Due to their molecular structure, more specifically the presence of oxygen bonds •this increases polarity Chlorophyll a has 5 oxygen groups Chlorophyll b has 6 oxygen groups Carotenoids have almost no oxygen groups

During which step are the centrosomes active? What do they do?

During early prophase •they move to opposite sides of cell •microtubules begin to grow outwards from centrioles -long protein filaments

Other than crossing over, what is the other major factor that allows genetic diversity? Where does this happen? How?

During metaphase I, duplicated homologous pairs are placed along the midline •this is after crossing over, each non sister chromatid is unique •some homologous chromosomes will be below, some will be above -multiple different orientations that can occur =source of genetic diversity

What does the image of proteins and lipids interacting with one another produce?

Dynamic group of molecules •dictate fluidity, permeability and thus transport across a membrane = fluid-mosaic model

Are cells dynamic or static?

Dynamic living things •lots of interacting parts and moving molecules

In terms of membranes, how do the two cell types differ?

E: contain lots of internal membranes (not just cell membrane) that form membrane boys structures called organelles (compartments) P: have no internal membrane, no separate compartments

Due to the first law relating mass to energy, what can we say about molecules?

Each molecule has a certain amount of energy which can be accounted for •does not explain why some of it is usable while some of it isn't (heat loss) •just says how energy conversion happens

Can processes in cellular respiration regulate themselves? Which structures allow this?

Each process in CR can regulate itself •the enzymes present in the 10 steps of glycolysis and other steps in Krebs cycle/ETC -each have its own active site which can be inhibited by competitive or allosteric (non competitive) inhibitors

Why do living organisms need energy? (Macro level)

Easier to understand what happens if don't get enough •become lethargic and tired •not able to perform every day functions •don't have the "energy" to do things

What type of reaction is seen with the building of bonds such as the building of ATP from ADP?

Edergonic process •the reactants have a lower energy state than the products -energy is absorbed •change in delta G is positive (energy is pumped in, increase in free energy)

What type of folding must a protein have to be considered functional?

Either a specific tertiary or quaternary structure

When does cytokinesis occur and what happens?

Either it immediately happens after telophase or overlaps with mitosis •the cytoplasm is divided in half to create two daughter cells -each have their copy of DNA -each has full set of organelles

What example of matter cannot be dissected into anything else (the smallest form)?

Elements

How are is energy used by the proteins in the ETC? (Mention players and their groups)

Energy is in the form of electrons which can enter proteins •membrane protein complex (complex 1) accepts electrons from NADH -FMN 1 chemical groups accepts electrons and is inside complex 1 -energy transfer = redox reaction

What occurs in the catabolic reaction in terms of energy? Why?

Energy is released in an outcome (exergonic) •Breaking the bonds in a polymer down to a monomer releases the energy within the bonds -called hydrolysis reaction

What occurs in the anabolic reaction in term of energy? Why?

Energy needs to be added in order to get an outcome (endergonic) •needs energy to create bonds between many monomers to form polymer (energy added to bonds) -called condensation reaction Ex: anabolic steroids: used to build muscles

What occurs in regeneration?

Energy still in the reduced organic compounds are used to reset the cycle

What are some examples of DNA damage sources?

Environmental •chemical pollutants •games and UV rays from sun Bodily •natural mechanisms/pollutants =cause damage within checkpoints that allows damage to progress and replicate

Which enzyme does the processing of pyruvate? How so?

Enzyme complex called pyruvate dehydrogenase •3 step process for enzymes + reactions take place -the enzyme does all of them —-> multi unit enzyme =In the end forms Acetyl CoA

What occurs in the process between glucose being converted into pyruvate (broad)?

Enzymes are breaking down covalent bonds between atoms •extracting the energy in bonds -placing it in activated carriers (ATP + NADH) (Arrows represent the formation of)

How do the terms: Enzyme, reactant and product connect?

Enzymes bring chemical reactants called substrates together in precise orientations so the electrons involved can from products

What is the intermediate step in alcoholic fermentation? What is produced?

Enzymes decarboxylate pyruvate •carboxyl group is broken off and CO2 (byproduct) is produced •creates intermediate molecule called Acetylaldhyde

What is the relationship between enzyme function and temperature/pH?

Enzymes function their best at specific temps and pH levels •at non optimal temps and pH's, the enzyme will take on a non optimal shape -it will still work but as well as the optimal conditions -can become such an extreme where enzyme denatures and there is zero activity

How many active sites does an enzyme have? What happens when a substrate is in it?

Enzymes generally have a single active site •when the substrate binds, the active site closes in on itself like a closed hand -not consciously doing this, chemistry of substrate + active site are compatible -causes them to "snuggle" Enzyme cannot bind to another substrate after this

What type of covalent bonds are formed between fatty acids and glycerol?

Ester linkages

Which type of cell is larger between Euk. and Pro.?

Eukaryote is lather

Where are the chromosomes found in a Eukaryote vs Prokaryote?

Eukaryote: Inside the nucleus Prokaryote: swimming around in a "nucleoid space"

What is the main distinction between eukaryotes from prokaryotes?

Eukaryotes have compartment inside the cell called the nucleus •houses genetic material =higher level of organization (but not more important) Prokaryotes do not have this compartment

How many carbon atoms do fatty acids have? How are they synthesized?

Even number of carbon atoms •joining of two carbon acetyl groups

Why do cells only use left handed amino acids isomers for protein synthesis?

Evolutionarily speaking, one common ancestor must have decided that it will only use left handed isomers •this gene was passed down the line until it is seen present today •our body and other animals will not utilize right handed amino acids -animals are the best source for left handed amino groups; that's why we eat each other

What do chromosomes look like in the G2 phase?

Exact same form as S phase •uncondensed and replicated

Which type of reaction is seen with the breakdown of glucose in cellular respiration?

Exergonic reaction •the reactants have a higher energy level than products -the difference in this value represents the amount of energy released (this is Free energy) =chemical potential energy taken and transformed into something else •negative change in energy since released

Which process is spontaneous? Is it really spontaneous??

Exergonic reactions; but this doesn't actually happen •some energy is needed to start the process of breaking down the glucose (illustrated on the hump of the energy graph) -energy conversion processes cost us some heat =it's paying for the activation energy of the reaction (need a little energy to make a of energy)

What process can vesicles use to help move materials outside the cell?

Exocitosis •post Golgi vesicles full of proteins fuse with the plasma membrane •contenta are deposited outside

Review of factors that affect diffusion and how

Extent of concentration gradient •higher = higher diffusion rate Mass • higher = higher Temp •higher = higher Solvent density •higher = slower diffusion rate Solubility •higher = higher Surface Area •higher = higher Plasma membrane thickness •higher = slower Distance traveled • higher = slower

Four types of lipids found in cells, how do they differ?

Fats (triglycerides) Phospholipids Steroids Waxes •differ in shape and function, how they bring fatty acids together

Macromolecule: Lipid Monomer name: Functions: Example:

Fatty acid Store energy + form membrane + steroids Fat cells

What are the building blocks of lipids?

Fatty acids

What is the monomer of lipids?

Fatty acids

How are females represented? Males?

Female = circle Make = square

How does the amount of ATP created in fermentation compare to CR?

Fermentation: only 2 ATP •very little energy compared to glucose a high energy compound CR: 30 ATP •full oxidation of glucose

Which cells possess telomerase? What implications does this have?

Fetal tissues, adult germ cells, and also tumor cells •especially prevalent in cancer -since there's an incredible amount of replication, the cancer cells would quickly die due to shortening DNA each time, yet telomerase lengthens the chromosome and prevents this from happening =by inhibiting telomerase activity, cancer can be stopped

In terms of cell connection, what are the two important classes of molecule? What is there overall purpose? (Not individual)

Fiber composite materials and stiffening agents •fiber composite makes up the wall and it can/won't possess stiffening agents Purpose is to help cells stick together.

What happens in mismatch repair?

First, mismatched bases are detected before/after DNA replication •occurs in the G1 and G2 phase of cell cycle Enzymes recognize mismatched base pair and remove section of strand that has it •then fills back in the gap with correct bases

What is structure of the alpha glucose monomers?

Form long polysaccharide sugar chains linked together by alpha linkages •they coil into long helical structures They branch when formed between carbon 1 of one strand and carbon 6 of another strand

Aldehyde group

Forms when the carbonyl group is located at the terminal end of the carbon chain and bonds with a hydrogen H-C=O

Who found the intermediary for protein synthesis?

Francois Jacob and Jacques Monod •realized that RNA exists in both nucleus and cytosol -it would carry the genetic code from DNA to ribosomes for protein synthesis Specifically, Messenger RNA/mRNA does this function (functionalizes protein synthesis)

What are genes? How are they seen on a DNA strand?

Functional coding sequences •they appear as portions of the DNA molecule and are separated by short regions -sequences along the long nucleic acid

What did Crick find in the codon experiment?

Functional polypeptide where only achieved with the correct sequence of three words •when deleting one or two letters, the reading frame shifted -the letters in RNA were not read correctly Ex The cat and the dog (we read it in three because we know the reading frame) •delete 1 letter: hec ata ndt do -can't interpret it properly because reading frame is off =proved the triplet codon hypothesis was correct

What occurs to the outputs of Calvin cycle?

G3P molecules are run through reactions •either makes starch to store it •or link glucose and fructose to make sucrose -mobile form of sugar which feeds plant cells

Where does meiosis occur in the body?

Gametes are produced in the reproductive organs •male=testes •female=ovaries These cells are capable to do meiosis (only locations)

Describe gamma rays vs radio waves

Gamma rays have a short wave length and thus have a lot of energy Radio waves have a long wavelength and thus have little energy

What direct/physical structure for communication is seen in animal cells?

Gap junctions •connect membranes together (But not in a structural way) -proteins do this, establish conduits for movement of molecules from one cell cytoplasm to the other Devices for direct cell-cell communication

What fills in the spaces between cellulose in plant cells?

Gelatinous polysaccharide •ex pectin Also protein

How can a trait be followed if it's not easily observable?

Gene sequences of individuals can be found to see if the trait is there •need to assess individuals to map traits on a pedigree

Is DNA replication accurate or faulty? Why?

Generally it is a very accurate process •less then one mistake per 1 billion bases -in one cell replication cycle, probably 3-4 total errors (missed by proofreading, needs to be repaired in G2) DNA polymerase is very selective in matching complementary bases (can also correct an error)

What were the results of Meselsons experiment?

Generation 0 is all high 15N Generation 1 is all hybrids or intermediate densities Generation 2 has 50/50 split for low and high density DNA •1/2 was 14N low, 1/2 was medium density =outcome predicted for semiconservative model •this is the mechanism for DNA replication

What are tumor suppressor genes?

Genes that code for regulators that help slow down the process of cell division •shuts down the cell cycle when necessary (could be damage of DNA) Ex: sentry complex BRCA (slow cycle down that checks DNA) •didn't allow cell to divide until it's determined totally safe/appropriate

What are oncogenes?

Genes that code for regulators that help speed up the cell cycle (act like a gas peddle) •proteins called oncogenic factors •help cells clear the checkpoint Ex: genes that codes for MPF cyclin and MPF Cdk (push cell through G2 checkpoint)

What occurs in mitosis? Who are the players?

Genetic material was replicated and is now partitioned into two separate clone cells •original cell = parent cell •clones = daughter cells

What kind of traits specifically do pedigrees track?

Genetic traits •not sicknesses such as Corona Virus -transmission viral disease •tracking diseases causes by genetic conditions -mutated form of genes create specific trait outcomes (reduce physiology) Ex: Cystic fibrosis

What is the genotype of the cell? What is the phenotype?

Genotype is the hereditary material or DNA itself Phenotype is the expression of proteins coded from the DNA •protein make up enzymes which have particular functions -if someone has an enzyme then they have that function and it shows up as a trait -vice versa (no enzyme = no appearance of function)

Peroxisomes structure

Globular organelles with 1 membrane •contain hydrogen peroxide

What is the starting molecule in both cellular respiration and fermentation? Is it always this?

Glucose •although, the body can use fats to get energy -other high energy macromolecules

What goes into glycolysis? Produce? Why is pyruvate important?

Glucose •and ATP Pyruvate •and ATP + NADH Important because it's the thing that fuels the next process •high energy intermediate that allows other processes to occur

What molecule is metabolism centered around? Why?

Glucose •this is the "sugar of life" -energy exchange molecule among living organisms -primary synthesized by photosynthesis (plants evolved to use largest carbon source: CO2) -primarily broken down in cellular respiration (animals evolved to use largest energy source: sugar) =links the two processes together, allows each process to support the other

What goes into glycolysis?

Glucose and 2 ATP

In the graph of change in free energy over the steps in CR, what is happening and what is the very general trend?

Glucose is being oxidized at each step and free energy is flowing out of it and into activated carriers (ATP, NADH, FADH2) •it is decreasing over time from a high energy state to a lower energy stage =this is an exergonic process and catabolic process

What is the first piece of lactic acid fermentation (2 parts)? What is being produced?

Glucose is being reacted to form pyruvate molecules •ADP is being used to produce ATP (being reduced) •NAD+ is being used to produce NADH (reduced)

What is special in the energy graph that happens in the first step of glycolysis? Why does this happen?

Glucose is increasing in free energy a small amount •ATP is being used to begin the process and it is being spent -energy is being absorbed by glucose -supercharges glucose + kicks it =need to overcome the activation energy barrier

What happens in the second half of glycolysis?

Glucose is oxidized and energy is released •4 ATP molecules exit this process with NADH =net 2 ATP and 2 NADH + 2 pyruvate Pay-off phase •energy investment is followed by energy pay off

Which protein does not have optical isomers?

Glycine

What hint does the name glyco-lysis provide to the function of this step? How is this seen?

Glyco means sugar •it shows that a sugar or glucose is going to be involved in this step Lysis means to split •it is a verb and represents that glucose will be split into two separate molecules =glucose (a hexose sugar) is split into 2 pyruvate molecules (triose sugars)

What are the three stages of CR that produce ATP? Do they do it in a direct or indirect way?

Glycolysis-direct (step 1) Krebs cycle-direct (step 3) ETC-indirect (step 4)

What occurs in the first 5 steps of glycolysis?

Goal is to supercharge glucose •use ATP to increase the molecules free energy •must surpass energy barrier to begin the process of CR or fermentation =spend 2 molecules ATP

What is ethanol?

Grain alcohol created when yeast cells ferment sugars in wheat •drinkable alcohol •also created when making bread dough (but burned away in baking)

What was the goal of mitosis in the life cycle?

Growth and repair of cells •to turn a zygote into a fully functioning adult organism •all cells from preexisting cells -same genetic info from zygote

What role do growth factors play in social control?

Growth factors are polypeptides or small proteins that tell cells to divide (facilitate social control; it's the signal) •if cells don't get growth factors, the cells won't divide -disorders with stunted growth (dwarfism) •can give artificial growth factors -like in plants or livestock so they grow larger and more to eat -causes secondary growth factors to cause harm to human beings (bovine growth factor ex)

Secondary structure of RNA

Happens when complimentary base pairing occurs in sequenced on one RNA molecule •forms hairpin loop -bases on one side are antiparallel and completa to the other side

Smooth Endoplasmic Reticulum (SER) structure

Has no ribosomes on its surface

What was Mendel's broad question about heredity?

He also questioned why offspring resemble their parents and how does the transmission occur? •did not favor the two previous theories

What did Francis Crick believe was important about the genetic sequence?

He believes that the sequence itself was it critical important, that it represented a code •code is information that could be read and used to create amino acids of polypeptide structure

How did Crick conduct his experiment in general terms?

He created a parent DNA sequence with 3 repeating nitrogenous bases •in three groups, he deleted 1 base pair/two base pairs/three base pairs -if the code is red in triplets, a functional protein will only appear if three bases were deleted to bring back the pattern

Why did the mice die according to Griffith in the fourth step of the experiment? What does it mean?

He did an autopsy on the mice and found fluid in the respiratory canal contained virulent S strain bacterial cells •was not added in before, only the heat-killed were activated =live R strain cells were the only thing that could have killed the mice •heat-killed S strain transformed the R strain to become S strain activated cells •new way for info to be inherited from generations -bacteria can inherent information from dead individuals

Where did the wrinkled phenotype go in the F1 generation?

He said that these traits "recede" •this is a hidden trait that will not express when a dominant trait is present -can be considered a shy trait =only shows up in certain circumstances/special conditions

What is Griffith find from his experiment (specific principle)? Why was this important?

He studied two strain of S. pneumoniae (bacteria) and found the principe of transformation =this provided information on hereditary molecule •factor responsible

What notation did Mendel develop to indicate the gene for a particular trait?

He used a letter to indicate the particular gene •capital of the letter represented the dominant allele/version •lowercase of letter presented recessive allele/lowercase -each individual possesses two letters because they have 2 determinants (sets of chromosomes)

How did Mendel detect the presence of recessive alleles in pea plants

He used something called a test cross •confirmed principle of independent assortment •could validate the ratios he was receiving to see if it's predictive =can use this to determine outcomes in other crosses

Which process did Mendel utilize in terms of fertilization for the pea plants?

He utilized cross-pollination •one plant fertilizes eggs in another individual •used sperm -produces diversity in the next generation=sexual reproduction =selective cross pollination meant he could study the transmission of specific traits in garden peas (Artificial selection; literally had a plant have sex with another plant)

What category of plants did Mendel use for his parent generation usually?

He worked with pure lines/true breeding •pea plant when mated with itself always produces same phenotypic outcome (in order to do this, it has to be homozygous for that trait) Ex: if a plant has green pee pods, it will always produce green pee pods when self pollinating •yellow never appear

Which enzyme catalyzes the breaking of the hydrogen bonds?

Helicase can functionally separate the two strands by breaking the bonds that connect the nucleotide bases

What do the centrosomes and centrioles do after/at end of telophase?

Help aid in elongating the cell •this is helpful for cytokinesis to occur, smaller surface area = easier to cut in half

What are the six-members rings called?

Hemiacetals

What occurs at the origin of replication?

Here a protein complex functions to separate the two strands of the double helix •open the helix by breaking the hydrogen bonds between the nucleotide bases -covalent (phosphodiester) bonds are not broken when opening the helix =creates replication bubble

What is interesting about the first step of the z scheme as it relates to CR?

Here water donates its electron and oxygen is formed (that's were the byproduct comes from) with hydrogen ions •this is exactly the opposite process of CR where oxygen accepts electrons and forms water =electron in ETC start off with really low energy

Sugars with 6 carbon atoms

Hexose sugar

Nucleus description

Highly organized information storage/retrieval compartment •contains cell's DNA (multiple linear chromosomes) -chromatin (DNA + proteins)

What is the function of the antenna complex?

Holds/contains pigments •arranges into light funneling decided (look like satellite dishes) =Transfers light energy to reaction center

Which "players" are seen in long distance cell communication?

Hormones and receptors

Saturation

How many carbon-valence positions are filled with hydrogen atoms

Carbohydrates structure (basic)

Hydrated hydrocarbons Because it's structure is simply carbon bonded to water multiple times •(CH2O)n

What is fatty acid made up of?

Hydrocarbon chain that is bonded to a carboxylic acid (COOH) functional group

What are lipids mostly made up of?

Hydrocarbons

Which R groups are hydrophilic?

Hydroxyl (OH) and amino groups (NH3) are a dead giveaway •they can form hydrogen bonds

Which compound is especially important in terms of the spatial arrangement of carbohydrate atoms?

Hydroxyl (OH-) group Defines the type of simple sugar it is

How is the genetic code predictive?

If given the sequence of nucleotide bases in a strand of RNA (or DNA), one could predict the amino sequence in the protein it codes for •if given DNA remember to put into RNA language (complimentary)

Which R ground are usually hydrophobic?

If it only possesses hydrogen and carbon bonds •a sulhydral group does not mean it is polar

How can one tell if a trait is recessive from a pedigree?

If the trait skips generations entirely •trait has receded (like the wrinkled phenotype in Mendels experiment) -can hide in heterozygote and reappear in later generations

How does the first part of cell theory constitute a pattern?

If you look at all organisms in the living world, a pattern should arise •all of them will be made up of cells (cell based)

Why is the idea of haploid cells important?

Important in terms of new cell containing the same amount of genetic material as parent cell •eggs and sperm must have 1/2 of chromosomes (combine to from 1) -if not, each new generation doubles the chromosome number

Why can't the protein synthesis mechanism be directly led by DNA according to Crick?

In Eukaryotes: •DNA is found exclusively in the nucleus •ribosomes are found outside the nucleus in the cytosol -they are in different compartment, DNA cannot migrate Intermediary must exist to transport the information

What is free energy?

In an energy conversion process, a certain protein is lost in each process •the energy that is not lost but transferred represents free energy -it is energy that is available to do work or usable Ex: inside the chemical potential of a molecule (Called Gibbs free energy)

What example can show direct/physical communications?

In cardiac myocite •one cell alone pulses in rhythm •two cells together in close interaction pulse in unison -thru association can communicate and pulse together •three cells not in tight connections will all pulse at different rhythms

What function do the two gap phases share? Is it important?

In each phase, DNA is being checked for errors •most important role because DNA has to have a perfect coding for the cell to function properly

What occurs in each step of glycolysis? What is the result?

In each step, chemical bonds are either broken or rearranged •this represents the release of energy to form ATP •also the reduction of NAD+ to hold the electrons released =energy releasing steps

What were the results of the Hershey experiment?

In experiment 1 •Radioactive DNA was in the pellet -it was injected into the bacteria cells and is a component of the HM In experiment 2 •radioactive protein found in the supernatant -it stayed on the outside of the cell with the virus (makes up the coat) so not a part of the HM =genes are made up of DNA (viral genetic material) •all evidence says DNA is the hereditary material, concluding experiment

How does the substrate concentration affect catalysis by enzymes in general?

In general they speed up enzyme-catalyzed reactions •as more substrates are present it increases the chance of them binding to the enzyme and creating products -they have to be in perfect orientation and speed so more chances = more success

What in particular causes growth factors to promote cancer?

In general, these signals trigger cyclin synthesis •when a cell is cancerous, it will overproduce cyclin in G1 Cyclin then binds to Cdk to activate them and activate S phase proteins •in cancer, too much cyclin will cause the continue activation of Cdk and phosphorylation of proteins -immortalize cells to produce cancer

How does the number of chromosomes in the cell change from metaphase to anaphase? What does this mean for the cell?

In metaphase, there was 46 chromosomes in total, each being two sister chromatids (23 pairs) •in anaphase, the number doubles to 92 total chromosomes and 46 pairs (sister chromatids each become there own chromosome) =each part of the cell now has a complete cell of chromosomes which are identical copies •can now create daughter cells which has copy of every chromosome

How do electrons fill the shells?

In order of increasing energy by occupying the lowest energy shells first

What is the "catch" with the glycolysis process?

In order to conduct this process, energy must be spent •the activation energy barrier has to be satisfied in order for the enzymes to do their jobs (reactants formed to products)

Mendel asked the question of whether the sex of the parent that has the recessive trait mattered. How did he test this?

In other words, does sex matter in passing down this particular trait? •conducted experimental called reciprocal cross -two separate crossed

When do condensed chromosomes appear? Why do they do this?

In preparation for mitosis (small amount of time) •all the rest of the cell cycle, chromosomes are uncondensed They need to be organized and easy to transport for mitosis •much easier when they're highly condensed/small

In terms of making mRNA? How is it different from replication (think semiconservative model)?

In semiconservative model, both strands of DNA are used as a template Vs. In transcription, only one of the DNA strands (after unraveling) is read by RNA polymerase to create mRNA •only a single template strand

Where does glycolysis occur? Why does it occur here?

In the cytosol •independent of oxygen so it's independent of mitochondria (same with fermentation) =must happen in the cytosol then

Where does fermentation occur?

In the cytosol (along with glycolysis) •not in mitochondria!

What was George Gamow's prediction of the relationship between genetic codes (DNA) and protein?

In the mRNA molecule "words" existed which could be read by the ribosome and each work would equal one amino acid •words were called codons and each codon is made of 3 bases/letters of RNA -each 3 letters related to single amino acid (and only 1)

Why do the chromosomes decondense and the nuclear envelope form ASAP in telophase?

In their condensed form, they don't have any functional purpose •can't be read for gene expression •DNA is not susceptible =processes have to occur again so DNA needs to decondense and become functional again •nuclear envelope is necessary for starting this process

Can organisms do cellular respiration with oxygen? How does this happen?

In very unique scenarios, yes (considers anaerobic respiration) •alternative electron acceptor can be used in the ETC -genetically encoded thing (our cells encoded to use oxygen)

Where does alcholic fermentation occur?

In yeast cells •

How is fluidity connected to permeability?

Increases in temp: •increase thermal energy •increases kinetic energy •increase fluidity =increases permeability There's is a direct relationship (more fluid equals more permeable)

Was the translating of RNA nucleotides to the language of amino acids important? Why?

Incredibly important to all of biology •every single organism shared this aspect of biology (central dogma) -allows us to unlock the code for how an organism is built (all of the functions of an organism can be explained through their structure)

Cells

Individual livimg units of any organism

Hormones def and how transported

Information-carrying signaling molecules •circulates throughout the body (often through blood stream, not always)

What does the pedigree reveal?

Inheritance mechanism for a trait •if the trait is inherited as a dominant or recessive trait =can use to study traits behavior in people (like genetic disorders)

What are the three phase of transcription?

Initiation, elongation and termination

What are the three phase of translation?

Initiation, elongation, and termination •similar to transcription but different in the specifics of each step

What are the two steps of the cell cycle?

Interphase •about 80% of the total cell cycle •not dividing -instead growing and preparing for division Mitotic phase •20% •cell is dividing

How does preparation phase of cell division for meiosis compare to mitosis?

Interphase is an equivalent process G1: growing/accumulation of resources S Phase: duplicate the genome G2: getting ready to enter cell division

What are the two types of molecular bonds?

Ionic bonds and covalent bonds

How is the G1 phase seen in rapidly dividing cells?

Is is short that it is practically eliminated •directly after mitosis, cells immediately start growing and acquiring resources -occurs once become daughter cell •DNA replication occurs immediately after

What is the critical component of initiation in terms of the gene sequence? How does it help? What about its counterpart and function?

Is it called a promoter •gene sequence found upstream (before/left) of the actual coding sequence -represents start region for the gene -on the other hand, there is a nucleotides downstream of this that is the start site of transcription called +1 site (first DNA template letter transcribed into RNA Terminator is the counterpart •located downstream of the actual coding sequence •signifies end of the transcription = initiation starts at promoters and end at terminators

Why do organisms need energy? (Micro level)

It "costs" something to maintain homeostasis •constant inside environment that is distinct from outside environment -inside space needs to be distinct from outside space Ex: costs money to maintain your house, keep the inside away and different from nature

What benefit exists from an organism being multicellular?

It allows the organism to perform functions that are not just seen in one cell but many cells when they are formed into a tissue/organ Ex: single skin cell—> can do a few skin functions Tissue of skin cells—> achieve greater function by protecting body 2. Region of epithelial tissue, has simple comulgar and goblet cells •both have different functions, by making it into a connective complex, it takes on multiple functions

Why do spindle fibers attach to a particular place on each chromatid? What is this process called?

It allows them to place the chromosomes along a linear alignment •single file along line = metaphase plate This is metaphase •marks half way point in mitosis

What occurs to pyruvate in fermentation? (In terms of breakdown and accepting) (also the function of fermentation)

It can be broken down into a derivative •substitutes the role of oxygen and accepts electrons from NADH -this creates NAD+ which allows glycolysis to continue to produce ATP -example of substrate level phosphorylation (get to that later)

What is the significance of electron transfer in biology?

It can be equated with the transfer of energy (electrons cause a molecule to have higher energy) •whenever trying to follow energy, follow the electrons being swapped -usually in the form of hydrogen ions (electrons moving with it)

What is the potential of a glucose molecule in terms of anabolism?

It can be used to build all of the biological macromolecules •can build all the building blocks through some accessory elements Summary: 1. Take glucose molecule and break it down -releases energy 2. Take those components of glucose and use that energy produced to build the building blocks 3. Create biological macromolecules (all of us) Catabolism fuels anabolism =we are what we eat literally

What is important about a molecules shape/structure?

It can be used to find it's related function

What is the function of the Calvin cycle?

It captures carbon dioxide from the atmosphere and used it to synthesize sugar •more specifically, it creates G3P and sugar creation is done from this output •can do this due to the energy of NADPH and ATP created in the light-dependent cycle •can happen at night and during the day

What is the concentration of cyclin in the cell cycle? Why is it like this?

It changes •increases through interphase •peaks in M phase (mitosis) •then decreases totally during the rest of M phase -it's concentration cycles (builds up, falls down, builds up again) with the cell cycle -that's why it's called cyclin =this is the independent variable in the reaction, when it's concentration becomes high it will bind with Cdk and create MPF •this causes cell division to occur •makes sense that it's concentration rises right before mitosis and then falls to stop the cell from dividing (when it doesn't need to)

What does selective mean in selective permeability?

It controls what comes in vs what comes out of the cell membrane

What is metastasis?

It correlated with malignant tumors •when the tumor/cancer cells enter the bloodstream/lymphatic vessels and are transported to other tissues -will start a new cancer growth in a new part of the body

Why is the release of heat a trend in the energy cycle?

It costs something to convert one form of energy to another •this can be seen in the release of heat -all energy exchanges have some loss of heat, none are 100% efficient

What is the overall function of the primary cell wall?

It defines the shape of the cell by counteracting the turgor pressure experienced by the central vacuole

What is important about polymers?

It dictates how everything in the human body is built

What does the functional group placement in sugars dictate?

It dictates the type of chemistry the monosaccharide can participate in (structure relates to function)

What does the spectrum of light portray? How does one read it?

It displays different types of light in the form of low energy to high energy •the side that has short wavelengths correlated with high energy •side with long wavelength correlates to low energy

What happens to the parent cell in mitosis?

It does not persist, it is divided into two separate cells and creases to exist as an entity

How does temperature affect enzyme activity (specific)?

It effects the movement of the substrates and the enzymes •substrates need to have a perfect kinetic energy to connect with the active sights on enzymes and bind -if too fast, they'll bounce off each other -if too slow, they won't come together fast enough to form the bond (negative charges will repel) -needs to be just optimal

What was so special about S. pnm bacteria?

It exists as two different strains: R and S strain 1. R strain •appears rough, colonies are dry and jagged -due to lacking of outer covering called a capsule 2. S strains •smooth, gelatinous and gooey -due to having a capsule =having capsule is virulence •S strains are virulent and can cause disease •R strains are benign -characteristics allowed Griffith to perform his experiment

How does the second part of cell theory constitute a process?

It explains the how or the mechanism; how the pattern comes to exist •it explains that cells come from preexisting cells

What is special about the minimal ATP production in the Krebs cycle?

It first created the molecule GTP (guanosine triphosphate) •then it will be converted into ATP

What is the first law of thermodynamics?

It focuses on energy conversation and also incorporates enthalpy (H) •the total amount of matter and energy in the universe is constant -not destroyed or created Think about E=mc^2 (both constant and interchangeable)

What is the structure of the origins of replication as the separating of strands begins? Function?

It forms an opening called the replication bubble •each end of the bubble has two convergence points (single strand attached to separated single strand) -called replication forks (2 per bubble) —> active sites of DNA replication (functional purpose) -replication occurs at both forks at the same time —> separating strands at each fork •bacterial cell —> circular molecule being separated from both sides •eukaryote—> long linear strands has multiple points -going outward in both directions, called bidirectionally =get the molecule synthesized half the time if only starting at one end/fork

How does the z scheme work?

It functions very similarly to the ETC 1. Water is the electro donor, donates electron to photosystem II (these are very low in charge) 2. Light catapults electron to higher energy •this increases their free energy 3. Free energy extracted in ETC •some get pulled out to produce ATP •other electron are funneled into second photosystem I 4. Absorbs another photon of light and brings free energy even higher 5. Another ETC extracts then energy •produces NADPH

What is the concentration of cyclin-dependent kinase in the cell cycle? Why is it like this?

It has a constant (high) concentration throughout the entire cell cycle •never fluctuates =this is the independent variable in the reaction, when it's concentration becomes high it will bind with Cdk and create MPF •this causes cell division to occur •makes sense that it's concentration rises right before mitosis and then falls =this is the dependent variable of the reaction •it will only from MPF when cyclin concentration is high •doesn't matter if it's high, it won't cause cell division -the fact that it's a constantly high amount makes sense

What is the structure of an ATP molecule?

It has three components: nucleotide building block for RNA 1. Three phosphate groups •when one is broken off to form ADP, energy is released -therefore = energy lies in the bonds between phosphate groups 2. Sugar group of ribose 3. Nitrogenous base of adenine

At which intervals (phases) of the cell cycle does MPF concentration increase? Decrease?

It increases during interphase and decreases during mitosis

What happens to the ATP produced in the light dependent reaction?

It is NOT used to fuel cell functions such as transport •it is strictly fuel for the Calvin cycle (Plants have their own mitochondria to create ATP for that other stuff)

What is NADH?

It is a an activated carrier similar to ATP but different in form and function •redox factor: stores energy in the form of high energy electrons -can be seen as added hydrogen atoms with electrons (not phosphate groups) •the structure is a di-nucleotide -similar form of ATP but double each part (hint cant hold way more energy than ATP)

Does the cell cycle have power over mitosis?

It is a control mechanism and will determine if the cell is ready/needs to divide •mitosis cannot occur without the cell cycles first step

What is special about the linkage between two monosaccharides?

It is a covalent bond between oxygen (not carbon) •called glycosidic linkage The monomers can be identical or difft and the location of the bond can vary

What is the transition state in relation to enzymes?

It is a hypothetical "halfway point" in the substrate bound enzyme •when an enzyme is forming a product, there is halfway point where bonds are being created/destroyed but not finished yet -it looks a little like reactant and product

What is significant about carbon?

It is a key element that organic organisms possess (carbon=organic)

What is entropy?

It is a measure of disorder or randomness in a system

How does the replisome function?

It is a multi protein complex composed of one helicase, 2 DNA polymerases (III) and 1 primase •this association allows the lagging strand template to loop -this causes the strand to re-orient itself 3 dimensionally so that the DNA polymerases are facing the same direction and moving together -the leading strand and lagging strand have the same orientation =makes sure that the lagging strand has the same rate of synthesis as the leading strand •they both finish in the same amount of time

What is the structure of DNA polymerase III?

It is a multi sun unit complex •has part called the sliding clamp which holds the DNA in place •then the actual polymerase which adds in the complementary bases

What is so special about the phosphate group in a phospholipid

It is a polar molecule and the fatty acids are nonpolar This creates an amphipathic chemistry

By looking at a graph of the ETC, what kind of process is going on? What's happening to the free energy over time? Does this make sense?

It is a series of redox reactions or electron exchange processes •the first structure is reduced by NADH and has a high free energy •the electron are passed down the line, each one becoming less charged in the process -free energy is slowly decreasing over the transfer of each complex =makes sense, this energy is coupled with the pumping of hydrogen ions across the membrane (requires the energy that was released)

What establishes the action of certain metabolic processes in the body?

It is all genetically encoded •In regard to CR and fermentation, you need the genes to create the enzymes •enzymes are critical in both processes

What is a redox reaction? Mention reduced and oxidized

It is an electron exchange process •the electrons on one entity exchanges those electrons with another entity Made up of reduced and oxidized •reduced means that atoms have a lower electrical charge = more negative -they accepted electrons in the exchange •oxidized means that atoms have more positive change = less negative -they gave up electrons in the exchange

What is ATP's function?

It is an energy transfer molecule •by breaking down into the form ADP (breaking bond between terminal phosphate group and rest of molecule), it can release energy to power a structure •by forming back into ATP, is stores energy to use for a later time =centerpiece for coupling energy; heart of metabolic process

What is the fiber composite see in animal cells called? What does it consist of?

It is called an extracellular matrix (ECM) •consist of network of elastic collagen proteins (not carbs) -embedded in gelatinous layer of carbs

Why/how do secondary structures form?

It is caused by hydrogen binding •the oxygen in the carbonyl group (of one amino acid) bonds to the hydrogen in the amino group (of another amino) •the peptide must bend to allow this bonding to occur

What is final product after the 5' cap and poly A tail is added to mRNA?

It is considered a fully mature mRNA that is ready to go into the cytosol environment (Leaves through nuclear por complexes) •will be bound by ribosome and used for translation

What is translation in respect of central dogma?

It is considered the second half •the interrogation of mRNA information into amino acid polypeptide information -protein will carry out its function and establish phenotype •interpret based in mRNA into the language of polypeptides

What do chromosomes look like in G1 phase? (2 qualities)

It is considered uncondensed and unreplicated/unduplicated •lots of spaghetti noodles intertwined and random

Where does mitosis happen in the body? Function in body?

It is for the production of body/Somatic cells Functions in: •growth •wound repair •tissue expansion (reproduction)

Where does pyruvate go after glycolysis?

It is funneled into the inner chamber of the mitochondria •mitochondrial matrix Now it awaits processing

How is the 3' end protected in mRNA?

It is given a poly (A) tail for insulation •consists several hundred adenine (A) nucleotides added to the 3' end -extends mRNA life by protecting them from degradation

How is the 5' end protected in mRNA?

It is gives a 5' cap •this is guanosine (G) nucleotide -called 7-methylguanylate =additionally, it served as recognition signal for translation enzymes

What is step one for cellular respiration (and also fermentation) in general?

It is glycolysis •glucose is broken down to from two pyruvate molecules -the energy is extracted and put into activated carriers

How does cholesterol affect membrane permeability?

It is largely hydrophobic with a small polar group •OH group interacts with polar heads slightly •rest is nonpolar and associated with tails =adds on to the hydrophobic reactions occurring between tails •molecular glue so makes membranes less permeable

Why does the ring structure form when glucose dissolves in water?

It is more stable in that structure than in linear form

What is the rotational ability of a polypeptide?

It is mostly held together by single covalent bonds which have the ability to rotate •yet, double bonds (carbonyl group) do not allow for rotation/inflexible •both flexible and inflexible structure

Will the reactants reach the transition state with an enzyme present?

It is much more likely that they will •the enzyme catalyzes the reaction by loading the activation energy (free energy needed to reach transition state) -now the reactants inherent energy is enough to generate products

Which key parts anatomy wise is missing from the RNA "bubble"?

It is not the same as replication •there is no replication bubble because it will not expand across the chromosome -only opens a single gene •there is no lagging and leading synthesis -only continuous synthesis because RNA does not need a primer -5' to 3' direction

At its condensed form at the beginning of mitosis, how many chromosomes are there if a species only has 1 pair?

It is only 1 chromosome (even though it's duplicated) •two DNA molecules (one original and one replicated) =because connected by centromere, it is still 1 chromosome

Why is there a lot of small jagged lines in the free energy graph rather than just one constantly decreasing line or one line straight down?

It is released in small separate bits •each small piece of energy is accepted by an electron carrier Must happen due to large amount of energy in glucose •too much energy in one step to control •heat released would be so high that cells and body would disintegrate -like trying to harness a lightning bolts

What kinds of figure resembles the energy diagram? How so?

It is similar to a food chain •energy is flowed from 1. CO2 is made into sugar by plants 2. Sugars in plants are consumed by animals 3. Animals use sugar for energy 4. Animals die and decomposers break the molecules down and recycle them 5. Starts anew - not webbing affect or species specific =reference is helpful to understand it

What types of conditions are seen with the Krebs cycle? What else is it called?

It is still aerobic because it's liked to a final process that requires oxygen or an electron acceptor •if not for the electron acceptor, this process would not receive the inputs it needs to forms outputs Also called: citric acid cycle and TCA cycle

What happens to biological molecules that are altered by string acids and bases?

It messes up ionic compounds

Where does lactic acid fermentation occur?

It occurs in human beings •red blood cells -do not possess mitochondria, do this instead •muscle cells -sometimes you exercise so hard that not enough oxygen is getting to your muscles -cells make small amounts of ATP to continue exercise

Where does the first checkpoint occur? Is it important?

It occurs in late G1 phase and it the most impetus to one •determined it cell with continue through cell cycle/divide or exit cycle and enter G0 state =gives daughter cells correct genome with high fidelity

What a the function of both slime layer and capsule? (Glycocalyces)

It prevents the bacterial cell from drying out and helps in surface attachment

What is the function of the phosphate group in nucleotides?

It provides a linkage site for other nucleotides to form polymers •it is negatively charged, makes both nucleotides and nucleic acids negatively charged

What is pyruvates function in fermentation?

It provides the mechanism to regenerate NAD+ •molecule still has energy and can work as electron acceptor -Intermediate to accept electrons from NADH to reform NAD+ =continuing of glycolysis

What is the purpose of fermentation?

It regenerates NAD+ which allows glycolysis to continue and create energy (minimal amounts) for the cell

What does the replication bubble signify in DNA?

It represents the active sight of DNA replication •it is happening in those exposed stranded areas -specifically, once it's formed, active sights are on each replication fork

What is the take home message with the graph of ETC?

It shows how first, NADH and FADH2 donate their higher energy electrons to proteins •this energy is contributed, indirect, through redox reactions to create ATP (Creating the hydrogen ion buffer)

Why is the example of 1 bacteria cells creating millions critical to understanding cell theories implications?

It shows that all single celled organism came originally from a single cell •this gives them all common ancestry •in terms of multicellular organisms, they all came from preexisting cells too and are thus also connected by common ancestry =all have a tie back to originally starting cell (contributes to evolution)

What does the Punnett Diagram show? What does it now show?

It simply shows the possible genotypes/phenotypes of the offspring from the cross •a probability of fertilization It does NOT show the process of segregation •not meiosis and creation of separate gametes -this is seen on the outside of the punnet diagram (not really) (how populate outside with gametes)

How long does it take for a cell to complete one cell cycle? How about the substeps?

It takes 24 hours for a cell to complete one cycle (some faster some not at all) •G1 = 7-9 hours •S = 6-8 hours •G2 = 4-5 hours •mitosis = rest of the day (2 hours)

What would occur if there was a mutation where the skin didn't possess desmosomes?

It would be extremely fragile due the tight junctions not being present in the cells •cause skin lesions

Why doesn't hydrogen lose and electron and form ionic bonds?

It would make the atom too unstable, it's properly is to share

What is the energy created in by the complexes called? What is it?

It's called a proton motive force •H+ is the protons, and a gradient is established -they want to come back —> establishes the potential energy to create ATP

What function does DNA polymerase have? Specifically DNA pol III

It's name hints that it creates a DNA polymer (DNA nucleic acid) from nucleotides •pol III is the major enzyme for bacterial DNA synthesis

What are the two forms starch can be found in?

It's unbranched form is amylose and it's branched from is amylopectin

Who discovered the secondary structure of DNA?

James Watson (American) and Francis Crick (English)

What happens if just one amino acid group is switched with another in terms of order?

Just a single change to an amino acid (order included) can change the function in radical ways •it is extraordinary specific and our DNA has this code

What does kin mean? Karyo?

Kin means movement Karyo means chromosomes/genetically material •movement of chromosomes Cyto means cell •movement of cell into two

How do materials in the nucleus get sent out into the cytoplasm and eventually to the organelles? (Such as ribosomal RNA)

Large openings called nuclear pore complexes are found in the nuclear envelope •this allows material to move between the nucleus and cytoplasm

What are glococalyces made of?

Layers of gelatinous polysaccharides and/or polypeptides •no elastic fibers

In a bubble, is leading synthesis and lagging synthesis present in only 1 replicated strands of both? Explain how

Leading and lagging synthesis both appear on a single strand •if one side of the bubble has a leading strand m, it's strand is being directed towards the fork -this means it has 3' —> 5' towards the fork •yet that same strand on the other side of the bubble will have its synthesis going away from the form -still 3' —> 5', but now away from the form and this form a lagging strand Vice versa is true =leading and lagging strands offset each other •creates 4 different quadrants of strand synthesis -if quadrant 1 and 3 will be, for example, lagging synthesis -quadrants 2 and 4 will be leading synthesis

What is one layer (one of the two phospholipids) in a lipid bilayer called? How many of these are seen in total?

Leaflet Two in total (one inner boundary facing the cell; one other boundary facing the extra cellular environment) -inner leaflet + outer leaflet

What is the catch for doing anaerobic CR vs Aerobic? Why?

Less ATP will be made doing it anaerobically (26 v 30) •due to free energy difference between glucose and oxygen -not as high between glucose and substitute electron acceptor

What occurs when someone eats a vegetable like lettuce?

Lettuce is about 90% water can the test is cell wall material (beta glucose) •insoluble to any digestive enzymes so it forms dietary fiber (don't get energy) • 1. travels through alimentary canal and "scrubs the walls" by loosening bacteria/molecules •2. Collect lots of water and adds to liquid and bulk to fecal matter

Behavior of molecules with respect to their polarity/nonpolarity?

Likes will interact •non polar will interact with nonpolar •polar will interact with polar

Lipids vs Carbs energy storage

Lipids are able to store more energy per unit than carbs/more dense •can make a candle out of fat but not out of sugar

What are the four types of carbon-based macromolecules? How do they differ?

Lipids, carbohydrates, proteins, and nucleic acids unique structure and function

Receptors def and how seen in body

Listen/receive to the hormones sent out by other cells •made up of proteins that bind hormones and other signaling molecules -this elicits cascade of responses

What forms organic molecules?

Long chains of carbon atoms

Hydrocarbons

Long chains of carbon covalently bonded with hydrogen atoms filling their valence shells (sometimes oxygen as well)

What are the chromosomes made up of (as seen in eukaryotic cells?

Long double helix of DNA that is wrapped around proteins •called histones

What shape does saturated fatty acids take?

Long linear shape

What is especially lacking in the photo of the bacterial cells?

Long lines that run crisscross and make loops around one another •no internal membranes (no internal organelles) Easily seen in a Eukaryotic cell =but, always exceptions

What does the Krebs cycle produce?

Lots of CO2 •due to the breaking of covalent bonds and rearranging of other bonds (electrons) •this releases energy and forms many molecules of NADH and a couple of FADH2 Small amounts of ATP made (phosphorylation of ADP)

What is the third checkpoint? When does it occur? What happens?

M phase checkpoint (final) •occurs right at metaphase when chromosomes are in metaphase plate •Checks that: -mitotic spindles are correctly attached to kinetochores of sister chromatids -all lines up for centromere separation in anaphase (Helps prevent wrong number of chromosomes in daughter cells=stops Down's syndrome)

What is the T2 virus made out of? (Protein or DNA)? Why is this important?

Made out of both protein and DNA, but Hershey didn't know which part was which •certain portion called coat stayed on the outside of the cell •certain portion that was the HM injected inside the cell -new viral particles is made inside cell Goal was to figure out what the part that stays outside is made out of •then can figure out what was injected inside the cell =what's on the outside of the cell is basis for experiment

What is the anatomy of a chlorophyll molecule? (a and b)

Made up of two units 1. Long "tails" made of isoprene subunits 2. Head consisting of large rings structure with a magnesium atom in the middle

How does osmosis affect plant, algae, and fungal cells that have cell walls?

Main point is that the cell wall is rigid and will not easily change shape •plasma membrane can only expand to cell wall limit so it won't burst •even if water leaves plasma membrane, the cell wall will not shrink -cell membrane detached and constricts cytoplasm =plasmolysis also called wilting

What structure is involved in cytokinesis? What do they do?

Mainly the actin-myosin ring •it creates a new cytoskeleton network -helps cut the cell in half =produced two new daughter cells

What occurs in late prophase I? (Chemistry wise)

Major event is a process called crossing over •homologous chromosomes are lined up to where complimentary nucleic acid sequences are directly connected (identical sequence for genes) -allows a mechanism "homologous recombination" -sequences on one nucleic acid swap with sequences in complimentary nucleic acid (adenine guanine etc) =creates hybrid chromosomes that are recombinant •possess information from both paternal and maternal DNA in a single strand

Which cells usually possess cholesterol?

Mammalian cells possess it in their cell membranes

Examples of saturated fatty acids

Meat, dairy, butter, muscle fat (lard) •stearic acid, arachidic, palmatic

How is meiosis related to heredity?

Meiosis is a sexual reproduction process that produced gametes •these cells contain a complete copy of chromosomes (1n=haploid) -one from dad and mom •combines to form individual/zygote =meiosis (and random assortment) produced the genetic information an offspring will inherit •directly affects heredity

What are the 3 sources of genetic diversity in sexual reproduction? What does it cause

Meiosis: 1. Crossing over 2. Random alignment of chromosomes on metaphase plate (metaphase I) Fertilization: 3. Random union of gametes •represents most unique part due to us having control -four gametes can form with any pattern with four other gametes, multiplex by the total number produced in the sexual reproduction organs =causes random assortment of maternal and paternal chromosomes (genes)

How does Mendels works work with the cell division theory and the information found from Hershey's experiment?

Mendel said that particles were passed down from paren generations to offspring •meiosis showed that this material was segregated into gametes -Hershey's experiment showed that this material is chromosomes that are made out of DNA =DNA provided link between mitosis/meiosis and Mendelian genetics

Which model of heredity was actually proven correct? (Studies done recently)

Mendels Particulate model of inheritance •composed of two principles 1. Segregation 2. Independent assortment

Which researchers proved the correct hypothesis for DNA replication?

Meselson-Stahl •determined which mechanism used for DNA replication -intricate experiment

Why are fats a good source of energy?

Metabolism creates energy by breaking covalent bonds, there are many covalent bonds in a fatty acid hydrocarbon chain

Ionic bonds occur between...

Metal and nonmetal atoms that effectively transfer an electron from the former to the latter

What are centrosomes? What do they contain?

Microtubule-organizing centers •contain structures called centrioles -they help to form and organize the mitotic spindle during mitosis

What must occur if there is an error not fixed by proofreading?

Mismatch repair (another repair mechanism) will fix the error

Difference between daughter cells in mitosis vs meiosis?

Mitosis •genetically identical to parent cell -have the same amount of material Meiosis •not genetically identical •1/2 the genetic material of parent cells -function in life cycle called gametes (sperm and egg)

What process allows an organism to form from a single fertilized egg cell?

Mitosis allows this •maintains chromosome number All cells are identical copies of parent cells

Golgi apparatus function

Modifies lipids and proteins chemically (comes from ER) and distributes them to proper destination inside/outside cell •enter through cis face and exit through the trans face (secretory vesicles take them away)

What two factors effect the permeability of a membrane itself?

Molecular composition •type of fatty acid chain or presence of cholesterol Temperature

What is the result when two atoms bond?

Molecule

Why do molecules distribute themselves evenly (diffuse)?

Molecules all have inherent kinetic energy •this causes constantly collisions between molecules •when they collide they move in the opposite direction and spread out =ultimately average themselves out over time until even concentration throughout space

What is an isomer?

Molecules that have the same molecular formula but different structures

Examples of unsaturated fatty acids

Mono-unsaturated: olive oil, canola oil, avocados, 1 C=C bond Poly-unsaturated: corn oil, fatty fish multi C=C bonds •oleic acid, erucic acid

What is the overall process the ATP used to generate ATP? (Other than oxidative-phosphorylation)

More specific, it's called chemiosmosis •powered by the proton-motive force =chemically driven transfer of protons across membrane to make ATP Also, the process is accredited as the chemiosmotic hypothesis

What would happen if the body didn't possess enzymes?

Most biochemical processes wouldn't occur standard body temp, pressure and pH •the body and cell simply wouldn't function

What are most of the molecules that make up the ETC? What special groups do they contain?

Most molecules are proteins (integral and peripheral proteins) •they contain special chemical groups ——> facilitate redox reactions (the transfer of electrons) -chemical groups: flavins, iron-sulfur centers and hemes

What is the distinction between multicellular organisms and single cellular organisms in terms of fermentation?

Multi=lactic acid fermentation Singular= alcoholic fermentation

How is the DNA code redundant? Unambiguous?

Multiple amino acids are encoded for more than one codon (not a one to one function) Ex: proline, encoded by 4 different codons -redundancy exists in the 3rd base pair in the codon Code is unambiguous: one codon will only code for a single amino acid •GCG al wash coded for Ala

What is portrayed on a pedigree? Is there a notation?

Multiple generations of family members are seen on a pedigree •specific notation is used to show things such as relationship (mother/sister/daughter), sex, and expression of trait

What is the purpose of lactic acid?

Myth: responsible for pain of sore muscles after exercise Truth: it is just a byproduct; buildup of this in muscle cells during exercises, does not make them sore •muscles become damaged and torn, the repairing process interacts with neurons and this causes pain •lactic acid is gotten rid of through metabolic processes (in extreme scenarios it can be dangerous= acidosis)

In glycolysis, what needs to be present to make NADH?

NAD+ needs to be present •it accepts and stored the energy (in the form of electrons) generated in glucose breakdown Energy can't just go anywhere (it'll be too hot)

What goes into the electron transport chain? What comes out?

NADH and FADH2 enter •they fuel this process Also: oxygen ATP is the most important thing that comes out Also: Water

How does the graph of free energy and CR prove the importance of NADH?

NADH can store much more energy in it than. ATP •the graph does not decrease in a smooth pattern, instead jagged -high energy molecules cause a jagged drop due to a decrease in usable energy from glucose -every drop or jagged line —-> more oxidized form of glucose •NADH causes a much larger drop than ATP -it can store much more energy than ATP

What is the precursor step to the ETC? Where is it in the cell?

NADH has been built up by every single part of CR •other electron carries have been built (FADH2 and ATP) =glucose loaded the mitochondrial matrix with reduced electron carriers (even from glycolysis)

What is the process of NADH turning into ATP in general terms?

NADH provides energy to pump protons (hydrogen ions) across the Intermitochondrial membrane •establishes an electrochemical gradient •this dissociated the direct relationship =creates flexibility in how much ATP is produced, allows regulation Gradient is a source of potential energy that can be used (stored) •protons move back across membrane through facilitated diffusion •ATP synthase used this energy to transform ADP into ATP

How do R groups interact act with one another? What does this cause?

Nature of R groups can counteract the formation of hydrogen bonds in secondary structure •like charged R groups repel each other and opposite charges R groups attract each other •in the end, polar R tripod lie interior, nonpolar lie exterior -all intramolecular interactions =causes the final three dimensional shape

After Cricks codon experiment, who cracked the genetic code?

Nirenberg and Leder found which codons coded for amino acids •created a system to synthesize the 64 codons and then determined which of the 20 amino acids they coded for

Amine + amide contain...

Nitrogen

Does chemotherapy affect the brain?

No The brain possesses no centrioles so there's no cell division •no side effects in this area so people are completely lucid

Does heredity only consist of the genetic information passed down?

No •it is not just controlled by the genetics from the biological parents -this is called genetic heredity •complex heredity can come from non-biological sources -the environment for example

Can plant cells conduct cytokinesis the same way as animals cells? Why or why not?

No •plant cells have a rigid strong cell wall -no way it could be constricted because it's not flexible

Does an inverted micelle function as an effective cell membrane?

No It still cannot accommodate a water environment on both sides of the cell •this is seen in animal cells

What causes phospholipids to create the lipid bilayer in our cells? ATP?

No enzymes or ATP is required for this process •structures form spontaneously in the presence of water because it's more stable due to amphipathic nature =in reality, water causes it

Does lagging strand synthesis cause the replication time period to increase? Why?

No it does not cause an increase in time (but would if not for an attachment •DNA replicating factors come together to form a multi-subunit protein complex to solve this problem called a replisome -includes helicase, two polymerases III, and a primase -bond together to form multi-protein =they stay associated with each other and coordinate the synthesis more effectively

Could researchers find the exact position of an atoms? Why?

No, Due to the complexities of the speed of light

Did Griffith identify what was the transforming factor in his experiment?

No, he failed to identify biological factor that transformed R strain bacterial •new experiment by Avery answered this question

Does mitosis occur in phases and takes breaks inbetween?

No, it is a continuous process •occurs all at once and the divisions made (phases) are labeled/imaginary

Does the DNA synthesis (addition of complementary base pairs + hydrogen bonds + phosphodiester bonds) happen spontaneously? Which enzymes assist in this process?

No, it is an enzymatic driven process •primase and DNA polymerase play critical roles in the process

Is the DNA strand completely even in structure?

No, it's a spiral staircase that has long areas (major grooves) and short areas (minor grooves) •most structurally stable way DNA can exist (right handed twist)

Do all cells divide at the same rate? Why or why not?

No, some divide quickly, others slowly and some not at all Ex: skin cells extremely fast to replace dead cells •brain cells never divide Occurs because of regulatory mechanisms that control the rate of division

Is oxygen the only possible electron acceptor in the ETC? What is the problem with this?

No, sulfates nitrates and carbonates can be substituted •but they are not as electronegative as oxygen and will not always accept very decharged electrons -this means a high potential energy gradient can't be formed and not as much ATP can be made =called anaerobic respiration

Are all regulations seen in the cell cycle the same across species?

No, the tight regulations of the cell cycle are species, cell and organism specific •vary considerably

Can the mRNA codons be directly translated into amino acids? Which molecule helps?

No, there must be a helper or intermediary molecule in the process •Crick explained what the adapter was -took that interprets the codon structure in mRNA (reading frame) and into amino acid chains •physically associate codons with amino acids and at the same time for peptide bonds =small RNA molecule called transfer RNA

Can left and right handed optical isomers be used exactly the same?

No, they cannot be superimposed and thus because they're structure differs, the functions cannot be substituted

Can the primers be left alone after they serve their purpose? Why or why not?

No, they must be removed •they are a type of RNA molecule that is only there to start the synthesis process (assist polymerase III) -their chemistry would not compute with DNA so it just be removed and replaced with DNA

What is the tail of a phospholipid?

Non-polar side (hydrophobic) •made of fatty acids (hydrocarbon chains) =repels water

Was any CO2 produced in glycolysis? What is the importance here?

None was produced •No carbon dioxide has been produced but we know that's a byproduct of CO2 -there must be more steps =carbon dioxide reveals the complete breakdown of glucose and extraction of energy

Do cells send replicate damaged DNA?

Normally no, the cell cycle will be stopped •but things can go wrong and cause mutations within daughter cells •sometimes even on purpose -to create genetic diversity

How do the chromosomes usually appear in the cell?

Not as the iconic X shape •spaghetti like strand randomly formed into a jumble in the middle -it's uncondensed form =stays in this form the entire time except when the cell needs to divide

Can allosteric inhibition be overcome?

Not by the conventional route of increasing substrate concentration •the inhibitor will still change the shape of the enzyme regardless and this prevents binding with the substrate =it does cause a lowering in the maximal rate of production

Will exergonic proceses always be spontaneous?

Not necessarily due to the requirement of activation energy to begin the reaction •many instances where this just would occur

How did Mendel choose traits for studying in his experiments?

Not randomly but in a very specific process; 2 major qualifications 1. They had to have easily recognizable phenotypes •versions of a trait 2. Each trait had to have only 2 phenotypes

What is moved by mRNA? (Chromosome or no?)

Not the entire chromosome •recall that certain portions of chromosomes represents genes and now we that one gene codes for a single enzyme =RNA will transport a copy of only a single gene

When did scientists fully conclude that DNA was the hereditary material? How is that fascinating in terms of history?

Not until the mid 1900's •all the studies before with Mendelian inheritance, chromosomal theory, cell division mid to late 1800's to early 1900's -biological processes can be described without known the molecule responsible =even if not all the pieces are know, one can study the patterns and outcome to see how something functions

What is the cytoplasm in the nucleus called?

Nucleoplasm

Macromolecule: Nucleic acids Monomer: Functions: Example:

Nucleotide Store genetic info DNA

What are the monomers of Nucleic acids?

Nucleotides

What are the 3 different criteria used to identify simple sugars?

Number of carbon atoms, location of carbonyl group, and spatial arrangement of their atoms

What is feedback inhibition? What is the common theme example?

Occurs when an enzyme in a pathway is inhibited by the product of that pathway Ex: within a process, three enzymes are present to convert the reactant to an intermediate and finally to a product •each enzyme can stop the process through regulation •common theme= take product of the entire process and let it control very beginning -feedback inhibition (very useful) because efficient

What is allosteric regulation?

Occurs when molecule caused a change in enzymes shape (confirmation change) by binding to enzyme at a location other than the active site •specific kind of non-competitive inhibition Can actually change an enzyme to be able to bind or not be able to bind to substrates

What is competitive inhibition?

Occurs when molecule similar in size + shape to substrate "competes" with substrate for binding to active site on enzyme •it binds to the active site and blocks the substrate from binding (thus lowering the amount of products)

How is asexual production different in terms of the offspring produced?

Offspring are genetically identical to the parent and one another •clones

Where are glycoproteins and glycolipids found? Why is this important?

Often attached to the cytoskeleton within the cell or materials outside the cell •always on the extracellular membrane =this is important for defining what inside the cell vs outside the cell •cells need this help

What are the chunks created in discontinuous synthesis called?

Okazaki fragments •short discontinuous fragments seen in the lagging strand =found to be avg 100-200 base pairs longs in eukaryotes (vary from one species to the next)

On which fork is DNA replication occurring?

On both of them •each respective strand acts as a template and both forks expose the strands =this is called bidirectional replication (away from center of bubble in both directions)

In diploid cells, where does each copy of a chromosome come from? What are they called?

One copy from mother's egg cell and one copy from fathers sperm cell •father and mother contribute same genetic information -each component/copy is called homologous componentes

What is the main issue for treating cancers using modern day medication?

One form can be seen with stopping the mechanism used to move chromosomes —-> prevents cell division •but, treatments can't target specific cells so it effects the entire body -side effects of chemotherapy arises (hair loss, nausea, fatigue, immunocompromised

What occurs in energy conversion processes? What does each process include (pattern)?

One form of kinetic or potential energy may be converted into another •each process has a small loss in energy, usually heat

When performing DNA synthesis, which strand has some issues? (Talk about direction)

One of the templates has an opposite orientation than the template which created the leading strand •it has a 3' —> 5' orientation heading towards the replication fork -the synthesized DNA will be antiparallel to the leading strand -it is being synthesized away from the fork, it has 5' —> 3' direction away (orientation forces this) =this type of synthesis is called lagging strand discontinuous synthesis •will not have one long continuous strand but rather series of chunks

What does it mean that DNA strands and complimentary?

One strand can be read from another •base pairing rules

Which proteins will generally be more reactive? Which ones won't?

Ones with R groups: hydroxyl (OH), amino (NH3), carboxylic acid (COOH), and sulfhydral (SH) more reactive •ones with only chains composed of carbon and hydrogen are less reactive

How many different ways can the letter notation be used for a single trait? List them and give classification. (Use R/r for letter)

Only 3 different ways 1. RR (dominant homozygous) 2. Rr/rR (heterozygous) 3. rr (recessive homozygous)

When do low affinity enzymes achieve maximum rate?

Only at relatively high substrate concentrations

Peripheral proteins structure

Only found on one side of the membrane •can attach to other proteins or leaflets but not on both sides

Which preparations killed mice in Averys experiment? What did this mean?

Only the preparations that contained DNA in them •when DNA was removed, mixture with heat strained and R cells did not lead to Rea formation, mice survived •when DNA was present, the mice died =lead to believe that DNA is the hereditary material (protein was removed but still killed the mice = not genetic material)

Rule electrostatic relationships

Opposites will attract and therefore charges of opposites will attract and re-orient themselves to keep stable and

What is the total span of the cell cycle?

Orderly sequence of events Starting: formation of eukaryotic cell from duplication of chromosomes Finishing: cell undergoes division

How can cells form communication through plasmodemsata?

Organelles such as the ER can form tubules to send across the channel •allow two adjacent cells to have one continuous cytoplasm -allows them to coordinate activities

What occurs in reduction?

Organic compounds are phosphorylated by ATP and NADPH (reduced) •this produces glyceraldehyde 3-phosphate (G3P) molecules

Any molecule with carbon structure is called...

Organic molecule

Polymers

Organic molecules that are composed of chains of subunits (monomers)

Which types of molecules will water interact well with?

Other polar molecules (such as salt or sugar)

What causes the cyclin concentration to change?

Other signaling processes in the body •will cause the increase of transcription and translation -gene expression for making protein •a gene exists for the creation of cyclin -activated in G1 phase, more cyclin protein is created -deactivated in mitosis, cyclin concentration decreases until zero •gene exists for creation of Cdk -on at all times and explains the constant concentration of the protein

Is trans fats bad?

Our bodies transport it differently, it caused artherosclerosis and other heart problems

What is the name of ATP synthesis in the 4th step of CR? What is it?

Oxidative phosphorylation •In the ETC, cells can dissociate ATP synthesis from high energy molecules (provides an energy buffer between inputs between NADH and ATP) -this is indirect synthesis (not one to one) -buffer is the proton gradient =energy is being converted into something else before being used (potential energy in NADH —-> proton gradient ——> ATP

What is the oxidized form of NAD? What is the reduced form?

Oxidized is NAD+ -no extra hydrogen atom has bonded to the molecule -contain less electrons than protons Reduced from is NADH -picked up extra hydrogen so extra electron -has a higher energy

What is the final step to from the ring structure of glucose? What does it produce?

Oxygen atoms becomes bonded to a carbon atom to close off the ring The ring now has a carbon point bonded to one hydrogen atom and one hydroxyl group •two different ways these two groups can be structured

How and why is water formed?

Oxygen has 6 electrons Hydrogen has 1 electron •in order to gain a full valence shell, the oxygen atoms will share an electron with two hydrogen atoms •now each atom has a full valence shell and is more stable than before

What occurs between the pull of an oxygen atom and the two hydrogen atoms?

Oxygen has more protons than either of the hydrogens (6 v 1), this means that oxygen has a greater pull on the electrons than hydrogen has (opposites attract) •therefore electro negativity exists higher on the oxygen side and oxygen has a tendency to be in a negative state •hydrogen has tendency to be in a positive state/charge H2O functions like a magnet

What traits did Mendel study with his dihybrid cross? How did the offspring turn out for F1?

Pea shape and color •homozygous recessive parent -green wrinkled pea (rryy) (r=wrinkled, y=green) •homozygous dominant parent -yellow round pea (RRYY) (R=round, Y=green) •dominant parent can only donate the two dominate alleles (RY), vice versa for recessive parent =All F1 offspring were yellow and round in phenotype and heterozygous (RrYy) for genotype

What type of sugar(s) are in nucleotides (DNA vs RNA)?

Pentose (five-carbon) monosaccharide •ribose in RNA •deoxyribose in DNA (Carbon atoms in sugar numbered clockwise)

What are the linkages between amino acids called? Why are they special?

Peptide bonds •they are a single covalent bond between carbon (of carbonyl group) and nitrogen (of amino group) •through displacement/resonance, the electrons in the carbonyl group can migrate towards the nitrogen, creating an unusually strong single bond

Which category of traits are dominant and recessive used for?

Phenotypes •whether a trait is expressed or masked based on the presence of dominant or recessive traits (respectively) •3 dominant to one recessive —> phenotype ratio in F2 offspring

What is each nucleotide made up of?

Phosphate group, a sugar group and a nitrogenous base

What is the linkage between nucleotides called?

Phosphodiester bonds

What is the anatomy/process behind the glycolysis regulation?

Phosphofructokinase has two binding sites for ATP •one has a high affinity (the active site) -needs ATP as the substrate to create the product •one has a lower affinity (regulatory site) -ATP concentration high—-> ATP binds to this area and causes the enzyme to change shape -reaction rate drops immediately =allosteric inhibition which causes feedback inhibition

What are all plasma membranes and organelle membranes made out of?

Phospholipid bilayer

Since micelles don't work, how do lipids arrange themselves to be effective cell membranes? (Name and explanation)

Phospholipid bilayer can accommodate water on both sides •two sheets of lipids spontaneously interact with each other and the environment -head group is attracted to the water molecules -tail group is repelled by the water and attracted to one another = head groups face outside watery environment, tail groups face each other and form non-watery environment

The 2 lesser organic elements

Phosphorus and sulfur

What is another name for Nucleic acids? Why is it named this?

Phosphorylated hydrocarbons •because it is composed of carbon, hydrogen, oxygen, nitrogen and phosphorous

RuBisCO can perform carbon fixation and .... Why would it do this?

Photorespiration •reverse photosynthesis where ATP produces CO2 It's helpful when CO2 levels are low (allows it to continue producing more sugar) -negative side is that it lowers photosynthesis rates

What are the different types of photosystems? What is there function? Who do they look like (hint CR)?

Photosystem I and photosystem II Work together to use captured light to produce ATP and NADPH •associated with ETC and operate very similarly (but flipped)

How do plants use photons of light to produce energy?

Plants collect energy photons enter the cells and dislodges the electron. This energy can be transformed into bio luminescence or energy in photosynthesis.

What occurs if proofreading finds an error? What structural aspects allows this?

Polymerase backtracks and finds a mistake •will remove the mispaired base that it just added (breaks phosphodiester linkage and replaced the base pair) Can do this because of polypeptide subunit epsilon •after a base is added this subunit checks to make sure it's correct •if wrong, it works as exonuclease (removes incorrect dNTP from newly synthesized DNA)

What is the polymer of amino acids called?

Polypeptide

Unsaturated fatty acids and bonds

Possess one or more double covalent bonds between carbon atoms •this produces a kink/bend = prevents rotation, limits flexibility and changes the overall shape of fatty acid

What category of energy does chemical energy fall into? Why?

Potential energy; energy is stored in the bonds of molecules •molecules position of bonds, breaking of bonds, forming of bonds =all forms of energy transfer

How are ribose and deoxyribose difft? What does this mean for the sugar?

Presence/absence of a hydroxyl (OH) group on the second prime carbon •ribose yes •deoxyribose no =HO imparts polarity and thus chemical reactivity, H lacks this -RNA more reactive (photocopies) than DNA (hard drive)

What are the function of carotenoids?

Primarily, to absorb wavelengths not absorbed by chlorophylls •then pass in the light energy to chlorophylls =extending range of wavelengths that can drive photosynthesis Secondarily, they protect chlorophylls from photooxidative damage caused by UV light and other EM radiation (protection)

Glucose function and examples

Primary brain food and is the basic part of all sugars •starches, sucrose, artificial sweeteners

endomembrane system description + members

Primary system in cells for protein and lipid synthesis and secretion •rough ER •Smooth ER •golgi apparatus •vesicles (others like lysosomes)

Which enzyme solves the DNA polymerase issue? How does it do this?

Primase is a special type of RNA polymerase •builds a short RNA segment from scratch (don't need free prime OH group) -has to occur first in synthesis and lays down primer, then DNA polymerase can lengthen the strand -primer provides free OH group on 3' strand

What is the difference between prokaryotic and eukaryotic ribosomes?

Pro- 70s (svedberg unit) ribosomes •structurally different Eu- 80s ribosomes =critically important to certain antibiotic drugs •shut down ribosomes function in bacteria but don't touch eukaryotic ribosomes -clearing bacterial infections from human body

What did the blending hypothesis explain? Who favored this hypothesis?

Process of heredity creates offspring that are a "blend" (of traits) between their parents Ex: black sheep + white sheep = gray sheep child •botanist Carl Naegeli favored this (colleague of Gregor Mendel) =negated

What did Rosalind Franklin do?

Produced the x ray crystallographic data that Watson and Crick used for the helical model

Who is the main player in photosynthesis? What do they do in the molecular level?

Producers are the main players (plants) •use energy from the sun to strum together carbon atoms in carbon dioxide -form sugar/glucose

The relatively simple process of initiation, elongation and termination is for which organism?

Prokaryotes •found from studying E. Coli Not Eukaryotes

What are the two types of cells?

Prokaryotic and Eukaryotic cells

What are the three types of repair mechanisms? When do you they work?

Proofreading Mismatch repair Nucleotide excision repair Most work during G1 and G2 phase of cell cycle but some work during synthesis phase

How can the laws of thermodynamics be applied to energy?

Properties of these laws help explain the inherent loss of heat within energy conversion processes (especially the second law)

What are the different phases of mitosis? What is there importance?

Prophase, prometaphase, metaphase, anaphase and telephase •importance is not in memorizing them, but under why each phase occurs and how they're connected

Why did many scientists think protein was the hereditary molecule?

Protein is made up of different 20 amino acid chains •heredity is very complex so it needs to be specific to coding information Nucleic acid is only made up of 4 nucleotides •thought it wasn't complex enough

Which molecule is seen (in average) in the same amount of lipids in the cell membrane? What is it's function here?

Proteins •they have effects on transport and fluidity of the membrane

Which macromolecule in the cell membrane can change permeability?

Proteins embedded in the cell membrane can change permeability (amount + type depends)

How are tight junction structured?

Proteins in adjacent cells plasma membrane interact with each other •form tight connections with one another -forms tight connections between cells Cells are stitched/bound together

Molecular Chaperones (Chaperonins)

Proteins that help newly synthesized polypeptides fold correctly in cells

How is energy illustrated in subatomic particles?

Protons and neutrons move little and this have low energy Electrons orbit and fly around so they have very high energy Atoms represent matter and energy

How did Mendels results impact the blending theory? What did it allow him to establish?

Proved this theory was not correct •F1 were not blend of two parents -represents phenotypes of one parent -no half way point or blending of traits =created the principle of segregation •explained how one generation passes down genetic information to the next

Alpha glucose when consumed...

Provides energy which allows someone to run a marathon

What goes into pyruvate processing? What comes out?

Pyruvate (fuels this step) Comes out: Acetly CoA •this is what fuels the next step of the process Also: NADH + CO2

What is another name for pyruvate processing? What are the conditions in which it happens?

Pyruvate oxidation •occurs with aerobic conditions (not fermentation) -does this to prepare for the mitochondria

Which players transfer electrons in the ETC?

Q and heme containing protein cytochrome-c

What enzyme does the synthesizing in transcription? What does it consist of?

RNA polymerase •forms polymers from RNA nucleotide building blocks (NTP's) •direct link to primase (no 3 hydroxyl end needed) It is a holoenzyme (whole) with two parts: 1. Enzyme that does the synthesizing = core enzyme 2. Regulatory subunit that begins the process In the enzymes active sight, phosphodiester bonds are formed •located intersection of these channels

What happens if the body wants to start breaking down protein? (What goes where)

Recall proteins are made up of amino acids •protease break it into amino acids -amino acids needs to be de-aminated -ammonia (NH3) extracted and leaves carbon chain (Sometimes 2-6 carbons) Based on # of carbons it determines where in the cycle •end of glycolysis (3), pyruvate processing end (2), intermediates of the Krebs cycle (6-4)

What special structures are found in the complete ribosome?

Recall that it contains a large and small subunit •has binding pockets that house 3 tRNA molecules in the fully intact ribosome (only exist in fully assembled ribosome) -called A,P, and E sites =all are structurally different and help in allowing the ribosome to interpret mRNA informational

What is the function of NADH in the ETC?

Recall that it fuels the ETC because it's the input •NADH is high energy and can be used in electron transport processes -redox reactions: gives electrons and takes it out NADH allows electrons to be transferred/transported through extraction •leads to the formation of ATP from released energy

What happens if the body wants to start breaking down fats? (What goes where)

Recall that it's three fatty acid chains bonded to one glycerol molones Fatty acids: will be broken down into two carbon group •binded with coenzyme A -fed into Krebs cycle directly (bypass last step) Glycerol: 3 carbon molecule •fed into glycolysis as an intermediate •becomes pyruvate -then rest of process

What is the function of the reaction center?

Receives the light that is funneled from the antenna •light energy is captured here =the conversion of light energy to chemical potential energy •excited electrons transferred to electron acceptor (reduced)

How does nucleotide excision repair fix thymine dimers?

Recognizes this type of damage •carves the dimers out of the single strand -fills in the space with unaltered base pairs (uses the complementary strand) =functionializes the DNA again

How does redox reactions relate to energetic coupling?

Redox always consists of both a reduction and oxidation, the electrons had to come from somewhere! •can't reduce a molecule without oxidizing another In a sense, one molecule has a higher energy due to an increase of electrons, it exchanges (releases) those electrons to another molecule which accepts (absorbs) them to become higher in energy •fundamental to how energy is transferred in exergonic and endergonic processes

What phrase described the overall goal of Meiosis? What does it mean?

Reduction division •specific purpose that applies to fertilization in the life cycle -division of the genetic material in a parent cell to produce daughter cells with 1/2 amount

pH scale

Reflects the concentration of hydrogen ions (H+) in an aqueous solution

How are Eukaryotic genes different from prokaryotes?

Regions of the genes that are made into mRNA protein message include particular sequences •called intervening sequences or introns -break up message and must be removed •also exons or regions of coding that will be a part of the final mRNA =the gene is much longer than the actual corresponding mRNA

What two factors do cells use in general to control the cell cycle?

Regulators and checkpoints •no cell moves through cell cycle if not appropriate (needs special permission to conduct division) -permission comes from neighbor cells (they can communicate through chemical stimulus)

Anomers of glucose

Related molecules that are configured/structures in a slightly different manner in terms of the hydroxyl group

After the two experiments contained the labeled viral cells, what did Hershey do next?(not including last step)

Remember 2 separate experiments •infected E. coli bacteria with the viral cells that was radioactive DNA and viral cells with radioactive phosphorus -all done separately •stopped the process before the infection cycle was complete -coats were still present outside the bacterial cells -viral particles still inside bacterial •each cultures were placed in kitchen blender -agitation of mixing caused viral coats/particles to fall off bacterial cells -detached virus from bacterium

Monosaccharide

Repeating chains of hydrated carbons •simple sugars •building blocks of carbohydrates (monomers)

What specifically happens in interphase? (Direct link to mitosis)

Replication •the instructional/genetic material, in the form of chromosomes, are copied

What happens at the very end of the ETC?

Residual (leftover) energy is added to oxygen •oxygen key reactant

What is the process of how the energy is transferred called in the photosystems?

Resonance

Which structure (not really organelle) do both prokaryote and eukaryotes posses? What are their importance?

Ribosomes •macromolecule assembly of polypeptides and RNA molecules •two main part -large subunit and small subunit Function: make (synthesize) proteins (work horses of the cell) solely

What two terms did Mendel use to explain the ratio he found in the F2 generation?

Rounds seeds appeared the majority of the time (3 our of 4) •called the genetic determinate dominant traits (dominant = more prevalent) Wrinkled seeds appeared less so (1 out of 4 times) •called the genetic determinants recessive traits (recessive = less prevalent)

What enzyme fixes carbon? What is special about it?

RuBisCO Ribulose 1,5-bisphosphate carboxylase/oxygenase •most abundant protein on earth -since it creates glucose (starting molecule) every organism on earth relies on it

Capsule structure and function

S: It is a thick layer and is firmly attached F: helps pathogenic bacteria from being phagocytized (by making it extra greasy so immune cells can't attach to it)

What is the structure and function of fiber composite material?

S: made up of long filaments F: protects the cell against stretching forces •stops from tearing the cell in half or breaking a connection between two cells

What is the structure and function of secondary cell walls?

S: more rigid than primary cell wall F: this adds strength to the cell and acts as a stiffening agent (prevents compression) •called lignin (organic polymer) Ex: Wood

What is the structure and function of collagen fibers?

S: twisted rope of three chains which gives it a lot of structure F: creates a lot of flexibility in order for tissues to move and conform to support locomotion

Slime layers structure and function

S: very slim, whispy and not firmly attached F: important for surface attachment (hook onto cells of other organisms)

What is the difference between saturated and unsaturated fats at room temp?

Saturated fats are able to make many connections with its carbon bonds •these connections squeeze against one another and it takes a lot of energy to break them =this makes saturated fats solid at room temp Unsaturated fats have a kink which does not allow the carbon atoms to be packed together tightly •it takes less energy to break these bonds =unsaturated fat is a liquid at room temp

What does the second law of thermodynamics help clear up? (Need ti apply molecules)

Says that whenever the conversion of energy or matter happens, randomness/disorder is favored •molecules at many times come together to create more ordered structures (contradicts second law) -since there is conservation, every order process has its respective disorder process (this is heat loss) =we can get out energy from a molecule (usable), but it costs something •gotta keep up the environment and cause disorder (entropy is satisfied)

Quantum mechanics and electrons

Says the positions of electrons form some shelves that determine the overall shapes of atoms •Gives a shape where an electron can exist at a certain time

Example of selective adhesion with sea sponge?

Sea sponge is an organism with relatively few types of cells, very simple organisms •researchers dissociated all the cells •saw that connections formed between same cells rather than just randomly (selective adhesion) =In the end, sea sponge completely re-organized itself and regained function (Didn't look like original)

Which cells have lots of Golgi apparatus?

Secretory cells such as glands •salivary glands and immune cells (antibodies)

What were the three hypothesis for how replication occurred? What did reach say?

Semiconservative replication •of two new DNA double helixes, each consist of one new strand and one old strand -each old DNA strand is copied to generate new DNA strand, makes sense that old is linked to new Conservative replication •one double helix consist entirely of old DNA strand and one is two new DNA strands -original chromosome copies by remains unchanged Dispersive replication •each strand in both double helixes is a combination of information of new and old (like crossing over)

How can cells sense DNA damage during G1 and G2 checkpoints?

Sentry proteins exist in the cell •scan the DNA for damage during both checkpoints -if lots damage, signals to cell to stop progressing through checkpoints

What is BRCA?

Sentry/marker proteins that when not functioning correctly are the most common cause of breast cancer •most forms breast cancer -early screening tools if woman is preconditioned for this disease

Golgi apparatus structure

Series of flattened membranes that contain flattened sac like compartments called cisternae •cis face: area closes to ER •trans face: area furthest from ER

How do the condensed and uncondensed forms of DNA compare?

Similarities: •contain DNA/genetic material •have lots of protein in time -DNA + protein = chromatin Difference •protein helps either keep them unraveled (uncondensed) or to organize them into tight structures (condensed) •different states at different portions of the cell cycle

Which cells have lots of RER?

Similarly to ribosomes, cells that secrete lots of protein like the pancreas

How is the Krebs cycle regulated?

Since NADH is the primary product —-> it is the feedback inhibitor molecule of the process •inhibits then many enzymes in the cycle =as NADH builds up, cycle slows down ATP also works (so does FADH2) •but NADH happens in the very beginning so it's critical to not wasting raw materials •it's the primary output of the cycle

What is interesting about ATP being produced from photosystem 1 and NADPH being formed from photosystem 2?

Since NADPH can hold so much more energy, it's electrons can be catapulted twice by the energy of photons •ATP can't hold as much so it can only handle 1 time

What is the difference between sister chromatids and non-sister chromatids?

Sister chromatids: •identical copies of the same chromosome which make up one of the homogenous pairs -contain the exact same genes and sequences Non-sister chromatids: •each one is from each homogenous pair, they "bind" together in crossing over -each (hereditarily) presents maternal and paternal sources -code for the same genes but have slightly different letter sequences (not identical=blue eye color vs brown eye color)

Chloroplasts function

Site of photosynthesis (production of glucose) •stroma spaces convert light energy into chemical energy (stored in sugars)

What two factors determine if a solute can cross the lipid bilayer? How so?

Size and charge effect the rate of diffusion •tiny molecules cross much easier than large molecules -ex: O2 (covalent bond) freely permeable -proteins are too large to get across •uncharged molecules cross easier (hydrophobic yes, small polar yes) -H2O crosses easily (not as easy as O2) -ions are charged and cannot cross (bounce off) =chemical properties dictate whether molecule can cross

How can R groups differ?

Size, shape and chemical reactivity

What are the two subcategories of glycocalyces?

Slime layers and capsules •it can take on characteristics of each

How do capsules and slime layers sit in respect to the cell membrane?

Slime layers are on the bottom and capsules are above them

Veisicle structure

Small spheres of membrane; membrane bound sacs •formed by budding off the ER or Golgi

Which molecules will easily form a balanced concentration gradient in the cell?

Small uncharged molecules like O2 and CO2 •the lipid bilayer can't stop these molecules from traveling across •can't achieve concentration gradients

Supplementary organic elements (3)

Sodium, magnesium and calcium

What characterizes isotonic solutions?

Solute concentration are equal on the outside and inside of a cell •equal osmolarity to the cell

What are the ions?

Solutes (the thing being dissolved)

What characterizes a hypotonic solution?

Solution outside the cell has lower solute concentration than inside the cell •Lower osmolarity (more water) than fluid inside cell

What is the water?

Solvent (doing the dissolving)

Water is an excellent _____ for polar molecules and ions

Solvent (most molecules are polar)

Are isotopes stable or unstable?

Some are stable but the majority are unstable •they decay/split apart into smaller atoms and/or subatomic particles

What did critics say about Averys experiment? Who made the conclusive study?

Some said that all the protein could have not been removed •only a small amount left would still allow transformation =removal not 100%, could have been problem in the experiment •although important, experiment was not conclusive •Hershey and Chase did the final experiment -completely new experimental system

In terms of the last point, how is energy circulated in the world?

Someone eats lettuce and they get carbohydrates •that lettuce got its carbs from CO2 in the atmosphere -that person breathed out CO2 The matter we are made out of exists from other organisms, those organisms got those molecules from us =recycling completely of molecules (we are tied together)

Can malignant tumors be extracted surgically?

Sometimes but most likely no (especially in certain regions of the body) •not ice cream scoop tumor -after removal, it can still pop back up in neighbor tissues or other tissue

Protoplasmic space

Space inside the cells; carries out life's functions

What is the activation energy?

Specific amount of energy needed to get a reaction started/to occur (Ea) •it's the cost that needs to be paid or the barrier that needs to be crossed •difference between reactants/products and the peak in energy diagram =entropic cost to get the reaction started

Where does replication begin on DNA?

Specific places called the origin of replication •chromosomal sequences that function as starting points for proteins

What does each complex in the ETC represent? Why is that important?

Specific redox factors •can exchange electrons down a line (like a handshake) •each transfer is a coupled redox reaction -energy exchange process They are ordered in a specific fashion •each can accept electrons at a specific energy level and can pass it down

Who are the major players of anaphase? What are their conditions?

Spindle fibers •already attached to kinetochores, they "pull" on each sister chromatid and take them to opposite sides of the cell Sister chromatids •once they are pulled apart, they stop being chromatids and are once again called chromosomes (no more centromere)

What are the major players in Metaphase? What do they do/position?

Spindle fibers (located in each pole) •move the chromosomes into the middle of the cell by tugging on the kinetochores (in centromere region) •creates imaginaras plane called metaphase plate Chromosomes •still completely condensed, duplicated sister chromatids •three dimensional figures lined up in the middle (organized) -actually a whole disk just found in the middle of the cell

What occurs in metaphase I of meiosis?

Spindle fibers move the chromosome pairs to the equator •they are present not as a single file like but as two pairs (one paternal homologous chromosome, the other maternal) -at this point called tetrads

Precursor to steroid?

Squalene, made up of many difft fatty acids stringed together

What is necessary to know where a gene begins and ends?

Start and stop codons exist in the genetic code •start codon gives the start for the reading frame -special AUG codon (only one) -also coded for amino acid methionine •stop codon tell the reading frame it's time to stop translating here -three of these: UAA UAG UGA =establishes mechanism for translation

How does one read a genetic code table?

Step 1: first letter of the code will be on the left side of the table Step 2: second letter along the top Step 3: find third letter along the right side =can find the amino acid that any codon codes for

With steps of cellular respiration take place in mitochondria?

Steps 2 + 3 + 4 (pyruvate processing, Krebs cycle, ETC) •these processes are all aerobic as well (connection between the mitochondria and the dependence of oxygen)

Imagine a cell starts the G1 phase with 4 chromosomes, how many appear in the G2 phase?

Still 4 chromosomes •S phase occurred inbetween these processes -DNA was replicated •each chromosome before is now a double copy with two sister chromatids

Vesicle function

Storage and transport •carry lipids and proteins to appropriate targets -some times cells surface

Lysosomes function

Storage and waste processing •enzymes break down proteins/lipids/carbs/nucleic acids and even organelles -when not needed by the cell (Can also destroy pathogens)

What other substrates can be used in the catabolic pathways to make ATP? Why does this happen?

Stored lipids can be used •as well as proteins They are balanced out by anabolic pathways •they build other molecules with the free energy produced

Channels structure and function

Structure: amphipathic molecule with polar ends facing each side of the cell membrane •it is "gated" Function: acts a funnel for polar substances •can open and close depending on what the cell requires (can passively control concentration within cell)

Intermediate filaments structure and function

Structure: fibrous proteins bound together Function: purely structural -bear tension and maintain cell shape -anchor nucleus/organelles in place Ex: Keratin

Microtubules structure and function

Structure: hollow tubes •widest compartment Function: helps resist compression •helps vesicles love •pulls chromosomes during division •structural element of flagella, cilia and centrioles

Micro filaments (actin filaments) structure and function

Structure: most narrow of the filaments •composes of two globular units (actin Function: cell movement + communication mainly •also helps in cell rigidity

Which model organisms did Hershey study? In what ways?

Studied the bacteriophage (bacterial virus) T2 and bacterium Escherichia coli. (E. coli) •did not study the transmission bacterial DNA from organism to organism •studied how a virus infects a bacteria, how it gets its genetic material inside the bacterial cells -do viral genetic info consist of DNA or protein?

What is bioenergetics?

Study how energy flows between different organisms on the planet = How organisms exchange energy to fuel life's processes

What (in general) creates connections between cells in animals?

Substance similar to conductive jelly (like in ultrasound jelly) •holds the cells together •hydrated mosaic of materials flowing around Middle lamella like material

Knowing what it takes to replicate DNA? What is necessary before the S phase?

Substep of the cell cycle called G1 phase (gap) •this a time of growth of the cell •acquiring all the resources needed for DNA replication =brand new cell out of mitosis, wants to get bigger in size + acquire resources

What is the name of ATP synthesis in steps 1 + 3 of CR? How does it work?

Substrate-level phosphorylation •the phosphorylation of ADP directly from the release of energy creates ATP -enzyme-catalyzed transfer of phosphate group from intermediate substrate to ADP -one time one fashion (give bond to break —-> get ATP) =one style of making ATP

How can one picture chemical reactions occurring the cell?

Substrates are hurdling at each other in three dimensions •constantly striking one another -these are usually non products b/c they aren't the correct match or they aren't coming at the correct speed Also, the atoms in the substrate have a negative electron cloud that repels each other •this makes it even more difficult to form bonds and be productive

Macromolecule: carbohydrate Monomer name: ? Functions: ? Example:

Sugar Stores energy and structural material Potato

Does table sugar dissolve in water Im the same manner as table salt?

Sugar is sucrose and this molecule has a covalent bond (C12H22O11) •water is not strong enough to completely break down all the bonds, therefore sucrose molecules still remain in water

Glycoproteins and glycolipids

Sugars that have been joined to proteins and lipids by strong covalent bonds on the cell membrane

What other substances can be used in place of oxygen?

Sulfates, nitrates and carbonates can also be used •they can still proceed with the 4 steps of CR (complete oxidation glucose)

What occurs in the light-dependent reactions? What is used and produced?

Sunlight energy (solar) is captured •it can be used to create ATP and electron carrier NADPH (phosphorylated form) Water is used to release electrons and oxygen is produced as a byproduct

Chloroplasts structure

Surrounded by double membrane •inner membrane called thylakoid membranes -fluid of inner membrane called stroke •thylakoids stacks (interconnected + fluid filled stacks called granum) present made up of individual thylakoids •inside is thylakoid space

Nucleus structure

Surrounded by nuclear envelope/membrane •double membrane (two lipid by layers) •outermost continuous with rough ER

SER function

Synthesis of fatty acids and phospholipids (lipids in general) •carbohydrate metabolism •steroid metabolism •drug detoxification •calcium regulation •Gluconeogenisis

What happens when table salt is placed in water?

Table salt has an ionic bond and thus interacts with water (a polar molecules) •water surrounds the cations and anions and breaks a part their ionic bonds (water is stronger) •the polar associations between ions are broken and the water molecules surround each ion

Why are there so many different versions of cancer and each one is unique? (Broad explanation)

Take MPF as an example •made up of two protein subunits Similar promoting factors outside the G1 and G2 checkpoints -made up of their own protein subunits Also other regulator molecules (sentry, growth factors) =huge amount of factors for regulating the progression of the cell cycle •if any one is damaged/nonfunctioning = cancer will occur

How are the rings of steroids made (easy def)?

Take fatty acids, stringing together into longer chains and lastly folding them up into ring based structures

How can one represent secondary structure? Tertiary structure? Quaternary structure?

Take the string of beads and twist certain regions if it, you get this 2 structure •take those folded regions and mash it to from one big mass = 3 structure •link that mass with another protein mass = 4 structure

What occurs in fixation?

Takes carbon dioxide out of atmosphere and attacked it to other organic compounds (intermediates) •called carbon fixation (exact opposite of carbon decarboxylation seen in CR)

What is the overall job of the Krebs cycle?

Takes the rest of the energy found in bonds of acetyl groups and releases it •stores this energy in activated carriers (NADH and FADH2) •Pool energy into carriers and send it to the last step =finish oxidation of glucose

Will the reactants reach the transitions state without enzymes?

Technically yes, it is still a spontaneous process •but is is very rare (low probability) -the reactants have their own inherent kinetic energy but surpass the barrier very slowly -not at all helpful for the cell

What did the experiment by Frye and Edidin (1970) prove?

That the plasma membrane is not static but instead fluid/dynamic

How does Cdk specifically phosphorylates enzymes?

The Cdk holds on to a molecule of ATP in its active site •when it binds to a cyclin, it causes the dephosphorylation of Cdk which caused the jumase to phosphorylate an enzyme

What happened in Mendels experiment when true breeding plant for round seeds mated with a true breeding plant for wrinkled seeds?

The F1 offspring/hybrids were produced •every single one of them every single time was round -wrinkled never showed up in the F1 generation

Which checkpoint defect is the most common cause of cancer?

The G1 checkpoint •most important one •mistake will cause huge implications (cancer)

What is the Calvin cycle the exact opposite of?

The Krebs cycle •NADPH and ATP are being oxidized to form their substrates •CO2 is being incorporated rather than released

What is energy? (Formal definition)

The ability to do work

What is energy? (informal definition)

The ability to do work isn't very helpful... •examples are the best way to understand it -the attraction of particles to one another (create bonds) -fuel: you can eat energy (chemical energy) through sugar =lots of different types and it's seen in lots of different ways

What mechanism allows cells to create the pattern piece of cell theory?

The ability to make copies of themes levels (process) •almost all cells can do this •perpetuates a species into survival

What is catalysis?

The action to speed up a chemical reaction •usually facilitated by an enzyme •also makes the reaction go easier (higher probability)

When the polypeptide bends in secondary structure, what two forms are seen?

The alpha helices and the beta pleated sheets

What feedback mechanism exists with Mitosis-promoting factor?

The appearance of two protein subunits hints at this •Cdk can only function when it is attached to a cyclin protein •Cdk, when functional, phosphorylates enzyme that degrades cyclin =this helps prevent Cdk from making the cell divide constantly, instead happens in a controlled way

What occurs when the valence shell is not filled?

The atoms are likely to gain or lose electrons to achieve a stable electron configuration (this is what dictates its chemical properties)

Electronegativity

The attraction of an atoms nucleus for the shared electrons in a covalent bond (Larger atoms are more electronegative than smaller ones)

Atomic mass

The average mass of all the isotopes of an element

How does Mendel's principles of inheritance apply to meiosis?

The behavior of gamete formation is explained through the principles 1. Principle of segregation: says that gametes carry only 1 allele (one HD) due to segregation of alleles •in Metaphase I, homologous chromosomes with alleles/genes are separated independently into two different cells -produced haploid gametes, in meiosis I this created 4 gametes with one copy of the chromosome 2. Genes are assorted independently of each other b/c located on different chromosomes •In metaphase I, chromosomes line up at the metaphase plate in multiple ways -genes on the nonhomologous chromosome assort independent of one another

How can cellular respiration be linked to energetic coupling?

The breakdown of glucose is an exergonic process •releases energy This energy it utilized to create ATP (from ADP) so it's endergonic •the energy required comes from glucose, it's absorbed and utilized Breakdown of ATP releases energy to do something else so it's exergonic -provides the necessary energy for an endergonic process =the energy flows throughout our body and it's transferred between energetic coupling •satisfies the first law of thermodynamics as well

Hydrolysis reaction

The breakdown process of polymers •each reaction used a single molecule water to split a large molecule into monomeric subunits •gains a water in the new chemical formula

What is the final outcome of pyruvate processing? Where did those products come from?

The carbon atom was broken and this released energy (electrons) •transferred to create NADH

What is the process of a cell getting ready for mitosis called? What is included in it (not specific)?

The cell cycle: interphase •lots of growth needs to occur •the DNA of a cell needs to be replicated

In most situations, how do small/nonpolar molecules move across the membranes of cells spontaneously?

The cell uses the principle of diffusion and concentration gradient to have these molecules come into the cell •this principle is due because of inherent kinetic energy (These molecules also meet no resistance from the membrane due to their chemical nature)

What occurs in anaphase I?

The centromere are NOT being split, sister chromatids remain attached •duplicated homologous chromosomes are transported to opposite sides of the cell =produced haploid meiotic I cells

What allows synapsis to occur? What advantage does this create?

The cohesin proteins form a network called the synaptonemal complex •acts like glue for the synapsed chromosomes (homologous chromosomes); cements non sister chromatids Allows crossing over to occur because it's done in a very particular way

Nucleus function

The command center of the cell that contains the chromosomes or genetic material

What was Mendels Model Organism? Why?

The common garden pea (pisum sativum) •easy to grow •short reproductive cycle -life cycle is only (3 months) •each plant produces large # peas -pea = new organism, it's a seed and has embryo inside of it -can grow new plant from seed •control matings -which plants mated with each other •traits were recognizable

What is the overall purpose of cellular respiration?

The complete oxidation of glucose which can then be used to create ATP

What specifically happens in mitosis?

The copied chromosomes are partitioned into daughter cells •2 daughter cells genetically identical to parent phase

Can a cell finish cell division if the mechanism for moving the chromosome fails? (In anaphase) Can this be beneficial?

The correct functioning of motor proteins to walk the chromosome down spindle microtubules is a critical process •cell division cannot complete if this isn't working =when cells divide uncontrollably, it could control these cells by shutting down the mechanism (can treat tumors)

What happens when a monosaccharide such as glucose is dissolved in water or in solid form?

The covalent bonds will have the ability to rotate around one another, which allows glucose to rotate into a six-members ring structure

What is the introplasmic space of a bacterial cell?

The cytoplasm •all the internal contents of the cell •structurally, not much going on (lots of ribosomes; DNA)

How did Watson and Cricks model explain replication (broad)?

The double helix could be unzipped to separate the two strands •each strand now acts as a template to produce another DNA helix -nucleotides added to the new strand to create complementary bases

What part of DNA has hints to the questions researchers asked?

The double helix structure of DNA molecule itself

Why is oxygen a perfect molecule for end of the ETC?

The end of the ETC produces electrons that have lost most of their charge •very low energy states But oxygen is so electronegative that it accepts any electrons

What is the final (broad) step for mature mRNA in Eukaryotes? Why is this necessary?

The ends of the linear sequence must be protected •5' cap and poly (A) tail is added to the 3' end DNA is located in nucleus and ribosomes are in the cytosol •nuclear environment is safe while cytosol is dangerous -enzymes could destroy the ends and message will be nonfunctional

What happens when the polysaccharides are branched?

The energy storage increases and becomes more dense

What is the importance of oxygen in the ETC? (General)

The entire process depends on the availability of oxygen •this an electron acceptor at the very end of the chain •this forms water

How does the body break apart glycogen and starch?

The enzymes amylase (released in saliva and by the pancreas) and phosphorylase breaks down the alpha glycosidic linkages in starch and glycogen •broken down subunits can be used to make ATP (energy)

Why are the cells in a eukaryotic organism diploid? (Think of process of making organism)

The first cell the organism came from is a fertilized egg cell •this was a diploid cell -Union of sperm and egg cell (1n + 1n = 2n; haploid) to make a zygote Then that cell divides to make trillions and all descendants are diploids

Which part of central dogma correlates to transcription? How so?

The first half •the process of DNA being turned into RNA -specifcally mRNA

What are the first three steps of cellular respiration for? And how about the last one? (Function ATP broad)

The first three (glycolysis, pyruvate processing, Krebs cycle) all function to pool high energy activated carriers •they bring it to the last step, the electron transport chain (ETC) In ETC, the energy is collected from the carriers and used to from ATP

Why did each codon have to be made of 3 letters according to Gamow?

The four nitrogenous bases needed to code for 20 unique amino acids •a triplet or three based code would allow the minimum amount to code for each amino acid -1 based code = 4 possible combinations (can't be, not enough) -2 based code = 16 (not enough for 20) -3 based code = 64 (more than enough for 20 amino acids)

What does the rate of a chemical reaction depend on?

The free energy contained by the reactants and the activation energy necessary to achieve the transition state •can the reactants have enough energy to break down the barrier and start the process of becoming products

The cell theory listed a structural and functional part, which part does this unit analyze?

The functional part •all cells are made of preexisting cells, but how? -cell cycle and mitosis answer this question

What occurs to micelles when the lipid/water ration changes? (Huge amounts of lipids and very small amounts of water)

The heads would all be attracted to the water molecules (forms a circle) •this traps the water into a sphere (opposite of usual composition) The tails would be repelled from the water inside •they face the outside which has no water =creates an inverted micelle

What occurs during DNA supercoiling?

The helicase creates torsional strain (tightening) •over or under twisting changes the structure of DNA helix -cannot bind to proteins due to altering of major and minor grooves =functions are comprismsed

What are the two ways the carbon ring can form?

The hydroxyl group can be placed either down in orientation (other side of carbon 6) or up in orientation (same side of carbon 6)

What caused tertiary structures to be formed?

The interactions between the R groups or between R ground and the backbone

What function to beta polysaccharides have?

The lattice formation makes great structural material in living organisms •amylase can't touch these

What is the light I see from plants?

The light which the plant cannot absorb so it must reflect it •sunlight (white light) hits them in all wavelengths of light and they can't absorb all of it =white light has all the colors of light in it

Where can peroxisomes be found in abundance?

The liver •functions to break down alcohol

During elongation, where does the newly synthesized RNA travel to? Where is the unzipped portion of DNA located?

The mRNA leaves through an exit site once it's been synthesized The unzipped double helix only exists inside the active site of the core enzyme •as soon as it enters it is unzipped by DNA pol, and it immediately reanneals once it leaves -single stranded DNA is not located outside the enzyme, no large bubble is seen as in replication

What important background knowledge did Hershey and Chase know?

The mechanism begins a virus infecting a bacterial cell •tail fibers are used for attachment outside bacterial cell -can then insert its hereditary material (HM) inside the cell =HM makes bacterial cell produce copies of itself •new viral particles are produced and released from host cell

How are chromosomes transported during anaphase? (Specific; structure and function)

The microtubule is dissociating while the chromosome's kinetochore is walked along microtubule Ex: microtubule is like train tracks and kinetochore is the head train + chromosome is the body Players: •microtubules -just long filaments made up of protein, they can disassemble into amino acid groups •motor proteins -structures that connect with the kinetochores "crown" and walk it along the spindle fiber

receptor-mediated endocytosis

The movement of specific molecules into a cell by the inward budding of membranous vesicles containing proteins with receptor sites specific to the molecules being taken in; enables a cell to acquire bulk quantities of specific substances.

Why is the breaking apart of ATP an energy releasing process?

The negative charges (4 total) in the phosphate groups repeal each other •by releasing a lone phosphate (hydrolysis), it produced a burst of energy

What happens to the chromosome over time when telomerase is present?

The newly synthesized Okazaki fragment covers some of the telomere region each time replication occurs •this makes the chromosome lengthen over time =better than shortening

What occurs to the membrane around the chromosome in prometaphase? Why?

The nuclear envelope breaks down •this allows the spindle fibers to attach microtubules to condensed chromosomes -spindle fibers can't cross the nuclear envelope, can't move the chromosomes =instead, spindle fibers on either side of cell attach microtubules to their respective sister chromatid

Electron configuration of atoms

The number of electrons in each of an atoms electron shells

What is the idea of "ploidy level"? What are the different types?

The numbers of copies of each chromosomes in the cells •diploid: each cell has two copies of every chromosome (2n) -2 copies of chromosome 1... 23 in humans •haploid: each cell (gametes) have only 1 copy of every chromosome (1n)

In simple terms, what about the replication process causes the occurrence of leading and lagging strands?

The orientations of the template which will affect the orientations of the new strands •they just be antiparallel to each other •can only travel in the 5' to 3' direction (need free hydroxyl group)

Valence shells

The outermost energy shell of an atom, containing the valence electrons involved in the chemical reactions of that atom (dictate the chemical properties and interaction) •does not always have to be filled

What problems does the overhang of linear chromosomes cause?

The overhang or the single strand left over by the primer will be disintegrated •enzymes exonucleases will get rid of them -the original chromosome will have shortened and lose genetic information =if happens over time (especially when cells replicate quickly), the chromosome will shorten each time where important genes are compromised •causes genetic mutations and problems

How exactly did Mendel use true breeding and hybrids in his experiments?

The parental generation was also a pure lime that differed in one trait (sometimes) •the hybrids created where offspring called the F1 generation (first filial)

What happens when a phospholipid is placed in water?

The polar head interacts with water while the nonpolar tail repels water •they immediately arrange themselves into a double layer, with the heads on the outside (interacting with water) while the tails are insulated on the inside =creates a bilayer membrane

What is the "head" of a phospholipid?

The polar side of the molecule (hydrophilic) •phosphate group =causes it to interact with water

Polysaccharide

The polymer of carbs which is formed from the condensation reaction of monomers (monosaccharides) •hydroxyl groups react together to create an oxygen and water molecule

What are the two types of Nucleic acids?

The polymers are ribonucleic acid (RNA) and deoxyribonucleic acid (DNA)

What caused the hydrogen bonds to form a particular fold in secondary structure?

The primary structure or the original placement/order of amino acids •some amino acids are more likely to form alpha or beta structures

What principle explains the ratio found in the offspring of dihybrid F1 generation crosses (F2)? How?

The principle of independent assortment •explains gamete formation (outside the punnet diagram) •simply extension of segregation =says, when tracking two genes at once they follow the principle of segregation •sort themselves into gametes independent of each other (one has no impact on the other) -this independence gives equal representation of possibilities in gametes (no total domination by one type)

What is energy coupling?

The process of cells pairing endergonic/non spontaneous process to an exergonic/spontaneous process •energy released in endergonic process is fueling the energy requirement of endergonic process

How is feedback inhibition efficient?

The product of the reaction inhibits the very first enzyme at the start of the reaction •no intermediate enzymes will create intermediate molecules -energy will not be burned to create something that not useful halfway done =not burning raw materials which won't turn out to be a product

How did breaking a gene lead to the one gene one enzyme hypothesis?

The production of a null mutant effectively breaks a gene •a specific phenotype could be broken as a result -phenotype is controlled by enzymes, therefore the enzyme would be broken as well =genes contain the information needed to make proteins/enzymes Called the one-gene, one-enzyme hypothesis

What happened the F1 generation were crossed with each other in a dihybrid cross? (F2 generation specifically)

The protection of gametes in this case are various (4 possibilities) •4 genotypes that can be found in gametes -RY, rY, Ry, ry (each carries copy of r and y) •produced 4x4 diagraman with 16 different fertilization possibilities -gametes combine to create the double set of alleles (2 copies R and 2 copies Y) =Create 4 different phenotypical combinations •round yellow, round green, wrinkled yellow, wrinkled green •ratio is 9:3:3:1

What occurs in terms or structure when a polypeptide interact with water?

The protein can twist and bend into more complex forms •double bonds between nitrogen and carbon cannot twist •causes the primary structure to consist of "stiff" segments (double bonds) and segments that rotate around the alpha carbon atoms

What is the special way ATP synthase makes ATP? (Motion) how does this happen?

The protein will spin and generate the molecules (mechanically spin) •when protons flow into the F0 subunit, it causes the stalk to spin -hydrogen ions drive this process •specifically, it causes shape change that transfers to F1 by gamma stalk -knob senses changes, and this provides catalysis for ATP -bets subunits in knob make ATP

What is the second step of lactic acid fermentation? What is produced?

The pyruvate molecules accepts electrons from NADH and becomes •NAD+ is regenerated (oxidized) from NADH •lactate (lactic acid) is being formed as a byproduct (not the goal, it just is formed)

How does substrate concentration affect catalysis by enzymes at low substrate concentration? (Not general)

The rate of production increases linearly when at low concentration •as more substrates are added, the enzymes work faster and produce more product in shorter amounts of time -true only at low concentration because the enzyme can handle it

What is a substrate?

The reactant in a chemical reaction •the thing the enzyme binds to/reacts on

How does the Benedict's regent test prove that glucose is reduced?

The regent consist of copper 2+ ions, and when it is mixed with glucose and heated, it will change into Cu + •this is a more reduced from •glucose donated the electron and became oxidized =glucose has energy to provide for the cell •the receiver here was copper, but in the cell the receivers are activated carriers

What is the backbone of a polypeptide made out of? How is this helpful?

The repeating pattern of anime groups, alpha carbine, and carboxylic acid groups •if you find the peptide bond, you can tell where one amino group begins and the other ends

What determines a molecules overall polarity?

The shape and arrangement of polar and nonpolar covalent bonds

What can one tell from the shape of an atoms subshell?

The shapes of the molecules it may form with other atoms

What occurs in the elongation phase of transcription?

The sigma molecule has left the core enzyme, synthesis occurs •RNA pol moves along the DNA template and synthesize RNA in the 5' ——> 3' direction =same as DNA pol III

What happens after the cell responds to the hormone?

The signal has to be turned off •allows cell to listen for additional signals (keeps cell sensitive) -drug addiction is affected by this (hit cells too much where lose sensitivity)

What is the active site on an enzyme? What is it's importance?

The site where the enzyme binds it substrate •a pocketlike area that is formed from specific amino side chains -because it's structure is so specific, it's functions is to bind to only 1 type of substrate (creates overall specificity of the enzyme) -this determines which substrate is specific for that enzyme =if hexokinase, glucose will fit like a glove but fructose or sucrose will fall right out •it is specific for glucose

Monomers

The small units or building blocks for polymers/macromolecules

What is the terminology for when salt dissolves in water?

The sodium and chloride ions dissociate you produce an aqueous solution

How do solutes move in respect to the concentration gradient? What happens after ample time?

The solutes will move from regions of higher concentration to regions of lower concentration •moving down concentration gradient Ex: drop perfume, molecules will spread outward form that corner to the rest of the room (rest of room has no perfume molecules before) Eventually, solutes will have moved completely down the gradient and the concentration will be equalized

What characterizes a hypertonic solution?

The solution outside the cell has a higher solute concentration than inside the cell •outside has higher osmolarity (less water)

Exoplasmic space

The space outside of the cell/not controlled by the cell (non living) •has to do relative to the structure, there is exoplasmic space in the mitochondria

What dictates the size, shape and function of polypeptides?

The structure of the amino acids •this is caused by folds upon folds and if the doesn't get the unique 3D structure, it won't function properly

organic chemistry

The study of carbon containing molecules

What is metabolism? How does this relate to biochemistry?

The sum total of all energy manipulating processes in living cells •biochemistry is the study of how energy manipulates chemical reactions in living cells =metabolism is the overarching concept in biochemistry

What does the entire process of energy cycle depend upon?

The sun •life on earth would not exist without energy from the sun =all heat being released isn't recycled, it's lost in the voids of space, sun provides lost energy (becomes unusable)

Why is the lagging strand synthesized in a discontinuous fashion?

The synthesis occurs away from the fork, and at the same time helicase is opening the form further in the opposite direction •polymerase III travels until it runs out of template or enters the opposite side of the bubble -during this time helicase opens up more of the single stranded template (which is now covered with SSBP) =this leaves a chunk of newly synthesized template with nothing on either side (called Okazaki fragments) •pol III must "travel" backwards and fill in the gap the helicase has unzipped -but a primer needs to first be placed to start the process (primase) -this process occurs over and over again and it is a discontinuous process

What occurs in elongation of translation?

The tRNA shuffles in a sequence through A, P and E sites in the large subunit of the ribosome •each new tRNA adds new amino acid to the growing chain

What is the function in the parts of a chlorophyll molecule?

The tail is hydrophobic (only carbon bonded to hydrogen) •embeds the molecule in the thylakoid membranes Head region is where the light is absorbed •mainly because of the magnesium atom

What type of permeability is experienced with unsaturated fatty acid tails?

The tails are kinked and cannot form tight packing •further apart and can move more frequently -this decreases the hydrophobic interaction between the tails =they are not as sticky and are more permeable

What is the phase transition in membrane biology? What is it effects to on permeability?

The temperature in which membranes go from a gel phase to liquid crystalline phase •called melting temp of membrane Two ways affects permeability b/c of increased kinetic energy •increases the surface area -phospholipids spread out (more space inbetween them) •thickness decreases -tails overlap and membranes are thinner =both changes increase permeability

What is a product?

The thing that is produced as a result of the action of an enzyme

Tertiary structure

The three dimensional final fully folded functional form of a polypeptide

What type of permeability is experienced with saturated fatty acid tails?

The tight formation of the tails increase lateral (hydrophobic) interaction •creates little movement or space between tails =this creates sticky nature and thus decreases the permeability (molecules can't squeeze through, they will have to touch hydrophobic tails)

What is heredity?

The transmission of traits from parents to their offspring

When synthesizing DNA on two antiparallel strands, which strand has no issues? (Talk about direction of synthesis)

The two original strands and antiparallel to each other •one is going in to 3' —> 5' direction (towards fork) •one is going into the 5' —-> 3' direction (away from fork) DNA can only be synthesized in the 5' -> 3' direction •only one strand can be synthesized towards the replication fork (other other is being synthesized opposite due to antiparallel) •the strand which is 5' —- 3' is going away from the fork, but it's newly synthesized strand will be going 3' —> 5' direction (towards the fork) -it is called the leading strand As helicase is unwinding the double helix, the leading strand is traveling in the direction of the replication fork, and can continuously be synthesized to create more DNA =called leading strand synthesis in 5' —> 3' direction

What is a polypeptides primary structure?

The unique sequence of amino acids it contains

What defines the primary structure of a nucleic acid?

The unique sequence of nucleotide bases •similar to polypeptide amino acid sequences

Instead of sigma factors, what do Eukaryotes possess? Do they have similar function? Explain.

The use general/basal transcriptional factors •they start transcription similarly -match RNA pol with the correct promoter region giving it correct orientation

What is glycolysis (broad)

The very first step of sugar catabolism •present in both CR and fermentation •10 step process

What happened when Mendel cross pollinated the F1 population? What was seen in the F2 generation?

The wrinkled seed trait actually reappeared in this new generation •specifically in 1/4 of the total plants •ratio always existed, 3 round for every 1 wrinkled appeared in =found in every single trait with F2 generation

What occurs to cells over time that do not possess telomerase? Implications?

Their genetic code shortens over time and it causes cell death •this is the basis behind aging of living organisms -tissues decline in function =researchers believed that giving every cell telomerase will stop aging •actually more complicated and the hypothesis is only partially true •will actually cause cancer (makes cells push through cell division

Why do bacterial cells not need stiffening agents?

Their small size reduces the risk of them being crushed •the wall acts as the stiffening agent (polysaccharides)

Why do cells exhibit selective adhesion?

There are adhesion proteins found on the cell surface which allows specific connections to be formed -connections are cell, tissue and species specific (Explains rejection of organ transplant)

What different kinds of hormones are there? Why is this distinction important in terms of transport?

There are hormones which are steroid based (made out of lipids) •they easily diffuse into the cell membrane and make connections with receptors There are protein based hormones (made out of polypeptides) •this can't diffuse through the cell membrane

How can a selectively permeable membrane use the principle of a concentration gradient?

There are many situations where a solute is highly concentrated on one side of the membrane while low concentration on the other •this occurs when the molecule is not freely permeable to the membrane •the membrane can maintain this concentration gradient for its purposes =this creates a potential source of energy

What different types of receptors are there? Why are they present?

There are ones which float in the cytosol •they come into contact with steroid hormones which can diffuse There are ones present as integral receptors in the cell membrane •they come into contact with protein hormones that can't diffuse

What is the anatomy of a promoter (2 components) that make it functional?

There are two regions that make it function •-10 box and the -35 box (names code from location = #'s represent bases from 5' transcription start site) •sigma factors will bind to the two regions in order to start transcription -this allows the RNA pol to be properly oriented to move downstream along the code

What is the relationship between NADH and ATP in the ETC? (Don't explain process)

There is not a direct process as seen in the previous three steps •NADH does not automatically become formed into ATP, it just helps/provides the energy for this action A buffer/intermediate exists

What occurs in isotonic solutions? How is this seen with the cell?

There will be no net movement of water molecules across the membrane (still moving but equal in direction) •cell will stay the same size

What kind of relationship to ionic bonds have?

There's is very short term, one atoms donates and electron and the other accepts it •this creates a full valence shell for both atoms, they are more stable when by itself

What are carotenoids?

These are accessory pigments •they absorb blue and green light •transmit yellow, organs and red light

Why will glycolysis not occur if ADP and NAD+ are not present?

These are activated carriers or cofactors •enzymes will break down glucose into pyruvate but can only do this with those cofactors -assist in the process

What are optical isomers?

These are amino groups that are exactly the same in arrangement of ground around the car in atom, but they are mirror images of themselves •there is a left handed and right handed optical isomer

What two broad processes can metabolism be divided into?

These are called metabolic pathways •anabolic processes •catabolic processes

What are malignant tumors?

These are cancerous tumors (invasive) •can spread through body via lymph and blood vessels -creation of secondary tumors in new unrelated organs •no wall of separation; instead unclear border between tumor and healthy cells

What are stomata? What is there purpose?

These are leaf structures that allow gas exchange to occur •these allow CO2 to enter the plant cells -this allows the process of the Calvin cycle to occur

What are inhibitory molecules?

These are molecules that are not part of the enzyme itself and regulate enzyme activity

What is significant about the number three and five carbon prime in nucleotides?

These are the carbons that create linkages for the nucleotides to form nucleic acid polymers

What are hereditary determinants?

These are the genes located on the strands of chromsomes •made up of DNA =they contain information passed from one generation to the next (heredity)

What are homologous chromosomes?

These are two separate chromosomes that contain the same genetic information (both chromosome 1 or 2 or 3...) •one of the pair came from the mother and other dad (originally) •they code for the same genes, but might be different versions (not identical copies)

Cytoskeleton proteins function in prokaryotes...

These create filaments which gives the cell shape and structure (causes the hot dog shape)

How do glycoproteins and glycolipids act as recognition?

These molecules are unique for individuals (not the same for everyone) •When activated, immune cells travel to other body cells and interact with these molecules on the cell membrane •if the molecules don't match the other cells in the body, immune cells will attack -organ/tissue transplants are rejected in this way

How are steroids signaling molecules?

They act like hormones and tell your body what to do

What is the general trend in all of the parts of cellular respiration in terms of extracting energy?

They all collect the energy released through glucose and reduce activated carriers to hold this energy •these carriers are all pooled together in the same place at the very end of the chain =the energy is released in the last step of the process (more like formed into a bond and then released) •this energy is released slowly in controlled way

What is the function of the three checkpoints in total?

They allow a cell to progress through all phases/steps of the cell cycle only when it's appropriate •if not appropriate, keeps cell in G0 state =if this isn't working correctly and damages cell moves forward, large implications for the body

What do extracellular structures do?

They allow cells to associate with each other and interact with their environment

What is the other major function glycocylated molecules?

They allow the cells to establish extracellular connections •function in cell to cell identification

How are metal ions related to enzymes? What is their function?

They are a type of cofactor for enzymes (non organic) •hello the enzyme stabilize substrates •help in redox reactions

What is important to notice about the 4 gametes produced in meiosis II? What does this represent?

They are all genetically unique of the parent cell and of each other •this was due to crossing over —-> unique combinations of chromosomes Due to the parental material being shuffled and swapped in gamete production •each individual that may come from two gamete formation will be unique from anyone else

What are the function photosynthetic pigments?

They are capable of collecting light in the visible portion of EM spectrum (absorb photons of light) •molecules •they can absorb certain wavelengths of light and then transit/reflect those not absorbed

What do chromosomes look like in the time right before and during mitosis? What connects them?

They are condensed and replicated •iconic X shape Structure called centromere connects them

What happens to the primers which helped form the Okazaki fragments?

They are created by primase and are RNA segments •RNA can start from scratch because they're more reactive -DNA can be built from this DNA polymerase I has repair function •called exonuclease activity •toss out RNA primers DNA ligase •forms the final phosphodiester linkages to seek the Okazaki fragments together

What are the condition of chromosomes in prophase (specific)?

They are duplicated sister chromatids •starting to condense (not condensed and not uncondensed, a middle ground)

If the chromosomes and genes are replicated, what does that make the daughter cells? Is replication important then?

They are exact clones of one another •pure asexual reproduction Replication is so important that it requires 100% accuracy and nothing less

How is Meiosis II similar to mitosis?

They are exactly similar in the process •only exception is that one of the homologous pairs is present in the cell -this generates a haploid cell when sister chromatids are pulled apart (breaking the centromeres) =creation of 2 daughter cells per meiosis I cell •total of 4 gamete cells with 1/2 genetic material of original cells

What is the structure of a desmosome?

They are formed as localized-clumped tight junctions •on either side of the two inside membrane is it is a large raft of floating proteins •in the middle (between the two outer membranes), membrane proteins create links between the two rafts -creates large and strong attachment point •have fibers of the cytoskeleton attached to the rafts

Stiffening agents function in cell is...

They are glue like substances which protect the cell against compression (crushing) forces •make cell + neighbors rigid so maintain distance and are not smashed together

What occurs to the genotypes/phenotype when pure-line individuals mate?

They are homozygous, each can only donate 1 type of allele (either dominant or recessive) •offspring will all be heterozygous genotype for that gene =dominant allele will express over the recessive, phenotype will always be the same as parents •F1 hybrid is carrier for recessive gene information

How do sister chromatids compare to each other genetically?

They are identical •letter to letter of genetic code (nucleotide sequences) duplicates =sequence identical

How are the promoters different in Eukaryotic cells? What is the most important one? What is the implication of this?

They are more complex and divers •because three different RNA pols, each promoter attracts a different one Most important promoter that attracts RNA pol II is the TATA box •function is the same as the -10/-35 boxes prokaryotes •TATA binding proteins bonds to these =more complexity allows for greater level of regulation of the transcription process in Eukaryotes

What do starch and glycogen have in common?

They are nothing more than a-glucose monomers joined by alpha 1, 4-glycosidic linkages

Now is the G1 phase seen in nondividing cells?

They are permanently stuck in the G1 phase •called G0 phase •will not take into account of environment or neighbor cells -will not divide no matter what

Why do the centrioles move to opposite sides of the cell?

They are placing themselves in an optimal location •easier to grab the chromosomes when ready and pull to opposite poles of cell =the cell can divide now

How is photosynthesis and cellular respiration connected?

They are the perfect counterpoints of each other •photosynthesis needs the CO2 produced in cellular respiration •cellular respiration needs the glucose and oxygen formed in photosynthesis =without one of them, the other could not function correctly (dependent) Work together and support each other

What are pedigrees? What are they used for?

They are tools/diagram created by geneticists •used to track a single genetically inherited trait within a family -only 1 trait -genetic trait

How are the exergonic and endergonic reactions related?

They are used to fuel one another or or coupled •in order to get the necessary the necessary energy is create a bond, it will use the energy released from breaking another bond (energy is conserved) Ex: use energy to pump up a bike tire, the tire has no absorbed the energy as work (higher pressure)

When two water interact, what happens?

They attract one another, the negative side bonds with a positive side of another water molecule and vice versa •this creates stability

What key similarity does the backbone of a nucleic acid share with a polypeptide?

They both have directional backbones •one end has an unlinked number 5 prime phosphate •other end has unlinked number 3 prime hydroxyl group

Since pea plants have both sex organs, what process can they do? What did Mendel do to fix this?

They can fertilize themselves through self-pollination •male parts fertilize female parts —> sex with itself Mendel prevented this from ruining his experiments •removed male reproductive organs from each flower

How do cells make tighter interactions in animals? Types?

They can possess specialized proteins bound to membranes that makes the connections string •tight junctions •desmosomes

How do membranes respond to changes in temperature?

They change the composition of their membranes to keep efficient permeability •change lipid, protein, and cholesterol components

Are chromosomes pulled during anaphase? What instead is occurring (broad)?

They chromosomes are not "pulled" by the microtubules •instead, they remain stationary and disassemble as the chromosomes moves toward centrosomes

What happens to chromosomes in prophase? Why is it important?

They condense into the X shape •this allows them to be organized easier for transport -not all spaghetti and random, but small condensed packaged that can be moved

Why are carbs such an efficient form of energy?

They contain an abundance of carbon-hydrogen and carbon-carbon bonds which can be broken down to release energy

What is so special about chloroplasts?

They contain their own DNA and grow/divide independently from the cell

How did researchers determine how RNA synthesis occurs? (Experiment summary)

They created a reaction b/w 3 element: 1. Ribonucleotides (NTP's) 2. RNA pol enzymes 3. DNA strand with only thymine base pairs •will RNA be made with only A base pairs? =yes, the DNA template could be used to make RNA nucleic acids •RNA strand came out with only A base pairs -RNA molecules are a photocopy (temporary) for DNA molecules

How did Meselson-Stahl set up their experiment? What steps were involved?

They created heavy nitrogen (15N) which is heavier than regular nitrogen (14N) due to one extra neutron •grew E. coli in the presence of heavy nitrogen -heavy nitrogen became incorporated into all of the bacterial cells DNA -did for multiple generation —> all DNA was homogenous for heavy nitrogen •switched bacteria cells to light nitrogen (14N) -only allowed to replicate 1-2 generations -isolated bacterial DNA and separated it in the centrifuge =could distinguish heavy DNA and light DNA

How do polysaccharides give identity to a cell?

They decorate the cell from the outside by forming glycoproteins and glycolipids •the glycoproteins function in cell to cell recognition and signaling

Why did Mendel stop studying a few particular traits? Which ones did he choose?

They did not have an easily seen, two phenotypes •instead they wouldn't appear so well Chose: •Seed/pod/flower color •Seed/pod position •flower/pod position •stem length =each one has two clear distinctions between phenotypes •no inbetween or blending (did not want to touch blending hypothesis)

Why must introns be removed?

They do not represent coding sequences that can be translated into polypeptide •must happen for translation •processes occur to remove them from pre-mRNA messages

What occurs when ions build up on one side of the plasma membrane? (2) what is this called?

They establish 1. Concentration gradient 2. Electrical gradient (charge distribution) =electrochemical gradients

What is the structure of transfer RNA? Secondary and tertiary

They fold themselves into a series of stem loops •called cloverleaf secondary structure with 3 separate hair pin loops (2D) Tertiary structure is L-shaped (3D)

How do plants conduct cytokinesis?

They from a cell plate in the middle of the cell •created when Golgi apparatus secreted vesicles -vesicles interact to form cell membrane and cell wall material (Laying down brick wall in middle of cell)

What function to proteins have in the membrane (in terms of large polar molecules)?

They functionalize transport to occur between the cell membrane by affecting permeability •dictate which molecules can get across and which don't (also in which direction)

Why can prokaryotes survive with no membrane bound organelles?

They have a very small cell size •allows things to diffuse easily in and out, all throughout the cell •everything can do the same job and be efficient at the same time

How do plants use wax?

They have an outer layer to prevent water from escaping •keeps them hydrated

What effect does the enzyme have on the free energy produced?

They have no effect in the change in free energy of the reactants and products •the enzyme is not consumed in the reaction

What is special about mitochondria? Why is this there?

They have their own DNA and ribosomes (grow and divide separately from cell) •theory of endosymbiosis -used to be separate organism until engulfed by eukaryote

Instead of just one RNA polymerase, what do Eukaryotes possess?

They have three type of RNA polymerase: I, II, and III •RNA pol II does most of the synthesis for proteins (creating mRNA)

What must be the case for two reactants to form a product in a reaction?

They have to collide with one another in a very precise orientation •also, they have to have enough kinetic energy to overcome the repulsion of their negatively charged electrons =most collisions, even with enzymes, are non-productive

What does DNA have to do to transform into for transport?

They have to prepare beforehand •condensing chromosomes •growing larger •creating more building blocks

What role did Srb and Horowitz have in the one gene one enzyme hypothesis? What new technique did they use?

They performed the actual experiments that would either prove or disprove the hypothesis •used the same N. crassa bread mold with radiation to create null mutants They used a genetic screen to identify/separate specific mutants •ones that had problems in metabolic pathways -specifically, bread molds that could not make the amino acid arginine

After the viral cells were separated from the bacteria cells, what did Hershey do and why?

They placed each sample/culture into a centrifuge machine •bacteria cells were denser so they collected in the bottom of the tube into a pellet •viral cells were less dense so they floated in the supernatant =where did the radioactivity end up? •if in pellet with bacteria -that labeled molecule was injected in the bacteria cells •if radioactivity in supernatant -labeled molecule was stayed outside cell virus (did not contribute HM)

Which of the two subcategories do plant cells have in terms of extracellular material?

They possess both fiber composite material and a stiffening agent

How can the enzyme decrease the activation energy barrier?

They possess cofactors and many of which are electron shuttles •they facilitate the decrease in energy by providing the necessary energy

What occurs in cells that can only do substrate level phosphorylation?

They require glucose in order to make energy for bodily processes •one to one; if no glucose immediately present then they can't make ATP -when out of food no more energy —-> need to shut down systems to ration energy

When researchers studied cell to cell associations, what did they notice about how the cells interact with each other (in terms of forming connections)?

They saw that cells have selective adhesion •this means that when cells dissociate from the tissue, they will only form connections with the same type of cells -will not connect with other types of cells or other species cells

What is NADH and FADH2 major function?

They shuttle/carry electrons reduced molecules to oxidized molecules •especially seen within the electron chain

What happens when bases are mixed with biological molecules?

They steal ions (H+)

How do bacterial cells move?

They use a structure called flagella •small tails that the cell uses to spin like a propeller in liquid environment

How do geologists and archaeologists use the decay it isotopes?

They use it to date materials radiometrically Ex: Unstable isotopes of carbon in uranium are used for dating the fossilized remains of organisms

How did researchers determine which solutions could pass through a lipid bilayer?

They used a special beaker which has a partition separating the left and right sides •partition has a whole which is formed by bilayer of lipids -use different solutions on one side and see if they can move through bilayer to other side

How do plants cells make connections with their primary walls?

They walls are glued together to form a layer •made up of gelatinous pectin carbohydrates •called the middle lamella

What would occur if chromosomes didn't condense in mitosis?

They would have to be transported in their noodle form •this has a high probability of the strands being tangled, torn, and damaged in anaphase -abnormalities would occur

How can one represent primary structure?

Think of a string of beads that can be attached to one another and moves/folded in many ways

How can tumor suppressor genes cause cancer?

Thinking of it as a car (brake peddle) 1. Put a brick on the brake peddle •cell can't progress through cell cycle because tumor suppressors creating too many regulators to stop •new cells aren't being created 2. Cable is cut between brake and fuel source •suppressor genes do not create any regulators to stop the cell at checkpoints -mistakes in DNA and others will be present in future daughter cells (BRCA ex) =causes tumors/cancer in both situations

How can oncogenes cause cancer?

Thinking of oncogenes as a car (gas peddle specifically) 1. Brick placed on gas peddle •oncogene is constantly producing the positive regulators and having the cell go though division constantly 2. Cut the cable between gas peddle and fuel source •the oncogene won't produce any regulators to cause the cell cycle to move on -problem because cells need to be replaced =both will cause tumors/cancer

Cell (plasma membrane)

This bounds the cell or separates the extracellular environment from the intracellular environment (Intra contains concentrated mix of chemicals)

What occurs in regards genotypes/phenotypes when the F1 generation is crossed?

This can also be a self fertilization process, all are heterozygotes •segregation —> two hereditary determinants are separated into gametes •two alleles (one dom/recessive) into gametes -female: will donate 1/2 time dominant allele, 1/2 recessive allele -male: same exact thing =this is segregation •outcome is offspring that have genotypes RR, Rr, rr -phenotypes for dom are present 3/4 of the time

What occurs if during DNA replication, an enzyme makes a mistake?

This causes a mutation •this can occur in a sensitive area of the chromosome -coding area called gene =has large implications for the function of the cell

What does the energy lost in energy conversion steps represent?

This energy is not destroyed, but also not available for work •it is simply lost to the energy cycle

What is the function of pectin in the primary cell wall?

This is a hydrophilic molecule •helps water hydrate the wall of the plant cell and keep it moist -this creates permeability and helps water move in and out of the plant cell

Why do proteins fold at all?

This is a spontaneous process due to the formation of hydrogen bonds and other interactions •it is to make the protein more energetically stable than in its unfolded form

How is time portrayed in a pedigree?

This is a time axis •letter d. (Year) •also Roman numbers on the side show generation = Oldest generation placed on top and youngest on the bottom

What role does helicase have in DNA replication?

This is an enzyme which separates the strands of the helix (breaks hydrogen bonds) •helic = helix, ase = separate •exposes each strand and causes the replication bubble to form

How can decide which genes should be transcribed during the cell cycle?

This is called gene regulation •the cell makes choices -these choices are influenced by bacterial cells sigma factors/general transcriptional factors in Eukaryotic cells -turning genes on and off for transcription

What is the extracellular components around bacteria called (in general)? Which of two classes of molecules is it?

This is called glycocalyces • it is considered fiber composite material

How does the RNA polymerase know when to end elongation?

This is called the termination phase •RNA meets the termination signal called the terminator -sequence in a gene that signifies end of that gene Two ways that termination process occurs 1. Special secondary structure of the mRNA (hair pin loop) causes the DNA template to be released from RNA pol and reanneale with itself •mRNA is released and is identical photocopy of DNA coding strand (except Uracil + NTP's)

What occurs to the strand that is not read from in transcription? What is it?

This is considered the non-template strand •when mRNA is synthesized from the template strand, it will look exactly like the non template strand -causes my commentary bases -T will be U's =therefore this strand is called the coding strand

What is a cofactors? What is their importance?

This is non-protein structure •they bind with enzymes in order to help them carry out binding with substrates (their function) -considered helper molecules

What is the stroma and it's significance?

This is the fluid filled space between the thylakoid and inner chloroplast membranes •this were the Calvin cycle takes place

What happens at the inflection point of a substrate concentration vs reaction rate graph?

This is the point where the line changes from linear rate to leveling off and saturation •the enzyme will slow down in how fast it can create products due to time restrictions •usually at 1/2 the maximal velocity =will continue leveling off until hits diminishing returns

What is the purpose of crossing over?

This is the process of swapping non-sister chromatid information •chromosomes (chromatids) that are purely recombinant (not the same as before, not the same as parent DNA) =increased genetic diversity

What is meant by the synapsis of homologous chromosomes? Is it important?

This is when a series of glue like proteins (ex Cohesin) line the chromosomes perfectly (gene for gene) •they press then right up to each other (sandwhich them) It is very important •allows error checking process to determine if homologous paired properly

What is the process of post-translational modifications?

This is when the protein must fold into its secondary and tertiary structures in order to be functional as enzymes •secondary seen with alpha helixes and beta pleated sheets •Molecular chaperones helps speed up the translation into tertiary structures (other polypeptides help fold) Other times macromolecules are added to the polypeptide •membrane bound proteins receive special lipid groups -meant for exoplasmic space are glycocylated with carbs (glycoproteins) Proteins furthermore altered by enzymes that add or remove phosphate group •switch protein from active state to inactive state

What occurs when a molecule becomes glycocylated?

This is where molecules such as lipids and proteins are modified to include a carbohydrate group •produces glycolipids and glycoproteins

What are the alleles together called?

This makes up the genotype in an organism •the full genetic information in an organism, not just which allele is expressed

Which part of meiosis (I or II) does reduction division? How?

This occurs in meiosis I •this process can be seen specifically in prophase I/metaphase I -chromosomes are paired up as homologous pairs (rather than single file down a line) -line up at metaphase plate (2 by 2); each of the pair facing opposite side of the cell -instead of sister chromatids being pulled apart, homologous are pulled apart =2 daughter cells with half the copies of genetic material (1/2 # of chromosomes) as parent cell (each cell has one homologous chromosome from the dad or mom) •division of genetic material created haploid 1n

What does the process of passive transport entail?

This occurs in usually two circumstances 1. Molecules move across the membrane without the help of transport proteins 2. When transport proteins assist in moving molecules without the use of energy (just in response to concentration gradient)(facilitated diffusion)

What occurs in initiation of translation?

This process begins at a start codon (AUG) on the mRNA •ribosome binding site precedes a specific start codon that small subunit recognizes -tells the ribosome to start transcription here •initiator tRNA then brined to AUG sequence •large subunit bonds last and completed initiation complex

Why does the molecule need to be phosphorylated in step 2?

This supercharged the fixed carbon •allows it to participate in sugar synthesis late (Exact opposite step of CR, energy is extracted from the supercharged glucose molecule)

What are conformational changes? What does it affect?

This the change of an enzymes shape caused by different temperatures, pH's and physical properties •it affects the enzymes ability to bind substrates and catalyze reactions

What was the importance of choosing the phenotypes in that particular way?

Those phenotypes were very reliable in always appearing in the plant and not "mixing" •it allowed him to track the passing down of traits from each generation with validity =learn something form how this process occurs

If one turn of the Calvin cycle fixes one molecule of CO2, how many are required to produce the necessary G3P?

Three turns of the cycle are required to produce one three carbon molecule of G3P

How to prokaryotic cells replicate?

Through binary fission •process where two equal halves are produced from 1 cell (clones) -DNA copied and placed in opposite sides of the cell

How are polypeptides formed?

Through the condensation reaction of amino acids •the carboxylic acid group of one acid bonds to the amino trout it another acid

Difference between thylakoid membranes and inner chloroplast membrane...

Thylakoid membrane is the structure that surrounds thylakoid •this is where chlorophyll is housed (pigments) •thylakoids thus capture energy Inner membrane surrounds the entire cell

Hydrogenate

To add hydrogen to unsaturated fats

What is the overall function of the Krebs cycle? How does the energy come out?

To completely oxidize acetyl CoA (glucose derivative) and release the electrons to activated carriers •this energy is collected by NADH, FADH2, and ATP (Primary output is NADH) •CO2 is a byproduct that proves carbon bonds were broken to release energy

What are the purpose of membranes?

To create boundaries between the inside of the cell (organelles) and outside of the cell

What is the primary function of phospholipids?

To form membranes

What is the overall function of pyruvate processing? How does this happen (micro scale)? Include products of intermediate phase

To prepare pyruvate for further processing in the Krebs cycle •it has to break a carbon bond off from pyruvate (was triose now only two) -creates two carbon group = acetyl group -stripped carbon turns into carbon dioxide (first step generate CO2) •acetyl group is linked to a cofactor: coenzyme A -makes acetyl-CoA -this is an activated carrier bc transporting energy from pyruvate to Krebs cycle

Why do cells use active transport?

To produce an internal environment that is different from the external environment •they want to purposely establish chemical or electrical gradients across the membrane Ex: interior of living cells more negative charge than outside -cells have higher potassium and lower sodium concentrations than outside the cell

How do tight junctions and desmosomes help the body?

Together they allow 4 main types of tissue to be formed •connective, epithelial, muscle and nervous =can tell the difference from the amount of tight junctions/desmosomes present

What was the procedure in the Frye - Edidin experiment?

Took human cell and mouse cell •tagged proteins with flourescent antibodies =made the cells fuse with each other to create hybridized cells Ex: two soap bubbles coming together to make one big one

How did researchers discover ATP's mechanical motion?

Took portions of ATP synthase and attached actin filament rope to gamma subunit •fluorescent molecule attached to rope at end •placed under microscope and provided with ATP -worked backwards and started to create ADP and Pi =the fluorescent label lit up and spun in a circle in a constant rate

Keeping in mind the energy cycle, what formula can be used to calculate total energy?

Total e = Free e - heat loss

What did the acquired characteristics hypothesis explain? Who favored it?

Traits are present in parents and get modified through use (parents life needs) and then passed on to their offspring Ex: adult giraffes strain necks to reach food—-> neck lengthens —-> longer neck condition is passed on to offspring •proposed by Lamarck and favored by Darwin =use something a lot, it'll get passed down •but also negated

What is the primary RNA transcript? What must happen to it?

Transcription in Eukaryotic cells by RNA pol II build this form (pre-mRNA) •it contains both exons and introns Since introns are non coding segments, they must be removed •this occurs simultaneously with the transcription process in the nucleus -this process is called splicing

Fats other name

Triglycerides

Sugar with three carbon atoms

Triose sugar

T/F: Glycogen is always highly branched

True

What are benign tumors?

Tumors that are non invasive and noncancerous •usually walled off/separated from the surrounding tissues and cells -can see clear distinction/line =do not spread from the tumor

What does DNA structure consist of? (Macro scale)

Two antiparallel nucleic acid strands that twist upon each other to form a double helix

chemical bonds occur when...

Two atom, interacting through their valence electrons, from an association that is energetically more stable than it is for the atoms to be apart

What are the protein subunits that compose MPF? How does their names hint their function?

Two different polypeptide 1. Cyclin •means repetitive, round and round, etc... 2. Cycling dependent (protein) Kinase •-Ase root = enzyme (so has function of enzyme) -puts phosphate groups on other proteins (Since dependent, only does its function when associated with cyclin) =both of them together comprise MPF

What is involved within stomata? (Players)

Two guard cells are involved •they change shape to open or close physical pores on surface it leaves

Why are there so many expensive steps in the Krebs cycle?

Two main reasons 1. The goal is to drain acetyl CoA (glucose) of every chemical potential bond it can possible break •wants to digest glucose down to the core and produce max ATP =this takes multiple steps to ensure it worked properly 2. Not all of the energy can be released at once, bonds must be broken one at a time •if they were all done at once, it would create to much free energy —-> damage the cell =needs to do it in small steps

nonpolar covalent bond example

Two oxygen atoms forming a covalent bone, each tugs on the electrons an equal amount •electrons are an equal distance from the nuclei of both atoms

What specifically is a test cross?

Two parents are crossed •one is homozygous recessive for trait(s) •one has a dominant phenotype but unknown genotype =genotype of the other parents can be inferred by the offspring genotypes (working backwards and then check) •can tell it homozygous or heterozygous for each trait •if recessive in F1 = heterozygous in unknown parent •only dominant F1= homozygous unknown parent Important to keep in mind this is a 4x1 diagram (one parent only produces one type of gamete)

How do Eukaryotic cells replicate?

Two parts, mitosis and cytokinesis •mitosis: cells make copies of the their chromosomes •cytokinesis: cells split themselves in half =more complex process than fission

What is a reciprocal cross? What did Mendel conclude?

Two separate crosses/experiments •one cross has the male parent with the dominant trait and the female with the wrinkled trait •other cross has male with recessive trait, female with dominant trait -nature is to test if sex matters (different outcomes if it matters) =he found that the exact same outcome occurred (identical) •both sets of offspring had all round pods -sex doesn't matter (butttt X chromosome)

What was the initial set up for the Hershey experiment? (What did they have to grow; how did they do this?)

Two separate experiments done simultaneously: one for DNA the other for protein 1. •grew viral cells in radioactive phosphorus (32P) -incorporated into newly synthesized DNA (phosphorus group structural component) -radioactive label for tracking DNA •grew viral sense in radioactive sulfur (35S) -sulfur a part of protein, incorporated into new proteins -radioactive label for tracking protein

What do chromosomes look like in the synthesis phase?

Uncondensed and replicated/duplicated •still in its spaghetti form •but now an identical copy intertwined as well with the original copy

Steroids structure

Unique lipids, made up of four ring structure

What is peculiar about Eukaryotic chromosomes being linear? Specifically about the end of a chromosome?

Unlike bacteria (circular), eukaryotes have endings on their linear chromosomes •when the replication forks gets to the end of the double helix there is a problem -the lagging strand has an RNA primer on both ends that allowed DNA polymerase III to function -it needs to be replaced, but then no 3' end (hydroxyl group) will exist to make a commentary strand ending (pol I needs this) -part of the strand is unreplicated and will not be seen on the new strand =this is called the overhang

What did Avery hypothesis the factor could be?

Used Griffith's experiment system to find if the transforming factor was: 1. Protein 2. RNA 3. DNA

How is the genetic code universal?

Used for every living organisms (exceptions) •universal for all life on earth = ties all life together on earth based on evolution

What is the purpose of meiosis in the life cycle?

Used in sexual production, production of gametes •cells will be used to form a new offspring -egg cell fuses with sperm cell; genetic info combines to from a whole individual

Poly unsaturated fatty acid shape

Usually takes in a U shape (many kinks)

How do materials arrive to lysosomes?

Usually through vesicles as the form of transportation

What does the process of active transport entail?

Usually when the molecules are moving against their concentration gradient (from low to high) •it requires an intake of energy •"pumped" across membrane

Apart from heat loss, what is the major advantage for CR being so many steps?

Variety of intermediaries allow the potential to fuel anabolism •glucose can be used to synthesize RNA and DNA •acetyl CoA can be used to create fats and phospholipids •many intermediaries in the Krebs cycle can be used to synthesis amino acids

Isotopes

Versions of atoms of a particular element with alternate numbers of neutrons in their nuclei

Are biofilm harmful to the host?

Very harmful if they function as pathogens •tend to have slime layers and capsules •cause more serious infections because they have more properties then just alone -can be seen more resistant to antibiotics

What is in the middle of the electromagnetic spectrum that has importance to us? Why?

Visible light •this is the only from of light that we can see with naked eyes -only sensitive to specific wavelengths of EM (400 nm - 700nm light) =rainbow of colors 400=blue violet 700= orange red

What is Vmax of an enzyme? What is Km of an enzyme?

Vmax= the maximal rate the enzyme can achieve Km= the substrate concentration at half maximal velocity •represents binding affinity

What occurs in a hypotonic solution (relative to the inside of the cell)? How is this seen in the cell?

Wager will movie into the cell by osmosis •cell will swell and possibly burst

Which early 20th century scientists expanded on Mendels work? What was their theory called?

Walter Sutton and Theodor Boveri Created chromosome theory of inheritance -says meiosis is linked to patterns of inheritance that Mendel observed in pea plants

How does temperature effect the permeability of membranes?

Warmer it is ——> increases permeability Colder it is ——> decreases permeability

Hydrophobic

Water fearing (usually nonpolar)

What occurs in a hypertonic solution (relative to inside of cell)? What is this seen with cells?

Water will move out of the cell by osmosis •the cell shrinks •relative to the inside of the cell

How do two strands of DNA come together

Watson and Crick said two DNA strands line up in opposite directions of each other •called antiparallel (5'3' bond to 3'5') •forms ladder of nitrogenous bases being the rungs Nitrogenous bases bond together (through hydrogen bonds) to become complementary pairs •cytosine with guanine ( •thymine with adenine -purine (a + g) pairs with pyrimidine (c + t) =these processes allow DNA replication to occur

Signal processing steps, how does it respond to the hormone?

Way for the cell to interpret the information •dictates what will happen in the end Cell will change somehow •change in gene expression, metabolism, growth and division

How does meiosis correspond to ploidy level?

We know that gametes are haploid cells and are needed for sexual reproduction •meiosis is the process that cuts the ploidy level in half to create gametes •2n —-> 1n Allows: 1 n + 1n —> 2n to create an organism

What is the difference between alcoholic germination and lactic acid fermentation?

What is being done to the pyruvate •an intermediary step is added as well as new enzymes working on pyruvate molecule

When is nucleotide excision repair used?

When DNA is damaged rather than mismatched •specifically damage from UV light

How is the expressed trait represented?

When a shape is filled in solid = trait is expressed When a shape is left unfilled = trait has receded

How is trans fatty acids made? And history?

When cooking it is easy when oils are in there solid form (such as butter with cookies) •not possible with saturated fast bc of its properties •saturated fat is expensive (animals) and hard to use at times if it's liquid -cheaper too produce plant based oils Crisco= taking plant based oils and bubbling hydrogen gas through the oil •hydrogenate the fat, not fully but partially saturated -causes hydrocarbon chain to loose it's kinks; rearranges into linear shape

When is nucleotide excision heavily relied on?

When going outside and exposing the skin to UV light •this repair mechanisms helps fix the DNA altered by the sun

How is the fiber composite seen in plant cells?

When new cells form, they secrete a primary cell wall which acts as a fiber composite •most important example is cellulose which is seen in long strands bundled into microfibrils =prevent stretching

When does a tumor occur?

When one or more cells in an organism divide uncontrollably •creates mass of cells that could potentially have genetic or other defects

How are molecules movement related to people's movement?

When people are in close quarters with one another, they will try and create an equal amount of space between one another •molecules act in the same way, they will distribute themselves evenly within an available space

When does a concentration gradient exist?

When solute concentration is more concentrated in one area than it is in the other •normally only occurs briefly Ex: drop perfume in one corner of classroom, larger concentration gradient in that corner than rest of room

When does osmosis occur?

When solutions with different concentrations are separated by a membrane that is permeable to water but not the solutes

In what situation will there be a different concentration gradient of oxygen in the body? CO2?

When taking a large breath, the alveolar sacs will posses a higher concentration of oxygen than the blood •oxygen diffuses down the concentration gradient naturally and into the blood Carbon dioxide is present largely in the blood rather than sacs when deep breath taken out •it moves down its concentration gradient and into the sacs

Ketose sugars

When the carbonyl group is found in the middle of the carbon chain and forms a ketone group

Aldose sugars

When the carbonyl group is located at the terminal end of monosaccharide and forms an aldehyde group

What question do researchers ask about DNA replication?

When the strands are replicated, how does the old information appear with the new information? •does it mix together, stay apart, or a little bit of both? •starting DNA double helix and need to create a new copy = total of two -these are the chromatids created in synthesis of interphase

What is the negative with stomata being open during day and not at night?

When they open water can potentially be lost •occurs in dry and hot weather (Problematic in Arizona)

What is special about the decay of isotopes?

When they split apart it releases energy which can be harnessed and used

How is quaternary structure formed?

When two or more polypeptide chains form a single entity •they do this through Intermolecular interactions

What dictates wether an amino acid is polar or nonpolar?

Whether it's side chain is a polar or nonpolar molecule (look for electronegative bonds)

When Mendel began studying two traits at one time, what did he question?

Whether the inheritance of one trait will impact the inheritance of another •whether the principle of segregation holds true it parents differ in more than one trait Ex: does the transmission of hair color effect the transmission of the color in offspring

Why big question does cell theory not answer?

Why do individuals in an isolated population look nothing like ancestors (red tulip and yellow tulip field) •not explain specialization and diversification of cells (neurons vs lung vs marrow)

How does the substrate concentration affect catalysis rate in high concentrations of substrates?

With higher and high concentrations, the reaction rate will level off or become saturated •it takes time for enzymes to conduct catalysis and release the products -this creates a limit on how fast an enzyme can really go even if it can get a substrate immediately after it's done Ex: enzyme that breaks bonds •can do it easily with low concentration bc gets its every second •higher now it gets substrate every half a second, can't do it that fast •gets one every 1/4th of a second, it doesn't make it go any faster

How is competitive inhibition overcome?

With in an increase in substrate concentration •the substrate molecules now have a higher probability of binding to the active site than inhibitor molecules do =therefore this inhibition does not affect the maximal rate of production

How are nucleotide sequence written in respect to their backbone?(prime numbers)

Written the 5 prime to 3 prime direction •reflects mechanics of how nucleotide are added to growing nucleic acid

How does the survivability of cells of XP patients compare to cells of healthy individuals exposed to UV light?

XP patients have a decreased amount of cells that survive •die faster as well

Are there boy and girl pea flowers?

Yes and no •both female and male reproductive parts are present -female organ produces egg cells/structures than collect pollen grains that carry sperm cells -male organs produce pollen grains -pollen grains contact female organ, sperm cells leave grain and travel to egg cells for fertilization =creates zygotes which grow up into plants which can have lots of seeds for new organisms

Does the cell cycle pause at checkpoints?

Yes and no •if there are problems, the regulators in each checkpoint will cause a pause to determine how to fix it •if there are no problems, no stop will occur -cell cycle will continuously move past this checkpoint =similar to the metal detector in a TSA checkpoints (just walk through and keep waking)

Can prokaryotes do CR even tho they have no mitochondria?

Yes, all of the processes instead occur in their cytosol •archae species as well •not a prerequisite for pyruvate to enter mitochondrial matrix (can happen without this too) •ETC actually occurs across the cell membrane

If an R group is hydrophobic, can an amino acid to interact with other molecules in water filled cells?

Yes, although that part is hydrophobic, when an amino acid interacts with water the amine group picks up a hydrogen atom (becomes positive) and the carboxylic acid group looses a hydrogen (becomes negative) •creates an overall polar molecule

Do all organism follow the semiconservative model of DNA replication? What does this mean?

Yes, every organism follows this mechanism •all organisms have evolutionary ties to one another -related to each other

Did Mendel tackle the idea of diploidy level?

Yes, he realized that individuals cannot just mix their two copies of chromosomes to create offspring •this would make offspring with double the normal alleles/chromosomes (4 total copies) -F1 hybrid with 4 copies will make F2 with 8 copies =each parent contributes half of their genetic material •this is the principle of segregation

Is pyruvate still important after glycolysis?

Yes, it is still a highly energized molecule •three carbon molecule to be exact •single covalent bonds can be broken to yield energy =glucose is not completely oxidized yet

Does feedback inhibition occur in pyruvate processing?

Yes, the enzyme pyruvate dehydrogenase allows this •negative feedback inhibition: large amounts of CO2, NADH, Acetyl CoA -shuts down process •positive feedback inhibition: large amounts of reactants pushes forward reaction

Do cells use the principle of a concentration gradient and diffusion?

Yes, this one of the driving forces for transport within the cell •solutes will travel from one side of a membrane to the other depending on the concentration gradient

What model shows how the photosystems work together? How do they work together?

Z scheme •shows that together they form an enhancement effect -photosynthetic output more than doubles when cells exposed to red and far-red light

What is the dual charge molecule of amino acids called?

Zwitterionic/zwitterions

What is an absorption spectrum?

a graph plotting a pigment's light absorption versus wavelength (which ones absorb and which ones don't) •allows us to study the properties of photosynthetic pigments

What occurs in termination of translation?

a stop codon triggers the release of the polypeptide and the ribosomal complex disassembles •mRNA can be used again to make additional copies of the polypeptide until the cytosol caused degradation

What is a coenzyme? How do they function?

an organic type of cofactors •they help create a more specific active site for the substrate to fit in •derives from B vitamins + act as activated carriers Ex: the active site in an enzyme is a square but the substrate is in the shape of a triangle •the coenzyme is the shape of the triangle and when it binds to the enzyme a new shape is formed which better fits the substrate

Is mitosis sexual or asexual?

asexual •it is making identical copies of itself, not the formation of an egg cell =cells are clones

Ketone group

carbon double bonded to an oxygen (carbonyl group) with a bond to carbon on either side (in middle of monosaccharide) C | C = O | C

Functional groups

chemical groups attached to carbon skeletons that give compounds their functionality •these are the patterns of organic molecules

Examples of steroids

cholesterol, estrogen, testosterone, oestrone, cholic acid, corticotestosterone

What are dihybrid crosses?

crosses that examine the inheritance of two different traits •parents that are both heterozygous for two traits

vesicle location

cytoplasm (travel all over)

What does permeable mean?

degree to which fluid or particles can pass through

What is wavelength?

distance between crests •can be used to determine energy

Kinetic energy

energy of motion •most visible manifestation of energy Ex: bolder rolling down a maintain

trans fats shape and other name

fatty acids with hydrogens on opposite sides of the double bond •partially hydrogenated oils (bad for us)

What are mitotic spindles? What are they made up of? What is there function?

fibers attached to centrioles and extend from one side of the cell to another •basic building block is microtubules which in groups are called spindle fibers Function is to attach to the chromosomes and pull them to opposite ends of the cell

What are the steps of the Calvin cycle?

fixation, reduction, regeneration

What are a stack of thylakoids called?

grana

Does water have a high or low specific heat?

high specific heat, due to the great cohesion between water molecules there needs to be a lot of energy to drive them apart

Enzyme affinity

how tightly an enzyme is bound to a substrate •affected by both shape and charge -complimentary shapes and opposite charges provide the highest affinity between and enzyme and substrates

cis unsaturated fatty acid

hydrogen atoms are nearly always on the same side of the two carbon atoms that are double bonded, low melting point, oils/liquids

Alcohol group

hydroxyl group •carbon atom bound to oxygen and hydrogen

solid water is ______ dense than liquid water

less (ice floats)

What is the polymer fatty acids?

lipids

Denaturation

loss of normal shape (unfolding) of a protein due to heat or pH change •do not function normally

Lysosomes structure

membranous sacs •lumen is acidic + has enzymes (Exoplasmic space)

Rough Endoplasmic Reticulum structure (RER)

membranous tubules (contain lumen) and flattened sacs with attached ribosomes •located directly outside the nuclear envelope (attached to it)

Centrosome

microtubule organizing center located near the nucleus of animal cells •contains two centrioles tips pull chromosomes to separate areas during cell division

Rough ER function

modification and packaging of newly synthesized proteins •proteins pass through lumen where they are folded or have side chains added

What are the two types of covalent bonds

nonpolar and polar

Are all cancers first tumors?

not all of them •cancers of blood (blood cells) •not tumor forming, cancers of certain cells that migrate all over the body

What are Heterozygotes? What happens in segregation?

organism that inherits two different alleles for a given gene •Can donate two types of alleles in meiosis -half gametes will have dominant allele and half will have recessive allele

How does the pH effect an enzyme? (Specific)

pH affects the enzymes shape and reactivity •If too high/low, interferes with the bonds holding the enzyme together -changes the shape of the active site and denatures the enzyme.

Sugar with 5 carbon atoms

pentose sugar

What are the particles of light? Do they all store the same amount of energy?

photons •packets if light No, some have high levels of energy while others have low energy

Endocytosis

process by which a cell takes material into the cell by infolding of the cell membrane (usually by vesicles)

What is the kinetochore?

protein structure on chromatids (specifically centromere region) where the spindle fibers attach during cell division to "pull" sister chromatids apart

Ribosomes function

protein synthesis (proteins are extremely important to the body; critical organelle) •abundant in cells that synthesize lots of proteins (pancreas/liver)

What are the two types of nitrogenous bases?

purines and pyrimidines

Potential energy

stored energy that results from the position or shape of an object Ex: boulder sitting on the top of a steep hill

Atomic number

the number of protons in the nucleus of an atom Upper left corner

Mass number

the sum of the number of neutrons and protons in an atomic nucleus (bottom number)

What is the starting components that are necessary for transcription?

•RNA polymerase •single factors/general transcription factors •DNA template strands -possess promoters for starting and terminators for ending

How are polymers of nucleotides formed?

•hydroxyl group is located within the phosphate group which is linked to the number 5 prime carbon •hydroxyl group is located on number 3 carbon of sugar (for both RNA and DNA) -hydroxyl ground bond (condensation reaction) to create a link between the oxygen group of the phosphate and the carbon group of the sugar

What factors affect whether cells can pass the G1 checkpoint?

•nutrients must be sufficient -need enough food for the cell to grow •social signals -growth factors from neighboring cells need to be present (the go ahead signal) •cell size -large enough to split into two functional daughter cells •DNA check -has to be undamaged -about to make entire copy of it and give it to a daughter cells—> don't want the copy messed up •tumor suppressors must be present -regulatory proteins that can stop cell cycle if not working correctly

What is the relationship between the level or organization in a cell vs in the human body? (Mention organelles and organs)

•the skin is similar to the cell membrane -establishes what is inside vs outside •in the digestive tract (alimentary canal), represents an outside space within an inside space -swallow marble and comes out the other end without touching inside space of body, therefore, digestive tract is an outside space =level of organization helps body keep the inside parts separate from the outside parts (can be within one another) •eukaryotic cells represent this -have outside spaces inside the cell =keeps processed separated inside them Conclusion: allows the cell to be the smallest unit of life