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Exam 3 (also study Exam 1 and Exam 2 )

Terms in this set (113)

Ch 20 (Done)
What drive DNA polymerization?
Use of ATP coupled to cleave the pyrophosphate product
Ch 20 (Done)
What other activity is often associated with DNA polymerases? Why?
Proofreading!
Avoid mutations
Ch 20 (Done)
What enzyme(s) are required to unwind DNA for replication?
Helicases: •Unwind DNA
Topoisomerases: •Cut DNA strands to release tension
Ch 20 (Done)
What model best describes DNA replication forks?
Trombone Mechanism
Ch 20 (Done)
What is responsible for the use of thymidine instead of uracil in DNA?
Overcome oxidative deamination
Ch 20 (OS)
What is common to all DNA repair systems?
Differs between base and nucleotide excision repair mechanisms?
•Different: DNA glycosylase vs helicase
•Same: Endonuclease, DNA polymerase, DNA ligase
Ch 20 (OS)
Why is recombination important for DNA repair/replication?
What is the advantage of being diploid?
•Advantage: Gives a template for accurately filling in double stranded break in DNA in a helix
Ch 20 (Done)
What controls access to packaged DNA?
Histone Code/ Histone Modification
Ch 20 (Done)
What about DNA polymerase activity leads to Okazaki fragments?
Directionality in polymerization (5' to 3')
Ch 20
What is the key aspect of the DNA polymerases at such forks?
•They are attached
•They need primers to start
•They work with other enzymes
Ch 21
How is RNA polymerase recruited to promoters for transcription?
With transcription factors and enhancer elements with a mediator.
Ch 21
How does transcription (i.e. RNA polymerases ) deal with nucleosomes?
Through histone modification for enhancing/repressing expression:

•Specifically methylation and acylation
Ch 21
What is required for the release of RNA pol II to elongate mRNA in eukaryotes?
Poly-phosphorylation of the c terminal tail
Ch 21
What is added to the 5' / 3' ends of eukaryotic mRNA ?
5' cap (7-methyl guanosine) , 3' poly-Adenosine Tail
Ch 21
Does all the gene sequenced in eukaryotes encode protein? What is an intron/exon?
No: lots of genes have introns which are regions of the gene that are "spliced" out in mRNA processing.
Exons are the regions that are retained in the transcript.
•Note, splicing can vary depending on the tissue for diversity in protein form
Ch 21 (Done)
Which types of RNA undergo universal modification?
Ribosomal RNA and tRNA
Ch 21 (Done)
Why can RNA form complex structures?
Alternative Base Pairing and 2' OH
Ch 21 (Done)
Why can short double-stranded RNA potentially act as drugs?
RNA interference
Ch 22 (OS)
Which enzyme/RNA is most critical for the accuracy of translation?
This question is stressing the importance of
!amino acyl-tRNA synthetases !

•Have exquisite fit to tRNA to insure the correct amino acid is added per tRNA
Ch 22 (OS)
How is the redundancy in the genetic code reflected in codon-anticodon base-pairing?
Multiple tRNAs encode for the same amino acid and differ in their third or "wobble" position
Ch 22 (Done)
Which bases allow wobble in the tRNA anticodon?
Inosine allows for the most wobble
guanine and uracil also allow for some wobble.
Ch 22 (Done)
Which component of the ribosome is responsible for (peptide bond formation) (reading mRNA)
Peptide bond = A Site
Reading mRNA = A site
Ch 22 (Done)
What makes up the bulk of the ribosome?
Ribosomal RNA
Ch 22
What are the major components/subunits of the ribosome?
Major components: RNA/Protein
Major Subunits: Large and small subunit
•Large subunit composed of various smaller RNA subunits for both prokaryotes and eukaryotes
Ch 22 (Done)
How is translation terminated -ie what binds to the stop codon and what does it do?
Stop Codons released by release factors not tRNA
Ch 22
How is the start codon (beginning AUG) defined in prokaryotes/eukaryotes?)
•Prokaryotes use Shine-Delgarno sequence and special tRNA for f-MET
•Eukaryotes Identify starting site by proximity to 5' cap
Ch 22 (C)
What is the general role of GTPase activity of
IF-2
EF-Tu
EF-G
RF-3
IF-2: Delivers initiator tRNA to P site of ribosome
EF-Tu: Delivers aminoacyl-tRNA to A site of ribosome during elongation
EF-G: Binds to A site to promote translocation following peptide bond formation
RF-3: Binds to A site to stop codon and induces peptide transfer to water
Ch 22
Where are polypeptides/proteins destined for secretion/plasma membrane synthesized?
ER membrane, directly through translocon into ER luminal side
Ch 3 (Done 3x)
What is the central dogma in biology?
The central dogma in biology is that genomic information is stored in DNA, transcribed into mRNA, and translated into protein to perform cellular functions
Ch 3 (Done 3x)
What is the key difference between RNA and DNA and why is this important?
The key difference between RNA and DNA is the presence/absence of the !!2' hydroxyl group!! (or oxygen). The 2' alcohol group allows for additional hydrogen bonding and more unique RNA structure beyond helices!!(more reactivity).!!

!!Note this reactivity means RNA can act as a catalyst!!

Thymine (DNA)
Uracil (RNA)
Ch 3 (Done 3x)
What underlies the helical nature of nucleotide polymers?
The hydrophic effect begins the process of pushing the DNA strand together, !!The Van Der Waals interactions!! of the stacked nitrogenous bases ultimately gives rise to helix formation"
Ch 3 (Done 3x)
What advantage does the CRISPR technology offer for genetic engineering?
CRISPR technology allows for greater specificity in mutation and also enables large scale manipulations in organisms. For example with CRISPR it is possible to selectively remove an entire gene cluster
Ch 4 (Done 3x)
What are the major types of amino acids?
Hydrophobic: Alanine
Polar: Serine, Threonine, Cysteine
Charged: Aspartate
Ch 4 (Done 3x)
What are the types of primary, secondary, tertiary, and quaternary structure and what it important about it?
Primary: just the sequence

Secondary : alpha helices are coiled motifs created
Beta-sheets (parallel and antiparalel)
-both arise due to hydrogen bonding in backbone

Tertiary : how the whole peptide comes together,
Composed of multiple motifs and interactions between side chains.

Quaternary: often multiple peptide chains come together to form larger complex. IE, two separate sub-units in a dimer
Ch 4 (Done 3x)
What drives protein folding?
Protein folding is driven by the !!hydrophic effect!! that drives the non-polar regions of amino acids together to form a !!"glass like state" !!from which local areas of secondary structure begin to form.
Ch 4 (Done 3x)
How are protein structures determined?
x-ray crystallography or nuclear magnetic resonance (NMR).
Ch 5 (Done 3x)
Can all proteins carry out their functions alone?
No, many proteins require cofactors to properly function. Example: myoglobin and hemoglobin !! requires a heme-iron group to transport oxygen.!!
Ch 5 (Done 3x)
How is it that myoglobin has higher affinity for oxygen than hemoglobin?
Myoglobin has a higher affinity for oxygen because it stabilizes the binding of oxygen to the heme group with a histidine residue.

Also, Hemoglobin also undergoes !!cooperative binding!! with it's four subunits that facilitates oxygen release through conformational change." (aka exhibits cooperativity, also know as allostery)
Ch 5 (done 3x)
Which filaments are most, least, and middle level dynamic and what is it about these structural proteins that makes them dynamic?
Most: Actin Filaments
Aka microfilaments
small subunit size and asymmetry
Middle Level: Beta tubules

Aka microtubules
Least: Intermediate Filaments
Do not use ATP to polymerize very static
Ch 5 (Done 2x)
What type of enzymatic activity unifies dynamic filaments and motor proteins?
atp/gtp-ases.
Ch 5 (Done 3x)
What motor protein moves cargo via microtubule tracks?
!!Kinesin!! is the motor protein that moves cargo via !!microtubule tracks.!!
Ch 5 (Done 3x)
What are the type of movements that describe myosin and kinesin motor mechanisms?
Myosin = rowing
Kinesin = walking
Ch 6 (Done 3x)
How do enzymes increase the rate of a reaction/what stage of the reaction do they bind most tightly?
they change the reaction coordinate. Enzymes bind most tightly to the transition state in the reaction.
Ch 6 (Done 3x)
What aspect of a reaction diagram tells you about rate/spontaneity?
Spontaneity:
If reactants are higher energy than products, reaction will be spontaneous. (aka negative free energy change)
Rate:
The lower the activation energy, the faster the rate.
Ch 6 (Done 3x)
Do all enzymes that share the same -ase name catalyze the exact same reaction?
No, for example serine proteases differ in their !!specificity/affinity!! for peptide cleavage due to changes the binding pockets of their active sites.
Ch 7 (Done 3x)
Must enzymes with multiple substrates bind them all at the same time?
No, some enzymes bind them at different times, either !!sequentially or non-sequentially!!. Example: Pentose phosphate pathway

One type of enzyme that always uses multiple substrates are !!transferases!!
Ch 7 (Done 2x)
What parameters of enzymatic activity are quantified by the Michaelis-Menten equation?
Km is used to compare the approximate affinity of an enzyme to its substrate
Ch 7 (Done 2x)
What enzymatic activity constant changes in the presence of a competitive inhibitor
Vmax stays the same, Km increases.
Ch 7 (Done 2x)
What enzymatic activity constant changes in the presence of noncompetitive/ mixed inhibitor & why?
Vmax decreases, Km increases
Ch 7 (Done 2x)
Define catalytic efficiency and why it is important to enzymatic activity in vivo
!!Catalytic efficiency!! is the ratio of product turn over relative to substrate concentration.

!!Mathematically = Kcat/Km!!
High catalytic efficiency: good activity at low concentrations.
In the body substrate concentration is relatively low, so in order to have sufficient product formation a high catalytic efficiency is needed.
Ch 7 (Done 2x)
How can enzymatic activity be regulated?
1.by covalent modification
2.Translocation of the enzyme
3.allosterically modified
4.changed on the transcriptional level
Ch 8 (Done 2x)
Which type(s) of lipids contains parts derived from serine?
Sphingolipids contain a backbone made from serine.
Ch 8 (Done 2x)
How is membrane fluidity maintained?
overall cholesterol has a ______ effect on membrane fluidity
!!Cholesterol!! has fused rings so it does not bend== it makes membranes !!less fluidand and have a higher melting point.!!

overall cholesterol has a !!"chaperone"!! effect on membrane fluidity
Ch 8 (OS)
Recall the different kinds of membrane associated proteins
!!All integral membrane proteins are "stuck" in the membrane , peripheral membrane proteins and lipid-linked proteins can reversibly disassociate from the membranes.!!
Ch 8 (Done 2x)
Which kind(s) of integral membrane protein can be predicted from sequence data and why?
Which is hardest to predict?
Single transmembrane helices are possible to predict from sequence,
Stretches of roughly 20 non-polar amino acids

Note, a Beta Barrel transmembrane protein would be the hardest to predict
Ch 8 (Done 2x)
What does the !!fluid mosaic!! model predict about membrane protein movement?
membrane proteins can diffuse laterally in a membrane

they can !!not!! diffuse in the transverse direction
Ch 9 (Done 2x)
What kind of ion channels are involved in nerve impulses/synaptic signaling?
nerve impulses : !!voltage gated.!!

synaptic signaling: voltage gated pre-synapse and ligand gated post-synapse
Ch 9 (Done 2x)
What mechanism ensures directional movement of the action potential?
by gate inactivation following channel opening with the "ball in chain motif"
Ch 9 (Done 2x)
How can ion channels be "gated"?
!!Ball and chain motif!! that swings into the channel pore and plugs it.
Ch 9 (Done 2x)
Which membrane proteins primarily/secondarily generate chemical gradients?
primary chemical gradients: Pumps that use ATP

Co-transporters facilitate secondary chemical gradient generation
Ch 9 (Done)
What drives membrane fusion?

What does it release?
!!voltage gated calcium channels!! opening, causing Ca influx that causes the !SNARE Complex to assemble/ coil together releasing neurotransmitters!
Ch 10 (OS)
What is the usual target of lipid hormones? (Hydrophobic molecules)
Lipid hormones (steroids) bind receptors at or on the plasma membrane
Ch 10 (Done 2x)
How do G protein-coupled receptors amplify their signal?
!GPCR's indirectly! activate g-proteins that go on to cause enzymatic protein kinase cascades through !secondary messengers.!
Ch 10 (OS)
How are receptors deactivated and their signals turned off?
hydrolysis of the phosphate groups of the bound GTP

secondary messengers' signals are also cleaved by water with phosphodiesterases.
Ch 10 (OS)
How are receptors deactivated and their signals turned off? STAR
For Calcium ions acting as secondary messengers, they must be !!pumped back into the ER with ATP Pumps!!

Sometimes receptors cannot "turned off" by hydrolyzing the bound GTP: Ex, when an agonist is bound to the receptor.
In this case, the receptor can be:

1. Phosphorylated
2. Be silence by Arrestin binding
Ch 10 (Done)
How do tyrosine kinase receptors amplify their signal?
Tyrosine kinase receptors have a !!conformational change!! across their transmembrane region that causes cytosolic residues auto-phosphorylate, !!directly!! activating other enzymes.
Ch 11 (Done 2x)
How many carbons are minimum/usual in carbohydrates?
minimum: three
common: six (glucose).
Ch 11 (Done 2x)
What distinguishes lactose and sucrose?
Lactose bond =
Galactose Beta (1, 4) alpha glucose

Sucrose bond =
Glucose alpha(1-2) beta fructose
Ch 11 (Done 2x)
What is the consequence of the difference between starch/glycogen and cellulose?
Cellulose is more extended, and a long linear sheet

Starch is more compacted, and forms helices
Ch 11 (Done) (OS)
What is the purpose of glycoproteins/ peptidoglycans?
Glycoproteins: host self-recognition and protein spacing.

Peptidoglycans: structural purposes such as building cross-linked cell walls
Ch 11 (OS)
What is the purpose of proteoglycans?
Proteoglycans are sugar with a peptide backbone so they are able to act as a sponge for water and reduce mechanical compression in cartilage.

"Hydrated shock pads"
Ch 11 (Done 2x)
Why is the hydrolysis of ATP energetically favorable?
1. Negative Charge Repulsion
2. Resonance stability
More resonance in free form (inorganic phosphate form)
Ch 11 (Done 2x)
What is the primary product from oxidization of carbon and what carries this?
electron capture == Electrons are the primary product
Ch 11 (Done 2x) (OS)
What is another bond (besides phospoanhydrides) who hydrolysis is energetically highly favorable?
Thioester
Ch 11 (Done 2x)
What are the key 2 and 3 carbon intermediates in central metabolism ?
3 Carbon:
Glyceraldehyde-3-phosphate
Pyruvate

2 Carbon:
Acetyl-Coa
(Done 2x)
In what form is energy input during glycolysis?
investment phase in the form of ATP
(Done 2x)
Which steps of gluconeogenesis require energy input?
•Every step that uses ATP or NADH
(Done 2x)
Committed step in gluconeogenesis is
Phosphoenolpyruvate carboxykinase
(Done 2x) (OS)
Why do yeast make ethanol an mammals make lactate?
Under annerobic conditions, organisms need a molcule to !!dump electrons!! too. Yeast reduce acetaldehyde to ethanol to dump electrons and !!reform NAD+!! .
Mammals do essentially the same process but make Lactate instead, also to!! reform NAD+!!
(Done 2x)
What are the products of the non-oxidative phase of the pentose phosphate pathway?
•Fructose-6-phosphate
•Glyceraldehyde-3-phosphate
(Done 2x)
What are the major products of the oxidative phase of the pentose phosphate pathway?
•NADPH and Ribose-5-phosphate
(Done 2x)
What are the major products of a "Full" Pentose Phosphate Pathway ("A Full Cycle")
•NADPH
(Done 2x)
What are the major products of the pyruvate dehydrogenase complex
Acetyl-CoA, and NADH.
(Done 2x)
What type of oxidation provides less energy?
FADH2 (QH2)

Both are oxidation, but more bonds to oxygen gives more energy than increasing the number of bonds to carbon.
(Done)
Which enzymes are most highly regulated in the citric acid cycle and why?
There are three most high regulated enzymes:
1. Citrate synthase = starting point of the cycle
2. Isocitrate dehydrogenase => forms NADH and CO2
3. alpha-ketoglutarate dehydrogenase => forms NADH and CO2
*Note the steps where C02 leaves, highly regulated
(Done)
Which enzyme directly links the citric acid cycle and electron transport chain?
Succinate Dehydrogenase aka complex II
(Done)
How do these co-factors differ in their affinity for electrons and what is the resulting energy used for?
Order: NADH <QH2 <Cytochrome C <Ferredoxin

Keep in mind, lower affinity means giving up is higher energy
(Done)
Which state of ubiquinione (co-enzyme Q) is particularly important for proton pumping by complex III? (oxidation state)
(•Q - ) form that donates an electron to complex three
(Done)
Which is the key aspect of the c subunit of the atp synthase?
•That it binds to protons and allows them to diffuse across the membrane in a way that is coupled to ATP synthesis

•Protons bind/are released from !!Aspartate 61 residue!!
(Done)
What drives the import of ADP/Pi into the mitochondria
•The chemical gradient drives ATP/ADP translocation.
•The proton gradient (electrochemical gradient) is used to bring new Pi into the mitochondrial matrix
(Done)
What is a key difference between the proton motive force in chloroplasts versus mitochondria?
Chloroplasts: !!chemical gradient!!
Mitochondria: electrochemical gradient
(Done)
What is the key function of Photosystem II in photosynthesis?
•excite an electron that can be transferred to QH2 and ultimately travel to Photosystem I.
(Done)
What is the key function of the oxygen evolving complex in photosynthesis?
regenerates cytochrome p680+ by oxidation of water .
(Done)
What is the key function of cytochrome b6f in photosynthesis?
•help strengthen the electrochemical gradient across the thylakoid membrane
(Done)
What is the key function of photosystem I in photosynthesis?
reduce NADP+ to NADPH
(Done) (OS)
What drives fixation of CO2 by rubisco?
Coupling carbon fixation to !!splitting ("lysis")!! the six carbon backbone into two, resonance stabilized
3-phosphoglycerate molecules
(Done) (OS)
•How can photosynthesis avoid splitting 02 (photorespiration)?
Fixing CO2 into a four carbon intermediate (malate)
(Done)
what pathway evolved due to the inefficiency of this (rubisco)?
C4 pathway.
(Done)
•What compound is key to the CO2 concentrating mechanism of C4 plants?
Malate
(Done)
What dictates the specificity of mammalian fatty acid synthases for palmitate?

What is the most common fatty acid?
•A thioesterase domain (TE) cleaves most commonly chains 16 carbons in length
palmitate the most common fatty acid.
(Done) (C)
How does liver alter its metabolism in response to starvation?
The liver redirects acetyl-coA to form ketone bodies, aka !! beta-hydroxybutyrate)!!


These can be rebroken down to use as fuel in tissues.
!!Broken back down to Acetyl-Coa!!
(Done)
What distinguishes fatty acid degradation versus biosynthesis
•Biosynthesis: Uses Cis-double bonds
•Degradation: Converts cis-bonds to trans bonds
(Done)
How many electrons are directly captured in one cycle of unsaturated fatty acid B-Oxidation?
Unsaturated: two electrons
Saturated: Four electrons
(Done)
What type(s) of energy is used by nitrogenase to fix nitrogen?
Electrons (From ferredoxin)
-ATP
(Done)
How does amino acid degradation and biosynthesis overlap in mammals?
Degradation of amino acids often directly produces other amino acids via transamination, deacylation, or hydroxylation.
(C)
How does amino acid degradation and biosynthesis overlap in mammals? Serine goes to What and Phenylalanine
Serine degraded to cysteine or glycine

Phenylalanine oxidize to Tyrosine
(Done)
What is the last common purine nucleotide
inosine-monophosphate
(OS)
In what form is nitrogen from purines/pyrimidines/ and amino acids excreted by mammals
Purines: Adenine, guanine, and uric acid
pyrimidines: Ammonia, Urea, and Uric acid
(Done)
In what form is nitrogen moved from muscles to the liver
Alanine
(Done)
In what form is pyruvate moved from muscles to the liver
Transported as lactate
(Done)
Adrenaline exhibits a similar effect to what other hormone that affects central fuel metabolism
glucagon
(Done)
What enzyme is key to the ability of the pancreatic islet cells to sense high blood glucose levels
•Glucokinase.
•It has a wider range of sensing capabilities than hexokinase which is nearly 100% activated at low concentrations.
(OS)
What type(s) of central catabolism do/do not take place in the mitochondria
Do: Citric Acid, Oxidative Phosphorylation, B Oxidation, Ketogenesis, Urea cycle
Do not:
Glycolysis, Gluconeogenesis, pentose phosphate pathway, fatty acid synthesis, urea cycle, nucleotide synthesis
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