Exam 2
Avidin and B7 have a Kd of 1 x 10^-15 while insulin and its receptor have a kd of 1 x 10^-10. How much stronger is the interaction between Avidin and B7 than the interaction between insulin and its receptor? A. 5 B. 5000 C. 10,000 D. 1.5 E. 100,000
E. 100,000
ATP binding to myosin leads to what? A. Rigor mortis B. "Cocking" of the myosin head C. Muscle contraction D. The "power stroke" E. Dissociation of the actin/ myosin binding
E. Dissociation of the actin/ myosin binding
Which fo the following statements about enzymes is false? A. Enzymes are highly selective in the reaction they catalyze B. Enzymes can drive an unfavorable reaction by coupling it to a favorable one, either directly or via activated carrier molecules C. Enzymes make reactions occur faster than without catalysis D. Enzymes form covalent bonds with their substrate to form a reaction product E. Enzymes can make an unfavorable reaction by lowering the activation energy
E. Enzymes can make an unfavorable reaction by lowering the activation energy
Intermediate filaments are primarily for long term or __ whereas actin microfilaments and microtubules are much more __
Intermediate filaments are primarily for long term or (load-bearing) whereas actin microfilaments and microtubules are much more (dynamic)
You alter tryptophanyl synthetase so that it still binds the tRNA but now it attaches serine to the tRNA. What would be the effect?
tryptophan in sequence replaced with serine
Describe treadmilling
add to + end of actin microfilament monomers (G-actin) while subunits lost from - end
Many antibiotics are isolated from fungi which often compete with bacteria for ecological niches. A common mechanism for toxicity is inhibition of protein synthesis. Why don't they stop protein synthesis in humans?
eukaryotic and prokaryotic ribosomes are different
Describe what happens in the spliceosome.
-2' OH in branch point "attacks" donor site -OH on 3' carbon in donor site forms new phosphodiester bond -phosphate on 5' carbon in acceptor site forms new phosphodiester bond
Describe the following molecules: actin, intermediate filaments, microtubule
-Actin: a polymer of individual ATP bound subunits, usually in a helix of two strands. The weakest of the cytoskeletal elements, but very flexible and dynamic -IFs: consists of diverse monomers arranged into dimers then tetramers. Not Bound to nucleotides. Very strong and not very flexible -Microtubule: Made of dimers arranged into a tube of 13 strands. Not very flexible
You wish to know whether BRT binds to RNE. You affix BRT to a matrix then add cell lysate. Finally you elute your "prey" RNE by washing with high salt. What should you see in the cell lysate lane and the elution lane in this gel?
-Cell lysate lane: smear of all proteins being shown -Elution: only see "prey" RNE protein
You're trying to elucidate that job of a particular gene and you find that it has a DNA binding domain and a domain with a sterol binding site (LBS). NLS is a nuclear localization signal. What sort of roll might this protein play?
-DNA binding domain: transcription factor -LBS: hormones -protein brings steroids to nucleus for transcription -protein is glucocorticoid receptor
Describe the following motor proteins: dynein, myosin, kinesin
-Dynein: uses ATP hydrolysis to move towards the - end of the microtubule -Myosin: uses ATP hydrolysis to move cargo on actin microfilaments -Kinesin: uses ATP hydrolysis to move cargo towards the + end of the microtubule
With regards to protein folding, rank the bond strength of the following interactions: hydrogen bonds, Van der Waals interactions, covalent (disulfide or peptide bonds)
-Hydrogen bond: Middle -Van der Waals: Weakest Covalent: Strongest
What do kinases and phosphatases do?
-Kinase: add a phosphate to a protein -Phosphatase: remove a phosphate from a protein
If an additional cryptic exon was added to the polypeptide and it pushed the following exons out of frame, would the protein work?
-No, wouldn't work correctly -May work but probably not same function
What are the polymers and monomers of actin microfilaments?
-Polymer: F-actin -Monomer: G-actin
What types of bonds are important for each level of structure? -Primary -Secondary -Tertiary -Quaternary
-Primary: covalent -Secondary: H bonds -Tertiary: H bonds, electrostatic, van der waals interactions and some covalent -Quaternary: H bonds, van der waals
What job are the following molecules responsible for? -RNA polymerase II -TFIID -U1 -Sigma factor -RNA in the spliceosome -TFIIH
-RNA polymerase II: responsible for transcribing mRNA in eukaryotes -TFIID: binds to the TATA box in eukaryotes -U1: binds the donor site during splicing -Sigma factor: binds to prokaryotic RNA polymerase and helps ensure that the RNA polymerase only binds to promoters -RNA in the spliceosome: catalyzes the splicing of exons together -TFIIH: melts DNA strands using ATP and phosphorylates RNA polymerase leading to transcription initiation in eukaryotes
Why don't antibiotics work on viruses?
-don't have ribosomes, they use the host's ribosomes
What mutation could lead to an outcome where an additional cryptic exon is added to the mRNA? (pre-mRNA: exon 1 - exon II - exon III) (mRNA: exon 1 - cryptic exon - exon II - exon III)
-mutation of additional donor site -mutation in spliceosome
Puromycin blocks the A site in eukaryotic and prokaryotic ribosomes. It has one big side effect so people don't use it on other people. What step does it inhibit in protein synthesis?
-tRNA can't bind to the A site -no new amino acids can be added
What job are the following molecules responsible for? -tRNA -EF-Tu -Aminoacyl-tRNA synthetase -EF-G -Release factor
-tRNA: base pairs to mRNA before adding amino acids in peptide bonds -EF-Tu: checks to make sure that tRNA and mRNA are base pairing correctly -Aminoacyl-tRNA synthetase: covalently bonds amino acids to tRNA -EF-G: moves the ribosome so tRNA moves from A to P site -Release factor: terminates translation
How does GTPase activity alter the activity of RAS. That is why do the GTP bound and GDP bound protein have different functions?
-they have different shapes -RAS is allosteric activator of different proteins
You're working in a lab to understand the role of a particular gene in your favorite organism Solenodon cubanus, a venomous insectivore. The gene codes for a protein that contains an N-terminus hydrophobic α helix and a RAS like domain. What could you predict about the protein?
-will find hydrophobic α helix in the inside of a protein or attach to the cell membrane -RAS like domain means the protein is a GTPase -one end is hydrophobic N-terminus other end is GTPase -extends across membrane
If the codon is 5' - CAU - 3', what's the anti-codon?
5' - AUG - 3'
What's the anticodon for 5' - GCA - 3'?
5' - UGC - 3'
Which of the following are roles proteins can play in a cell? A. Signal Molecule B. Motor - moving cargo around C. Mechanical support D. Enzymatic catalysis E. Signal Receptors F. Transcription factors G. Creating the peptide bond in a ribosome H. Transducing the energy of a protein gradient into ATP
A. Signal Molecule B. Motor - moving cargo around C. Mechanical support D. Enzymatic catalysis E. Signal Receptors F. Transcription factors H. Transducing the energy of a protein gradient into ATP -creating peptide bonds in a ribosome are done by peptidyl transferase (rRNA)
What's the intermediate filament's role in the cell? A. Strengthen cell to cell contacts B. Aid in separating chromosomes during mitosis C. Structural support of the nucleus and cell membrane D. Aid in cell movement
A. Strengthen cell to cell contacts C. Structural support of the nucleus and cell membrane
It has been experimentally determined that sigma binds with greater affinity to the trp operon than the lac operon promoter. What does this information tell you? A. The Kd of lac operon-sigma binding is higher than trp operon-sigma B. The Kd of trp operon-sigma binding is higher than lac operon-sigma C. The promoter sequence of the lac operon promoter are different than at the trp operon promoter
A. The Kd of lac operon-sigma binding is higher than trp operon-sigma C. The promoter sequence of the lac operon promoter are different than at the trp operon promoter
Phosphofructinase catalyzes the following reaction of fructose-6-phosphate to fructose-1,6-biphosphate. You know the sign for for ΔG of ATP ➝ ADP + P and this reaction happens in cells all the time. A. The combined reaction of hydrolyzing ATP and adding a phosphate to fructose-6-phosphate has a -ΔG B.Fructose-6-phosphate ➝ fructose-1,6-biphosphate has a +ΔG C. The enzyme alters the ΔG of adding a phosphate to fructose-6-phosphate D. ATP is an allosteric regulator of phosphofructokinase
A. The combined reaction of hydrolyzing ATP and adding a phosphate to fructose-6-phosphate has a -ΔG B.Fructose-6-phosphate ➝ fructose-1,6-biphosphate has a +ΔG
Enzymes can accelerate the rate of reactions by over a million fold A. True B. False
A. True
Peptide bonds are planar but there's relatively free rotation around the α carbon A. True B. False
A. True
Which of the following are jobs carried out by the cytoskeleton according to the chapter? A. Vesicle movement B. Positioning organelles within a cell C. Help give the cell its 3D shape D. Moving signals through the blood E. "Crawling" of a cell on a substrate
A. Vesicle movement B. positioning organelles within a cell C. Help give the cell its 3D shape E. "Crawling" of a cell on a substrate
What must be bound to actin microfilaments in order to function?
ATP
What is true of protein folding? A. All of the information necessary to fold a protein correctly is in its amino acid sequence B. The free energy of the correctly folded protein is at its minimum C. A "denatured" protein can be "renatured" given appropriate conditions
All are true
Which are true? A. Peptidyl transferase catalyzes the formation of peptide bonds. It's an rRNA B. The P site holds the growing polypeptide chain C. Aminoacyl tRNA synthetase catalyzes the addition of amino acids to the 3' end of tRNA D. EF-Tu is a GTPase that ensures proper pairing between codon and anticodon
All are true
Threonine's R group has a 2 carbon chain with a hydroxyl on the first carbon. Which of the following would apply to theronine? A. This amino acid would likely be in an α helix crossing a lipid bilayer B. This amino acid would be in an α helix and could make hydrogen bonds to a hydrophobic amino acid through the NH and CO groups in the peptide bonds C. This amino acid would make hydrogen bonds to other amino acids in the interior of a protein through its R group D. This amino acid would be able to form salt bridges with aspartic acid and glutamic acid
B. This amino acid would be in an α helix and could make hydrogen bonds to a hydrophobic amino acid through the NH and CO groups in the peptide bonds C. This amino acid would make hydrogen bonds to other amino acids in the interior of a protein through its R group
You add aminoacyl tRNAs that have the tryptophan anticodon but are bound to lysines. How would this affect the cell? A. Transcription would not be attenuated so the trp structural genes would not get made even with lots of tryptophan B. Transcription would be attenuated so the trp structural genes would not get made even in the absence of tryptophan C. Tryptophans would be put into proteins in place of lysines D. Lysines would be put into proteins instead of tryptophans
B. Transcription would be attenuated so the trp structural genes would not get made even in the absence of tryptophan D. Lysines would be put into proteins instead of tryptophans
What changes when an enzyme is added to a reaction? A. ΔG B. Energy of the transition state C. The direction of the reaction D. Activation energy
D. Activation energy
Valine's R group is an isopropyl chain. Where would you find valine in a cytosolic protein?
inside the protein
You're developing a drug to inhibit an enzyme. How might you go about decreasing its Kd? A. Lower the concentration of the drug B. Increase the concentration of the drug C. Alter the enzyme's sequence to bind the drug (ligand) more tightly D. Add groups to the drug that will hydrogen bond to amino acid R groups in the active site E. Increase its size F. Decrease its concentration
D. Add groups to the drug that will hydrogen bond to amino acid R groups in the active site -Kd = [protein][ligand]/ [complex] -can't do C since you'd have to alter enzymes of humans
The product of a biochemical pathway acts as an allosteric inhibitor of the enzyme that catalyzes an early step in synthesis. This is called: A. Allosteric modification B. Phosphorylation C. Catalysis D. Feedback inhibition
D. Feedback inhibition
If you were to create a model of surface interactions between two proteins, which type(s) of protein modeling might you use? A. Backbone model B. Ribbon C. Wire model D. Space-filling model
D. Space-filling model
The specificity on an enzyme substrate interaction is determined by A. The concentration of substrates B. The location of the protein C. hydrogen bonding between the substrate and enzyme D. The R groups of the amino acids in the active state E. The type of transition state needed for the reaction
D. The R groups of the amino acids in the active state
If the interaction between the protein and ligand is weak. What should we see? A. [A] > [B] B. [A] = [B] C. You'd have a lot of [AB] even if [B] has low concentration D. You'd get more [A] then [AB] when [B] has low concentration
D. You'd get more [A] then [AB] when [B] has low concentration -you'd get more of each on its own than in a complex
Which are examples of allosteric regulation of an enzyme? A. RAS, a GTPase, binds to Raf and activates Raf's kinase function without phosphorylating Raf B. SOS replaces the GDP bound to RAS with a GTP activating RAS C. RAS, a GTPase binds to GTP and can hydrolyze it to GDP
A. RAS, a GTPase, binds to Raf and activates Raf's kinase function without phosphorylating Raf
Phosphofructokinase attaches a phosphate to fructose-6-phosphate. It binds ATP in two places - the catalytic site (active site) and the allosteric site. Allosteric binding by ATP inhibits the enzyme. Which site has the lower Kd? A. Allosteric site B. Active site
B. Active site -want glycolysis to happen when ATP low
Which are true of allosteric regulation A. Allosteric regulators of enzymatic activity usually bind to the active site of the enzymes B. Allosteric regulators can be proteins or other biological and non-biological molecules C. Frequently, allosteric regulators exert their influence by leading to changes in protein form D. Allosteric regulators inhibit function, they can't promote it
B. Allosteric regulators can be proteins or other biological and non-biological molecules C. Frequently, allosteric regulators exert their influence by leading to changes in protein form
Which are true about secondary structure? A. H bonding between R-groups stabilizes β strands B. Amino acids in beta strands can have hydrophobic R-groups, hydrophilic R-groups, or a mixture C. The R-groups in an α helix point out like spokes from a bicycle axle D. The R groups in β strand alternate pointing above and below the plane of the peptide chain
B. Amino acids in beta strands can have hydrophobic R-groups, hydrophilic R-groups, or a mixture C. The R-groups in an α helix point out like spokes from a bicycle axle D. The R groups in β strand alternate pointing above and below the plane of the peptide chain
A mutation at the 3' end of an mRNA (in a normal codon not a stop codon or the UTR) could lead to A. An alteration of an amino acid at the N-terminus of the protein B. An alteration of an amino acid at the C-terminus of the protein C. A change in primary structure of the protein D. An alteration of tertiary structure
B. An alteration of an amino acid at the C-terminus of the protein C. A change in primary structure of the protein D. An alteration of tertiary structure
In humans the C-terminal domain or "tail" of RNA polymerase II consists of 52 repeats of a seven amino acid sequence, a serine in the fifth position is an important target of TFIIH. What effects might a mutation that substitutes a glycine for this serine have? A. Lower affinity of the polymerase for the promoter B. Decreased initiation of transcription C. Inability of TFIIH to "melt" the DNA D. Transcriptional errors
B. Decreased initiation of transcription -focus on the kinase activity, initiating transcription -you've mutated RNA polymerase II tail not TFIIH so phosphorylation won't work as well
An enzyme can make an energetically unfavorable reaction +∆G into a favorable one -∆G A. True B. False
B. False
Enzymes alter the activation energy of a reaction thus changing the overall ∆G A. True B. False
B. False
Tertiary structure is composed only of a mixture of α helices and β strands A. True B. False
B. False
The attenuation mechanism for restricting tryptophan operon transcription is a good example of allosteric regulation A. True B. False
B. False
If a protein is post-translationally modified and changes structure as a result, has primary structure of the protein changed? A. True B. False
B. False -e.g. ubiquitination, phosphorylation, glycosylation
What is/ are the most likely interactions between the R group of Tyrosine (phenol) and the guanine base of GDP? A. Covalent B. Hydrogen bond C. Van der Waals D. Ionic bond salt bridge
B. Hydrogen bond C. Van der Waals
What kind of interactions will arginine make with other amino acids? Arginine has a 3 carbon chain, a nitrogen, then a carbon attached to 2 nitrogens. A. Van der Waals interactions B. Hydrostatic interactions "salt bridges" C. Covalent bonds D. Hydrogen bonds
B. Hydrostatic interactions "salt bridges" D. Hydrogen bonds
Where are the R groups arrayed in a beta sheet? A. All on one side B. Interspersed on both sides of the beta sheet C. Depends on whether they are inside the protein or facing the aqueous solution
B. Interspersed on both sides of the beta sheet
When affinity between ligand and protein is very high what should be true? A. The substrate will probably be present in very high concentration in the cell B. Kd should be low C. The active site should have strong bonds to the ligand D. Kd should be high
B. Kd should be low C. The active site should have strong bonds to the ligand
Is the Kd for the enzyme/ substrate complex higher or lower than the Kd for the enzyme/ product complex? A. Higher B. Lower
B. Lower
Do enzymes change the "free energy" of the reactants and products in a chemical reaction? A. Yes B. No
B. No
A mutation in the RNA of the U2 snRNP would lead to what effects? A. No recognition of donor site by spliceosome B. No recognition of the branch point by the spliceosome C. Potential splicing error D. No recognition of acceptor site by spliceosome
B. No recognition of the branch point by the spliceosome C. Potential splicing error
Phosphorylation of nuclear lamins changes which of the following in protein structure? A. Primary B. Quaternary C. Tertiary D. Secondary
B. Quaternary
What changes when PrP shifts to prion form? Normal PrP has 4 α helices while diseased PrP has 4 β sheets and 2 α helices A. Primary B. Secondary C. Tertiary D. Quaternary
B. Secondary C. Tertiary D. Quaternary
Enzymes can A. Alter the chemical equilibrium to encourage product formation B. Stabilize the transition state of reactants to products C. Alter the ΔG of a reaction D. Lower the activation energy of a reaction
B. Stabilize the transition state of reactants to products D. Lower the activation energy of a reaction
Which mutation would lead to no attenuation, but still allow for transcription and translation of the trp operon A. The 2-3 hairpin doesn't form B. The 3-4 hairpin doesn't form C. The 1-2 hairpin doesn't form
B. The 3-4 hairpin doesn't form
GTPases are in their active state when A. They hydrolyze GTP B. They are bound to GTP C. They are bound to GDP D. They phosphorylate GDP
B. They are bound to GTP
Coenzymes differ from proteins because A. They don't fit into the active site, but instead bind to an allosteric site B. They aren't proteins C. Bacteria don't need them D. They can be recycled, but they are altered chemically by the enzymatic reaction
B. They aren't proteins D. They can be recycled, but they are altered chemically by the enzymatic reaction
The trp operon A. Is an example of feedback inhibition B. Tryptophan inhibits an enzyme directly C. If you raised the Kd of the repressor for tryptophan feedback inhibition wouldn't work
A. Is an example of feedback inhibition C. If you raised the Kd of the repressor for tryptophan feedback inhibition wouldn't work -repressor isn't an enzyme; not involved in reaction but is a protein (TF) -feedback inhibition doesn't have to have enzyme
What would be true of a protein-ligand interaction with very high affinity? A. Kd would be low B. Kd would be high C. Kd would vary depending on concentration of the protein
A. Kd would be low
Under what conditions will the trp structural genes get transcribed and translated? A. Low tryptophan B. Hairpin 3-4 formed C. Hairpin 2-3 formed D. Low glucose E. Stalled ribosome F. Few aminoacyl trp-tRNAs
A. Low tryptophan C. Hairpin 2-3 formed E. Stalled ribosome F. Few aminoacyl trp-tRNAs
You're working in a molecular biology lab studying a particular protein and your PI tells you that you're going to mutate the 6th amino acid changing it from valine to alanine. You are changing an amino acid close to which end? Which end of the coding strand should you target? A. N-terminus B. C-terminus C. 5' end D. 3' end
A. N-terminus C. 5' end
A mutation in the RNA of the U1 snRNP would lead to what effects? A. No recognition of donor site by spliceosome B. No recognition of acceptor site by spliceosome C. No recognition of branch point by spliceosome D. No intron splicing using spliceosome
A. No recognition of donor site by spliceosome D. No intron splicing using spliceosome
Which are post-translational modifications to proteins? A. Phosphorylation B. Disulfide bonds C. Ubiquitination D. Glycosylation E. Chaperone interactions
A. Phosphorylation C. Ubiquitination D. Glycosylation
In an SDS-PAGE gel, detergents are added to unfold proteins completely. What level of structure remains? A. Primary B. Tertiary C. Quaternary D. Secondary
A. Primary
You're measuring the Kd of your protein of interest at 30 °C, but you realize your protein comes from an organism that normally lives at 37 °C so you measure the Kd at that temperature as well. Which temperature would have the higher Kd? A. 30 °C B. 37 °C
A. 30 °C
Protein structural domains A. Are stable sub-structures in a portion that appear in many different proteins B. Often fold separately from the rest of the protein C. Are combinations of secondary structure motifs like the helix-turn-helix domain
A. Are stable sub-structures in a portion that appear in many different proteins B. Often fold separately from the rest of the protein
Why do misfolded proteins aggregate? A. Because hydrophobic R groups get exposed to the external surface of the protein B. Because the cell sequesters them this way before sending them to the proteosome C. Because chaperones are unable to interact with all proteins D. Because they have more beta-sheets than alpha helices
A. Because hydrophobic R groups get exposed to the external surface of the protein
How do researchers ensure that only primary structure is preserved on an SDS-PAGE gel? A. Boil/ heat proteins B. Add detergent with a charged head group C. Disrupt proteins using a french press or waring blender D. Use an electric current to separate the proteins in the gel E. Add beta-mercaptoethanol to disrupt di-sulfide bonds
A. Boil/ heat proteins B. Add detergent with a charged head group C. Disrupt proteins using a french press or waring blender E. Add beta-mercaptoethanol to disrupt di-sulfide bonds
Which steps of mRNA maturation happen only in eukaryotes? A. Export from nucleus B. Addition of 5' cap to mRNA C. Production of poly-cistronic mRNAs D. Poly-adenylation E. Removal of introns
A. Export from nucleus B. Addition of 5' cap to mRNA E. Removal of introns
When [protein] = [complex], how much of the total protein is in the complex? Kd = [protein][ligand]/ [complex] A. Half B. All C. Can't tell
A. Half half in complex half not [A] + [AB] = total protein in complex
What correctly characterizes hydrogen bonding in secondary structure? A. Hydrogen bonding occurs between the amino groups and oxygens along the polypeptide backbone B. Secondary structure is held together solely by covalent bonds C. Hydrogen bonds occur between R groups and the polypeptide backbone D. Hydrogen bonds are between R groups
A. Hydrogen bonding occurs between the amino groups and oxygens along the polypeptide backbone
Which are true concerning intermediate filaments? A. IFs are important in maintaining the structure of neuron axons B. Similar to microtubules and microfilaments IFs are composed of repeating identical subunits C. IFs polymerize and depolymerize repeatedly D. Unlike microtubules and microfilaments, IFs don't use nucleotides to help drive polymerization
A. IFs are important in maintaining the structure of neuron axons B. Similar to microtubules and microfilaments IFs are composed of repeating D. Unlike microtubules and microfilaments, IFs don't use nucleotides to help drive polymerization
What is true about various protein structure models? A. In a space fill model it's difficult to see secondary structure B. The wireframe model makes secondary structure very clear C. Secondary structure can't be deduced from the backbone model D. A ribbon model cannot be used to deduce primary structure
A. In a space fill model it's difficult to see secondary structure D. A ribbon model cannot be used to deduce primary structure
Which are true of hemoglobin? A. In order to be functional hemoglobin must also bind an organic molecule called heme that isn't actually covalently bonded to the protein B. The sickle cell mutation is due to a truncation of one of the hemoglobin monomers C. Hemoglobin is composed largely of alpha helical secondary structures folded into a globular tertiary structure D. The functional form of hemoglobin is a heterotetramer
A. In order to be functional hemoglobin must also bind an organic molecule called heme that isn't actually covalently bonded to the protein C. Hemoglobin is composed largely of alpha helical secondary structures folded into a globular tertiary structure D. The functional form of hemoglobin is a heterotetramer
If you were to isolate the amino acid asparagine, where would you find it and what kind of bonds would it be making with other amino acids through its R group? Asparagine has a short 3 carbon chain attached to a NH2 and a C=O A. Inside the protein interacting with hydrophilic amino acids B. Inside the protein interacting with hydrophobic amino acids C. Facing the aqueous environment D. Hydrogen bonds E. Van der Waals interactions F. Covalent bonds G. Salt bridges
A. Inside the protein interacting with hydrophilic amino acids C. Facing the aqueous environment D. Hydrogen bonds
What level of protein structure should be evident on the nitrocelluose membrane in Western Blot? A. Primary B. Secondary C. Tertiary D. Quaternary
A. Primary
Prp is a prion protein that leads to Creutzfeldt-Jacob disease in humans. What is different between the normal Prp protein and the abnormal one? A. Its primary structure is altered so that there are more hydrophobic R groups facing the cytosol B. A helices have re-folded into β strands with hydrophobic R groups facing the cytosol C. It induces the refolding of many different types of proteins D. It induced other correctly folded Prp proteins to misfold
B. A helices have re-folded into β strands with hydrophobic R groups facing the cytosol D. It induced other correctly folded Prp proteins to misfold
Prion proteins A. The prion protein is an infectious agent that in its native folding form can lead to amyloid plaques B. A single mutation in a gene in a somatic cell for a prion protein can cause that protein to induce misfolding in other prion proteins C. Prion proteins are the leading cause of Alzheimer's D. A single mutation in a gene in a somatic cell for a prion protein can cause a hereditary mutation in families
B. A single mutation in a gene in a somatic cell for a prion protein can cause that protein to induce misfolding in other prion proteins
Which actin state has the highest affinity for other actin molecules? A. ATP hydrolysis leads to a conformation change that encourages binding to other monomers B. ATP bound C. ADP bound
B. ATP bound
Smilin is a protein that causes people to be happy. It's inactive in unhappy people. The mature mRNA isolated from a number of different unhappy individuals in the same family was found to lack an internal stretch of 173 nucleoties that are present in the non-mutant Smilin mRNA. The DNA sequences of the Smilin genes from the happy and unhappy persons were compared and they only differed by just one nucleotide change - no nucleotides were delted. Moreover, the change was found in an intron. What would have caused the internal deletion in the mRNA? A. Donor site mutated B. Acceptor site mutated C. Branch site mutated
B. Acceptor site mutated -missing an exon (2) -spliceosome would look for next acceptor site -splice from acceptor site of exon 1 to beginning of exon 3
One way an enzyme can work is by coupling a reaction with a -∆G to one with a +∆G. For instance, in the "harvesting" part of glycolysis, phosphoglycerate kinase takes a phosphate form 1,3 bisphosphoglycerate and adds it to ADP. Which of the following are true? A. The enzyme uses the hydrolysis of ATP to drive the reaction B. ADP ➝ ATP has a -∆G C. 1,3 bisphosphoglycerate ➝ 3-phosphoglycerate has a -∆G D. ADP ➝ ATP has a +∆G E. The overall reaction has a -∆G F. The overall reaction has a +∆G
C. 1,3 bisphosphoglycerate ➝ 3-phosphoglycerate has a -∆G D. ADP ➝ ATP has a +∆G E. The overall reaction has a -∆G
Which sort of protein would be likely to need a chaperone? A. All three B. A membrane protein with hydrophobic amino acids facing the membrane C. A large cytosolic protein with large stretches of hydrophobic amino acids D A small cytosolic protein composed largely of hydrophilic α helices E. Just the cytosolic proteins
C. A large cytosolic protein with large stretches of hydrophobic amino acids
A decrease in cellular ATP concentration would directly affect which of these? A. Intra-peptide folding during translation B. tRNA/ mRNA pairing C. Aminoacyl-tRNA synthetase D. Hsp70 interaction with hydrophobic patches E. Transcription
C. Aminoacyl-tRNA synthetase D. Hsp70 interaction with hydrophobic patches E. Transcription -needed for transcription for phosphorylation of the mRNA tail and adding nucleotides to a growing chain needs nucleotides in their triphosphate forms -Hsp70 is heat shock protein that uses ATP to bind exposed hydrophobic amino acids
Chaperones A. Help most proteins fold correctly B. Are what allow amino acids to interact locally in protein folding C. Help get proteins out of nonfunctional minimal energy states to their proper native state D. Interact with DNA to form nucleosomes
C. Help get proteins out of nonfunctional minimal energy states to their proper native state
CTP inhibits the synthesis of pyrimidine rings of cytosine, uracil, and thymine. CTP is used in the synthesis of pyrimidine rings. Why is it a good inhibitor? A. It's the product of the reaction B. It's plentiful in the cell C. If there's a lot of CTP it suggests there's enough pyrimidines in the cell D. CTP ➝ CDP is a -∆G so it can be coupled to the reaction
C. If there's a lot of CTP it suggests there's enough pyrimidines in the cell -inhibition doesn't require reaction coupling
Which of the following are true concerning TFIIH function in eukaryotic transcription? A. TFIIH is phosphorylated in order to position the RNA processing enzymes B. TFIIH is a regulatory transcription factor C. TFIIH acts as a helicase, melting DNA D. TFIIH's kinase activity results in transcriptional initiation E. TFIIH positions the polymerase for transcription
C. TFIIH acts as a helicase, melting DNA D. TFIIH's kinase activity results in transcriptional initiation
In terms of microtubules what leads to catastrophe? A. Loss of tubulin dimers from the minus end of the microtubule B. Hydrolysis of GTP tubulin dimers before they are added to a growing microtubule C. When addition of GTP bound tubulin dimers slows so that the GTP cap gets small D. Exchange of GTP for GDP by GEFs
C. When addition of GTP bound tubulin dimers slows so that the GTP cap gets small
If the interction is very strong between a protein and its ligand. What should we see? A is the protein and B is the ligand. A. [A] > [B] B. [A] = [B] C. You'd have a lot of [AB] even if [B] concentration low D. You'd get more [A] than [AB] when [B] has low concentration
C. You'd have a lot of AB even if B concentration low
