Enzyme Amino Acids and Bond – Biochemistry Exam

Enzyme Amino Acids and Bond – Exam

This is Biochemistry exam based on topics of enzyme, amino acids and the bond linking polymers and amino acids.


Amino acids with non-ionizable side chains are zwitterions when they are


a) in any solution
b)in solutions with pH>pKa value of their acidic group and pH<pKa value of their basic group – correct
c)in solutions with pH>pKa value of their acidic group and pH>pKa value of their basic group
d) in solutions with pH<pKa value of their acidic group and pH<pKa value of their basic group
e)in solutions with pH<pKa value of their acidic group and pH>pKa value of their basic group


According to the Henderson-Hasselbalch equation, when the concentrations of proton acceptor and proton donor are the same, then


a) the carboxylic acid is totally neutralized
b) only salt forms are present
c) pH = pKa – correct
d) pKa = log [proton acceptor/proton donor]
e) the pH is neutral


what information can be gained by comparing the sequences pf proteins that have the same or similar function in different species?


a) to determine evolutionary relationships and relatedness of species
b) to determine sequences that are conserved among species since they are likely to be important to the function and stability of the proteins
c) to locate highly variable residues which contribute little to the structure and function of the protein
d) all of the above – correct
e) none of the above


The R group of an amino acid determines if it is


a) hydrophilic or hydrophobic
b) polar or nonpolar
c) charged or uncharged
d) an acid or a base
e) all of the above- correct


What is the major driving force for protein folding?


a) the hydrogen bonds that stabilize alpha helices and beta sheets
b) van der waals forces
c) ionic forces (salt bridges)
d) covalent bonds, like disulfide bonds between cysteine residues
e) the increase in the entropy of the solvent when the protein folds- correct


which statement explains the cleaning action of soap on greasy dishes?


a) the soap changes the water-solubility of the grease so that it is easily dissolved by the water
b) the soap hydrates the grease with its polar head groups and holds it in suspension
c) the soap chemically breaks down the grease into smaller, more water-soluble molecules
d) the grease is trapped inside the hydrophobic interior of micelles made of soap molecules- correct
e) the soap protonates the grease, increasing its pKa, and thus the forward rate constant, k1, for dissolution


How many fragments will result from the treatment of trypsin on the following protein?
Gly-Lys-Ala-Thr-Trp-Arg-Val-Ser-Tyr-Gln-Lys-Ile


a) 0
b) 1
c) 2
d) 3
e) 4 – correct


Disulfide bridges can form in proteins _____________


a) only between cysteine residues side-by-side in the protein sequence
b) between cysteine residues that are close in 3D space, but not necessarily close in primary structure- correct
c) between 2 cysteine residues in proteins
d) between any 2 methionines or cysteines
e) only inside the cell where it is a reducing environment


Dilute amounts of acetic acid (CH3COOH, pKa = 4.76) are mixed in buffered solutions of pH = 2 and pH = 7


a) since it is an acid, it will be in the acidic form, and thus positively charged in both solutions.
b) it will be present predominantly as a positively charged species at pH = 2
c) it will be present predominantly as a negatively charged species at pH = 2
d) it will be present predominantly as a positively charged species at pH = 7
e) it will be present predominantly as a negatively charged species at pH = 7 – correct


You are sequencing a protein sample via Edman degradation, and after the first round of degradation, you identify amino acids derivatives. Which of the following are reasonable explanations for this result?


a) the sample is impure and contains multiple different proteins
b) the protein is composed of several different subunits
c) the protein is partially degraded
d) all of the above – correct
e) none of the above)


Alanine, valine, leucine, and isoleucine are important in 3D structure because they


a) are branched
b) are highly hydrophobic – correct
c) are highly hydrophilic
d) attract water molecules


Which will be different for a catalyzed reaction versus an uncatalyzed reaction?


a) activation energy – correct
b) ground state energy
c) free energy change
d) all of the above


In an enzyme reaction involving one enzyme and one substrate, the rate of the reaction depends on 


a) substrate concentration
b) enzyme concentration
c) both substrate and enzyme concentrations- correct
d) the enzyme concentration at first and the substrate concentration later on


the initial velocity of an enzyme reaction (v0) describes)


a) the concentration of the enzyme at maximal velocity 
b) the concentration of substrate at maximal velocity 
c) the concentration of both at the start of the reaction
d) the rate of the reaction when the substrate and enzyme are first mixed- correct


The Michaelis constant Km, is equal to the ___________. 


a) max velocity that any given enzyme reaction can achieve
b) substrate concentration which gives the best enzyme assay for an enzyme reaction 
c) substrate concentration when the rate is equal to half its maximal value- correct
d) max velocity divided by 2


The expression Vmax = K2[E]total applies when 


a) [S] is low, and the kinetics are first order in [S]
b) [S] is low, and the kinetics are zero order in [S]
c) [S] is high, and the kinetics are first order in [S]
d) [S] is high, and the kinetics are zero order in [S]- correct
e) generally valid as long as Michaelis-Menten kinetics are obeyed


Enzyme activity can be modified by protein phosphorylation, i.e., by adding phosphate to the side chains of:


a) tryptophan
b) serine
c) threonine
d) tyrosine
e) b, c, and d- correct


Acyl-group-transfer reactions often involve which coenzyme?


a) coenzyme A – correct
b) NAD+
c) cytochrome C
d) all of the above


The metal ions in metalloenzymes are firmly bound at the active site of the enzyme. In catalase and cytochromes they are found attached to ___________


a) sulfur clusters
b) phosphate
c) vitamins
d) hemes- correct


The compounds alpha-D-fructofuranose and B-D-fructofuranose are _________


a) enantiomers
b) mutamers
c) anomers- correct
d) conformational isomers


What type of bond links the monomers of the polysaccharide?


a) carbohydrate ester bond
b) glucotide bond
c) aldo-keto bond
d) glycosidic bond- correct
e) epimeric bond


A cutthroat trout during the winter will be relatively rich in _________, allowing it to live in the icy cold waters of Yellowstone lake


a) arachidonic acid
b) unsaturated fatty acids – correct
c) saturated fatty acids
d) eicosanoids
e) all of the above


Facilitated diffusion (passive transport) through a biological membrane is 


a) generally irreversible
b) driven by the ATP to ADP conversion
c) driven by a concentration gradient- correct
d) endergonic
e)all of the above


In the adenylyl cyclase signaling pathway the second messenger(s) are ________


a) ATP and GTP
b) protine kinase A
c) cyclic AMP – correct
d) AMP
e) GBy


According to Chargaff’s observations of nucleotide composition of DNA samples 


a) % of (G + C) + % of (A + T) = 100%
b) A = T
c) G = C
d) %A + %G +%C + %T = 100%
e) all of the above- correct


Adenylate and AMP each contain ________ phosphate group(s)


a) 0
b) 1- correct
c) 2
d) 3
e) none of the above


The tetranucleotide AGTC (in DNA) has a free hydroxyl group on 


a) A
b) A, G, T, and C
c) C- correct
D) G, T, and C


Regions of DNA that are most easily unwound have 


a) about half G and half C
b) alternating A and G
c) Greater G:C content
d) Greater A:T content- correct


the processivity of E. coli DNA polymerase 3 holoenzyme accounts for all the following except


a) the relatively small number of enzymes needed to replicate the entire chromosome
b) the directionality of polymerization- correct
c) the rapid rate of polymerization
d) the ability of a single holoenzyme to add many nucleotides to a growing DNA chain


Why is DNA damage in human skin cells from exposure to excessive UV light not completely reverse by photoreactivation?


a) DNA photolyase in humans is activated only under conditions of heat shock
b) humans lack a photoreactivation repair mechanism- correct
c) the presence of histones greatly slows photoreactivation, thus humans depends primarily on other forms of DNA repair
d) photoreactivation is specific for the removal of thymine dimers. Thymine dimers do not form in human DNA


In the Holiday model describing recombination


a) homologous sequences line up
b) strands of DNA are nicked
c) DNA strands associate with the homologous strand (strand invasion)
d) strands rotate then are cleaved at the crossover point
e) all of the above- correct


Genes that encode for proteins that are need for basic metabolic processes (such as glycolysis) are called _______ genes


a) essential 
b) housekeeping- correct
c) core
d) cardinal


Which is not a property of RNA polymerase?


a) polymerizes in the 5′-3′ direction
b) catalyzes the formation of phosphodiester linkages
c) polymerizes a reaction assisted by pyrophosphate hydrolysis
d) has exonuclease proof-reading abilities- correct


Pause sites are regions ________ sometimes causing transcription to stop completely. 


a) rich in GC base pairs- correct
b) rich in AT base pairs
c) without palindromic sequences
d) where Nus A is not present


Which is not true about the lac repressor?


a) its genes is part of the lac operon and is transcribed along with lacZ, lacA, and lacY.- correct
b) when it binds to DNA, it forms a loop-type structure.
c) it likely blocks both RNA polymerase binding as well as transcription initiation
d) it binds to DNA by interaction of an alpha helix with the major groove


What is the 5′ -> 3′ for an amino acid with the codon CAG?


A) GAC
b) CUG- correct
c) GUC
D) CTG


Unlike bacterial mRNA, eukaryotic mRNA must undergo __________ before it may be used for translation


a) splicing
b) capping
c) polyadenylation
d) export to the cytoplasm
e) all of the above- correct


How are the termination codons different from other codons?


a) they contain thymines
b) the termination codon always codes for methionine
c) they are not recognized by an tRNA molecules- correct
d) their conformations do not allow them to fit properly in the A site of the ribosome


Which statement is not true about catabolic pathways?


A) catabolic pathways generally provide a net release of energy
b) catabolic pathways generally result in a net consumption of ATP- correct
c) catabolic pathways generally liberate smaller molecules from larger ones.
d) catabolic pathways include the citric acid cycle
e) catabolic pathways are usually oxidative, not reductive processes


Which thermodynamic quantity is used to determine if a reaction in a cell is spontaneous?


a) Delta G”
b) Delta G- correct
c) Delta H
d) Delta S


For a step in a reaction pathway to serve as a control point it should be ___________


a) irreversible
b) endergonic
c) far from equilibrium
d) both A and C- correct
e) all of the above


Enzymes that catalyze the same reaction are called ________


a) isozymes- correct
b)complementary enzymes
c) cofactors
d) catalytes


The sequence of glucose oxidation to lactate in peripheral tissues of lactate to the liver, formation of glucose from lactate in the liver, and delivery of glucose back to peripheral tissues is known as the _____________. 


a) glyoxylate cycle
b) kreb’s cycle
c) Cori cycle- correct
d) gluconeogenesis cycle
e) TCA cycle


Which of the following is not regulated in glycolysis?


a) pyruvate kinase
b) phosphoglycerate kinase- correct
c) hexokinase
d) PFK-1


7 of the 10 reactions in the glycolytic pathway have free energy values close to 0. What does this tell us about the reactions?


a) they are not near equilibrium reactions
b) they are not control points for pathway regulation
c) they are reversible reactions
d) all of the above- correct
e) none of the above


The glycolytic pathway oxidizes glucose to 2 molecules of pyruvate and produces a net of 2 ATP. ATP allosterically inhibits the Phosphofructokinase-1, that catalyzes the third step of glycolysis. This is an example of ____________. 


a) feed-forward activation
b) feedback inhibition- correct
c) negative cooperativity
d) competitive inhibition
e) negative inhibition


Transfer of the phosphoryl group from PEP to ADP is an example of 


a) mutase reaction
b) isomerization
c) dehydrogenase
d) substrate-level phosphorylation- correct


In eukaryotes the enzymes of the citric acid cycle are found in the ____________.


a) cytosol
b) mitochondria- correct
c) nucleus
d) endoplasmic reticulum


The net effect of the eight steps of the citric acid cycle is to 


a) completely oxidize an acetyl group to carbon dioxide- correct
b) convert pyruvate to succinate
c) produce NAD+ and Q
d) produce B ATP for every pass through the cycle


Most of the energy released in citric acid cycle reactions is conserved in ________


a) GTP
b) ATP
c) NADH and QH2- correct
d) ADP


In the mitochondria NADH and QH2 are essentially oxidized by ___________ since it is the ferminal electron acceptor. 


a) carbon dioxide
b) hydrogen peroxide
c) ozone
d) oxygen- correct


Energy from electron transport reactions is stored as a ______________ gradient that is higher in the intermembrane space than in the mitochondrial matrix


a) electron
b) ATP
c) proton- correct
d) NAPH


The carbonic acid (H2CO3)/bicarbonate (HCO3-) conjugate pair maintain the pH of blood plasma at 7.4. What is the ratio of bicarbonate to carbonic and in the blood? (pKa of H2CO3 = 6.4)


a) 10- correct
b) 1
c) 0.1
d) 1:1
e) insufficient data given to solve this problem


The pKa values of glutamate’s alpha carboxyl group, alpha amino group, and side chain are 2.1, 9.5, and 4.1, respectively. What is the isoelectric point of glutamate?


a) 1.3
b) 3.1- correct
c) 5.2
d) 7.9
e) 9.5


Every third residue in collagen is invariably a glycine because glycine 


a) forms H-bonds which help stabilize the protein
b) makes the protein rigid
c) is required for hydroxylation
d) forms covalent cross links
e) allows tightly wound helix formation- correct


The major driving force responsible for protein folding is 


a) the formation of hydrogen bonds in alpha helices and beta sheets
b) the increased disorder in the surrounding solvent as the protein folds- correct
c) the resulting increase in the order of the protein
d) the formation of multiple salt bridges between charged side chains like glutamate and lysine
e) van der waals forces


A fatty acid designated w-3


a) has 3 double bonds
b) is saturated
c) has a double bond 3 carbons from the alpha carbon
d) has a double bond 3 carbons from the end of the chain- correct
e) contains a triple bond between two carbon atoms


Much of the stability of the double-stranded DNA structure is the result of 


a) hydrogen bonding between purines
b) the phosphodiester backbone
c) the angle of the planes of the bases with respect to the helix axis
d) the stacking interactions between base pair- correct


The processivity of E. coli DNA polymerase 3 holoenzyme accounts for all the following except 


a) the relatively small number of enzymes needed to replicate the entire chromosome
b) the directionality of polymerization- correct
c) the rapid rate of polymerization
d) the ability of a single holoenzyme to add many nucleotides to a growing DNA chain


the replication of DNA is ___________ because ______________


a) conservative; one strand of parental DNA is retained in each daughter DNA
b) conservative; each daughter molecule has 2 new strands copied from the parental DNA template
c) semiconservative; one strand of parental DNA is retained in each daughter DNA- correct
d) semiconservative; each daughter molecule has 2 new strands copied from the parental DNA template


Transcription termination


a) occurs at certain DNA sequences where the elongation complex is unstable
b) sometimes requires a specific protein, rho, which facilitates disassembly
c) often occurs near pause sites
d) all of the above- correct


An operon is ________


a) a set of genes whose transcription is controlled by a single promoter- correct
b) the site of repressor binding
c) a protein that activates the transcription of a whole class of genes
d) a multisubunit complex responsible for the splicing of exons


Shifting of the reading frame by one nucleotide results in ___________


a) the production of a completely different protein that is likely non-functional- correct
b) a substitution only at the first amino acid
c) the generation of homologous proteins
d) a protein that has one less or one more amino acid


Ten people are sitting in a row. Their objective is to whisper a secret from one person to the next all the way down the row. The first person whispers the secret to the second person and so on. After the third person, the second person notices the ninth person has fallen asleep in their chair, so she gets up, goes down the row and shakes person 9 awake. This example is similar to ________. 


a) allosteric control
b) positive cooperativity
c) feed-forward activation- correct
d) negative modulation


Which statement is not true about catabolic pathways?


a) they have a net release of energy
b) they have a net consumption of ATP- correct
c) they liberate smaller molecules from larger ones
d) they include the citric acid cycle


The citric acid cycle oxidizes pyruvate, and some of the pathway intermediates are starting materials for many biosynthetic pathways. This means that the citric acid cycle is ____________


a) amplifying
b) catabolic
c) anabolic
d) amphibolic- correct


Linoleate is an essential fatty acid in mammalian diets because mammalian cells ___________. 


a) synthesize it from arachidonate
b) do not use this acid for biosynthesis
c) can use it to synthesize eicosanoids
d) do not have a desaturases that acts beyond the carbon-9 position- correct


what type of reaction is shown below? Amino acid + alpha-ketoglutarate <–> alpha-keto acid + Glutamate


a) reductive amination
b) oxidation
c) Transamination- correct
d) Hydrolysis


The excretory products of uric acid catabolism vary among organisms depending on their ability to ______________


a) tolerate the end-product
b) remove the end-product to less toxic products
c) solubilize the end product
d) remove an end-product like ammonia to the environment
e) all of the above- correct


During fasting, when glycogen supplies are depleted, ___________ become a major source of carbon for gluconeogenesis


a) amino acids- correct
b) nucleic acids
c) fatty acids
d) lactate and pyruvate


In the Cori cycle, gluconeogenesis occurs in _______ and glycolysis in _________


a) liver; muscle- correct
b) liver; liver
c) muscle; muscle
d) muscle; liver


Photorespiration in plants involves the _________


a) fixation of carbon dioxide to a four carbon acid
b) light-dependent uptake of O2 catalyzed by rubisco, followed by the release of CO2- correct
c) reduction of surface-exposed disulfides in the regulation of rubisco
d) exclusive fixation of carbon dioxide at night by plants such as cacti


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