Biochem exam 1 (ch.1-6) Flashcards

Which of these statements about hydrogen bonds is not true?

A) Hydrogen bonds account for the anomalously high boiling point of water.

B) In liquid water, the average water molecule forms hydrogen bonds with three to four other water molecules.

C) Individual hydrogen bonds are much weaker than covalent bonds.

D) Individual hydrogen bonds in liquid water exist for many seconds and sometimes for minutes.

E) The strength of a hydrogen bond depends on the linearity of the three atoms involved in the bond.

Dissolved solutes alter some physical (colligative) properties of the solvent water because they change the:

A) concentration of the water.
B) hydrogen bonding of the water.
C) ionic bonding of the water.
D) pH of the water.
E) temperature of the water.

Which of the following is not among the four most abundant elements in living organisms?

A) Carbon
B) Hydrogen
C) Oxygen
D) Nitrogen
E) Phosphorous

In eukaryotes, the DNA is found in the:

A) Nucleoid
B) Nucleus
C) Cytoplasm
D) Ribosomes
E) Plasma membrane

The three-dimensional structure of macromolecules is formed and maintained primarily through noncovalent interactions. Which of the following are examples of noncovalent interaction?
A) carbon-carbon bonds
B) hydrogen bonds
C) hydrophobic interactions
D) ionic interactions
E) van der Waals interactions

A) All of them
B) A and B
C) Only C, D, and E
D) Only D and E
E) B, C, D, and E

The major carrier of chemical energy in all cells is:

A) acetyl triphosphate.
B) adenosine monophosphate.
C) adenosine triphosphate.
D) adenine triphosphate
E) cytosine tetraphosphate

Which of the following properties of water does not contribute to the fitness of the aqueous environment for living organisms?

A) Cohesion of liquid water due to hydrogen bonding.
B) High heat of vaporization.
C) High specific heat.
D) The density of water is greater than the density of ice.
E) The very low molecular weight of water.

Phosphoric acid, H3PO4, is tribasic, with pKa’s of 2.14, 6.86, and 12.4. The ionic form that predominates at pH 3.2 is H2PO4-
A) True
B) False

The conjugate base of RNH3+ is RNH2
A) True
B) False

Hydrophobic interactions make important energetic contributions to:

A) binding of a hormone to its receptor protein.
B) enzyme-substrate interactions.
C) membrane structure
D) three-dimensional folding of a polypeptide chain
E) all of the answers are correct

By adding SDS (sodium dodecyl sulfate) during the electrophoresis of proteins, it is possible to:

A) determine a protein’s isoelectric point.
B) determine an enzyme’s specific activity
C) determine the amino acid composition of the protein
D) preserve a protein’s native structure and biological activity
E) separate proteins exclusively on the basis of molecular weight

The peptide alanylglutamylglycylalanylleucine has:

A) a disulfide bridge.
B) five peptide bonds
C) four peptide bonds.
D) no free carboxyl group
E) two free amino groups.

The average molecular weight of the 20 standard amino acids is 138, but biochemists use 110 when estimating the number of amino acids in a protein of known molecular weight. Why?

A) The number 110 is based on the fact that the average molecular weight of a protein is 110,000 with an average of 1000 amino acids.
B) The number 110 reflects the higher proportion of small amino acids in proteins, as well as the loss of water when the peptide bond forms.
C) The number 110 reflects the number of amino acids found in the typical small protein, and only small proteins have their molecular weight estimated this way.
D) The number 110 takes into account the relatively small size of nonstandard amino acids.
E) The number 138 represents the molecular weight of conjugated amino acids.

Two amino acids of the standard 20 contain sulfur atoms. They are:

A) cysteine and serine
B) cysteine and threonine
C) methionine and cysteine
D) methionine and serine
E) threonine and serine

Amino acids are ampholytes because they can function as either a(n):

A) acid or a base
B) neutral molecule or an ion
C) polar or a nonpolar molecule.
D) standard or a nonstandard monomer in proteins
E) transparent or a light-absorbing compound

An octapeptide composed of four repeating glycylalanyl units has:

A) one free amino group on an alanyl residue
B) one free amino group on an glycyl residue and one free carboxyl group on a alanyl residue
C) one free amino group on an alanyl residue and one free carboxyl group on a glycyl residue
D) two free amino and two free carboxyl groups.
E) two free carboxyl groups, both on glycyl residues

Which of the following statements about aromatic amino acids is correct?

A) All are strongly hydrophilic
B) Histidine’s ring structure results in its being categorized as aromatic or basic, depending on pH
C) On a molar basis, tryptophan absorbs more ultraviolet light than tyrosine.
D) The major contribution to the characteristic absorption of light at 280 nm by proteins is the phenylalanine R group.
E) The presence of a ring structure in its R group determines whether or not an amino acid is aromatic.

In a mixture of the five proteins listed below, which should elute second in size-exclusion (gel- filtration) chromatography?

A) cytochrome c Mr = 13,000
B) immunoglobulin G Mr = 145,000
C) ribonuclease A Mr = 13,700
D) RNA polymerase Mr = 450,000
E) serum albumin Mr = 68,500

The chirality of an amino acid results from the fact that its α carbon:

A) has no net charge
B) is a carboxylic acid
C) is bonded to four different chemical groups
D) is in the L absolute configuration in naturally occurring proteins
E) is symmetric

The formation of a peptide bond between two amino acids is an example of a(n) ______________ reaction.

A) cleavage
B) condensation
C) group transfer
D) isomerization
E) oxidation reduction

All proteins have primary, secondary, tertiary and quaternary structure.

A) True
B) False

The functional differences, as well as differences in three-dimensional structures, between two different enzymes from E. coli result directly from their different:

A) affinities for ATP.
B) amino acid sequences.
C) their roles in the metabolism of E. coli.
D) secondary structures.

A peptide was incubated with 1-fluoro-2,4-dinitrobenzene (FDNB) and then hydrolyzed; 2,4-dinitrophenylphenylalaine was identified by HPLC. Digestion with the enzyme carboxyeptidase (cleaves the peptide bond on the N-terminal side of the C-terminal residue) yielded an tetrapeptide and leucine. Identify the C-terminal amino acid. Use the three letter code in your answer.

A peptide was incubated with 1-fluoro-2,4-dinitrobenzene (FDNB) and then hydrolyzed; 2,4-dinitrophenylphenylalaine was identified by HPLC. Digestion with the enzyme carboxyeptidase (cleaves the peptide bond on the N-terminal side of the C-terminal residue) yielded an tetrapeptide and leucine. How many amino acids are in the peptide?

A peptide was incubated with 1-fluoro-2,4-dinitrobenzene (FDNB) and then hydrolyzed; 2,4-dinitrophenylphenylalaine was identified by HPLC. Digestion with the enzyme carboxyeptidase (cleaves the peptide bond on the N-terminal side of the C-terminal residue) yielded an tetrapeptide and leucine. Identify the N-terminal amino acid - use the three letter code in your answer.

Which of the following “weak” interactions stabilize secondary structure in proteins?
A) hydrogen bonds.
B) hydrophobic interactions.
C) carbon-carbon bonds
D) peptide bonds

Roughly how many amino acids are there in one turn of an α helix?
A) 1
B) 2.8
C) 3.6
D) 4.2

Amino acid residues commonly found in the middle of a β turn are:
A) Ala and Gly.
B) Pro and Gly.
C) those with ionized R-groups.
D) two Cys.

In an α helix, the R groups on the amino acid residues:
A) alternate between the outside and the inside of the helix.
B) are found on the outside of the helix spiral.
C) generate the hydrogen bonds that form the helix.
D) stack within the interior of the helix.

Amino acids residues found in a parallel beta sheet are always found close together in the primary sequence of the protein.

A) True
B) False

An allosteric interaction between a ligand and a protein is one in which binding of a molecule to a binding site affects binding of additional molecules to the same site.
A) True
B) False

Which of the following molecules is a homotropic modulator of oxygen binding to hemoglobin?
A) Oxygen
B) H+
C) Carbon dioxide
D) 2,3-bisphosphoglycerate
E) Carbon monoxide

The amino acid substitution of Val for Glu in Hemoglobin S results in aggregation of the protein because of ___________ interactions between molecules.
A) covalent
B) disulfide
C) hydrogen bonding
D) hydrophobic
E) ionic

Amino acids residues found in a parallel beta sheet are always found close together in the primary sequence of the protein.

A) Fe2+ binding
B) heme binding
C) oxygen binding
D) subunit association
E) subunit dissociation

Carbon dioxide produced in the tissues forms carbamates with the N-terminal _________ residues of hemoglobin

A) Histidine
B) Phenylalanine
C) Heme
D) Glycine
E) Aspartate

A prosthetic group of a protein is a non-protein structure that is permanently associated with the protein
A) True
B) False

Leghemoglobin is an oxygen-binding protein in root nodules that contain bacteria which fix atmospheric nitrogen. Which of the following is true if leghemoglobin is like myoglobin, not hemoglobin?

A) There are four oxygen binding sites
B) The oxygen binding curve is hyperbolic
C) There is cooperative oxygen binding
D) The oxygen binding curve is sigmoidal
E) Oxygen binding changes the heme configuration from T to R

2,3-bisphosphoglycerate has no effect on O2 affinity in hemoglobin, but it can force heme into the R-state
A) True
B) False

Which of the following forms a hydrogen bond with O2, but is not one of the six coordination bonds with heme?

A) His F8, the proximal His residue
B) A nitrogen atom in the protoporphyrin ring
C) His E7, the distal His residue
D) Iron (Fe)
E) Phe CD1, which is at the same plane as the protoporphyrin ring

Which of the following is not correct concerning 2,3-bisphosphoglycerate (BPG)?
A) It binds at a distance from the heme groups of hemoglobin.
B) It binds with lower affinity to fetal hemoglobin than to adult hemoglobin.
C) It increases the affinity of hemoglobin for oxygen.
D) It is an allosteric modulator
E) It is normally found associated with the hemoglobin extracted from red blood cells.

Which of the following statements about a plot of V0 vs. [S] for an enzyme that follows Michaelis-Menten kinetics is false?

A) As [S] increases, the initial velocity of reaction V0 also increases.
B) At very high [S], the velocity curve becomes a horizontal line that intersects the y-axis at Km.
C) Km is the [S] at which V0 = 1/2 Vmax.
D) The shape of the curve is a hyperbola.
E) The y-axis is a rate term with units of μm/min.

The following data were obtained in a study of an enzyme known to follow Michaelis-Menten kinetics: V0 values (μmol/min) Substrate added (mmol/L) 217 0.8 325 2 433 4 488 6 647 1,000. The first number in each pair is the V0 values and the second number is the concentration of substrate.The Km for this enzyme is approximately:

A) 1 mM.
B) 1,000 mM.
C) 2 mM
D) 4 mM
E) 6 mM

The role of an enzyme in an enzyme-catalyzed reaction is to:

A) bind a transition state intermediate, such that it cannot be converted back to substrate
B) ensure that all of the substrate is converted to product
C) ensure that the product is more stable than the substrate.
D) increase the rate at which substrate is converted into product.
E) make the free-energy change for the reaction more favorable

Enzymes are potent catalysts because they:

A) are consumed in the reactions they catalyze
B) are very specific and can prevent the conversion of products back to substrates
C) drive reactions to completion while other catalysts drive reactions to equilibrium
D) increase the equilibrium constants for the reactions they catalyze
E) lower the activation energy for the reactions they catalyze.

The concept of “induced fit” refers to the fact that:

A) enzyme specificity is induced by enzyme-substrate binding.
B) enzyme-substrate binding induces an increase in the reaction entropy, thereby catalyzing the reaction.
C) enzyme-substrate binding induces movement along the reaction coordinate to the transition state.
D) substrate binding may induce a conformational change in the enzyme, which then brings catalytic groups into proper orientation.
E) when a substrate binds to an enzyme, the enzyme induces a loss of water (desolvation) from the substrate.

In competitive inhibition, an inhibitor:

A) binds at several different sites on an enzyme.
B) binds covalently to the enzyme.
C) binds only to the ES complex
D) binds reversibly at the active site
E) lowers the characteristic Vmax of the enzyme.

Which one of the following statements is true of enzyme catalysts?

A) Their catalytic activity is independent of pH.
B) They are generally equally active on D and L isomers of a given substrate.
C) They can increase the equilibrium constant for a given reaction by a thousand-fold or more.
D) They can increase the reaction rate for a given reaction by a thousand-fold or more.
E) To be effective, they must be present at the same concentration as their substrate.

The number of substrate molecules converted to product in a given unit of time by a single enzyme molecule at saturation is referred to as the:

A) dissociation constant.
B) half-saturation constant
C) maximum velocity
D) Michaelis-Menten number
E) turnover number

Phenyl-methane-sulfonyl-fluoride (PMSF) inactivates serine proteases by binding covalently to the catalytic serine residue at the active site; this enzyme-inhibitor bond is not cleaved by the enzyme. This is an example of what kind of inhibition?

A) irreversible
B) competitive
C) non-competitive
D) mixed

Enzyme X exhibits maximum activity at pH = 6.9. X shows a fairly sharp decrease in its activity when the pH goes much lower than 6.4. One likely interpretation of this pH activity is that:

A) a Glu residue on the enzyme is involved in the reaction.
B) a His residue on the enzyme is involved in the reaction
C) the enzyme has a metallic cofactor.
D) the enzyme is found in gastric secretions
E) the reaction relies on specific acid-base catalysis.

All of the amino acids that are found in proteins, except for proline, contain a(n):

A) amino group.
B) carbonyl group.
C) carboxyl group.
D) ester group.
E) thiol group.

Which of the following statements about buffers is true?

A) A buffer composed of a weak acid of pKa = 5 is stronger at pH 4 than at pH 6.
B) At pH values lower than the pKa, the salt concentration is higher than that of the acid.
C) The pH of a buffered solution remains constant no matter how much acid or base is added to the solution.
D) The strongest buffers are those composed of strong acids and strong bases.
E) When pH = pKa, the weak acid and salt concentrations in a buffer are equal.

Which of the following is true about the properties of aqueous solutions?

A) A pH change from 5.0 to 6.0 reflects an increase in the hydroxide ion concentration ([OH-]) of 20%.
B) A pH change from 8.0 to 6.0 reflects a decrease in the proton concentration ([H+]) by a factor of 100.
C) Charged molecules are generally insoluble in water.
D) Hydrogen bonds form readily in aqueous solutions.
E) The pH can be calculated by adding 7 to the value of the pOH.

The pH of a solution of 0.1 M NaOH is:

A) 0.1
B) 1.0
C) 12.8
D) 13
E) 14

The pH of a solution of 1 M HCl is:

A) 0
B) 0.1
C) 1
D) 10
E) -1

A hydronium ion:

A) has the structure H3O+.
B) is a hydrated hydrogen ion.
C) is a hydrated proton.
D) is the usual form of one of the dissociation products of water in solution.
E) all of the above are true.

A true statement about hydrophobic interactions is that they:

A) are the driving force in the formation of micelles of amphipathic compounds in water.
B) do not contribute to the structure of water-soluble proteins.
C) have bonding energies of approximately 20-40 Kjoule per mole.
D) involve the ability of water to denature proteins.
E) primarily involve the effect of polar solutes on the entropy of aqueous systems.

The pH of a sample of blood is 7.4, while gastric juice is pH 1.4. The blood sample has:

A) 0.189 times the [H+] as the gastric juice.
B) 5.29 times lower [H+] than the gastric juice.
C) 6 times lower [H+] than the gastric juice.
D) 6,000 times lower [H+] than the gastric juice.
E) a million times lower [H+] than the gastric juice.

A compound has a pKa of 7.4. To 100 mL of a 1.0 M solution of this compound at pH 8.0 is added 30 mL of 1.0 M hydrochloric acid. The resulting solution is pH:

A) 6.5
B) 6.8
C) 7.2
D) 7.4
E) 7.5

The Henderson-Hasselbalch equation:

A) allows the graphic determination of the molecular weight of a weak acid from its pH alone.
B) does not explain the behavior of di- or tri-basic weak acids
C) employs the same value for pKa for all weak acids.
D) is equally useful with solutions of acetic acid and of hydrochloric acid.
E) relates the pH of a solution to the pKa and the concentrations of acid and conjugate base.

Consider an acetate buffer, initially at the same pH as its pKa (4.76). When sodium hydroxide (NaOH) is mixed with this buffer, the:

A) pH remains constant.
B) pH rises more than if an equal amount of NaOH is added to an acetate buffer initially at pH 6.76.
C) pH rises more than if an equal amount of NaOH is added to unbuffered water at pH 4.76.
D) ratio of acetic acid to sodium acetate in the buffer falls.
E) sodium acetate formed precipitates because it is less soluble than acetic acid.

A compound is known to have a free amino group with a pKa of 8.8, and one other ionizable group with a pKa between 5 and 7. To 100 mL of a 0.2 M solution of this compound at pH 8.2 was added 40 mL of a solution of 0.2 M hydrochloric acid. The pH changed to 6.2. The pKa of the second ionizable group is:

A) The pH cannot be determined from this information.
B) 5.4
C) 5.6
D) 6.0
E) 6.2

Three buffers are made by combining a 1 M solution of acetic acid with a 1 M solution of sodium acetate in the ratios shown below.

1 M acetic acid 1 M sodium acetate
Buffer 1: 10 mL 90 mL
Buffer 2: 50 mL 50 mL
Buffer 3: 90 mL 10 mL

Which of these statements is true of the resulting buffers?

A) pH of buffer 1 < pH of buffer 2 < pH of buffer 3
B) pH of buffer 1 = pH of buffer 2 = pH of buffer 3
C) pH of buffer 1 > pH of buffer 2 > pH of buffer 3
D) The problem cannot be solved without knowing the value of pKa.
E) None of the above.

A 1.0 M solution of a compound with 2 ionizable groups (pKa's = 6.2 and 9.5; 100 mL total) has a pH of 6.8. If a biochemist adds 60 mL of 1.0 M HCl to this solution, the solution will change to pH:

A) 5.60
B) 8.90
C) 9.13
D) 9.32
E) The pH cannot be determined from this information.

In which reaction below does water not participate as a reactant (rather than as a product)?

A) Conversion of an acid anhydride to two acids.
B) Conversion of an ester to an acid and an alcohol.
C) Conversion of ATP to ADP.
D) Photosynthesis
E) Production of gaseous carbon dioxide from bicarbonate.

Which of the following properties of water does not contribute to the fitness of the aqueous environment for living organisms?

A) Cohesion of liquid water due to hydrogen bonding.
B) High heat of vaporization.
C) High specific heat.
D) The density of water is greater than the density of ice.
E) The very low molecular weight of water.

Name and briefly define four types of noncovalent interactions that occur between biological molecules.

Explain the fact that ethanol (CH3CH2OH) is more soluble in water than is ethane (CH3CH3).

Explain the fact that triethylammonium chloride ((CH3CH2)3N•HCl) is more soluble in water than is triethylamine ((CH3CH2)3N).

Explain with an appropriate diagram why amphipathic molecules tend to form micelles in water. What force drives micelle formation?

(a) Briefly define "isotonic," "hypotonic," and "hypertonic" solutions. (b) Describe what happens when a cell is placed in each of these types of solutions.

Define pKa for a weak acid in the following two ways: (1) in relation to its acid dissociation constant, Ka, and (2) by reference to a titration curve for the weak acid.

What is the pH of a solution containing 0.2 M acetic acid (pKa = 4.7) and 0.1 M sodium acetate?

You have just made a solution by combining 50 mL of a 0.1 M sodium acetate solution with 150 mL of 1 M acetic acid (pKa = 4.7). What is the pH of the resulting solution?

For a weak acid with a pKa of 6.0, show how you would calculate the ratio of acid to salt at pH 5.

Suppose you have just added 100 mL of a solution containing 0.5 mol of acetic acid per liter to 400 mL of 0.5 M NaOH. What is the final pH? (The pKa of acetic acid is 4.7.)

Which of the following statements about aromatic amino acids is correct?

A) All are strongly hydrophilic.
B) Histidine's ring structure results in its being categorized as aromatic or basic, depending on pH.
C) On a molar basis, tryptophan absorbs more ultraviolet light than tyrosine.
D) The major contribution to the characteristic absorption of light at 280 nm by proteins is the phenylalanine R group.
E) The presence of a ring structure in its R group determines whether or not an amino acid is aromatic.

Which of the following statements about cystine is correct?

A) Cystine forms when the —CH2—SH R group is oxidized to form a —CH2—S—S—CH2— disulfide bridge between two cysteines.
B) Cystine is an example of a nonstandard amino acid, derived by linking two standard amino acids.
C) Cystine is formed by the oxidation of the carboxylic acid group on cysteine.
D) Cystine is formed through a peptide linkage between two cysteines.
E) Two cystines are released when a —CH2—S—S—CH2— disulfide bridge is reduced to —CH2—SH.

What are the structural characteristics common to all amino acids found in naturally occurring proteins?

Only one of the common amino acids has no free -amino group. Name this amino acid.