Biochem Exam 1

Predict the net charge on tyrosine when pH is at 7, and 11.6. (pKa side chain is 10.5) A. 0 & 0, respectively B. 1 & -1, respectively C. 0 & -2, respectively D. 0 & -1, respectively

C. 0 & -2 respectively

What is the difference in magnitude or the ration of sizes between 1. elements and simple organic compounds or monomers 2. Monomers and polymers 3. polymers and organelles 4. eukaryotic cells and bacteria

1/10, 1/10, 1/100, 1/10

What is the pI for lysine? pK1 = 2.3, pK2 =9.0, pK3 = 10.5 a. 10.5 b. 13.0 c. 9.7 d. 7.0 e.8.0

c. 9.7

Which statement about protein-ligand binding is CORRECT? a. The Ka is independent of such conditions as salt concentration and pH. b. The Ka is equal to the concentration of ligand when all of the binding sites are occupied. c. The larger the Ka, the smaller the Kd (dissociation constant). d. The larger the Ka, the faster is the binding. e. The larger the Ka (association constant), the weaker the affinity.

c. The larger the Ka, the smaller the Kd (dissociation constant).

The interactions of ligands with proteins: a. are relatively nonspecific. b. are relatively rare in biological systems. c. are usually transient. d. are usually irreversible. e. usually result in the inactivation of the proteins

c. are usually transient.

Which statement regarding the acid-base characteristics of the 20 common amino acids is false? a. many exist as zwitterions at physiological pH b. they can act as buffers c. each has three pKa values d. they have a characteristic isoelectric point

c. each has three pKa values

Which disease is NOT one characterized by or associated with an unfolded protein aggregate? a. Parkinson disease b. All of these diseases are linked to unfolded protein aggregates. c. diabetes d. scurvy e. Alzheimer disease

d. scurvy

The pKa of α-amino group in Histidine is 9.2. At pH 9.2 it exists as: A. His0 and His- in equal amounts B. His0 and His+ in equal amounts C. His- D. His0

A. His0 and His- in equal amounts

Compute the polarity and the net charge for glutamic acid at pH 0 is __ , pH 6 is __, pH 7 is __, and pH 11 is __. A. +1, 0, -1, -1 B. +1, -1, 0, -2 C. +1, -1, -1, -2 D. -1, -1, -1, -2

C. +1, -1, -1, -2

What is the charge status of Asp at pH 7.0? A. -2 B. 0 C. -1 D. +1

C. -1

Titration of valine by a strong base, for example NaOH, reveals two pK's. The titration reaction occurring at pK2 (pK2 = 9.62) is: A. —NH2 + OH- ⟶ —NH- + H2O B. —COOH + —NH2 ⟶ —COO- + —NH3+ C. —NH3+ + OH- ⟶ —NH2 + H2O D. —COOH + OH- ⟶ —COO- + H2O

C. —NH3+ + OH- ⟶ —NH2 + H2O

Sort out the following acids as strong or weak: (1) Ka = 10-3, (2) Ka = 1.2X102, (3) pKa = -7, (4) pKa = 10 a. (1) Strong, (2) Weak, (3) Strong, (4) Weak b. (1) Weak, (2) Strong, (3) Weak, (4) Strong c. (1) Weak, (2) Strong, (3) Strong, (4) Weak d. All of the above e. None of the above

a. (1) Strong, (2) Weak, (3) Strong, (4) Weak

What would be the charge on cysteine at pH 5, 7 and 10.6? a. 0, 0, -2 b. 1, 0, -1 c. Either of the above d. 0, 0, -1 e. 0, +1, -1

a. 0, 0, -2

What is the pI for acidic amino acids? pK1 = 2.2. pK2=4.2, pK3 = 9.6 a. 3.2 b. 6.8 c. 9.6 d. 7.0 e. 5.0

a. 3.2

Certain amino acids occur more frequently in one type of secondary structure. Which of the following is CORRECT for this phenomenon? a. Branched aliphatic side chains such as isoleucine do not occur often in α helices because of destabilizing steric clashes, and proline rarely occurs in a helices because its ring structure disallows the required dihedral angles. b. Any of the given options can fit into the criteria c. Side chains that contain hydrogen-bond donors, such as phenylalanine, do not prefer αhelices because they compete for hydrogen bonding with main-chain NH and CO groups d. Proline occurs in α helices because its ring structure allows the required dihedral angles e. Branched aliphatic side chains such as isoleucine occur often in α helices because of stabilizing steric clashes

a. Branched aliphatic side chains such as isoleucine do not occur often in α helices because of destabilizing steric clashes, and proline rarely occurs in a helices because its ring structure disallows the required dihedral angles.

The joining of two amino acids via a peptide bond (the process of protein synthesis) has a positive DG value. What does this imply? a. Forming a peptide bond is endergonic and must be coupled to another reaction b. Forming a peptide bond increases the entropy of a system c. Forming a peptide bond is exergonic and must be coupled to another reaction d. Forming a peptide bond is spontaneous and does not need to be coupled to another reaction. e. Forming a peptide bond is spontaneous and can sometimes be coupled to another reaction

a. Forming a peptide bond is endergonic and must be coupled to another reaction

The conjugate base of H2PO4-1 is: a. HPO4^-2 b. PO4^-3 c. HPO4^-3 d. H2PO4^-1 e. H3PO4

a. HPO4^-2

Which of the images below depict a protein-folding pathway with no stable folding intermediates? a. I and III b. I c. II and IV d. III e. IV

a. I and III

Which of these cases has maximum buffering action? a. 10% formate ion & 90% formic acid b. 100% formate ion and 0% formic acid c. 50% and 50% d. 90% and 10%

c. 50% formate and 50% formic

Which statement about living systems is NOT true? a. Living systems are in equilibrium with their surroundings b. Living organisms can be described as an open system c. Living systems maintain a more-or-less constant composition d. Living systems have efficient mechanisms to convert chemical energy from one form into another e. Living systems exist in a dynamic steady-state

a. Living systems are in equilibrium with their surroundings

When energy is used by a system, can it be "used up"? a. No. energy can be converted into kinetic and potential energy b. Yes, it is used up when the energy source is depleted c. No, all energy is converted into kinetic energy d. Yes, it is used up when all energy is converted into chemical energy. e. No, all energy is converted into potential

a. No. energy can be converted into kinetic and potential energy

The uncommon amino acid selenocysteine has an R group with the structure —CH2—SeH (pKa ≈ 5). In an aqueous solution, pH = 7.0, selenocysteine would: a. be a fully ionized zwitterion with no net charge. b. be found in proteins as D-selenocysteine. c. never be found in a protein. d. be nonionic. e. not be optically active.

a. be fully ionized zwitterion with no net charge

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.

a. concentration of the water

Which organelle is found in both plant and animal cells? a. mitochondrion b. ribosome c. chloroplast d. glyoxysome e. starch granule

a. mitochondrion

The pH of a sample of blood is 7.4, while gastric juice is pH 1.4. The blood sample has: a. one million times lower [H+] than the gastric juice b. 0.189 times the [H+] as the gastric juice c. 6 times lower [H+] than the gastric juice d. 5.29 times lower [H+] than the gastric juice e. 6000 times lower [H+] than the gastric juice

a. one million times lower [H+] than the gastric juice

Which factor is NOT known to be involved in the process of assisted folding of proteins? a. peptide bond condensation b. disulfide interchange c. heat shock proteins d. chaperonins e. peptide bond isomerization

a. peptide bond condensation

Which interactions are NOT considered to be "weak" in proteins? Correct! a. peptide bonds b. van der Waals forces c. hydrogen bonds d. hydrophobic interactions e. ionic bonds

a. peptide bonds

Kendrew's studies of the globular myoglobin structure demonstrated that: a. the structure was very compact, with virtually no internal space available for water. b. highly polar or charged amino-acid residues tended to be located interiorally. c. "corners" between α-helical regions invariably lacked proline residue. d. myoglobin was completely different from hemoglobin, as expected. e. the α helix predicted by Pauling and Corey was not found in myoglobin.

a. the structure was very compact, with virtually no internal space available for water.

A Ramachandran diagram of ψ versus ф angles is separated into four quadrants. In which quadrant would you expect to find data descriptive of a β-pleated sheet? a. top left b. bottom left c. bottom right d. both top right and bottom left e. top right

a. top left

Predict the charge on glutamic acid when the pH is 0, 7, and 12. a. -1, 0, and -2 b. +1, -1, and -2 c. +1, 0, and -2 d. 0, +1, and -1

b. +1, -1, and -2

To make an acetate buffer at pH 4.76 (pK = 4.76) starting with 500 mL of 0.1 M sodium acetate (pK = 4.76), what do you require? a. 500 mL of acid b. 25 milli moles of monoprotic acid c. 250 mL of base d. 250 mL of acid

b. 25 milli moles of monoprotic acid

Which of the following processes can take place at 300K without violating the second law of thermodynamics? a. H=85 kJ mol-1, S=+125 J mol-1 b. H=-85 kJ mol-1, S=-125 J mol-1 c. H=+85 kJ mol-1, S=-125 J mol-1 d. H=+85 kJ mol-1, S=+125 J mol-1

b. H=-85 kJ mol-1, S=-125 J mol-1

Which group of amino acids would be MOST likely to be found in the core of protein that is folded into a three-dimensional structure and soluble in water? a. V, T, and R b. I, M, and V c. F, Y, and W d. N, Y, and K e. M, S, and Y

b. I, M, and V

Which image below shows that there are folding intermediates with substantial stability along nearly every folding pathway? a. None of the answers is correct b. IV c. I d. III e. II

b. IV

Which statement about protein-ligand binding is CORRECT? a. The larger the Ka, the faster is the binding. b. The larger the Kd (dissociation constant) , the smaller the Ka c. The larger the Ka (association constant), the weaker the affinity. d. The Ka is equal to the concentration of ligand when all of the binding sites are occupied. e. The Ka is independent of such conditions as salt concentration and pH.

b. The larger the Kd (dissociation constant) , the smaller the Ka

A D-amino acid would interrupt an α helix made of L-amino acids. Another naturally occurring hindrance to the formation of an α helix is the presence of: a. a negatively charged Arg residue. b. a Pro residue. c. a positively charged Lys residue. d. two Ala residues side by side. e. a nonpolar residue near the carboxyl terminus.

b. a Pro residue.

Which group of single-celled micro-organisms has many members found growing in extreme environments? A) bacteria. B) archaea. C) eukaryotes. D) heterotrophs. E) none of the above.

b. archaea

Of the 20 standard amino acids, only ___________ is not optically active. The reason is that its side chain ___________. a. alanine; is a simple methyl group b. glycine; is a hydrogen atom c. glycine; is unbranched d. lysine; contains only nitrogen e. proline; forms a covalent bond with the amino group

b. glycine; is a hydrogen atom

Proteins in their functional, folded conformation are called _____ proteins. a. unique b. native c. intrinsic d. inherent e. natural

b. native

Long-range interactions between residues on a single polypeptide chain could BEST be classified as _____ structure. a. quaternary b. tertiary c. secondary d. primary e. globular

b. tertiary

How many charged groups are present in the peptide alanylglutamylglycylalanylleucine at pH 7? a. 5 b. 4 c. 3 d. 2 e. 1

c. 3

The MOST important contribution to the stability of a protein's conformation appears to be the: a. sum of free energies (positive sign) of formation of many weak interactions among the hundreds of amino acids in a protein. b. sum of free energies of formation of many weak interactions between its polar amino acids and surrounding water. Correct! c. entropy increase from the decrease in ordered water molecules forming a solvent shell around it. d. maximum entropy increase from ionic interactions between the ionized amino acids in a protein. e. stabilizing effect of hydrogen bonding between the carbonyl group of one peptide bond and the amino group of another.

c. entropy increase from the decrease in ordered water molecules forming a solvent shell around it.

Which statement regarding amino acids that are being studied is true? a. at physiological pH, they have no charges b. all of the R groups are either polar or charged c. five of the ones used in making proteins are either acidic or basic d. not all of them are used in making proteins

c. five of the ones used in making proteins are either acidic or basic

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 alanyl residue and one free carboxyl group on a glycyl residue. c. one free amino group on a glycyl residue and one free carboxyl group on an alanyl residue. d. two free amino and two free carboxyl groups. e. two free carboxyl groups, both on glycyl residues.

c. one free amino group on a glycyl residue and one free carboxyl group on an alanyl residue.

Which statement is NOT a distinguishing feature of living organisms? a. There exists a high degree of organizational complexity b. organisms change over time c. organisms do not need to interact with their environment d. the structure of components influences their functions.

c. organisms do not need to interact with their environment

The α-keratin chains indicated by the diagram below have undergone one chemical step. To alter the shape of the α-keratin chains—as in hair waving—what subsequent steps are required? a. chemical reduction and then shape remodeling b. chemical oxidation and then shape remodeling c. shape remodeling and then chemical oxidation d. chemical reduction and then chemical oxidation e. shape remodeling and then chemical reduction

c. shape remodeling and then chemical oxidation

At the isoelectric pH of a tetrapeptide: a. the amino and carboxyl termini are not charged b. there are four ionic charges c. the total net charge is zero d. only the amino and carboxyl termini contribute charge e. two internal amino acids of the tetrapeptide cannot have ionizable R groups

c. the total net charge is zero

Calculate the concentration of acetate in 0.2 M solution of actic acid at pH 5.0 a. 0.0012 M b. 0.19 M c. 0.0127 M d. 0.127 M

d. 0.127 M

If a protein is not folded correctly or becomes partially unfolded, what could NOT be a consequence? a. The protein may be refolded. b. The protein may be remodeled by a chaperone. c. The protein may form an inactive aggregate that leads to disease. Correct! d. All of the given consequences are possible. e. The protein may be degraded by the proteasome.

d. All of the given consequences are possible.

What is common for 'parallel' and 'anti-parallel' b-sheets a. the orientation of the hydrogen bonding b. the orientation of the amide crosslinks c. the quaternary structure of the protein d. Hydrogen bonding between the β-strands e. the topology of the reverse turns

d. Hydrogen bonding between the β-strands

Which mutation would be MOST likely to result in amyloid formation? a. Lys → Arg b. Gln → Glu c. Trp → Ile d. Lys → Phe e. Tyr → His

d. Lys → Phe

By convention, polypeptides are read in which order? a. C- to N-terminus b. 3' to 5' c. 5' to 3' d. N- to C-terminus

d. N- to C-terminus

Which of the following is TRUE of intrinsically unstructured proteins? a. They are rarely found in eukaryotes. b. They are also known as metamorphic proteins c. They assume a defined structure when in monomeric form d. They are rich in charged and polar amino acids.

d. They are rich in charged and polar amino acids.

An allosteric interaction between a ligand and a protein is one in which: a. binding of the ligand to the protein is covalent. b. multiple molecules of the same ligand can bind to the same binding site. c. binding of a molecule to a binding site affects binding of additional molecules to the same site. d. binding of a molecule to a binding site affects binding properties of another site on the protein. e. two different ligands can bind to the same binding site.

d. binding of a molecule to a binding site affects binding properties of another site on the protein.

The amino acid substitution of Val for Glu in Hemoglobin S results in aggregation of the protein because of _____ interactions between molecules. a. disulfide b. covalent c. hydrogen bonding d. hydrophobic e. ionic

d. hydrophobic

What functional groups are present on this molecule? CH2-CH2-CHO | OH a. hydroxyl and ester b. hydroxyl and ketone c. hydroxyl and carboxylic acid d. hydroxyl and aldehyde e. ether and aldehyde

d. hydroxyl and aldehyde

Which organic molecules can be considered "alive"? a. carbohydrates b. nucleic acids c. proteins d. None

d. none

Proteostasis is the cellular process by which: a. proteins are modified. b. proteins are degraded. c. proteins are synthesized. d. protein levels are maintained. e. proteins are folded.

d. protein levels are maintained.

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.

d. ratio of acetic acid to sodium acetate in the buffer falls.

Using the Ramachandran plot below, identify the secondary structure adopted by an amino acid with phi(ф) and psi (Ψ) angles of -90 and -60 degrees, respectively. a. β sheet b. twisted β sheets c. left-handed α helix d. right-handed α helix e. Amino acids will not adopt this conformation

d. right-handed α helix

Which type of structure refers to particularly stable arrangements of amino acid residues in a protein that give rise to recurring patterns? a. quaternary structure b. primary structure c. None of the given options fit into the criteria d. secondary structure e. tertiary structure

d. secondary structure

The aqueous solution with the LOWEST pH is : a. 0.1 M acetic acid (pKa=4.86) b. 10^-12 M NaOH c. 0.1 M formic acid (pKa=3.75) d. 0.01 M HCl e. 0.1 M HCl

e. 0.1 M HCl

Which backbone arrangement BEST represents that of two peptide bonds? a. Cα—N—C—C—N—Cα b. C—N—Cα—Cα—C—N c. Cα—N—Cα—C—Cα—N—Cα—C d. Cα—Cα—C—N—Cα—Cα—C e. Cα—C—N—Cα—C—N

e. Cα—C—N—Cα—C—N

Carbon monoxide (CO) is toxic to humans because it: a. binds to the globin portion of hemoglobin and prevents the binding of O2. b. binds to myoglobin and causes it to denature. c. binds to the heme portion of hemoglobin and causes heme to unbind from hemoglobin. d. is rapidly converted to toxic CO2. e. binds to the Fe in hemoglobin and prevents the binding of O2.

e. binds to the Fe in hemoglobin and prevents the binding of O2.

What is the most abundant element in the universe? a. nitrogen b. hydrogen c. phosphorous d. oxygen e. carbon

e. carbon

Which of the following is a reflection of the total energy change in a chemical reaction, a measure of the number and kinds of bonds that are made and broken? a. delta S b. delta G c. delta T d. delta E e. delta H

e. delta H

What maintains the secondary structure of a protein? a. peptide bonds b. ionic bonds c. phosphodiester bonds d. disulfide bonds e. hydrogen bonds

e. hydrogen bonds

In the binding of oxygen to myoglobin, the relationship between the concentration of oxygen and the fraction of binding sites occupied can best be described as: a. random. b. linear with a negative slope. c. linear with a positive slope. d. sigmoidal. e. hyperbolic.

e. hyperbolic

Which of the following is a similarity between all prokaryotes and all eukaryotes? a. Both contain certain of the same membrane bound cell organelles (like mitochondria, golgi, etc) b. both have cytoskeleton c. both contain DNA in a nucleus d. all of these e. none of these

e. none of these

Patients with chronic hypoxia (low O2 levels) due to decreased lung function may adapt by increasing their circulating BPG levels. Predict which outcome will be TRUE for such a patient. a. The R-state of hemoglobin will be favored. b. None of the answers is correct. c. p50 for O2 will be decreased. d. O2 binding to hemoglobin will be hyperbolic. Correct! e. p50 for O2 will be increased.

e. p50 for O2 will be increased.

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.

e. relates the pH of a solution to the pKa and the concentrations of acid and conjugate base.

Which of the following does NOT consist of a double membrane? a. chloroplast b. Golgi body c. mitochondrion d. endoplasmic reticulum e. ribosome

e. ribosome

How do cells carry out endergonic reactions? a. they need only be promoted by interaction with an enzyme to overcome the activation barrier b. the temp is raised to increase entropy c. the pH is lowered to decrease the entalapy d. they are spontaneous e. they are coupled to an exergonic reaction

e. they are coupled to an exergonic reaction