Molec 1 Practice Exam 2

Which of the following weak attractive forces are involved in stabilization of the DNA double helical structure? a. Base stacking. b. 3' to 5' phosphodiester linkages. c. Disulfide bridges. d. Covalent bonds between the 3' end of one strand and the 5' end of the other.

a. Base stacking.

A protein interface is shown below. The symbols represent hydrogen bond acceptor (A), hydrogen bond donor (D), cysteine (C), hydrophobic (H), basic (+), and acidic (-) residues. To what would this interface bind? Assume you are looking through the protein that binds to the interface so that it lines up with the one below. A H + - C D a. D H - + C A b. A H + - C D c. - C D A H + d. C H A + - D e. - A - + D +

a. D H - A+ C A

DNA with a higher G:C content has a higher Tm because of a. a greater number of hydrogen bonds. b. G and C are more hydrophilic and therefore resist exposure to water more than A and T. c. G and C are more hydrophobic and therefore resist exposure to water more than A and T. d. None of the answer choices are correct.

a. a greater number of hydrogen bonds.

In a β-sheet, the side chains of adjacent amino acids in the polypeptide chain a. always emerge on opposite sides of the plane of the sheet. b. sometimes emerge on opposite sides of the plane of the sheet. c. never emerge on opposite sides of the plane of the sheet. d. emerge on the same or opposite sides of the plane of the sheet, depending on whether it is parallel or antiparallel.

a. always emerge on opposite sides of the plane of the sheet.

With regards to both hydrogen bonding and any H/CH3 groups, a protein can distinguish between which of the following in the minor groove? a. an A:T and G:C. b. a G:C and C:G. c. an A:T and T:A. d. All of the answer choices are correct.

a. an A:T and G:C.

The acyl carrier protein, found in fatty acid synthase, directly interacts with (physically contacts via its amino acids) a. coenzyme A and fatty acid synthase. b. phosphofructokinase. c. the growing fatty acid chain. d. pyruvate kinase.

a. coenzyme A and fatty acid synthase.

When ribonuclease was treated gently with chemicals such as urea and reducing agents, a. it denatured but the structure could be restored upon removal of the chemicals. b. it was irreversibly denatured. c. it required chaperones to restore its function. d. it aggregated via hydrophobic residues, leading to inclusion bodies. e. disulfide bridges could not be restored upon removal of the chemicals.

a. it denatured but the structure could be restored upon removal of the chemicals.

The advantage of positively-supercoiled DNA is that it a. keeps DNA wound up under high temperatures. b. is more resistant to endonucleases. c. stores energy that aids in strand separation. d. allows topoisomerase to access the DNA more easily.

a. keeps DNA wound up under high temperatures.

The following could represent either a ____________-handed DNA helix or ____________- supercoiled DNA. a. left ; positively b. left ; negatively c. right ; positively d. right ; negatively

a. left ; positively

SH2 domains bind to a. phosphotyrosine. b. proline-rich sequences. c. calcium. d. acetylated histone tails. e. ubiquitinated amino acids.

a. phosphotyrosine.

In the leucine zipper family of DNA binding proteins, a. two subunits come together to form a dimer, also called a coiled coil. b. repeating appearance of polar amino acids such as leucine and valine occurs. c. two faces in two adjacent helices are packed against each other, burying hydrophilic side chains away from H2O. d. None of the answer choices are correct.

a. two subunits come together to form a dimer, also called a coiled coil.

Protein structure is determined by a. weak forces and the primary sequence. b. strong bonds. c. the order of the protein's nucleotides. d. All of the answer choices are correct.

a. weak forces and the primary sequence.

The image below shows a. DNA bound to ADP. b. a protein bound to ADP. c. CoA bound to fatty acid synthase. d. hemoglobin bound to heme. e. vinculin bound to a peptide of talin.

b. a protein bound to ADP.

Cdk requires the presence of both cyclin and phosphorylation of the T loop to activate. This is a. called multi-activation. b. an 'and' gate. c. considered to be an outdated pathway. d. only found in higher mammals.

b. an 'and' gate.

Tautomers of the common forms of A/T/G/C a. are only found in prokaryotes and archaea. b. are often sources of error in the genetic code. c. result from the removal of water from the 3' OH on the sugar of one nucleotide. d. are found at the same concentrations in the cell as conventional nucleotides. e. are found at greater concentrations in the cell as conventional nucleotides.

b. are often sources of error in the genetic code.

You discover a protein that has an antiparallel β-sheet, a 310 helix, an PTB domain, and a leucine zipper. You would expect this protein to a. have a hydrophillic core. b. bind to DNA and phosphorylated proteins. c. bind to NAD+ and proline-rich sequences. d. be involved in vesicle trafficking and protein phosphorylation. e. bind to DNA and histones.

b. bind to DNA and phosphorylated proteins.

The DNA bases that are incorporated into your DNA are a. nucleotides that are directly from ingested food without any further processing. b. built up from amino acid building blocks as precursors. c. built up from RNA building blocks as precursors. d. built up from CO2 and H2O via carbonic anhydrase. e. built solely from sugar precursors.

b. built up from amino acid building blocks as precursors.

Topoisomerase's tyrosine binds to the phosphate backbone with its tyrosine via a. hydrogen bonding. b. covalent bonding. c. ionic bonding. d. van der Waals interactions. e. disulfide bridges.

b. covalent bonding.

You are studying a multidomain enzyme, but do not know its structure. You could predict that the polypeptide chain of the active site is ____________ and the polypeptide chain of each domain is ____________. a. continuous; discontinuous b. discontinuous; continuous c. continuous; continuous d. discontinuous; discontinuous

b. discontinuous; continuous

A peptide bond's partial double bond character results from a. steric hindrances between side chains, amino and carboxyl groups, and adjacent peptides. b. resonance between a carbonyl and imino conformation. c. pi stacking interactions between the carboxyl group of one amino acid and the amino group of the next. d. Delocalization of the pi electron orbitals over the alpha carbon and R group.

b. resonance between a carbonyl and imino conformation.

The functional groups (i.e. primary amines, carbonyls) on the DNA bases that interact with DNA- binding proteins are _________ of the same functional groups that are involved in the hydrogen bonding that allows for base pairing. a. all b. some c. none

b. some

The melting point (Tm) is the point at which a. the DNA starts to denature. b. 25% of the DNA is denatured. c. 50% of the DNA is denatured. d. 75% of the DNA is denatured. e. all of the DNA is denatured.

c. 50% of the DNA is denatured.

The purines are _________, and pyrimidines _________. a. A and T; G and C b. G and C; A and T c. A and G; T and C d. T and C; A and G e. A and C; T and G

c. A and G; T and C

Which of the following describes the smallest segment of a protein? a. Scaffold. b. Domain. c. Motif. d. Quaternary structure. e. Multidomain.

c. Motif.

Which of the following is FALSE regarding enzymes with quaternary structure? a. Quaternary enzymes will correctly interact with substrates that are moving through the cell more frequently than if the enzyme was free of the quaternary complex. b. Quaternary enzymes are subject to a different mechanism of control than enzymes free of quaternary complexes. c. Quaternary enzymes follow standard Michaelis-Menten kinetics. d. Each individual subunit of a quaternary enzyme will interact with other subunits to allow for cooperativity. e. Quaternary enzymes with multiple subunits can be regulated by a single activator or inhibitor.

c. Quaternary enzymes follow standard Michaelis-Menten kinetics.

Which of the following best describes DNA? a. Two parallel strands, both in the 5' to 3' direction. b. Two strands held together by H bonds between pyrimidines. c. Two strands, each with 3'/5' covalent phosphodiester linkages. d. Two antiparallel strands consisting of amino acids.

c. Two strands, each with 3'/5' covalent phosphodiester linkages.

Multiple domains are advantageous because they a. increase the time it takes a protein to fold. b. increase the time it takes a protein to be translated by the ribosome. c. allow for protein specialization. d. destabilize the protein.

c. allow for protein specialization.

The EF-hand domain, found in calmodulin, binds to a. armadillo repeats. b. Src-homology domains. c. calcium. d. chromo and bromo domains. e. zinc.

c. calcium.

In the pathway below, the arrow from Product B to Enzyme #3 demonstrates __________, and the arrow from Product D to Enzyme #1 demonstrates __________. a. feedback inhibition ; feed-forward activation b. positive feedback ; negative feedback c. feed-forward activation ; feedback inhibition d. negative feedback ; negative feedback e. positive inhibition ; negative inhibition

c. feed-forward activation ; feedback inhibition

You're working with a protein that has a tyrosine and lysine, but no serines, threonines, or asparagines. This protein can be modified in all of the following ways EXCEPT a. phosphorylation. b. acetylation. c. glycosylation. d. ubiquitination.

c. glycosylation.

Multidomain proteins are created as a result of all of the following EXCEPT a. gene duplications. b. retrotransposons. c. monosomies and trisomies. d. DNA polymerase slippage. e. unequal crossing over.

c. monosomies and trisomies.

Francis Crick made a key connection between the B-form DNA diffraction and a. the structure of fatty acid synthase. b. its water content. c. the structure of hemoglobin. d. the A-form DNA.

c. the structure of hemoglobin.

The structure below is a(n) a. parallel β-sheet. b. antiparallel β-sheet. c. α-helix. d. Greek key. e. β-barrel.

c. α-helix.

Below is a DNA base, with various carbons and nitrogens numbered. Which atoms of this base participate in base pairing in DNA? a. 1 and 2. b. 4 and 5. c. 4, 5, and 6. d. 3 and 4. e. 2 and 3.

d. 3 and 4.

5. Double-stranded DNA is stable due to a. base stacking. b. base pairing. c. water being excluded from the hydrophobic interior of the molecule. d. All of the answer choices are correct.

d. All of the answer choices are correct.

How can a single phosphorylation cause protein activation? a. It can decrease hydrophobicity. b. It can increase interactions with other amino acids on the protein, causing conformational changes. c. It can allow for binding partners to recognize the phosphorylated protein. d. All of the answer choices are correct.

d. All of the answer choices are correct.

RNA can form tertiary structures because it a. forms unique base pairing not found in DNA. b. is not constrained by the double helix so can twist and turn to make more self- interactions. c. can form a unique U:A:U base triple. d. All of the answer choices are correct.

d. All of the answer choices are correct.

RNA stability results from a. the binding of divalent metal ions to the backbone. b. hydrogen bonding between the bases. c. proteins that help to maintain tertiary structure. d. All of the answer choices are correct.

d. All of the answer choices are correct.

Which of the following can prevent formation or lead to destabilize an α-helix? a. Multiple adjacent + or - charged amino acids. b. Glycine. c. Proline. d. All of the answer choices are correct.

d. All of the answer choices are correct.

Which of the following is correct about two adjacent peptide bonds and the bond angles? a. Orientation about planar peptide bonds can be described by two angles, φ and Ψ. b. Within proteins, these angles are constrained by the need to maximize the formation of secondary bond angles among functional groups within peptide backbone while minimizing steric interference. c. Bulky R groups are typically on opposite sides. d. All of the answer choices are correct.

d. All of the answer choices are correct.

Tm for DNA increases as a. GC content decreases. b. AT content increases. c. AC content decreases. d. GC content increases.

d. GC content increases.

Why are human proteins on average larger than bacterial proteins? a. Larger enzymes can perform a single reaction more efficiently than smaller enzymes because of their larger active site. b. Bacteria are streamlined so that their proteins are smaller and more efficient. c. Bacteria contain larger structural proteins that bring the average up. d. Many proteins found separate in bacteria are fused in humans. e. Bacterial proteins are not as "good" as human proteins.

d. Many proteins found separate in bacteria are fused in humans.

The structure below is of a. double helical DNA. b. the ribosome. c. the hammerhead ribozyme. d. tRNA. e. intergenic DNA.

d. tRNA.

DNA contains _________ base pairs per turn. a. 0.34 b. 2 c. 3.6 d. 7 e. 10.5

e. 10.5

Which of the following is NOT a class of amino acid side chains? a. Polar. b. Basic. c. Acidic. d. Nonpolar. e. Electrostatic.

e. Electrostatic.

Which of the following is TRUE regarding Z DNA? a. It consists of alternating adenines and thymines. b. It is not found in the human body. c. It is considered "right-handed". d. It contains guanine only in the standard anti conformation. e. It is believed to play an important role in the body during transcription.

e. It is believed to play an important role in the body during transcription.

Which of the following is FALSE regarding multi-domain proteins? a. Each domain is usually a continuous polypeptide chain. b. Individual domains assist in protein folding by reducing the number of possible conformations. c. Individual domains are usually stable on their own if cleaved from other domains with a protease. d. Multiple domains allow for protein specialization and regulation. e. Many multi-domain bacterial proteins are synthesized as separate proteins in humans.

e. Many multi-domain bacterial proteins are synthesized as separate proteins in humans.

Which of the following is TRUE regarding base pairing in DNA? a. Nucleotides form base pairs with one another by van der Waals bonding. b. A and G have all hydrogen bond donors, and T and C all hydrogen bond acceptors. c. A and C are found mostly in the enol form and T and G in the imino form. d. Pyrimidines take on the amino conformation, and purines the keto conformation. e. None of the answer choices are correct.

e. None of the answer choices are correct.

Proteins are held together internally by all of the following EXCEPT a. hydrogen bonds. b. ionic bonds. c. disulfide bridges. d. hydrophobic interactions. e. hydrophilic interactions.

e. hydrophilic interactions.

Proteins can be activated in all of the following ways EXCEPT by a. proteolytic cleavage. b. protein-protein interactions. c. mechanical tension. d. signal transduction. e. α-carbon modification.

e. α-carbon modification.