BC Exam 1 chapter 4

Cells deal with misfolded proteins by a. storing them for later energy use. b. collecting and excreting them from the cell. c. aggregating them to maintain the cell's structural integrity. d. degrading them to individual amino acids.

d

How many possible unique triplet codons could there be in a genome? a. 3 b. 20 c. 36 d. 64

d

The dipole moment associated with a peptide bond proceeds from which amide? a. the C to the O atom b. the C to the N atom c. the O to the H atom d. the H to the O atom

d

After analyzing all the structures of proteins found in the Protein Data Bank, scientists have found that four general classes of protein structures exist, based on their secondary structure themes. Name the four classes of general protein structures.

1. a helix 2. b sheet 3. mixed a and b 4. a adjacent to b

List the levels of protein structure and give a brief description of each.

1. amino acid sequence 2. H bonding for alpha helix/beta pleated sheets 3. 3d structure, side group interactions 4. multiple subunits

In the famous experiment where Christian Anfinsen unfolded and refolded the protein RNaseA, in what order was the denaturant and reductant removed to give an inactive protein? Why was the protein inactive?

B then urea removed, disulfide bonds can't reform

In the multi-subunit protein family called immunoglobulins, the different subunits are held together by both covalent and noncovalent forces. What are the covalent forces that hold subunits together in immunoglobulins?

Cysteine disulfide bonds covalently bond

Which of the following statements about β-sheet structures is true? a. The individual strands of all β-sheet structures are connected by turns, helices, or loops. b. All amino acid side chains in antiparallel and parallel β-sheet structures point to one side of the sheet. c. Parallel β-sheet structures have backbone amides that directly hydrogen bond between strands, whereas antiparallel β-sheets have hydrogen bonds that are offset. d. All β-sheet structures form a spiraling backbone chain.

a

To what organic reaction class does peptide bond formation belong? a. condensation b. isomerization c. oxidation d. addition

a

Using the table below, determine the kind of gene mutation illustrated. ATG_AAT_CAC → ATG_AAG_CAC a. missense mutation b. nonsense mutation c. frameshift mutation d. silent mutation

a

What is the dominant secondary structure found in hair keratin? a. α-helices b. disulfide bonds c. β-sheets d. loop structures

a

Which statement about amino acids is true? a. Most common natural amino acids in proteins are L-amino acids. b. All naturally occurring amino acids in proteins are chiral. c. Most naturally occurring amino acids in proteins are D-amino acids. d. Naturally occurring amino acids in proteins occur as a mixture of enantiomers.

a

Describe generally how a gain-of-function protein folding disease can lead to cell death.

aggregation, interferes with normal cell function

An α-helix has the sequence: NH3 +-Ser-Glu-Gly-Asp-Trp-Gln-Leu-His-Val-Phe-Ala-Lys-Val-Glu-COO-. The carbonyl oxygen (in the peptide bond) of the histidine residue is hydrogen bonded to the amide nitrogen of a. Asp. b. Lys. c. Trp. d. Ala.

b

How many β-turns or β-loops are required to construct a β-sheet composed of four antiparallel strands? a. 0 b. 3 c. 4 d. 5

b

Of the three proposed models of globular protein folding, which one describes formation of an initial disordered protein interior, followed next by ordering of secondary and tertiary structures? a. mutant globule b. hydrophobic collapse model c. framework model d. nucleation model

b

The peptide bond a. is most stable in the cis configuration. b. has a mix of single and double bond characters. c. can rotate around the carbonyl and N bond but not around the α-carbon and N bond. d. can function as a weak acid and weak base.

b

The protein fold known as the Rossman fold is found in proteins that commonly bind a. α-helices. b. nucleotides. c. cytochromes. d. membranes.

b

What is the minimum number of amino acids needed to make one turn of an α-helix? a. 3 b. 4 c. 6 d. 7

b

How many possible protein primary structures are there for a tripeptide given the 20 amino acids? a. 32 0 b. 400 c. 203 d. 1.27 × 10130

c

In a standard α-helix, __________ H bonds and __________ dipole moments are found per amino acid, which stabilizes the α-helical structure. a. 1; 1 b. 1; 2 c. 2; 1 d. 2; 2

c

Protein tertiary structures a. require the formation of disulfide bonds in order to achieve their native state. b. are always irreversibly destroyed by the addition of denaturants, such as urea and salts, even when the denaturants are subsequently removed. c. are often disrupted by the either very low pH or very high pH values as a result of alterations in the ionization states of acidic or basic amino acids. d. are generally poorly defined and cannot be determined experimentally.

c

The proteins collagen, silk fibroin, and hair keratin have all of the following in common, EXCEPT that they a. are fibrous proteins. b. are composed of repeating amino acid sequences. c. are composed of α-helical structures. d. play important structural roles in biology.

c

What is the difference between clamp-type and chamber-type chaperone proteins? a. One uses ATP and the other does not. b. One folds proteins, whereas the other just protects them from unfolding. c. They are shaped differently. d. One type is found extracellularly and one intracellularly.

c

Which of the following statements is true about α-helices? a. The center of the helix is an open channel. b. There are about seven amino acids per helical turn. c. The amide backbone dipoles line up in one direction. d. The helical backbone structure is stabilized by ionic interactions.

c

Which of the following statements regarding protein domains is true? a. Each protein has one unique domain. b. Multiple domains require multiple subunits and a quaternary structure. c. A domain can be composed of smaller structural units called motifs. d. A domain is a region absent of α-helices and β-sheets.

c

Which statement about the α-helix is true? a. The hydrophobic interior of α-helices is stabilized by the side chains of hydrophobic amino acids. b. The amino acid side chains point out to the sides with every third amino acid roughly lining up on one side of the helix. c. α-Helices have backbone amide groups that are hydrogen bonded to amino acid side chains. d. α-Helices have 5 amino acids per one turn of the helix.

c

Draw the resonance structures that stabilize the peptide bonds found in proteins.

c=o to c-o n-c to n=c

Which of the following statements about α-helices and β-sheets are FALSE? a. They are both incompatible with the amino acid proline. b. They both interact with other protein elements through amino acid side chains that stick out. c. They both contain a recurring pattern of hydrogen bonds from one peptide bond to another peptide bond. d. They both give rise to similar tertiary structures.

d

Which one of the following statements comparing alpha keratin and silk fibroin is true? a. Both have covalently cross-linked strands. b. Both are primarily α-helical in character. c. Both fibers are intracellularly located. d. Both fibers are heavily stabilized by hydrogen bonds.

d

Which statement regarding protein secondary structures is correct? a. β-strands allow α-helices to interact with one another. b. Protein α-helices alternate with β-strands in stabilizing protein structure. c. Protein α-helices are left handed, whereas β-sheets are right handed in arrangement. d. Protein α-helices and β-strands differ in that α-helices are stabilized by intrahelical hydrogen bonds, whereas β-strands are stabilized by hydrogen bonds across adjacent strands.

d

Shown is the titration curve for the amino acid aspartic acid. Draw the predominant protonation state of aspartic acid found at point A in the curve.

only deprotonate COOH to COO- other end is NH3

List reagents and conditions that denature proteins.

reagents: acid, bases, urea conditions: temp, pH, pressure

Arrange the following in order of increasing complexity: secondary structure, tertiary structure, motif, and domain.

secondary, motif, domain, tertiary

Describe the proposed model of globular protein folding called the nucleation model.

small part folds correctly, becomes folding nucleus, everything else folds around it