Chapter 2 Protein Composition and Structure
Use the following to answer questions 1-10:
Choose the correct answer from the list below. Not all of the answers will be used.
a) L-amino acids
e) secondary structure
f) tertiary structure
m) D-amino acids
____________ Chiral type of amino acids found in proteins.
____________ Another name for dipolar molecules.
____________ Disulfide bonds are formed by pairs of which amino acid?
____________ The amino acid with a pKa near neutral pH.
____________ When a peptide bond is formed, what molecule is also made?
____________ Where are proteins with extensive disulfide links likely to be found?
____________ This amino acid residue disrupts the helix because its side chain contains a unique ring structure that restricts bond rotations.
____________ Name of the plot that allows one to investigate the likely orientation of certain amino acid pairs.
____________ The type of structure to which helices, sheets, and turns are referred.
____________ The overall structure of a protein is referred to as
Fill in the Blank Questions
The amino acid that contains a weakly acidic phenolic group is _________________.
Ans: tyrosine Section 2.1
_______________ is a fibrous protein and is the primary component of wool and hair.
Ans: keratin Section 2.3
Every third residue in the protein collagen is ____________________.
Ans: glycine Section 2.3
Disulfide bonds in proteins can be reduced to free sulfhydryl groups by reagents such as _____________________.
Ans: mecaptoethanol Section 2.6
A protein is considered to be __________________ when it is converted into a randomly coiled structure without its normal activity.
Ans: denatured Section 2.6
______________________ is the major fibrous protein present in skin, bone, tendon, cartilage, and teeth.
Ans: Collagen Section 2.3
Collagen contains _____________________, a modified amino acid.
Ans: hydroxyproline Section 2.6
Agents such as ______________________ and guanidine hydrochloride denature proteins by disrupting the noncovalent interactions.
Ans: urea Section 2.6
_____________________________ refers to the spatial arrangement of subunits and the nature of their interactions
Ans: Quaternary structure Section 2.5
The ________________________ -sheet structure occurs when the two strands are oriented in opposite directions (N C).
Ans: antiparallel Section 2.3
Multiple Choice Questions
What determines a proteins function?
A) structure D) None of the above.
B) gene sequence E) All of the above.
C) N-terminal amino acids
Ans: A Section: Introduction
Key properties of proteins include
A) a wide range of functional groups.
B) an ability to possess either rigid or flexible structures as dictated by functional requirements.
C) the ability to interact with other proteins.
D) a and b.
E) All of the above.
Ans: E Section: Introduction
What charged group(s) are present in glycine at a pH of 7?
A) NH3+ B) COO C) NH2+ D) a and b E) a, b, and c
Ans: D Section: 2.1
At a pH of 12, what charged group(s) are present in glycine?
A) -NH3+ B) -COO C) -NH2+ D) a and b E) a, b, and c
Ans: B Section: 2.1
In what pH range is zwitterionic Alanine the predominate structure?
A) 02 D) 24
B) 914 E) 29
Ans: E Section 2.1
Which amino acids contain reactive aliphatic hydroxyl groups?
A) serine and methionine D) cysteine and methionine
B) serine and threonine E) cysteine and threonine
C) methionine and threonine
Ans: B Section: 2.1
Name three amino acids that are positively charged at a neutral pH.
A) lys, arg, and his D) lys, arg, and pro
B) his, arg, and cys E) arg, glu, and his
C) cys, arg, and met
Ans: A Section: 2.1
In the following peptide, which amino acid is the N-terminus?
A) Ala B) Phe C) Phe and Arg D) Arg E) None of the above.
Ans: B Section: 2.2
What is the approximate mass of a protein containing 200 amino acids? (Assume there are no other protein modifications.)
A) 20,000 B) 11,000 C) 22,000 D) 222,000 E) None of the above.
Ans: C Section: 2.2
Which individual won a Nobel Prize for his landmark work in sequencing the protein insulin?
A) Pauling B) McClintock C) Gilbert D) Maxam E) Sanger
Ans: E Section: 2.2
Why is the peptide bond planar?
A) Bulky side chains prevent free rotation around the bond.
B) It contains partial double-bond character, preventing rotation.
C) Hydrogen bonding between the NH and C=O groups limits movement.
D) None of the above.
E) All of the above.
Ans: B Section: 2.2
The configuration of most -carbon atoms of amino acids linked in a peptide bond is
A) cis. B) circular. C) parallel. D) trans. E) perpendicular.
Ans: D Section: 2.2
What structure(s) did Pauling and Corey predict in 1951?
A) helix B) sheet C) turns D) a, b, and c E) a and b
Ans: E Section: 2.4
Which of the following protein(s) contain examples of helical character?
A) keratin B) ferritin C) myosin D) tropomyosin E) All of the above.
Ans: E Section: 2.4
Where are and turns and loops often found?
A) in a hydrophobic pocket D) on the surface of proteins
B) on the interior cleft E) None of the above.
C) at the protein interface with ligand
Ans: D Section: 2.3
What are some of the modifications that proteins acquire?
A) cleavage and trimming of the protein D) a, b, and c
B) addition of carbohydrate groups E) b and c
C) phosphorylation of certain groups
Ans: D Section: 2.6
Which of the following amino acid residues would most likely be buried in the interior of a water soluble, globular protein?
A) Asp D) Lys
B) Ser E) Gln
Ans: C Section 2.5
How does a proteins amino acid sequence influence the tertiary structure?
Ans: A protein will spontaneously fold into a three-dimensional structure determined by the amino acid sequence.
What is the advantage of having 20 different amino acids available to form proteins?
Ans: The amino acids provide a rich diversity of functional groups, which can independently contribute to protein structure and function. In addition, many can be modified, increasing the diversity of functional groups.
What is the advantage of protein interaction and assembly with other proteins?
Ans: When proteins interact or assemble, new functions and specificity become available. Protein interactions allow new binding sites at the assembly interface, as well as providing multifunctional activity and specificity, such as found in polymerases and signal transduction.
What are the three aromatic amino acids?
Ans: phenylalanine, tyrosine, and tryptophan
Which amino acid side chains are capable of ionization?
Ans: The amino acids are: Asp, Glu, His, Cys, Tyr, Lys, and Arg.
How does the protein backbone add to structural stability?
Ans: The protein backbone contains the peptide bond, which has NH molecules and C=O (ketone) groups. Hydrogen-bond formation between the hydrogen on the nitrogen and the oxygen support the protein conformation.
Why are all the theoretical combinations of phi and psi not possible?
Ans: Steric hindrances of the side chains make certain combinations and angles impossible.
Describe some of the features of an helix.
Ans: The helix is coil stabilized by intrachain hydrogen bonds between the carbonyl oxygen of a residue and the amide hydrogen of the fourth residue away. There are 3.6 amino acids per turn. The hydrogen bonds are between amino acid residues that have two intervening residues. Thus, these amino acid residues are found on the same side of the coil. The helix is almost always right-handed, although left-handed helices are, in theory, possible.
What is the hydrophobic effect as it relates to protein structure?
Ans: The three-dimensional structure of a water soluble protein is stabilized by the tendency of hydrophobic groups to assemble in the interior of the molecule.
What is a protein domain?
Ans: A domain is a defined region of a protein. Often, a domain is defined by a particular function.
What are prions?
Ans: Prions are proteins that can assume (after infection or by other causes) a new protein structure, which is self-propagating. The disease has several variants, and at least one is fatal to humans.
In the ribonuclease experiments performed by Anfinson, what was the significance of the presence of the reducing agent mercaptoethanol?
Ans: The reducing agent reduced incorrectly paired disulfide bonds allowing them to reform with the correct pairing until the most stable conformation of the protein had been obtained.
What is the advantage of having certain regions of partially correct folded regions?
Ans: If some regions interact preferentially, lending stability to certain conformations as the protein folds, they can impact the overall structure of the protein.
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