Chapter: Amino Acids And Proteins

25 July 2022
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question
Which of the following statements regarding Anfinsen's denaturing experiments with ribonuclease A are valid? 1) Exposing the denatured protein to air oxidation and then dialysis to remove urea restored the protein to its original functionality. 2) Removing urea by dialysis and then allowing air oxidation of the denatured protein restored the protein to its original functionality. 3) Denaturing the protein with both urea and β-mercaptoethanol yielded an inactive protein. 4) Protein folding is determined by its primary sequence.
answer
Only statements 2, 3, and 4 are valid.
question
All amino acids have a chiral α-carbon EXCEPT ________.
answer
glycine
question
Using the information in table, explain how a point mutation could change a codon for Glu to a codon for Val.
answer
A change of the A in the GAG codon for glutamate to a U would change the codon to GUG, which codes for valine.
question
Do you expect the pI for the sickle-cell β-globin to be higher or lower than the pI for wild-type β-globin? Explain.
answer
The pI of the sickle-cell globin will be higher than the wild-type globin because the mutation replaces a negatively charged side chain with one that carries no charge.
question
Which statement correctly describes amphipathic (or amphiphilic) helices and sheets?
answer
Amphipathic helices and sheets have predominantly hydrophilic (or hydrophobic) residues on one face.
question
What are the N-terminal and C-terminal residues for the following peptide sequence? Peptide sequence: EASY
answer
E is the N-terminal residue; Y is the C-terminal residue.
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primary structure
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the interaction between two separate protein strands
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secondary structure
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the sequence of AA
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tertiary structure
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small sections of organized protein structure, such as helices
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quaternary structure
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the overall fold of a single protein strand, such as the globulin fold
question
Which of the following statements about protein quaternary structure are correct? 1) It involves a complex of two or more proteins interacting with each other. 2) The subunits of the structure can be either identical or different. 3) The interactions between subunits can give rise to indefinite growth of polymeric complexes. 4) Most assemblies of protein subunits have one or more defined axis of rotation.
answer
All of the listed statements are correct.
question
The side chain of histidine has a typical pKa value in the range of 6.5-7.4. However, when analyzing the pKa values in a particular protein, scientists determined that one particular His residue has an unusually low pKa value of 4.8. Which of the following statements correctly explain this anomaly? 1) The microenvironment around a residue can impact its pKa value. 2) A positively charged amino acid must be in close proximity to this residue. 3) A negatively charged amino acid must be in close proximity to this residue. 4) This residue must be located on the surface of the protein.
answer
Statements 1 and 2 are correct.
question
In considering protein secondary structure which of the following is INCORRECT? 1)The most common structures are the α helix and the β sheet. 2)A network of main-chain hydrogen bonds connect β strands in a β sheet. 3)The 310 helix is right-handed and often contains proline residues. 4)An α helix repeats after 18 residues and has 3.6 residues per turn. 5)The β strands can be in either parallel or antiparallel configuration.
answer
3)The 310 helix is right-handed and often contains proline residues.
question
The side chain of ________ has a pKa in the physiological pH range and is therefore often involved in proton transfer during enzymatic catalysis.
answer
histidine
question
Alpha amino acid structure
answer
Amino group attached to the carbon α to the carboxylic acid R - groups are the side chains that distinguish the 20 common amino acids When R is not a hydrogen atom, the α-carbon is an asymmetric center At neutral pH (~7) the amino acid nitrogen is protonated and the carboxylic acid is deprotonated to yield the zwitterion
question
All amino acids except ___ contain an asymmetric alpha carbon
answer
glycine
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Nonpolar amino acids
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P, M, G, A, V, L, I
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Nonpolar aromatic amino acids
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P, Y, W
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Nonpolar aliphatic amino acids
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G, A, V, L, I
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Polar Amino Acids
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S, C, T, N, Q
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Positively charged amino aicds
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H, K, R
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Negatively charged amino acids
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D, E
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The ___ of amino acids forms a peptide bond and releases water
answer
condensation
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The reaction that creates a peptide bond is or is not thermodynamically favorable?
answer
It is NOT and is coupled to ATP hydrolysis during protein biosynthesis
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Proteases
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Enzymes that cleave specific peptide bonds
question
How is the pka of glutamic acid effected when in proximity to a negative charge? pka = 4.2
answer
It is raised
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How is the pka of glutamic acid effected when in proximity to a positive charge? pka = 4.2
answer
It is lowered
question
As ph increases the overall charge on a peptide will become more ___
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Negative
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As ph decreases the overall charge on a peptide will become more ___
answer
postive