Chapter 1. Amino Acids, Peptides, and Proteins Flashcards
(93 cards)
1
Q
What are the four properties of proteinogenic amino acids?
A
- There is a central carbon with an amino group, carboxyl group, side chain, and hydrogen atom.
- All are α-amino acids.
- All are chiral (except for glycine).
- All are L-isomers.
2
Q
Is the following an L-amino acid or D-amino acid? Explain.
A
L-amino acid. The amino group is on the left side.
3
Q
Is the following an L-amino acid or D-amino acid? Explain.
A
D-amino acid. The amino group is on the right side.
4
Q
Which amino acids are nonpolar, nonaromatic?
A
- Glycine
- Alanine
- Valine
- Leucine
- Isoleucine
- Methionine
- Proline
5
Q
Glycine is the only proteinogenic amino acid that is considered achiral. Why?
A
Its R-group is a hydrogen atom.
*Remember: A molecule is chiral if it has four different groups attached to it.
6
Q
Which two amino acids contain a sulfur atom in their side chain?
A
Methionine and Cysteine
7
Q
Methionine and cysteine both contain sulfur in their side chain. Why is methionine considered to be nonpolar, while cysteine is considered to be polar?
A
The sulfur in methionine has a methyl group attached to it, which makes it nonpolar.
8
Q
Which amino acid has the amino group attached to the α-carbon?
A
Proline
9
Q
The amino group in proline is only attached to the α-carbon, which creates a ring. What effects does the ring in proline have?
A
The ring causes flexibility constraints, which limits proline’s position on a protein and effects its role in secondary structures.
10
Q
What are the 3-letter and 1-letter abbreviations for proline?
A
pro, p
11
Q
What are the 3-letter and 1-letter abbreviations for alanine?
A
ala, a
12
Q
What are the 3-letter and 1-letter abbreviations for valine?
A
val, v
13
Q
What are the 3-letter and 1-letter abbreviations for leucine?
A
leu, l
14
Q
What are the 3-letter and 1-letter abbreviations for isoleucine?
A
ile, i
15
Q
What are the 3-letter and 1-letter abbreviations for methionine?
A
met, m
16
Q
What are the 3-letter and 1-letter abbreviations for glycine?
A
gly, g
17
Q
What is the name of the following amino acid?
A
Glycine
18
Q
What is the name of the following amino acid?
A
Alanine
19
Q
What is the name of the following amino acid?
A
Valine
20
Q
What is the name of the following amino acid?
A
Leucine
21
Q
What is the name of the following amino acid?
A
Isoleucine
22
Q
What is the name of the following amino acid?
A
Methionine
23
Q
What is the name of the following amino acid?
A
Proline
24
Q
Which amino acids are considered to be aromatic? State whether each one is polar or nonpolar.
A
- Tryptophan (nonpolar)
- Phenylalanine (nonpolar)
- Tyrosine (polar)
25
What are the 3-letter and 1-letter abbreviations for tryptophan?
trp, w
26
What are the 3-letter and 1-letter abbreviations for phenylalanine?
phe, f
27
What are the 3-letter and 1-letter abbreviations for tyrosine?
tyr, y
28
What is the name of the following amino acid?
Tryptophan
29
What is the name of the following amino acid?
Phenylalanine
30
What is the name of the following amino acid?
Tyrosine
31
Phenylalanine and tyrosine both have a benzyl group in their side chain. Why is phenylalanine considered to be nonpolar, while tyrosine is considered to be polar?
Tyrosine has a hydroxyl group attached to its benzyl group, while phenylalanine does not.
32
Which amino acids are considered to be polar?
* Serine
* Threonine
* Asparagine
* Glutamine
* Cysteine
33
What are the 3-letter and 1-letter abbreviations for serine?
ser, s
34
What are the 3-letter and 1-letter abbreviations for threonine?
thr, t
35
What are the 3-letter and 1-letter abbreviations for asparagine?
asn, n
36
What are the 3-letter and 1-letter abbreviations for glutamine?
gln, q
37
What are the 3-letter and 1-letter abbreviations for cysteine?
cys, c
38
Asparagine and glutamine have a nitrogen in their side chain. What is a characteristic of the nitrogen atom?
The nitrogen in their side chain does not gain or lose protons with changes in pH.
39
Proteinogenic amino acids are considered to be L-isomers. This translates to (S)-absolute configuration. Which amino acid has an (R)-absolute configuration? Explain.
Cysteine. The -CH2SH bond has priority over the -COOH bond.
40
Cysteine's side chain is said to be prone to oxidation. Why?
The -SH bond is weaker than the -OH bond.
41
What is the name of the following amino acid?
Serine
42
What is the name of the following amino acid?
Threonine
43
What is the name of the following amino acid?
Asparagine
44
What is the name of the following amino acid?
Glutamine
45
What is the name of the following amino acid?
Cysteine
46
Why are serine and threonine considered to be polar?
They have an -OH group in their side chain that makes them polar and capable of hydrogen bonding.
47
Which amino acids are considered to be basic?
* Arginine
* Lysine
* Histidine
48
Which amino acids are considered to be acidic?
* Aspartic Acid
* Glutamic Acid
49
# Fill in the blanks.
\_\_\_\_ amino acids have a positive charge, while ____ amino acids have a negative charge.
**Basic** amino acids have a positive charge, while **acidic** amino acids have a negative charge.
50
What is the name of the following amino acid?
Aspartic Acid
51
What is the name of the following amino acid?
Glutamic Acid
52
What is the name of the following amino acid?
Arginine
53
What is the name of the following amino acid?
Lysine
54
What is the name of the following amino acid?
Histidine
55
What are the 3-letter and 1-letter abbreviations for arginine?
arg, r
56
What are the 3-letter and 1-letter abbreviations for lysine?
lys, k
57
What are the 3-letter and 1-letter abbreviations for histidine?
his, h
58
What are the 3-letter and 1-letter abbreviations for aspartic acid?
asp, d
59
What are the 3-letter and 1-letter abbreviations for glutamic acid?
glu, e
60
Which amino acid has three nitrogens in its side chain?
Arginine
61
Which amino acid has an imidazole ring? Explain.
Histidine. An imidazole ring is an aromatic ring with two nitrogen atoms.
62
Which amino acids are considered to be hydrophobic?
* Alanine
* Leucine
* Isoleucine
* Valine
* Phenylalanine
63
Which amino acids are considered to be hydrophilic?
* Histidine
* Arginine
* Lysine
* Glutamate
* Glutamine
* Aspartate
* Asparagine
64
What is the difference between hydrophobic and hydrophilic?
* Hydrophobic
* Water-hating.
* Amino acids with long alkyl side chains.
* More likely to be found in the interior of proteins, away from water.
* Hydrophobic
* Water-loving.
* Amino acids that are charged.
* More likely to be found on the surface of proteins.
65
Amino acids are said to be amphoteric species. Why?
* They have an acidic carboxylic acid and basic amino group.
* They can either accept a proton or donate a proton.
* How they react depends on their pH.
66
If the pH of an amino acid is less than the pKa, then it is \_\_\_\_.
Protonated.
\*Remember: Protonated means that it gains electrons. In this state, the amino has an NH3+ and COOH group.
67
# Fill in the blank.
If the pH of an amino acid is greater than the pKa, then it is said to be \_\_\_\_.
Deprotonated.
\*Remember: Deprotonated means that it loses electrons. In this state, the amino has an NH2 and COO- group.
68
What is the pKa of a molecule?
The pH at which half of the molecules of that species are deprotonated.
69
# Fill in the blanks.
The pKa of COOH is \_\_\_\_, while the pKa of NH2 is \_\_\_\_.
~2; ~9-10
70
What is the isoelectric point (pI) of a molecule?
The pH at which the molecule is electrically neutral.
71
# Fill in the blank.
When the pH of a solution is equal to the pKa, the solution acts as a \_\_\_\_.
buffer
72
The pI of acidic amino acids is \_\_\_\_, while the pI of basic amino acids is \_\_\_\_.
less than 6; greater than 6
73
What are peptides composed of?
Amino acid subunits, which are also called residues.
74
# Fill in the blanks.
\_\_\_\_ are peptides that contain 2-20 amino acid residues, while ____ are peptides that contain more than 20 amino acid residues.
Oligopeptides; polypeptides
75
# Fill in the blank.
The residues in peptides are joined together by \_\_\_\_.
peptide bonds
76
The residues in peptides are joined together by peptide bonds. What are three characteristics of this bond?
* It is a specialized form of an amide bond.
* The C-N bond has a partial double bond character.
* Rotation around this bond is limited.
77
How are peptide bonds formed?
It forms between the -COO- group of one amino acid and the NH3+ group of another amino acid.
78
# Fill in the blanks.
The formation of a peptide bond is an example of a ____ reaction because \_\_\_\_.
condensation/dehydration; it results from the removal of a water molecule
79
# Fill in the blanks.
Peptide bonds are broken by ____ because \_\_\_\_.
hydrolysis; it requires water
80
Peptide bonds are broken by hydrolysis since water is required. Who hydrolytic enzymes used in hydrolysis are trypsin and chymotrypsin. What is the difference between these two enzymes?
* Trypsin cleaves at the carboxyl end of arginine and lysine.
* Chymotrypsin cleaves at the carboxyl end of phenylalanine, tryptophan, and tyrosine.
81
Which protein structure is a linear arrangement of amino acids?
Primart
82
Which protein structure encodes all the information needed for coding?
Primary
83
Which protein structure is stabilized by the formation of covalent peptide bonds between adjacent amino acids?
Primary
84
Which protein structure is primarily the result of hydrogen bonding between nearby amino acids?
Secondary
85
What are the two common secondary structures of a protein?
alpha-helices and beta-pleated sheets
86
How are α-helices stabilized?
By intramolecular hydrogen bonds between a carbonyl oxygen atom and an amide hydrogen atom four residues down the chain.
87
Which protein structure is the protein's three-dimensional shape?
Tertiary
88
What are two ways that the tertiary structure of a protein can be determined?
* Hydrophobic and hydrophilic interactions between (R) groups.
* Creating salt bridges (disulfide bonds).
89
What are disulfide bonds?
Bonds that form when two cysteine molecules become oxidized to form cystine.
90
What are molten globules?
Intermediate states in the folding of a protein.
91
Finish the sentence.
The quaternary structure of a protein only exists for proteins that contain \_\_\_\_.
more than one polypeptide chain.
92
The quaternary structure of a protein is said to induce cooperativity/allosteric effects. What does this mean?
One subunit can undergo conformational or structural changes, which can either enhance or reduce the activity of the other subunits.
93
What are the two common ways that a protein can be denatured?
High heat or solutes (breaking disulfide bonds)
