Amino Acids, Peptides, and Proteins Flashcards
1
Q
What are the amino acids encoded in the genetic code called?
A
proteinogenic amino acids
2
Q
Which amino acid is achiral?
A
glycine
3
Q
Amino acids in eukaryotes are D or L?
A
L
4
Q
Amino acids are all S/R except for ______?
A
S except for cysteine
5
Q
Which two amino acids contain sulfur?
A
methionine and cysteine
6
Q
Glycine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
A
nonpolar
neutral
nonaromatic
neither
7
Q
Alanine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
A
nonpolar
neutral
nonaromatic
hydrophobic
8
Q
Valine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
A
nonpolar
neutral
nonaromatic
hydrophobic
9
Q
Leucine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
A
nonpolar
neutral
nonaromatic
hydrophobic
10
Q
Isoleucine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
A
nonpolar
neutral
nonaromatic
hydrophobic
11
Q
Methionine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
A
nonpolar
neutral
nonaromatic
neither
12
Q
Proline Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
A
nonpolar
neutral
nonaromatic
neither
13
Q
Tryptophan Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
A
nonpolar
neutral
aromatic
neither
14
Q
Phenylalanine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
A
nonpolar
neutral
aromatic
hydrophobic
15
Q
Tyrosine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
A
polar
neutral
aromatic
neither
16
Q
Serine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
A
polar
neutral
nonaromatic
neither
17
Q
Threonine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
A
polar
neutral
nonaromatic
neither
18
Q
Asparagine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
A
polar
neutral
nonaromatic
neither
19
Q
Glutamine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
A
polar
neutral
nonaromatic
neither
20
Q
Cysteine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
A
polar
neutral
nonaromatic
neither
21
Q
Aspartic Acid Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
A
polar
negative
nonaromatic
hydrophilic
22
Q
Glutamic Acid Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
A
polar
negative
nonaromatic
hydrophilic
23
Q
Lysine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
A
polar
positive
nonaromatic
hydrophilic
24
Q
Arginine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
A
polar
positive
nonaromatic
hydrophilic
25
```
Histidine
Polar/Nonpolar =
Charge =
Aromatic/Nonaromatic =
Hydrophilic/Hydrophobic =
```
polar
positive
aromatic
hydrophilic
26
How many pKa values do amino acids have and what are they?
at least two
the first one is the deprotonation of the carboxyl group around 2
the second one is the deprotonation of the amino group around 9/10
27
At very acidic pH values, amino acids tend to be _____ charged.
positively
28
What is the isoelectric point?
the pH at which the molecule is electrically neutral
29
pI of a neutral amino acid
pKa amino group + pKa carboxylic acid / 2
30
pI of a acidic amino acid
pKa R group + pKa carboxylic acid / 2
31
pI of a basic amino acid
pKa amino group + pKa R group / 2
32
What is a peptide bond?
a specialized form of an amide bond, which form between the -COO- group of one amino acid and the NH3+ group of another amino acid
33
Peptides read from the _-terminus to the _-terminus.
N to C
34
How do hydrolytic enzymes hydrolyze peptides?
Break apart amide bond by adding a hydrogen atom to the amide nitrogen and an OH group to the carbonyl carbon
35
Where does trypsin cleave?
carboxyl end of arginine and lysine
36
Where does chymotrypsin cleave?
at the carboxyl end of phenylalanine, tryptophan and tyrosine
37
What is the primary structure of a protein?
the linear arrangement of amino acids coded in an organism's DNA
38
What is the secondary structure of a protein?
the local structure of neighboring amino acids
39
What are two secondary structures?
alpha helix and beta sheets
40
Which bonds hold the secondary structure together?
hydrogen bonds
41
What is proline useful for?
found at the turns between beta sheets and start of alpha helix due to its kinking properties
42
What are fibrous proteins?
structures that resemble sheets or long strands
43
What are globular proteins?
structures that are spherical
44
What is tertiary structure?
three-dimensional shape
45
What determines the tertiary structure?
hydrophilic and hydrophobic interactions between the R groups
46
What are quaternary structures?
aggregate of smaller globular peptides (multiple polypeptides chains) that function as a protein
47
Four reasons for having quaternary structure?
(1) more stable by reducing the surface area of the protein complex
(2) reduce amount of DNA needed to encode the protein complex
(3) bring catalytic sites close together, allowing intermediates from one reaction to be directly shuttled to a second reaction
(4) Cooperativity/allosteric effects
48
What are conjugated proteins?
proteins with have covalently attached molecules known as prosthetic groups
49
What are lipoproteins?
proteins with lipid prosthetic groups
50
What are glycoproteins?
proteins with carbohydrate prosthetic groups
51
What are nucleoproteins?
proteins with nucleic acid prosthetic groups
52
What are prosthetic groups needed for?
- can direct protein to be delivered to a certain location
| - affect activity of protein
53
Which amino acids have chiral carbons in their side chains?
serine and threonine
