Amino Acids, Peptides and Proteins Flashcards
1
Q
What determines the properties of the amino acids
A
side chain – R group
2
Q
What are proteinogenic amino acids?
A
20 alpha oleic amino acids that are encoded but the human genetic code
3
Q
What type of amino acids have the carboxyl group and the amino group attached to the same carbon?
A
alpha amino acids
4
Q
Do the carboxyl group and the amino group have to be connected to the same carbon to be an amino acid?
A
no the carboxyl group and the amino group do not have to be connected to the same carbon to be an amino acid
5
Q
What determines the chemical properties of amino acids
A
R group
6
Q
Of the 20 proteinogenic amino acids, which are chiral
A
19
chiral - four different group attached to it
optically active
7
Q
Of the 20 proteinogenic amino acids, which are achiral
A
glycine – because the hydrogen atom is its R group so it does not have four different groups attached to it
8
Q
All chiral amino acids used in eukaryotes are _____
A
L-amino acids
9
Q
Which amino acids have an absolute S configuration
A
All the amino acids besides glycine and cysteine
10
Q
Which amino acids have an absolute R configuration
A
cysteine – the -CH2SH group has priority over the –COOH group
11
Q
What are D-amino acids
A
not in eukaryotes – found in antibiotics
12
Q
Alanine abbreviations
A
Ala
A
13
Q
Arginine abbreviations
A
Arg
R
14
Q
Asparagine abbreviations
A
Asn
N
15
Q
Aspartic Acid abbreviations
A
Asp
D
16
Q
Cysteine abbreviations
A
Cys
C
17
Q
Glutamic Acid abbreviations
A
Glu
E
18
Q
Glutamine abbreviations
A
Gln
Q
19
Q
Histidine abbreviations
A
His
H
20
Q
Isoleucine abbreviations
A
lle
I
21
Q
Leucine abbreviations
A
Leu
L
22
Q
Methionine abbreviations
A
Met
M
23
Q
Phenylalanine abbreviations
A
Phe
F
24
Q
Proline abbreviations
A
Pro
P
25
Serine abbreviations
Ser
| S
26
Threonine abbreviations
Thr
| T
27
Tryptophan abbreviations
Trp
| W
28
Tyrosine abbreviations
Tyr
| Y
29
Valine abbreviations
Val
| V
30
Which amino acids are non polar and non aromatic (7)
gal v mip
```
glycine g
valine v
alanine a
leucine l
methionine m
isoleucine i
proline p
```
31
What is the smallest amino acid
glycine -- single hydrogen atom as its R group
32
What are the aromatic amino acids
tryptophan
phenylalanine
tyrosine
33
What amino acids have polar side chains and are not aromatic
q cn st
```
Serine s
Threonine t
Asparagine n
Glutamine q
Cysteine c
```
34
Which amino acids have negatively charged acidic side chains
Aspartate -- aspartic acid
| Glutamate -- glutamic acid
35
Which amino acids have positively charged basic side chains
Lysine
Arginine
Histidine
36
What are some common properties of hydrophobic amino acids
long alkyl side chains
interior proteins
alaine, isoleucine, leucine, valine, phenylalanine
37
What are some common properties of hydrophilic amino acids
```
charged side chains
(positive - histidine, lysine,arginine)
(negative - aspartic acid and glutamic acid)
amides - asparagine and glutamine
surface proteins
```
38
What type of amino acids would be found on the interior of proteins
hydrophobic
39
What type of proteins would be found on the surface of proteins
hydrophilic
40
What is an amino acid
```
have four groups attached to an central carbon
an amino group
a carboxylic group
a hydrogen
an R group
```
41
Amino acids are amphoteric meaning
they can accept or donate protons
42
What is pKa of a group
is the pH at which half of the species are deprotonated
43
Do amino acids change based on the pH
yes, amino acids exist in different forms at different pH values
44
What happens to an amino acid at a low pH
at a low acidic pH the amino acid is fully protonated
45
What happens to an amino acid at a high pH
at a high basic pH the amino acid is fully deprotonated
46
What happens to an amino acid if the pH is near the pI of the amino acid
the amino acid is a neural zwitterion
47
What is the pI of an amino acid, what does pI stand for
pI is the isoelectric point
48
How do you determine the pI of an amino acid that does to have a charged side chain
pI of an amino acid without a charged side chain can be calculated by averaging the two pKa values
49
How do you determine the pI of an amino acid with a charged side chain
calculated by averaging the two pKa values that correspond to protonation and deprotonation of the zwitteron
50
Generally amino acids without charged side chains have a pI of about
6
51
Generally amino acids that are acidic and negatively charged have a pI
well below 6
52
Generally amino acids that are basic and positively charged have a pI of
well above 6
53
What reaction occurs when a peptide bond is formed
condensation or dehydration
| releasing one molecule of water
54
How many amino acid residues are in dipeptides
two amino acids
55
How many amino acid residues are in tripepties
three amino acids
56
How many amino acids are in Oligopeptides
more than 3 but less than 20
57
How many amino acids are in polypeptides
more than 20
58
When a peptide bond is broken, what reaction occurs
hydrolysis
59
What is the Primary structure of proteins and how is it stabilized
linear sequence of amino acids in a peptide
| stabilized by peptide bonds
60
What is the secondary structure of proteins and how is it stabilized
local structure of neighboring amino acids and is stabilized by hydrogen bonding between amino groups and nonadjacent carboxyl groups
alpha helices
beta sheets
61
What is Tertiary structure of a protein and how is it stabilized
3D shape of a single polypeptide chain
| stabilized by hydrophobic interactions, acid-base interactions, hydrogen bonding, and disulfide bonds
62
What is quaternary protein structure and how is it stabilized
interaction between peptides in proteins that contain multiple subunits
63
What is denaturation
loss of the 3D dimensional protein structure
64
How can proteins become denatured
heat and increasing solute concentrations
65
What are alpha helices, which type of protein structure does this correlate to
clockwise coils around a central axis
| secondary
66
What are beta pleated sheets, which type of protein structure do they correlate to
rippled strands that can be parallel or antiparallel
67
How does proline interrupt secondary protein structure
because of its rigid cyclic structure
68
When the pH is less than the pka, a majority of the species will be ____
protonated
69
When the pH is more than the pka, a majority of the species will be ____
deprotonated
70
All amino acids have ___ groups that can become deprotonated, so they have ___ pka values
two, two
71
The pka1 refers to the ___ group becoming deprotonated and the pka2 refers to the ___ group becoming deprotonated
pka1 - carboxyl group usually around 2
| pka 2 - amino group usually 9-10
72
The pka1 of the carboxyl group is usually around
2
73
The pka2 of the amino group is usually around
9-10
74
At a pH of 1, what happens to the amino acid
- usually becomes positively charged
- pka is below 9-10 so the NH group is positively charges so it is NH3+
- pka is below 2 so the COOH group is fully protonated and will be neutral
75
At a pH greater than 10, what happens to the amino acid
- usually becomes negatively charged
- pka is above 10 so the NH group is deprotonated and becomes NH2
- pka is above 2 so the COOH group is deprotonated and becomes COO-
76
At a intermediate pH of 7, what happens to the amino acid
- usually becomes neutral
- pka is below 9 so the NH group becomes protonated forming NH3
- pka is above 2 so the COOH group becomes deprotonated forming COO-
- overall the charge is neural, these are called zwitterions
- exist in water as internal salts
77
In a neural solution, most amino acids exist as
- positively charged compounds
- zwitterions
- negatively charged compounds
- hydrophobic molecules
- zwitterions
78
At pH 7, the charge on a glutamic acid molecule is
- -2
- -1
- 0
- + 1
- -1
79
Which of these statements concerning peptide bonds is false
- their formation involves a reaction between and amino group and a carboxyl group
- they are the primary bonds that hold amino acids together
- they have partial double bond character
- their formation involves hydration reactions
- their formation involves hydration reactions
80
How many distinct tripeptides can be formed form one valine molecule, one alanine molecule and one leucine molecule
- 1
- 3
- 6
- 27
- 6
81
Which of these is most likely to be preserved when a protein is denatured
- primary structure
- secondary structure
- tertiary structure
- quaternary structure
- primary
82
An alpha helix is most likely to be held together by
- disulfide bonds
- hydrophobic effects
- hydrogen bonds
- ionic attraction between side chains
- hydrogen bonds
83
Which of the following is least likely to cause denaturation of proteins
- heating the protein to 100C
- adding 8 M urea
- moving it to a more hypotonic environment
- adding a detergent such as sodium didecyl sulfate
-
84
Which of the following is least likely to cause denaturation of proteins
- heating the protein to 100C
- adding 8 M urea
- moving it to a more hypotonic environment
- adding a detergent such as sodium didecyl sulfate
- moving it to a more hypotonic environment
85
Which of these amino acids has a chiral carbon in its side chain
- serine
- threonine
- isoleucine
- I only
- II only
- II and III only
- I, II, and III
- II and III only
86
Adding concentrated strain base to a solution containing an enzyme often reduces enzyme activity to zero. In addition to causing protein denaturation, which of the following is another plausible reason for the loss of enzyme activity
- enzyme activity, once lost, cannot be recovered
- the base can cleave peptide residues
- adding a base catalyzes protein polymerization
- adding a base tends to deprotonated amino acids on the surface of proteins
- the base can cleave peptide residues
87
Which of these amino acids has a side chain that can become ionized in cells
- histidine
- leucine
- proline
- threonine
- histidine
88
In lysine, the pka of the side chain is about 10.5. Assuming the pka of the carboxyl and amino group are 2 and 9 respectively, the pI of lysine is closet to 5.5
- 5.5
- 6.2
- 7.4
- 9.8
- 9.8
89
Which of the following is a reason for conjugating proteins
- to direct their delivery to a particular organelle
- to direct their delivery to the cell membrane
- to add a cofactor needed for their activity
- I only
- II only
- II and III only
- I, II, and III
- I, II, and III
- to direct their delivery to a particular organelle
- to direct their delivery to the cell membrane
- to add a cofactor needed for their activity
90
Collagen consist of three helices with carbon backbones that are tightly wrapped around one another in a triple helix. which of these amino acids is most likely to be found in the highest concentration in collagen
- proline
- glycine
- threonine
- cysteine
- glycine
