Lecture 2 Flashcards
(145 cards)
1
Q
what is the operating system for nearly all biological functions?
A
the proteome
2
Q
what are 4 things common to all amino acids?
A
-alpha carbon
-Carboxyl group
-Amino group
-Variable R group
3
Q
The R groups in amino acids differ by what two things?
A
size and charge
4
Q
how many standard amino acids are there?
A
20
5
Q
what are the four types of R groups that categorize amino acids?
A
-nonpolar R groups
-polar R groups
-polar charged R groups
-aromatic R groups
6
Q
where are nonpolar R groups located?
A
the intertior of proteins where they don’t interact with water
7
Q
what were the 7 molecules shown in class with nonpolar R groups?
A
Glycine, alanine, proline, valine, leucine, isoleucine, methionine
8
Q
what were the 5 compounds shown in class with uncharged polar R groups?
A
serine, threonine, cysteine, asparagine, glutamine
9
Q
what are the 3 molecules shown in class with positively charged polar R groups?
A
lysine, arginine, histidine
10
Q
what are the 3 molecules shown in class with negatively charged polar R groups?
A
aspartate, glutamate
11
Q
true or false? if false, correct statement
polar charged R groups are (almost) always charged under
physiological conditions
A
true
12
Q
true or false? if false, correct statement
polar charged R groups can be either positively or negatively charged
A
true
13
Q
what are the 3 compounds shown in class with aromatic R groups?
A
phenylalanine, tyrosine, tryptophan
14
Q
true or false? if false, correct statement
Certain polar-uncharged amino acids can become charged
depending on the environment
A
true
15
Q
what compound is very versatile in catalyzing chemical reactions?
A
Histidine
16
Q
true or false? if false, correct statement
Histidine can act only as a base
A
false; Histidine can act as an acid and a base
17
Q
true or false? if false, correct statement
The position of an AA relative to its neighbors
DOES NOT affect stability of helix
A
false; The position of an AA relative to its neighbors
DOES affects stability of helix
18
Q
true or false? if false, correct statement
the microenviroment of the active site does not affect the protonation state of amino acids
A
false; the microenviroment of the active site DOES affect the protonation state of amino acids
19
Q
true or false? if false, correct statement
Proteins have diverse properties and an incredible
number of functions
A
true
20
Q
true or false? if false, correct statement
alpha helix and beta sheets meet the requirements of a secondary structure
A
true
21
Q
what is something that is very important for protein structure?
A
covalent links between polypeptide chains and subunits
22
Q
what configuration are all AA residues in proteins?
A
L-configuration
23
Q
are amino acids chiral or achiral?
A
chiral
24
Q
all AA are chiral except for what compound? what atom is repeated?
A
glycine; H
25
every AA has at least how many ionizable groups?
2
26
what is a compound?
a substance formed by two or more different types of elements chemically combined in a fixed proportion
27
what is a molecule?
a group of two or more atoms held together by chemical bonds
28
define zwitterion and at what pH does it occur?
a molecule that has both a positive and negative charge, but has a net charge of zero, making it electrically neutral; occurs at neutral pH
29
AA with ionizable R groups will have how many ionizable groups?
3
30
what are two things each ionizable group will have?
1. pKa
2.region of buffering capacity
31
what does pKa meassure?
it measures the tendency to lose s proton
32
how do ionizable groups act?
they act as acids with increasing pH (give up protons)
33
what type of environment stabilizes the protonated form?
a hydrophobic environment
34
what causes repulsion and can affect protonation state?
proximate amino acids of similar charged
35
the point at which the pH of a molecule has no net electrical charge is the ...
isoelectric point
36
how does the buffer zone on a titration curve look? what happens in these zones?
the relatively flat section of the curve where the pH changes very little with the addition of titrant
37
what are comprised of a wide variety of amino acid monomers with varied charge distribution?
proteins
38
what are four types of proteins?
-structural
-enzymatic
-carrier
-regulatory
39
where are structural proteins found?
hair, skin, eyes, muscle, silk
40
what do carrier proteins help with?
respiration and metabolism
41
what do enzymatic proteins help with?
digestion, blood clotting, replication, transcription, translation
42
what do regulatory proteins do?
coordinate events within and between cells
43
protein 3D structure depends on the ...
primary sequence of AAs
44
what happens if you change a single amino acid in the primary sequence?
small changes at the amino acids level can affect structure which can lead to sickness and disease
45
what is an example (shown in class) of changing a protein at the amino acid level? what is the outcome?
hemoglobin at 6 position changing from a Glu to Val can cause sickle cell anemia
46
what type of bonds link amino acids to make proteins?
peptide bonds
47
what are the 3 things to keep in mind about the polarity of peptides?
-it goes from left tor right
-free amino group is on the left - N Terminus
-Free carboxyl group is on the right – C Terminus
48
what property of the polypeptide depends on the R groups?
electrostatic property
49
what are the four levels of protein structure?
primary
secondary
tertiary
quaternary
50
name the protein structure:
Sequence of AAs
primary
51
name the protein structure:
Conformation of backbone
(main chain atoms only –no regard to side chains) (arrangement of
adjacent AAs)
-alpha helix or beta sheet-
secondary
52
name the protein structure:
How multiple secondary structures are arranged relative to each other in one polypeptide (arrangement of adjacent and distant AAs)
tertiary
53
name the protein structure:
Multiple polypeptides arranged
relative to each other to form
a protein with different subunits
quaternary
54
name the protein structure:
primary
55
name the protein structure:
secondary
56
name the protein structure:
tertiary
57
name the protein structure:
quaternary
58
what are peptide bond characteristics?
-Partial sharing of electrons between the carbonyl oxygen
and the amide nitrogen
-partial double bond character across the peptide bond
-no rotation around the C-N
59
phi and psi angles are influenced by ...
steric interference of R
groups
60
fill in the blank:
Atoms of the peptide bond are ____ and tend to form __________
polar; H-bonds
61
what are 3 requirements of secondary structures?
1. H-bond requirements of the polar peptide bond
2. minimizes steric strain
(limited movement of bonds due to rotation)
3. positioning of side chains to minimize interference
62
if a person has acidemia (increased [H+] in blood), what is the appropriate treatment?
hyperventilating
63
what does the bicarbonate system maintain?
blood pH
64
what is Le Chatelier's principle?
if a dynamic equilibrium is disturbed (change of conditions), then the position of equilibrium will shift to counteract the change to reestablish an equilibrium
65
is the tyrosine R- group:
a.hydrophobic
b.hydrophilic
c. amphiphilic
C. amphiphilic
66
what compounds have hydrophobic R-groups (shown in class)?
phenylalanine and tryptophan
67
Enantiomers:
a. are only associated with amino acids
b. can be specific types of diastereomers
c. are never mirror images of each other
d. can exist for molecules with more than one chiral carbon
d. can exist for molecules with more than one chiral carbon
68
what are asymmetric carbons called?
chiral center
69
if a molecule has n number of chiral carbons, how many stereoisomers will it have?
2^n
70
can enantiomers exist for molecules that have more than one chiral carbon?
yes
71
One turn of the helix = ____ A along
the axis
(____ amino acid residues)
5.4; 3.6
72
what type of contact do atoms in the core of the helix have?
Van der Waals
73
Do AA side chains point inward or outward from the helix in secondary structures?
outward
74
what two compounds (shown in class) are least likely to form a alpha helix?
Proline and glycine
75
why is proline least likely to form an alpha helix?
-No rotation around C-N bond
-Results in destabilizing kink
76
why is glycine least likely to form an alpha helix?
Too much
conformational flexibility
77
what are the two ways beta sheets can form?
parallel and antiparallel
78
what types of bonds are formed between neighboring strands in beta sheets?
H-bonds
79
in parallel beta sheets, strands run in ____ direction
same
80
in antiparallel beta sheets, strands run in ____ direction
opposite
81
what is the average number of strans per beta sheet?
6
82
what are two small compounds (shown in class) that are common in beta sheets?
glycine and alanine
83
what kind of linkage links antiparallel beta sheets?
beta-turns
84
what kind of linkage links parallel beta sheets?
beta loops
85
what two compounds (shown in class) are common to have beta-turns?
proline and glycine
86
the hydrophobic core houses what kind of amino acids?
hydrophobic
87
the hydrophobic core allows polar residues to participate in what kind of bonding?
H-bonding
88
the hydrophobic core allows charged residues to participate in what kind of bonding?
ionic-bonding
89
what are the three examples of folding possibilities shown in class?
beta-alpha-beta
beta-hairpin
alpha-alpha
90
a hydrophilic surface has what two things?
- charged amino acids
-polar residues
91
what is the part of a peptide chain that is independently stable or can undergo
movement as a single entity with respect to the entire protein called?
domain
92
will domains retain their individual structure if separated?
yes
93
what are polypeptide subunits associated with each other to form a multisubunit protein called?
oligomers
94
a homo-oligomer has ____ subunits
identical
95
a hetero-oligomer has ____ subunits
different
96
Associations between the different subunits are ____
noncovalent
97
What factors drive and stabilize the folding of proteins?
Proteins fold into the conformation that is the most thermodynamically stable - lowest Gibbs free energy
98
label:
1. denatured
2. native
99
what effect drives protein folding?
the hydrophobic effect
100
what will nonpolar groups do to minimize their contact with water?
aggregate to displace water molecules surrounding the protein
101
what are 3 weak noncovalent interactions that stabilize protein structures?
Van der Waals forces
hydrogen bonds
ionic interactions
102
what is a covalent interactions that stabilize protein structures?
disulfide bonds
103
describe the hydrophobic collapse into molten globule
Spontaneous collapse of the polypeptide into a
compact state (molten globule)
104
what are 4 things that drive protein folding?
1. Hydrophobic Effect (lowest Gibbs free energy)
2. Ionic Bonds (Salt Bridges) - Charged Amino Acids
3. Hydrogen Bonds*
4. Disulfide Bonds * *Stabilizing (After Folding)
105
protein folding in vivo often requires what?
chaperones
106
name the 1, 3 letter code and property of R groups for: glycine
Gly G; nonpolar r group
107
name the 1, 3 letter code and property of R groups for: alanine
Ala A; nonpolar r group
108
name the 1, 3 letter code and property of R groups for: proline
Pro P ; nonpolar r group
109
name the 1, 3 letter code and property of R groups for: valine
Val V; nonpolar r group
110
name the 1, 3 letter code and property of R groups for: leucine
Leu L; nonpolar r group
111
name the 1, 3 letter code and property of R groups for: isoleucine
Ile I ; nonpolar r group
112
name the 1, 3 letter code and property of R groups for: methionine
Met M ; nonpolar r group
113
name the 1, 3 letter code and property of R groups for: phenylalanine
Phe F; aromatic r group
114
name the 1, 3 letter code and property of R groups for: tryosine
Tyr Y ; aromatic r group
115
name the 1, 3 letter code and property of R groups for: tryptophan
Trp W ; aromatic r group
116
name the 1, 3 letter code and property of R groups for: serine
Ser S; uncharged polar r group
117
name the 1, 3 letter code and property of R groups for:threonine
Thr T ; uncharged polar r group
118
name the 1, 3 letter code and property of R groups for: glutamine
Gln Q ; uncharged polar r group
118
name the 1, 3 letter code and property of R groups for: asparagine
Asn N ; uncharged polar r group
119
name the 1, 3 letter code and property of R groups for: cysteine
Cys C ; uncharged polar r group
120
name the 1, 3 letter code and property of R groups for: lysine
Lys K ; positively charged r group
121
name the 1, 3 letter code and property of R groups for: histidine
His H; positively charged r group
122
name the 1, 3 letter code and property of R groups for: arginine
Arg R ; positively charged r group
123
name the 1, 3 letter code and property of R groups for: aspartate
Asp D; negatively charged r group
124
name the 1, 3 letter code and property of R groups for: glutamate
Glu E; negatively charged r group
125
name the compound:
glycine
126
name the compound:
alanine
127
name the compound:
proline
128
name the compound:
valine
129
name the compound:
leucine
130
name the compound:
isoleucine
130
name the compound:
methionine
131
name the compound:
serine
131
name the compound:
threonine
131
name the compound:
cysteine
132
name the compound:
asparagine
133
name the compound:
glutamine
133
name the compound:
lysine
134
name the compound:
arginine
135
name the compound:
histidine
136
name the compound:
aspartate
137
name the compound:
glutamate
138
name the compound:
phenylalanine
139
name the compound:
tyrosine
140
name the compound:
tryptophan
