2.04 Proteins Flashcards
1
Q
Most abundant and functionally diverse molecules in living systems
A
Proteins
2
Q
Proteins are linear polymers of _____
A
Amino acid
3
Q
Set of all the proteins expressed by an individual cell at a particular time
A
Proteome
4
Q
Aims to identify the entire complement of proteins elaborated by a cell under diverse conditions
A
Proteomics
5
Q
Goal is the identification of proteins and of their postranslational modifications whose appearance or disappearance corerelates with physiologic phenomenon, aging, or specific diseases
A
Proteomics
6
Q
Building blocks of proteins
A
Amino acids
7
Q
Only ____ AA are commonly found in mammalian proteins
A
20
8
Q
Except fo proline, each amino acid has
A
1 carboxyl group
1 amino group
1 unique side chain
9
Q
_____ dictates the function of the amino acid in a protein
A
Structure of the R-group
10
Q
Amino acids with aliphatic side chains
A
Glycine Alanine Valine Leucine Isoleucine
11
Q
Amino acids with hydroxylic goups
A
Serine
Threonine
Tyrosine
12
Q
Amino acids with side chains containing sulfur atoms
A
Cysteine
Methionine
13
Q
Amino acids with aromatic side chains
A
Histidine
Phenylalanine
Tyrosine
Tryptophan
14
Q
Imino acid
A
Proline
15
Q
AA with side chains containing basic group
A
Arginine
Lysine
Histidine
16
Q
AA with acidic groups and their amide
A
Aspartic acid
Asparagine
Glutamic Acid
Glutamine
17
Q
AA with nonpolar side chains
A
Glycine Alanine Valine Leucine Isoleucine Phenylalanine Tryptophan Methionine Proline
18
Q
Net charge of zero at physiologic pH
Promote hydrophobic interactions
A
Nonpolar side chains
19
Q
Nonpolar side chains cluster in the ______ of the protein in __________ and outside of the protein in hydrophilic environment
A
interior; aqueous solution
20
Q
Has the smallest side chain
A
Glycine
21
Q
Often occurs where peptides bend shaprly
A
Glycine
22
Q
First step of heme sythesis
A
Glycine + Succinyl CoA -> delta-ALA
23
Q
major inhibitory neurotransmitter in the spinal cord
A
Glycine
24
Q
major inhibitory neurotransmitter in the brain
A
GABA
25
major excitatory neurotransmitter
Glutamine
26
used in purine synthesis
Glycine
27
carries nitrogen from peripheral tissue
Alanine
28
branched-chain amino acids
Valine, Leucine, Isoleucine
29
Deficiency in branched chain alphaketoacid dehydrogenase
Maple syrup urine disease
30
Precursor of tyrosine
Phenylalanine
31
Deficiency of phenylalanine hydroxylase
Phenylketonuria
32
Metabolites that accumulate among PKU patients
phenyllactate
phenylacetate
phenylpyruvate
33
Has the largest side chain
Tryptophan
34
Tryptophan is the precursor for
Melatonin, Serotonin, Niacin
35
Transfer of methyl group as S-adenosylmethionine
Methionine
36
Methionine is precursor for
Homocysteine
37
Primary cause of myocardial infarction among patients with no known risk factors
Homocysteine
38
Contributes to the fibrous structure of collagen and interrupts alpha-helices in globular proteins
Proline
39
Phenylalanine derivatives
Tyrosine>L-dopa>Dopamine>Norepi>Epi
| Tyrosine>Thyroxine and Melanin
40
AA with uncharged polar side chains
Serine, Threonine, Tyrosine, Asparagine, Glutamine, Cysteine
41
Contains a sulfhydryl group that is an active part of many enzymes
Cysteine
42
Two cysteines can be connected by a covalent disulfide bond to form
Cystine
43
Precursor of L-dopa, Thyroxine, Melanin
Tyrosine
44
Phosphorylation site of enzyme modification
Serine
45
Serine is often linked to carbohydrate groups in _____
Glycoprotein
46
Sites for O-linked glycolsylation in Golgi apparatus
Serine, Threonine
47
Have a carbonyl group and an amide group that can also form hydrogen bonds
Asparagine, Glutamine
48
Site for N-linked glycosylation in endoplasmic reticulum
Asparagine
49
Deaminated by glutaminase resulting in the formation of ammonia
Glutamine
50
Major carrier of nitrogen to the liver from peripheral tissues
Glutamine
51
Negatively charged at physiologic pH because of the carboxylate group
Acidic side chains
52
Glutamate is precursor for ______ and _____
GABA, Glutathione
53
Positively charged because of the amine group
Basic Amino Group
54
Precursor of histamine
Histidine
55
Histidine is used in the diagnosis of _______
Folic acid deficiency
56
Test for folic acid deficiency
N-formiminoglutamate excretion test
57
Prescursor of creatinine, urea, nitric oxide
Arginine
58
Found in a handful of proteins, including certain peroxidases and reductases
Selenocysteine
59
Inserted into polypeptides during translation but is not specified by a simple three-letter codon
Selenocysteine
60
C
Cysteine
61
H
Histidine
62
I
Isoleucine
63
M
Methionine
64
S
Serine
65
V
Valine
66
A
Alanine
67
G
Glycine
68
L
Leucine
69
P
Proline
70
T
Threonine
71
R
Arginine
72
N
Asparagine
73
D
Aspartate
74
E
Glutamate
75
Q
Glutamine
76
F
Phenylalanine
77
Y
Tyrosine
78
W
Tryptophan
79
All AA are chiral except for ____
Glycine
80
Atom in a molecule that is bonded to 4 different chemical species, allowing for optical isomerism
Chiral
81
Exact mirror images of each other
Stereroisomers/optical isomers/enantiomers
82
All amino acids in proteins
L-configuration
83
D-configuration
free D-serine and D-aspartate in ______
D-alanine and D- glutamate in ______
Brain tissue;
| Cell walls of gram-positive bacteria
84
AA that cannot be synthesized by the body and must come from diet
Phenylalanine, Valine, Tryptophan, Threonine, Isoleucine, Methionine, Histidine, Arginie, Leucine, Lysine
85
Conditionally Non-essential Amino Acids
Histidine, Arginine
86
May be made in the body, but usually not enough in growing children
Arginine
87
May be recycled but should eventually be consumed since it is not made at all
Histidine
88
In PKU patients, this is considered an essential AA
Tyrosine
89
Protein structure
Primary
Secondary
Tertiary
Quaternary
90
Linear sequence of a protein's AA
Primary Sequence
91
Attaches alpha-amino group of one AA to the alpha-carbonyl group of another
Peptide bonds
92
Very stable, can only be disrupted by hydrolysis through prolonged exposure to a strong acid or base at elevated temperatures
Peptide bonds
93
Folding of short (3-30) contiguous segments of polypeptide into geometrically ordered units
Secondary structure
94
Regular arrangements of AA that are located near each other in the linear sequence
Secondary structure
95
Secondary structure is stabilized by excessive
Hydrogen bonding
96
2 main kinds of secondary structure
alpha helix
| beta pleated sheets
97
Most common
R-handed spiral structure with polypeptide backbone core, with side chains extending outward and H-bonds parallel to spiral
Alpha helix
98
___ AA per turn of the spiral
3.6
99
Alpha helix is disrupted by
Proline
Large R-groups (W)
Charged R-groups ()
100
Surfaces appear flat and pleated
| 1 or 2 peptide chains parallel to each other
Beta sheet
101
Beta sheet
| Between two polypeptides
Perpendicular interchain H-bonds
| Antiparallel
102
Beta sheet
| 1 polypeptide
Perpendicular intrachain H bonds
| Parallel
103
Reverses the direction of the polypeptide chain forming a compact and globular shape
beta bends, reverse turn, beta turns
104
often connect anti parallel beta sheets
| composed of 4 AA, with first AA in a hydrogen bond to the fourth AA
beta bends, reverse turns, beta turns
105
Beta bends
| Usually with
Proline and glycine
106
Stabilized by formation of hydrogen and ionic bonds
beta bends, reverse turns, beta turns
107
seen in half of an average globular protein
Non-repetitive (loop and coil) structures
108
Not random, but with less regular structure than alpha helix or beta sheet
Non-repetitive (loop and coil) structures
109
Many adopt a specific conformation stabilized through H-bond, salt bridge, and hydrophobic interactions with other portions of the protein
Non-repetitive (loop and coil) stuctures
110
Produced by packing side chains from adjacent secondary structural elements close to each other
Motif
| Supersecondary structures
111
beta-alpha-beta unit
Greek key
beta-meander
beta-barrel
Motif
| Supersecondary structures
112
overall 3 dimensional shape of the protein
Tertiary structure
113
An axial ratio of <3
globular proteins
114
An axial ratio of > 10
fibrous proteins
115
refers to the folding of domains and their final arrangement in the polypeptide
Tertiary structure
116
Tertiary structure is stabilized by
Disulfide bonds
Hydrophobic interactions
Hydrogen bonds
Ionic bonds
117
Fundamental structural and functional units of polypeptide
Domain
118
Combinations of motifs
Domain
119
structure of protein consisting of more than one polypeptide chain
Quaternary structure
120
One polypeptide chain
Monomeric
121
2 polypeptide chains
Dimeric
122
2 copies of same polypeptide
Homodimer
123
2 different polypeptide
Heterodimer
124
Several polypeptides
Oligomeric
125
Quaternary structure is held together mainly by
Noncovalent bond:
| H-bond, Ionic bond, Hydrophobic interactions
126
Disruption of a protein's structure
Denaturation
127
Results in the unfolding and disorganization of the protein's secondary and tertiary structures, which are not accompanied by hydrolysis of peptide bonds
Reversible under ideal conditions
Denaturation
128
Means of denaturation
```
heat
organic solvent
mechanical mixing
strong acids or bases
detergents
ions of heavy metals like Pb and Hg
```
129
Protein folding
| Native conformation
thermodynamically favored
130
Protein folding occurs in
modular or step-wise process
131
Hydrophobic regions settle in the interior forming
Molten globule
132
Specialized group of protein required for the proper folding of many species of proteins
Chaperones
133
Chaperones can also ____ that have become themodynamically trapped in a misfolded dead end by unfolding hydrophobic regions
Rescue proteins
134
Binds to hydrophic amino acids and shields them from solvent
Hsp70
135
Provides sheltered environment where polypeptide can fold until all hydrophobic groups are in the interior, preventing aggregation
Hsp60
| chaperonins
136
Facilitate formation of disulfide bonds that stabilizes protein's native conformation
Protein disulfide isomerase
137
Catalyzes trans to cis in proline
Proline cis-trans isomerase
138
Protein folding
| More common
In vitro
139
Protein has already been fully synthesized and will be denatured before allowing primary structure to initiate refolding
In vitro
140
Has refolding buffer
In vitro
141
protein denatured and then refolded by biochemical techniques
does not lead to complete unfolding
in vitro
142
folding happens while protein is being synthesized sequentially in the ribosome
results in intermediate structures
chaperones assist folding
in vivo
143
cotranslational folding
in vivo
144
cooperative folding
in vitro
145
cytosol provides crowded macromolecular environemnt
in vivo
146
significantly extended in the early stage of protein folding while the protein is being synthesized in the ribosome
in vivo
147
Fatal neurodegenerative diseases characterized by spongiform changes, astrocytic gliomas, neuronal loss resulting from the deposition of insoluble protein aggregates in neural cells
Prion disease
148
transmitted through the protein alone and there is no need to change DNA or RNA
Prion disease
149
Normal protein
| Lots of alpha-helices
PrPc
150
Pathologic conformation, lots of beta-sheets
PrPsc
151
Characteristic senile plaques and neurofibrillary bundles contain aggregates of the protein-beta amyloid
Alzheimer's disease
152
Potential mediator of the conformational translation of beta-amyloid from soluble alpha-helix
Apolipoprotein E
153
Virtually every life process depends on this class of molecules
Proteins
154
Optically inactive
| Its alpha-carbon has two hydrogen substituents
Glycine
155
Found in the interior of proteins that function in an aqueous environment and on the surface of proteins that interact with lipids
AA with nonpolar side chains
156
Found on the outside of proteins that function in an aqueous environment and in the interior of the membrane-associated proteins
AA with uncharged polar side chains/ acidic side chains/ basic side chains
157
Understanding the _____ structure of proteins is important because many genetic disease result in proteins with abnormal AA sequences, which cause improper folding and loss or impairment of normal function
Primary
158
Not broken by conditions that denature proteins, such as heating or high concentrations of urea
Peptide bonds
159
Collagen alpha-chain helix is an example of ______ structure
Secondary
160
Form of secondary structure in which all of the peptide bond components are involved in hydrogen bonding
Composed of two or more peptide chains
beta sheets
161
Often connect successive strands of antiparallel beta sheets
| Stabilized by the formation of hydrogen and ionic bonds
beta bends
162
Globular proteins are constructed by combining secondary structural elements (alpha helices, beta sheets, nonrepetitive sequences)
Supersecondary structures
163
Information needed for correct protein folding is contained in the ____ structure of the polypeptide
Primary
