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01 Cell > 2.04 Proteins > Flashcards

2.04 Proteins Flashcards

1
Q

Most abundant and functionally diverse molecules in living systems

A

Proteins

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2
Q

Proteins are linear polymers of _____

A

Amino acid

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3
Q

Set of all the proteins expressed by an individual cell at a particular time

A

Proteome

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4
Q

Aims to identify the entire complement of proteins elaborated by a cell under diverse conditions

A

Proteomics

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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

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6
Q

Building blocks of proteins

A

Amino acids

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7
Q

Only ____ AA are commonly found in mammalian proteins

A

20

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8
Q

Except fo proline, each amino acid has

A

1 carboxyl group
1 amino group
1 unique side chain

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9
Q

_____ dictates the function of the amino acid in a protein

A

Structure of the R-group

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10
Q

Amino acids with aliphatic side chains

A 
Glycine
Alanine
Valine
Leucine
Isoleucine
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11
Q

Amino acids with hydroxylic goups

A

Serine
Threonine
Tyrosine

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12
Q

Amino acids with side chains containing sulfur atoms

A

Cysteine

Methionine

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13
Q

Amino acids with aromatic side chains

A

Histidine
Phenylalanine
Tyrosine
Tryptophan

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14
Q

Imino acid

A

Proline

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15
Q

AA with side chains containing basic group

A

Arginine
Lysine
Histidine

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16
Q

AA with acidic groups and their amide

A

Aspartic acid
Asparagine
Glutamic Acid
Glutamine

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17
Q

AA with nonpolar side chains

A 
Glycine
Alanine
Valine
Leucine
Isoleucine
Phenylalanine
Tryptophan
Methionine
Proline
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18
Q

Net charge of zero at physiologic pH

Promote hydrophobic interactions

A

Nonpolar side chains

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19
Q

Nonpolar side chains cluster in the ______ of the protein in __________ and outside of the protein in hydrophilic environment

A

interior; aqueous solution

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20
Q

Has the smallest side chain

A

Glycine

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21
Q

Often occurs where peptides bend shaprly

A

Glycine

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22
Q

First step of heme sythesis

A

Glycine + Succinyl CoA -> delta-ALA

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23
Q

major inhibitory neurotransmitter in the spinal cord

A

Glycine

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24
Q

major inhibitory neurotransmitter in the brain

A

GABA

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25
Q

major excitatory neurotransmitter

A

Glutamine

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26
Q

used in purine synthesis

A

Glycine

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27
Q

carries nitrogen from peripheral tissue

A

Alanine

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28
Q

branched-chain amino acids

A

Valine, Leucine, Isoleucine

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29
Q

Deficiency in branched chain alphaketoacid dehydrogenase

A

Maple syrup urine disease

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30
Q

Precursor of tyrosine

A

Phenylalanine

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31
Q

Deficiency of phenylalanine hydroxylase

A

Phenylketonuria

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32
Q

Metabolites that accumulate among PKU patients

A

phenyllactate
phenylacetate
phenylpyruvate

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33
Q

Has the largest side chain

A

Tryptophan

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34
Q

Tryptophan is the precursor for

A

Melatonin, Serotonin, Niacin

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35
Q

Transfer of methyl group as S-adenosylmethionine

A

Methionine

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36
Q

Methionine is precursor for

A

Homocysteine

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37
Q

Primary cause of myocardial infarction among patients with no known risk factors

A

Homocysteine

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38
Q

Contributes to the fibrous structure of collagen and interrupts alpha-helices in globular proteins

A

Proline

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39
Q

Phenylalanine derivatives

A

Tyrosine>L-dopa>Dopamine>Norepi>Epi

Tyrosine>Thyroxine and Melanin

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40
Q

AA with uncharged polar side chains

A

Serine, Threonine, Tyrosine, Asparagine, Glutamine, Cysteine

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41
Q

Contains a sulfhydryl group that is an active part of many enzymes

A

Cysteine

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42
Q

Two cysteines can be connected by a covalent disulfide bond to form

A

Cystine

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43
Q

Precursor of L-dopa, Thyroxine, Melanin

A

Tyrosine

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44
Q

Phosphorylation site of enzyme modification

A

Serine

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45
Q

Serine is often linked to carbohydrate groups in _____

A

Glycoprotein

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46
Q

Sites for O-linked glycolsylation in Golgi apparatus

A

Serine, Threonine

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47
Q

Have a carbonyl group and an amide group that can also form hydrogen bonds

A

Asparagine, Glutamine

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48
Q

Site for N-linked glycosylation in endoplasmic reticulum

A

Asparagine

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49
Q

Deaminated by glutaminase resulting in the formation of ammonia

A

Glutamine

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50
Q

Major carrier of nitrogen to the liver from peripheral tissues

A

Glutamine

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51
Q

Negatively charged at physiologic pH because of the carboxylate group

A

Acidic side chains

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52
Q

Glutamate is precursor for ______ and _____

A

GABA, Glutathione

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53
Q

Positively charged because of the amine group

A

Basic Amino Group

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54
Q

Precursor of histamine

A

Histidine

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55
Q

Histidine is used in the diagnosis of _______

A

Folic acid deficiency

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56
Q

Test for folic acid deficiency

A

N-formiminoglutamate excretion test

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57
Q

Prescursor of creatinine, urea, nitric oxide

A

Arginine

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58
Q

Found in a handful of proteins, including certain peroxidases and reductases

A

Selenocysteine

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59
Q

Inserted into polypeptides during translation but is not specified by a simple three-letter codon

A

Selenocysteine

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60
Q

C

A

Cysteine

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61
Q

H

A

Histidine

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62
Q

I

A

Isoleucine

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63
Q

M

A

Methionine

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64
Q

S

A

Serine

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65
Q

V

A

Valine

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66
Q

A

A

Alanine

67
Q

G

A

Glycine

68
Q

L

A

Leucine

69
Q

P

A

Proline

70
Q

T

A

Threonine

71
Q

R

A

Arginine

72
Q

N

A

Asparagine

73
Q

D

A

Aspartate

74
Q

E

A

Glutamate

75
Q

Q

A

Glutamine

76
Q

F

A

Phenylalanine

77
Q

Y

A

Tyrosine

78
Q

W

A

Tryptophan

79
Q

All AA are chiral except for ____

A

Glycine

80
Q

Atom in a molecule that is bonded to 4 different chemical species, allowing for optical isomerism

A

Chiral

81
Q

Exact mirror images of each other

A

Stereroisomers/optical isomers/enantiomers

82
Q

All amino acids in proteins

A

L-configuration

83
Q

D-configuration
free D-serine and D-aspartate in ______
D-alanine and D- glutamate in ______

A

Brain tissue;

Cell walls of gram-positive bacteria

84
Q

AA that cannot be synthesized by the body and must come from diet

A

Phenylalanine, Valine, Tryptophan, Threonine, Isoleucine, Methionine, Histidine, Arginie, Leucine, Lysine

85
Q

Conditionally Non-essential Amino Acids

A

Histidine, Arginine

86
Q

May be made in the body, but usually not enough in growing children

A

Arginine

87
Q

May be recycled but should eventually be consumed since it is not made at all

A

Histidine

88
Q

In PKU patients, this is considered an essential AA

A

Tyrosine

89
Q

Protein structure

A

Primary
Secondary
Tertiary
Quaternary

90
Q

Linear sequence of a protein’s AA

A

Primary Sequence

91
Q

Attaches alpha-amino group of one AA to the alpha-carbonyl group of another

A

Peptide bonds

92
Q

Very stable, can only be disrupted by hydrolysis through prolonged exposure to a strong acid or base at elevated temperatures

A

Peptide bonds

93
Q

Folding of short (3-30) contiguous segments of polypeptide into geometrically ordered units

A

Secondary structure

94
Q

Regular arrangements of AA that are located near each other in the linear sequence

A

Secondary structure

95
Q

Secondary structure is stabilized by excessive

A

Hydrogen bonding

96
Q

2 main kinds of secondary structure

A

alpha helix

beta pleated sheets

97
Q

Most common
R-handed spiral structure with polypeptide backbone core, with side chains extending outward and H-bonds parallel to spiral

A

Alpha helix

98
Q

___ AA per turn of the spiral

A

3.6

99
Q

Alpha helix is disrupted by

A

Proline
Large R-groups (W)
Charged R-groups ()

100
Q

Surfaces appear flat and pleated

1 or 2 peptide chains parallel to each other

A

Beta sheet

101
Q

Beta sheet

Between two polypeptides

A

Perpendicular interchain H-bonds

Antiparallel

102
Q

Beta sheet

1 polypeptide

A

Perpendicular intrachain H bonds

Parallel

103
Q

Reverses the direction of the polypeptide chain forming a compact and globular shape

A

beta bends, reverse turn, beta turns

104
Q

often connect anti parallel beta sheets

composed of 4 AA, with first AA in a hydrogen bond to the fourth AA

A

beta bends, reverse turns, beta turns

105
Q

Beta bends

Usually with

A

Proline and glycine

106
Q

Stabilized by formation of hydrogen and ionic bonds

A

beta bends, reverse turns, beta turns

107
Q

seen in half of an average globular protein

A

Non-repetitive (loop and coil) structures

108
Q

Not random, but with less regular structure than alpha helix or beta sheet

A

Non-repetitive (loop and coil) structures

109
Q

Many adopt a specific conformation stabilized through H-bond, salt bridge, and hydrophobic interactions with other portions of the protein

A

Non-repetitive (loop and coil) stuctures

110
Q

Produced by packing side chains from adjacent secondary structural elements close to each other

A

Motif

Supersecondary structures

111
Q

beta-alpha-beta unit
Greek key
beta-meander
beta-barrel

A

Motif

Supersecondary structures

112
Q

overall 3 dimensional shape of the protein

A

Tertiary structure

113
Q

An axial ratio of <3

A

globular proteins

114
Q

An axial ratio of > 10

A

fibrous proteins

115
Q

refers to the folding of domains and their final arrangement in the polypeptide

A

Tertiary structure

116
Q

Tertiary structure is stabilized by

A

Disulfide bonds
Hydrophobic interactions
Hydrogen bonds
Ionic bonds

117
Q

Fundamental structural and functional units of polypeptide

A

Domain

118
Q

Combinations of motifs

A

Domain

119
Q

structure of protein consisting of more than one polypeptide chain

A

Quaternary structure

120
Q

One polypeptide chain

A

Monomeric

121
Q

2 polypeptide chains

A

Dimeric

122
Q

2 copies of same polypeptide

A

Homodimer

123
Q

2 different polypeptide

A

Heterodimer

124
Q

Several polypeptides

A

Oligomeric

125
Q

Quaternary structure is held together mainly by

A

Noncovalent bond:

H-bond, Ionic bond, Hydrophobic interactions

126
Q

Disruption of a protein’s structure

A

Denaturation

127
Q

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

A

Denaturation

128
Q

Means of denaturation

A 
heat
organic solvent
mechanical mixing
strong acids or bases
detergents
ions of heavy metals like Pb and Hg
129
Q

Protein folding

Native conformation

A

thermodynamically favored

130
Q

Protein folding occurs in

A

modular or step-wise process

131
Q

Hydrophobic regions settle in the interior forming

A

Molten globule

132
Q

Specialized group of protein required for the proper folding of many species of proteins

A

Chaperones

133
Q

Chaperones can also ____ that have become themodynamically trapped in a misfolded dead end by unfolding hydrophobic regions

A

Rescue proteins

134
Q

Binds to hydrophic amino acids and shields them from solvent

A

Hsp70

135
Q

Provides sheltered environment where polypeptide can fold until all hydrophobic groups are in the interior, preventing aggregation

A

Hsp60

chaperonins

136
Q

Facilitate formation of disulfide bonds that stabilizes protein’s native conformation

A

Protein disulfide isomerase

137
Q

Catalyzes trans to cis in proline

A

Proline cis-trans isomerase

138
Q

Protein folding

More common

A

In vitro

139
Q

Protein has already been fully synthesized and will be denatured before allowing primary structure to initiate refolding

A

In vitro

140
Q

Has refolding buffer

A

In vitro

141
Q

protein denatured and then refolded by biochemical techniques
does not lead to complete unfolding

A

in vitro

142
Q

folding happens while protein is being synthesized sequentially in the ribosome
results in intermediate structures
chaperones assist folding

A

in vivo

143
Q

cotranslational folding

A

in vivo

144
Q

cooperative folding

A

in vitro

145
Q

cytosol provides crowded macromolecular environemnt

A

in vivo

146
Q

significantly extended in the early stage of protein folding while the protein is being synthesized in the ribosome

A

in vivo

147
Q

Fatal neurodegenerative diseases characterized by spongiform changes, astrocytic gliomas, neuronal loss resulting from the deposition of insoluble protein aggregates in neural cells

A

Prion disease

148
Q

transmitted through the protein alone and there is no need to change DNA or RNA

A

Prion disease

149
Q

Normal protein

Lots of alpha-helices

A

PrPc

150
Q

Pathologic conformation, lots of beta-sheets

A

PrPsc

151
Q

Characteristic senile plaques and neurofibrillary bundles contain aggregates of the protein-beta amyloid

A

Alzheimer’s disease

152
Q

Potential mediator of the conformational translation of beta-amyloid from soluble alpha-helix

A

Apolipoprotein E

153
Q

Virtually every life process depends on this class of molecules

A

Proteins

154
Q

Optically inactive

Its alpha-carbon has two hydrogen substituents

A

Glycine

155
Q

Found in the interior of proteins that function in an aqueous environment and on the surface of proteins that interact with lipids

A

AA with nonpolar side chains

156
Q

Found on the outside of proteins that function in an aqueous environment and in the interior of the membrane-associated proteins

A

AA with uncharged polar side chains/ acidic side chains/ basic side chains

157
Q

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

A

Primary

158
Q

Not broken by conditions that denature proteins, such as heating or high concentrations of urea

A

Peptide bonds

159
Q

Collagen alpha-chain helix is an example of ______ structure

A

Secondary

160
Q

Form of secondary structure in which all of the peptide bond components are involved in hydrogen bonding
Composed of two or more peptide chains

A

beta sheets

161
Q

Often connect successive strands of antiparallel beta sheets

Stabilized by the formation of hydrogen and ionic bonds

A

beta bends

162
Q

Globular proteins are constructed by combining secondary structural elements (alpha helices, beta sheets, nonrepetitive sequences)

A

Supersecondary structures

163
Q

Information needed for correct protein folding is contained in the ____ structure of the polypeptide

A

Primary

01 Cell (22 decks)

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