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Flashcards in 2.04 Proteins Deck (163)
1

Most abundant and functionally diverse molecules in living systems

Proteins

2

Proteins are linear polymers of _____

Amino acid

3

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

Proteome

4

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

Proteomics

5

Goal is the identification of proteins and of their postranslational modifications whose appearance or disappearance corerelates with physiologic phenomenon, aging, or specific diseases

Proteomics

6

Building blocks of proteins

Amino acids

7

Only ____ AA are commonly found in mammalian proteins

20

8

Except fo proline, each amino acid has

1 carboxyl group
1 amino group
1 unique side chain

9

_____ dictates the function of the amino acid in a protein

Structure of the R-group

10

Amino acids with aliphatic side chains

Glycine
Alanine
Valine
Leucine
Isoleucine

11

Amino acids with hydroxylic goups

Serine
Threonine
Tyrosine

12

Amino acids with side chains containing sulfur atoms

Cysteine
Methionine

13

Amino acids with aromatic side chains

Histidine
Phenylalanine
Tyrosine
Tryptophan

14

Imino acid

Proline

15

AA with side chains containing basic group

Arginine
Lysine
Histidine

16

AA with acidic groups and their amide

Aspartic acid
Asparagine
Glutamic Acid
Glutamine

17

AA with nonpolar side chains

Glycine
Alanine
Valine
Leucine
Isoleucine
Phenylalanine
Tryptophan
Methionine
Proline

18

Net charge of zero at physiologic pH
Promote hydrophobic interactions

Nonpolar side chains

19

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

interior; aqueous solution

20

Has the smallest side chain

Glycine

21

Often occurs where peptides bend shaprly

Glycine

22

First step of heme sythesis

Glycine + Succinyl CoA -> delta-ALA

23

major inhibitory neurotransmitter in the spinal cord

Glycine

24

major inhibitory neurotransmitter in the brain

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