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Protein and Nucleic acid > SECONDARY, TERTIARY AND QUARTERNARY STRUCTURE OF PROTEINS > Flashcards

SECONDARY, TERTIARY AND QUARTERNARY STRUCTURE OF PROTEINS Flashcards

1
Q

Side chains capable of forming H bonds are usually located on the blank

A

Protein surface

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2
Q

Why hydrophobic interactions drive protein folding?

A

Because nonpolar side chains of AAs and other nonpolar solutes prefer to cluster in a nonpolar environment than to intercalate in a polar solvent such as water.

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3
Q

Forming a blank minimizes the interaction of nonpolar residues in water.

A

Hydrophobic bonds

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4
Q

Blank are much less common in the interior of a protein.

A

Polar AAs

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5
Q

Ionic interactions arise either as blank between opposite charges or blank between like charges

A

electrostatic attractions, repulsion

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6
Q

N-terminal and C-terminal residues of a protein or peptide chain usually exist in blank and carry (+) or (-) charges.

A

Ionized states

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7
Q

TRUE OR FALSE
Ability of a K to attract a nearby E weakened by dissolved salts.

A

True

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8
Q

Van der Waals interaction is blank

A

Ubiquitous

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9
Q

Both blank and blank are included in van der waals interactions

A

attractive forces and repulsive forces

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10
Q

Attractive forces are due primarily to instantaneous blank interactions that arise because of fluctuations in the e-charge distributions of adjacent nonbonded atoms.

A

dipole-induced dipole

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11
Q

Local conformations of the polypeptide that are stabilized by H bonds

A

Secondary structure

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12
Q

The H bonds that make up secondary structure involve the blank of one peptide group and the blank of another

A

amide proton and carbonyl oxygen

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13
Q

all of the carbonyl groups are blank along the helix axis

A

Pointing in one direction

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14
Q

All of the H bonds lie blank to the helix axis

A

Parallel

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15
Q

(-)ly charged ligands (phosphates) frequently bind to proteins near the blank of an a-helix

A

N-terminus

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16
Q

(+)ly charged ligands are only rarely found to bind near the of an a-helix

A

C-terminus

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17
Q

TRUE OR FALSE
The first 3 amide hydrogens and the last 4 carbonyl oxygens cannot participate in helix bonds.

A

False ( 4 amide hydrogens)

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18
Q

Can be visualized by laying thin, pleated strips of paper side by side to make a “pleated sheet” of paper

A

B-pleated sheet

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19
Q

Adjacent chains run in the same direction. The H bonds formed are bent significantly. hydrophobic side chains on both sides of the sheet.

A

Parallel B-pleated sheets

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20
Q

Adjacent chains run in opposite directions. Usually arranged with all their hydrophobic residues on one side of the sheet.

A

Antiparallel B-pleated sheets

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21
Q

The H bonds of B-pleated sheets structure are blank rather than intrastrand

A

Interstrand

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22
Q

TRUE OR FALSE
The optimum formation of H bonds in the parallel pleated sheet results in a highly extended conformation that in the antiparallel B-sheets

A

False (Slightly less)

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23
Q

TRUE OR FALSE
antiparallel B-sheets tend to be more regular than parallel B-sheets

A

False (Parallel B-sheets is more regular)

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24
Q

A form of keratin is synthesized in special glands in the spider’s abdomen.

A

Spider silk

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25
Q

As keratin protein is extruded from the spider’s glands, it endures shearing forces that break the H bonds stabilizing keratin a-helices, these regions then form blank arrays B-sheets.

A

Microcrystalline

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26
Q

These microcrystals are surrounded by blank, which adopt a highly disordered state composed of a-helices and random coil structures.

A

keratin strand

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27
Q

Polypeptide chain must possess the capacity to blank, blank and blank themselves to produce compact, globular structures.

A

bend, turn, reorient

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28
Q

Makes the B-turn a relatively stable structure

A

Hydrogen bond

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29
Q

What are the two major types of B-turns?

A

Type I and Type II

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30
Q

TRUE OR FALSE
Type I turns are more common than type II

A

True

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31
Q

Pro fits best in the blank and blank position of the type I and type II turns, respectively

A

3 and 2

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32
Q

Fit best in the 3 position of type II turn

A

Gly or any small residue

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33
Q

Arrangement of all atoms of a single polypeptide chain in 3D spaces

A

Tertiary structure

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34
Q

Discovered the 3D structure of hemoglobin?

A

Max Perutz

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35
Q

Discovered the 3D structure of myoglobin?

A

John Kendrew

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36
Q

Predominant constituents of claws, fingernails, hair and horns in mammals.

A

a-keratin

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37
Q

Stability of most proteins rises from:

A
  1. Formation of large numbers of intramolecular H bonds.
  2. Reduction in the surface area accessible to solvent that occurs upon folding.
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38
Q

A protein typically a mixture of blank and blank AAs

A

Hydrophobic and hydrophilic

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39
Q

What would happen if every side chain could make H bond to water?

A

The protein will not form a compact, folded structure.

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40
Q

Induces the formation of a compact structure- The folded protein

A

Hydrophobic effect

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41
Q

3 larges classes of proteins based on their structure and solubility

A

Fibrous proteins
Globular proteins
Membrane proteins

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42
Q

Contains polypeptide chains organized approximately parallel along a single axis, producing long fibers or large sheets. Plays a structural role in nature.

A

Fibrous proteins

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43
Q

TRUE OR FALSE
Membrane tend to be mechanically strong
and resistant to solubilization in
water and dilute salt solutions

A

False (Fibrous instead of membrane)

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44
Q

In other forms of keratin, covalent disulfide bonds form between blank residues of adjacent molecules, making the overall structure even more rigid, inextensible, and insoluble.

A

Cys

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45
Q

TRUE OR FALSE
when a hairstylist creates a
permanent wave (perm) in a hair
salon, disulfides in the hair are
first reoxidized and cleaved, then
reorganized and reduced to
change the degree of curl or wave

A

False (reduced and cleaved, reorganized and reoxidized)

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46
Q

On humid or rainy days, the H bonds in curled hair may blank, and the hair becomes frizzy.

A

rearrange

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47
Q

Found in silk fibers in the cocoons of the silkworm, bombyx mori, and also in spiderwebs

A

Fibroin protein

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48
Q

Found in bird feathers

A

B-keratin

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49
Q

A rigid, inextensible fibrous protein principal constituent of connective tissue in animals, including tendons, cartilage, bones, teeth, skin, and blood vessels.

A

Collagen

50
Q

TRUE OR FALSE
broken bones and tendon and
cartilage injuries to knees, elbows,
and other joints involve tears or
hyperextensions of the collagen
matrix in these tissues.

A

True

51
Q

Basic structural unit of collagen

A

Tropocollagen

52
Q

The most common collagen, predominates in bones, tendons, and skin.

A

Type I Collagen

53
Q

Type of collagen Found in cartilage

A

Type II Collagen

54
Q

Type of collagen found in blood vessels, consist of 3 identical polypeptide chains.

A

Type III Collagen

55
Q

TRUE OR FALSE
Because of the high content of Gly, Cys and Hyp, collagen fibers are incapable of forming a-helices and B-sheets.

A

False (Gly, Pro, and Hyp)

56
Q

TRUE OR FALSE
Long stretches of the polypeptide sequence are repeats of a Gly-Pro-Hyp, every 3rd residue is Hyp.

A

False (Gly)

57
Q

Are for more numerous than fibrous proteins

A

Globular proteins

58
Q

A small protein, a few short a-helices, a broad section of antiparallel B-sheet a few B-turns, and several peptide segments without defined secondary structure.

A

Bovine ribonuclease A

59
Q

TRUE OR FALSE
the space between the helices and
sheets in the protein interior is filled
efficiently and tightly with mostly
hydrophilic AA side chains

A

False (Hydrophobic)

60
Q

Most polar side chains in ribonuclease face the blank of the protein structure and interact with solvent

A

Outside

61
Q

TRUE OR FALSE
the folding of a globular protein
could be viewed as the aggregation
of multiple elements of primary structure

A

False (secondary)

62
Q

The interior of a globular protein is composed of conserved blank, and blank, the surface of a globular protein s different in several ways

A

Sheets and Helices

63
Q

The segments of the protein that are neither helix, sheet, nor turn. Most of these loop segments are neither coiled nor random.

A

Coil or random coil

64
Q

TRUE OR FALE
A globular proteins surface structure is not affected by the surrounding water molecule.

A

False (affected)

65
Q

The outward face of such an amphiphilic helixn consist mainly of blank and charged residues,, whereas the inward face contains mostly nonpolar and blank residues.

A

polar, hydrophobic

66
Q

TRUE OR FALSE
tertiary structure pack closely to one another and also intercalate with extended polypeptide chains.

A

False (Secondary)

67
Q

Protein composed of about blank AAs or less have a simple, compact globular shape.

A

250

68
Q

TRUE OR FALSE
Large proteins are usually made up of 3 or more recognizable and distinct structures.

A

False (2 or more)

69
Q

Compact, folded protein in structures that are usually stable by themselves in aqueous solutions.

A

Domains or modules

70
Q

A metabolic enzyme consisting of 2 subdomains large subdomains and consist of a B-sheets surrounded by 12 a-helices small subdomain.

A

Transacylase

71
Q

Loss of protein structure and function

A

Denaturation

72
Q

TRUE OR FALSE
Covalent bonds are affected to acids and bases

A

False (not affected)

73
Q

GUANIDINE HYDROCHLORIDE AND UREA
Altering the structure and dynamics of the water solvent

A

Indirect effects

74
Q

Binding to hydrophilic groups on the protein

A

Direct effects

75
Q

Proved that sequence determines structures.

A

Anfinsen’s Classic experiment

76
Q

TRUE OR FALSE
Mercaptoethanol unfolded the protein.

A

False (urea)

77
Q

TRUE OR FALSE
Urea reduced the disulfide bridges

A

False (Marcaptoethanol)

78
Q

Demonstrated that protein can fold reversibly

A

Christian Anfinsen’s experiment

79
Q

Led protein chemist to hypothesized that proteins must fold by specific folding pathways.

A

Levinthal’s paradox

80
Q

is a flexible but compact form characterized by significant amounts of secondary structure, no precise tertiary structure, and a loosely packed hydrophobic core.

A

Molten globule

81
Q

(Ken Dill) The folding process can be pictured as a blank of free energies- an energy landscape.

A

Funnel

82
Q

TRUE OR FALSE
most globular proteins oscillate
and fluctuate continuously about
their average or equilibrium
structures

A

True

83
Q

TRUE OR FALSE
Durability is essential for a variety
of protein functions: ligand binding,
E catalysis, and E regulation

A

False (Flexibility)

84
Q

Vibrations
Usually occur over small distances.
Arise from the kinetic energy within the protein.
A function of temp

A

Atomic fluctuations

85
Q

Slower motions
May extend over larger distances
Movement of a group of atoms covalently linked in such a way that the group moves as a unit.
Range from few atoms to hundreds of atoms.

A

Collective atoms

86
Q

Motions of groups of atoms
(individual side chains) or even
whole sections of proteins
Occur on a time scale of 10
-9 to 10 3.
Distances covered can be as large
as 1 nm.
Occur in response to specific
stimuli.

A

Conformational changes

87
Q

Adopt the most
stable tertiary structure possible

A

Globular proteins

88
Q

TRUE OR FALSE
Left-handed twisted B-sheets are
found at the center of a number of
proteins and provide an extended,
highly stable structural core

A

False (Right-handed)

89
Q

connect adjacent
(or nearly adjacent)
parallel B-strands

A

Crossovers

90
Q

connect adjacent
antiparallel B-strands.

A

Hairpins

91
Q

uses both automated algorithms
and manual inspection to describe
the structural and evolutionary
relationships between all the
proteins whose structures are
known.

A

SCOP2 (Structural Classification of Proteins Database)

92
Q

TRUE OR FALSE
4 groups under protein type
soluble
fibrous
membrane
Insoluble

A

False (intrinsically disordered proteins instead of insoluble)

93
Q

Closely related proteins that show
clear evidence of evolutionary
origin

A

Family

94
Q

TRUE OR FALSE
4 properties of all proteins in
SCOP2
Protein types
Folds
Folding relationships
Evolutionary relationships

A

False (structural classes)

95
Q

Brings together more distantly
related protein domains, again
based on common evolutionary
origin

A

Superfamily

96
Q

Number, arrangement, and
connections of secondary structure
elements

A

Folds

97
Q

TRUE OR FALSE
structure depends on function,
sequence depends on structure

A

False (structure depends on sequence,
function depends on structure)

97
Q

a common protein fold
consisting of 8 α-helices and 8 β-strands that alternate along the
peptide backbone to form a
doughnut–like tertiary structure. An enzyme that interconverts
ketone and aldehyde substrates
in the breakdown of sugars

A

TIM Barrel (Triose Phosphate Isomerase)

98
Q

TRUE OR FALSE
all proteins of similar
function possess similar
domains

A

False (Not all proteins)

99
Q

are Proteins
that help other Proteins to Fold

A

Molecular Chaperones

100
Q

Exist and function normally in a
partially unfolded state.
Do not possess uniform structural
properties but are essential for
basic cellular functions.

A

intrinsically unstructured proteins
(IUPs) or intrinsically disordered
proteins (IDPs)

101
Q

TRUE OR FALSE
predictive analysis of whole
genomes indicates that 2% of
bacterial and 4.2% of archaeal
proteins probably contain long
regions of disorder

A

False (2% of archaeal and 4.2% of bacterial)

102
Q

induced in cells by elevated
temperature or other stress
Hsp70

A

HSP (Heat Shock protein)

103
Q

TRUE OR FALSE
25% to 30% of prokaryotic proteins
are mostly disordered, and more
than half of eukaryotic proteins
have long regions of disorder

A

False (25% to 30% of eukaryotic proteins)

104
Q

an artificial intelligence program
developed by Alphabet/Google’s
DeepMind subsidiary that can
predict 3-dimensional structures of
proteins with high accuracy

A

AlphaFold

105
Q

provides open access to protein
models generated with this software

A

Alphafold Protein Structure Database

106
Q

complexes composed of
noncovalent assemblies of 2 or
more monomer subunits

A

Oligomers

107
Q

Oxidizes alcohol consumed in a
beer or mixed drink in the liver

A

Alcohol dehydrogenase

108
Q

A homodimeric enzyme which
when controlled by hormonal
signals modulate blood sugar
levels.

A

glycogen phosphorylase

109
Q

carries oxygen in the blood

A

Hemoglobin (HB)

110
Q

the subunits are arranged around
a single rotation axis

A

Cyclic symmetry

111
Q

TRUE OR FALSE
if there are 2 subunits, the axis is
referred to as a twofold rotation
axis

A

True

112
Q

additional subunits cannot be
bound

A

Closed structure

113
Q

can polymerize more or less
indefinitely, creating structures
that are both esthetically
attractive and functionally
important to the cells or tissue in
which they exist

A

Open structure

114
Q

αβ-dimeric protein that
polymerizes into long, tubular
structures that are the structural
basis of cilia, flagella, and the
cytoskeletal matrix

A

Tubulin

115
Q

causative agent of AIDS
enveloped by a spherical shell
composed of hundreds of coat
protein subunits, a large-scale,
but closed, 4 association

A

Human Immunodeficiency Virus (HIV)

116
Q

TRUE OR FALSE
surface-to-volume ratio
becomes larger as the radius
of any particle or object becomes smaller

A

False (surface-to-volume ratio
becomes smaller as the radius
of any particle or object becomes larger)

117
Q

TRUE OR FALSE
decreased surface-to-volume
ratios usually result in more
unstable proteins

A

False (Stable proteins)

118
Q

TRUE OR FALSE
more DNA is required to code for
a monomer that assembles into a
homomultimer than for a large
polypeptide of the same
molecular mass

A

False (less)

119
Q

increases in affinity at subsequent
sites

A

Positivity cooperativity

120
Q

decreases in affinity at
subsequent sites
binding of ligand to one subunit
can influence the binding behavior
at the other subunits

A

Negative cooperativity

Protein and Nucleic acid (6 decks)

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