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
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.
3
Q
Forming a blank minimizes the interaction of nonpolar residues in water.
A
Hydrophobic bonds
4
Q
Blank are much less common in the interior of a protein.
A
Polar AAs
5
Q
Ionic interactions arise either as blank between opposite charges or blank between like charges
A
electrostatic attractions, repulsion
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
7
Q
TRUE OR FALSE
Ability of a K to attract a nearby E weakened by dissolved salts.
A
True
8
Q
Van der Waals interaction is blank
A
Ubiquitous
9
Q
Both blank and blank are included in van der waals interactions
A
attractive forces and repulsive forces
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
11
Q
Local conformations of the polypeptide that are stabilized by H bonds
A
Secondary structure
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
13
Q
all of the carbonyl groups are blank along the helix axis
A
Pointing in one direction
14
Q
All of the H bonds lie blank to the helix axis
A
Parallel
15
Q
(-)ly charged ligands (phosphates) frequently bind to proteins near the blank of an a-helix
A
N-terminus
16
Q
(+)ly charged ligands are only rarely found to bind near the of an a-helix
A
C-terminus
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)
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
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
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
21
Q
The H bonds of B-pleated sheets structure are blank rather than intrastrand
A
Interstrand
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)
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)
24
Q
A form of keratin is synthesized in special glands in the spider’s abdomen.
A
Spider silk
25
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.
Microcrystalline
26
These microcrystals are surrounded by blank, which adopt a highly disordered state composed of a-helices and random coil structures.
keratin strand
27
Polypeptide chain must possess the capacity to blank, blank and blank themselves to produce compact, globular structures.
bend, turn, reorient
28
Makes the B-turn a relatively stable structure
Hydrogen bond
29
What are the two major types of B-turns?
Type I and Type II
30
TRUE OR FALSE
Type I turns are more common than type II
True
31
Pro fits best in the blank and blank position of the type I and type II turns, respectively
3 and 2
32
Fit best in the 3 position of type II turn
Gly or any small residue
33
Arrangement of all atoms of a single polypeptide chain in 3D spaces
Tertiary structure
34
Discovered the 3D structure of hemoglobin?
Max Perutz
35
Discovered the 3D structure of myoglobin?
John Kendrew
36
Predominant constituents of claws, fingernails, hair and horns in mammals.
a-keratin
37
Stability of most proteins rises from:
1. Formation of large numbers of intramolecular H bonds.
2. Reduction in the surface area accessible to solvent that occurs upon folding.
38
A protein typically a mixture of blank and blank AAs
Hydrophobic and hydrophilic
39
What would happen if every side chain could make H bond to water?
The protein will not form a compact, folded structure.
40
Induces the formation of a compact structure- The folded protein
Hydrophobic effect
41
3 larges classes of proteins based on their structure and solubility
Fibrous proteins
Globular proteins
Membrane proteins
42
Contains polypeptide chains organized approximately parallel along a single axis, producing long fibers or large sheets. Plays a structural role in nature.
Fibrous proteins
43
TRUE OR FALSE
Membrane tend to be mechanically strong
and resistant to solubilization in
water and dilute salt solutions
False (Fibrous instead of membrane)
44
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.
Cys
45
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
False (reduced and cleaved, reorganized and reoxidized)
46
On humid or rainy days, the H bonds in curled hair may blank, and the hair becomes frizzy.
rearrange
47
Found in silk fibers in the cocoons of the silkworm, bombyx mori, and also in spiderwebs
Fibroin protein
48
Found in bird feathers
B-keratin
49
A rigid, inextensible fibrous protein principal constituent of connective tissue in animals, including tendons, cartilage, bones, teeth, skin, and blood vessels.
Collagen
50
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.
True
51
Basic structural unit of collagen
Tropocollagen
52
The most common collagen, predominates in bones, tendons, and skin.
Type I Collagen
53
Type of collagen Found in cartilage
Type II Collagen
54
Type of collagen found in blood vessels, consist of 3 identical polypeptide chains.
Type III Collagen
55
TRUE OR FALSE
Because of the high content of Gly, Cys and Hyp, collagen fibers are incapable of forming a-helices and B-sheets.
False (Gly, Pro, and Hyp)
56
TRUE OR FALSE
Long stretches of the polypeptide sequence are repeats of a Gly-Pro-Hyp, every 3rd residue is Hyp.
False (Gly)
57
Are for more numerous than fibrous proteins
Globular proteins
58
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.
Bovine ribonuclease A
59
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
False (Hydrophobic)
60
Most polar side chains in ribonuclease face the blank of the protein structure and interact with solvent
Outside
61
TRUE OR FALSE
the folding of a globular protein
could be viewed as the aggregation
of multiple elements of primary structure
False (secondary)
62
The interior of a globular protein is composed of conserved blank, and blank, the surface of a globular protein s different in several ways
Sheets and Helices
63
The segments of the protein that are neither helix, sheet, nor turn. Most of these loop segments are neither coiled nor random.
Coil or random coil
64
TRUE OR FALE
A globular proteins surface structure is not affected by the surrounding water molecule.
False (affected)
65
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.
polar, hydrophobic
66
TRUE OR FALSE
tertiary structure pack closely to one another and also intercalate with extended polypeptide chains.
False (Secondary)
67
Protein composed of about blank AAs or less have a simple, compact globular shape.
250
68
TRUE OR FALSE
Large proteins are usually made up of 3 or more recognizable and distinct structures.
False (2 or more)
69
Compact, folded protein in structures that are usually stable by themselves in aqueous solutions.
Domains or modules
70
A metabolic enzyme consisting of 2 subdomains large subdomains and consist of a B-sheets surrounded by 12 a-helices small subdomain.
Transacylase
71
Loss of protein structure and function
Denaturation
72
TRUE OR FALSE
Covalent bonds are affected to acids and bases
False (not affected)
73
GUANIDINE HYDROCHLORIDE AND UREA
Altering the structure and dynamics of the water solvent
Indirect effects
74
Binding to hydrophilic groups on the protein
Direct effects
75
Proved that sequence determines structures.
Anfinsen's Classic experiment
76
TRUE OR FALSE
Mercaptoethanol unfolded the protein.
False (urea)
77
TRUE OR FALSE
Urea reduced the disulfide bridges
False (Marcaptoethanol)
78
Demonstrated that protein can fold reversibly
Christian Anfinsen's experiment
79
Led protein chemist to hypothesized that proteins must fold by specific folding pathways.
Levinthal's paradox
80
is a flexible but compact form characterized by significant amounts of secondary structure, no precise tertiary structure, and a loosely packed hydrophobic core.
Molten globule
81
(Ken Dill) The folding process can be pictured as a blank of free energies- an energy landscape.
Funnel
82
TRUE OR FALSE
most globular proteins oscillate
and fluctuate continuously about
their average or equilibrium
structures
True
83
TRUE OR FALSE
Durability is essential for a variety
of protein functions: ligand binding,
E catalysis, and E regulation
False (Flexibility)
84
Vibrations
Usually occur over small distances.
Arise from the kinetic energy within the protein.
A function of temp
Atomic fluctuations
85
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.
Collective atoms
86
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.
Conformational changes
87
Adopt the most
stable tertiary structure possible
Globular proteins
88
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
False (Right-handed)
89
connect adjacent
(or nearly adjacent)
parallel B-strands
Crossovers
90
connect adjacent
antiparallel B-strands.
Hairpins
91
uses both automated algorithms
and manual inspection to describe
the structural and evolutionary
relationships between all the
proteins whose structures are
known.
SCOP2 (Structural Classification of Proteins Database)
92
TRUE OR FALSE
4 groups under protein type
soluble
fibrous
membrane
Insoluble
False (intrinsically disordered proteins instead of insoluble)
93
Closely related proteins that show
clear evidence of evolutionary
origin
Family
94
TRUE OR FALSE
4 properties of all proteins in
SCOP2
Protein types
Folds
Folding relationships
Evolutionary relationships
False (structural classes)
95
Brings together more distantly
related protein domains, again
based on common evolutionary
origin
Superfamily
96
Number, arrangement, and
connections of secondary structure
elements
Folds
97
TRUE OR FALSE
structure depends on function,
sequence depends on structure
False (structure depends on sequence,
function depends on structure)
97
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
TIM Barrel (Triose Phosphate Isomerase)
98
TRUE OR FALSE
all proteins of similar
function possess similar
domains
False (Not all proteins)
99
are Proteins
that help other Proteins to Fold
Molecular Chaperones
100
Exist and function normally in a
partially unfolded state.
Do not possess uniform structural
properties but are essential for
basic cellular functions.
intrinsically unstructured proteins
(IUPs) or intrinsically disordered
proteins (IDPs)
101
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
False (2% of archaeal and 4.2% of bacterial)
102
induced in cells by elevated
temperature or other stress
Hsp70
HSP (Heat Shock protein)
103
TRUE OR FALSE
25% to 30% of prokaryotic proteins
are mostly disordered, and more
than half of eukaryotic proteins
have long regions of disorder
False (25% to 30% of eukaryotic proteins)
104
an artificial intelligence program
developed by Alphabet/Google’s
DeepMind subsidiary that can
predict 3-dimensional structures of
proteins with high accuracy
AlphaFold
105
provides open access to protein
models generated with this software
Alphafold Protein Structure Database
106
complexes composed of
noncovalent assemblies of 2 or
more monomer subunits
Oligomers
107
Oxidizes alcohol consumed in a
beer or mixed drink in the liver
Alcohol dehydrogenase
108
A homodimeric enzyme which
when controlled by hormonal
signals modulate blood sugar
levels.
glycogen phosphorylase
109
carries oxygen in the blood
Hemoglobin (HB)
110
the subunits are arranged around
a single rotation axis
Cyclic symmetry
111
TRUE OR FALSE
if there are 2 subunits, the axis is
referred to as a twofold rotation
axis
True
112
additional subunits cannot be
bound
Closed structure
113
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
Open structure
114
αβ-dimeric protein that
polymerizes into long, tubular
structures that are the structural
basis of cilia, flagella, and the
cytoskeletal matrix
Tubulin
115
causative agent of AIDS
enveloped by a spherical shell
composed of hundreds of coat
protein subunits, a large-scale,
but closed, 4 association
Human Immunodeficiency Virus (HIV)
116
TRUE OR FALSE
surface-to-volume ratio
becomes larger as the radius
of any particle or object becomes smaller
False (surface-to-volume ratio
becomes smaller as the radius
of any particle or object becomes larger)
117
TRUE OR FALSE
decreased surface-to-volume
ratios usually result in more
unstable proteins
False (Stable proteins)
118
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
False (less)
119
increases in affinity at subsequent
sites
Positivity cooperativity
120
decreases in affinity at
subsequent sites
binding of ligand to one subunit
can influence the binding behavior
at the other subunits
Negative cooperativity
