1
Q
describes the well-defined, three-
dimensional fold adopted by a protein
A
Tertiary structure
2
Q
Tertiary structure is determined by
A
amino acid sequence
3
Q
Protein structures are stabilized by
A
noncovalent interactions and forces
4
Q
thermodynamically the most stable, that
is, lowest free energy (G)
A
conformations
5
Q
proteins in any functional, folded conformations
A
natives
6
Q
tendency of a protein to maintain a native conformation
A
stability
7
Q
unfolded proteins have high
A
conformational entropy
8
Q
what stabilizes native conformations
A
chemical interactions
9
Q
what are weak (noncovalent) interactions and forces
A
- hydrogen bonds
- hydrophobic effect
- ionic interactions
10
Q
predominating weak interaction
A
hydrophobic effect
11
Q
highly structured shell of H2O around a
hydrophobic molecule
A
solvation layer
12
Q
what happened to solvation layer when nonpolar groups cluster together
A
decrease
13
Q
what happens to the net entropy when when nonpolar groups cluster together
A
favorable increase in net entropy
14
Q
Amino acids with hydrophobic R groups form a
A
hydrophobic protein core
15
Q
optimize hydrogen bonding
A
repeating secondary structures (alpha helices and beta sheets)
16
Q
interaction of oppositely charged groups
A
= ion pair = salt bridge
17
Q
dipole-dipole interactions over
short distances
A
van der Waals interactions
18
Q
individual interactions contribute how much to overall protein stability
A
little
19
Q
Why is Peptide Bond Rigid and Planar
A
- 3 covalent bonds separate the alpha carbons of adjacent
amino acid residues: C alpha—C—N—C alpha - resonance between the carbonyl oxygen and the amide
nitrogen - partial negative charge and partial positive charge sets up
a small electric dipole
20
Q
Can Peptide C—N Bonds Rotate Freely
A
NO
21
Q
atoms of the peptide group lie in a
A
single plane
22
Q
why can’t peptide C—N Bonds
rotate Freely
A
partial double-bond character of C—N peptide bond prevents rotation, limiting range of conformations
23
Q
(phi) and (psi) values are prohibited by
A
steric interference
24
Q
describes the spatial arrangement of the main-chain atoms in a segment of a polypeptide chain
A
secondary structure
25
(phi) and (psi) values remain
the same throughout the segment
regular secondary structure
26
common types of secondary structure
alpha helix, Beta conformation, Beta turn, and random coils
27
simplest arrangement, maximum
number of hydrogen bonds
alpha helix
28
backbone wound around an
imaginary longitudinal axis
29
protrude out from the backbone
R groups
30
between hydrogen atom attached to the
electronegative nitrogen atom of residue n and the electronegative carbonyl oxygen atom of residue n + 4
Intrahelical Hydrogen Bonds
31
are Intrahelical Hydrogen Bonds stable
yes
32
have an intrinsic propensity to form an alpha helix
amino acid residues
33
how can interactions between R chains spaced 3–4 residues apart stabilize alpha helix
formation of ion pairs and
hydrophobic effect can stabilize
34
how can interactions between R chains spaced 3–4 residues destabilize alpha helix
charge, size, and shape of R chains
can destabilize
35
introduces destabilizing kink in helix
proline
36
high conformational flexibility, take
up coiled structures
glycine
37
opposite orientation
antiparallel
38
what occurs more frequently antiparallel or parallel
antiparallel
39
same orientation
parallel
40
form between backbone atoms of
adjacent segments
H bonds
41
Amino Acid Residues Near the what of the alpha Helix Segment Affect Stability
End
42
align through
hydrogen bonds
small electric dipoles in each
peptide bond
43
negatively charged amino acids
often found near
NH3+ terminus
44
positively charged amino acids
often found near the
COO– terminus
45
Organizes Polypeptide Chains into Sheets
Beta Conformation
46
backbone extends into a zigzag
Beta Conformation
47
single protein segment
Beta strand
48
several strands in Beta conformation side by side
Beta sheet
49
Adjacent Polypeptide Chains in a Beta
Sheet Can Be
Antiparallel or Parallel
50
connect ends of two
adjacent segments of an antiparallel
Beta sheet
Beta turns
51
hydrogen bond forms between
first and fourth residue
52
what degree turn are B turns
180
53
how many residues involve Beta turns
4
54
– visualize all phi and psi angles
– test quality of three-dimensional protein structures
Ramachandran plots
55
overall three-dimensional arrangement
of all the atoms in a protein
tertiary structure
56
arrangement of 2+ separate
polypeptide chains in three-dimensional complexes
quaternary structure
57
archive of experimentally determined three- dimensional structures
Protein Data Bank (PDB)
58
structures assigned an identifier called the
PDB ID
59
PDB data files describes what:
* the spatial coordinates of each atom
* information on how the structure was determined
* information on its accuracy
60
four major types of protein groups based on polypeptide chains:
– fibrous proteins
– globular proteins
– membrane proteins
– intrinsically disordered proteins
61
lacking stable tertiary structures
intrinsically disordered proteins
62
arranged in long strands or sheets
fibrous proteins
63
folded into a spherical or globular
shape
globular proteins
64
embedded in hydrophobic lipid
membranes
membrane proteins
65
give strength and/or flexibility to structures
Fibrous Proteins
66
Tough, insoluble protective structures
of varying hardness and flexibility
α Helix, cross-linked by
disulfide bonds
67
Soft, flexible filaments
β Conformation
68
High tensile strength, without stretch
Collagen triple helix
69
alpha-keratin helix is a what kind of helix
right-handed alpha helix
70
amino acids that are rich in hydrophobic
residues
Ala, Val, Leu, Ile, Met, Phe
71
cross-links stabilized by
disulfide bonds
72
main protein in silk
fibroin
73
found in connective tissue
collagen
74
left-handed, repeating tripeptide unit Gly–X–Y, where X is often Pro and
Y is often 4-Hyp
secondary structure
75
right-handed twisting of 3 separate
polypeptides
tertiary and quaternary structure
76
is caused by a lack of vitamin C
scurvy
77
is required for the hydroxylation of proline and lysine in collagen
vitamin C
78
each globular protein has a
distinct structure, adapted fo
its
biological
function
79
recognizable folding pattern involving 2+
elements of secondary structures and the connection(s)
motif = fold
80
part of a polypeptide chain that is independently stable or could undergo movements as a single entity
domain
81
series of beta-alpha-beta loops arranged such that the beta strands form a barrel
alpha/beta barrel
82
Structural Classification of Proteins database
SCOP2
83
Intrinsically Disordered Proteins facilitates a protein to
interact with multiple binding partners
84
proteins with significant similarity in primary structure and/or tertiary structure and function are in the same what
protein family
85
2+ families that have little sequence
similarity, but the same major structural motif and have functional similarities
superfamilies
86
assembly of multiple peptide
subunits
quaternary structure
87
Segments not connected by peptide bonds
quaternary structure (4)
88
multisubunit protein
oligomer = multimer
89
the complex cellular process that maintains a healthy balance of proteins by regulating their production, folding, transport, and degradation
Proteostasis
90
Loss of Protein Structure Results in
Loss of Function
91
loss of three-dimensional structure
sufficient to cause loss of function
denaturation
91
what causes denaturation
heat, pH extremes, miscible organic
solvents, certain solutes, detergents
92
which Polypeptides structures fold first
local secondary structures
93
which interactions follow after secondary
longer range interactions
follow
94
it is mathematically impossible for protein folding to occur by randomly trying every conformation until the
lowest energy one is found
Levinthal’s Paradox
94
is a free-energy landscape model that explains how proteins fold into their specific three-dimensional shapes
free-energy funnel
95
high degree of conformational
entropy, high free energy
unfolded states
96
facilitate correct folding pathways or ideal microenvironments
chaperone proteins
97
bind to hydrophobic regions
Hsp70
98
required for the folding of proteins
that do not fold spontaneously
chaperonins
99
High degree of Beta-sheet structure
native
100
misfolded Beta amyloid promotes
aggregation
101
associated with extracellular amyloid deposition by neurons, involving the amyloid-beta peptide
Alzheimer disease
101
protein secreted in a misfolded state
and converted to an insoluble
extracellular fiber
amyloid fiber
102
misfolded form alpha-synuclein
aggregates into spherical filamentous masses called Lewy bodies
Parkinson disease
103
caused by defects in the membrane-
bound protein cystic fibrosis transmembrane conductance regulator (CFTR)
cystic fibrosis
104
misfolded brain protein
prion protein (PrP)
105
in the human cerebral cortex
Pyramidal cells
Biochemistry 1
flashcards
Decks in class (16)
# Cards
-
Chapter 2: Water: the Solvent of Life67
-
Chapter 3: Amino Acids, Peptides, and Proteins100
-
Chapter 4: The Three- Dimensional Structure of Protein108
-
Iclicker Questions for Exam 114
-
Exam 1 Practice Questions49
-
Chapter 4 for Exam 213
-
Chapter 5: Protein Function151
-
Iclicker Questions for Exam 224
-
Si practice question for Exam 2133
-
Chapter 6: Enzymes179
-
Chapter 7: Carbohydrates and Glycobiology123
-
Exam 2 Practice Exam Questions33
-
Iclicker Questions for Exam 366
-
Chapter 10: Lipids17
-
Si practice questions for Exam 3173
-
Exam 3 Practice Exam Questions64
