chapter 3 Flashcards
(116 cards)
1
Q
what specifies protein structure
A
amino acid sequence
2
Q
how are amino acids connected
A
peptide bonds
3
Q
repeating seq of atoms along core of polypeptide chain
A
polypeptide backbone
4
Q
what is attached to polypeptide backbone
A
side chains
5
Q
limit possible bond angles in polypeptide chain
A
constraints
6
Q
do constraints limit protein folding completely
A
no, long flexible chain can still fold a lot of ways
7
Q
folding of protein chain determined by what
A
many sets of non covalent bonds
8
Q
what kinds of interactions determine protein folding
A
h bonds, electrostatic interaction, vander waals
9
Q
non polar molecules tend to cluster where in protein
A
inside/core
10
Q
polar molecules will try to do what in protein folding
A
form H bonds with water
11
Q
protein fold into conformation w what
A
Lowest energy
12
Q
assist in protein folding
A
molecular chaperones
13
Q
a single conformation is always dynamic due to what
A
thermal energy
14
Q
temporarily exposed hydrophobic region associating with each other
A
protein aggregates
15
Q
what prevents protein aggregates in cytoplasm
A
chaperones
16
Q
alpha helix originally found where
A
alpha keratin
17
Q
beta sheet originally found where
A
fibroin
18
Q
cores of many proteins contain extensive regions of what
A
beta sheets
19
Q
regions of alpha helix common in where
A
cell membranes
20
Q
2 alpha helix have most of non polar chains on one side Calld what
A
coiled coil
21
Q
wehre do bonpolar SC face in coiled coil
A
facing inward
22
Q
structural unit that folds independently
A
domain
23
Q
how many aa make up domain
A
40-350
24
Q
modular unit from which larger protein constructed
A
domain
25
present in many different protein in eukaryotic cells, responds to cell signals to cause certain protein molecules to bind to each other, altering cell behavior
SH2 domain
26
tertiary structure of SH2 domain made of what
2 alpha helix, 1 antiparallel beta sheet
27
different domains often associate with different...
functions
28
important for cell signaling and regulation
intrinsically disordered region
29
what kind of protein is unlikely to help survival of a cell
unpredictable variable structure and biochemical activity
30
what does it take to change function of a protein completely
change of just a few atoms
31
large family of protein cleaving enzymes, include chymotropsin, trypsin, elastase
serien proteases
32
2 protein with more than 25% identity in AA seq usually share same
overall structure
33
humans have how many protein coding genes
20000
34
what techniques do we use to know about proteins struct, func
X-ray crystallography, NMR, cry-electron microscopy
35
what is estimated # of ways proteins fold in nature
2000
36
relates structures often imply what
related function
37
large protein have evolved through joining of pre existing domains in new combos
domain shuffling
38
subset of protein domains that are especially mobile
protein modules
39
examples of protein modules
SH2, immunoglobin, fibronectin type 3, Kringle module
40
each of the protein modules has what
stable core made of beta sheets
41
loops ideally fit for what
binding sites with other molecules
42
why do modules have genetic success
convenient framework for generation of new binding sites of ligands
43
SH2, Kringle are what
plug in type, n term and c term close together
44
duplicated domains with inline arrangement can be
readily linked in serious to form external structures
45
domain shuffling during vertebrae evolution gives rise to
many. combos of domains
46
human proteins and mustard weed are different how
human proteins are more complex
47
weak non covalent bonds allow protein to...
bind to each other to produce larger structure in cell
48
any region of protein surface that can interact with another molecule through sets of non covalent bonds
binding site
49
larger protein molecule made of 2 proteins connected by polypeptide chains
protein subunit
50
protein subunits together make what
quaternary structure
51
2 identical folded polypeptide chains form symmetrical complex of 2 protein SU
dimer
52
polypeptide chain folds up like ball with irregular surface
globular protein
53
enzymes tend to be what kind of protein
globular
54
simple elongated 3d structure
fibrous protein
55
large family of fibrous protein
alpha keratin
56
dimer wit long alpha helixes of each subunit forming a coiled coil
alpha keratin
57
kind of protein abundant outside of cell
fibrous protein
58
main component of ECM
fibrous protein
59
collagen main comp is what
3 long polypeptide chains, glycine every 3rd position
60
stabilize extracellular protein
covalent cross linkages
61
either tie together 2 amino acid in same protein or join together many polypeptide chains in large protein complex
covalent cross linkages
62
most common covalent cross linkage
disulfide bonds
63
disulfide bonds fail to form where
in cytosol
64
large structure built from one or a few repeating small subunits only needs what
small amount of genetic info
65
formation of closed structures does what
increases stability
66
many structures in cell are capable of what kind of assembly
self assembly
67
aid formation of complex structures
assembly factors
68
utilized for some cell func, can contribute to disease when not controlled
amyloid fibrils
69
amyloid fibrils made of what
self propagating beta sheets
70
beta strands in amyloid fibrils stacked how
fibril axis
71
accumulation of amyloid fibrils can do what
kill cells, damage tissue
72
where is especially susceptable to amyloid fibril accumulation
brain
73
most severe thing amyloid fibrils known to cause
neurodegenerative disease
74
special type of pathology, can readily spread form 1 organism to another
prion disease
75
useful purpose of amyloid fibrils
can be used to treat infections
76
attach to viruses or bacteria to mark them for destruction
antibodies
77
substance bound by protein
ligand
78
ability of protein to bind selectively based on what
non covalent bonds
79
region or protein associated with ligand
binding site
80
ligand will do what if water Is not present
form stronger H bonds
81
Identifying sites in protein domain that are most crucial to domains function
evolutionary tracing
82
what sites are most likely to be conserved
those that bind to other molecules
83
portion of surface of 1 protein contacts etended loop of polypeptide chain on a second protein
surface string
84
two rigid surface, can be very tight
surface-surface
85
feature of surface surface
large # of weak bonds
86
protein produced by immune system in response to foreign molecules
antibodies
87
target of antibody
antigen
88
y shaped molecule with 2 binding sites
antibody
89
enzymes that catalyze hydrolytic cleavage rxn
hydrolyses
90
break down nucleic acids by hydrolyzing bonds between nucleotides
nucleases
91
break down proteins
proteases
92
synthesize molecules by condensing 2 smaller molecules together
synthases
93
join together 2 molecules in e dependent process
ligase
94
catalyze rearrangement of bonds
isomerase
95
phosphate group addition
kinase
96
removal of phos group
phosphatase
97
first step in enzyme catalysis
substrate binding
98
vmax/enzyme conc
turnover number
99
conc of substrates that allows ten to proceed at half its max rate
km
100
catalyzes cutting of polysaccharide chains in cell walls
lysozyme
101
small organic molecules that help enzymes perform functions that are hard/impossible
coenzymes
102
binding of ligand on one unit can cause allosteric change on the other to help it better bind the same ligand
symmetrical protein assemblies
103
phosphorylation can attract what
positive ions
104
phosphorylation can form the part of the structure that what recognizes
binding sites of other proteins recognize
105
phosphorylation can disrupt what
protein protein interaction
106
enzyme catalyzed transfer of the terminal phosphate group of an ATP to hydroxyl group on serine, threonine, tyrosine
protein phosphorylation
107
what amino acids can be phosphorylated
hydroxyl group of serine, threonine, tyrosine
108
catalyzes reverse of protein phosphorylation
protein phosphatase
109
phosphate groups on proteins are continuously doing what
turning over
110
why do phosphate groups turn over
allows rapid switch from one state to another
111
first tyrosine kinase to be discovered
SRC protein
112
Short N term of SRC protein becomes what
covalently linked to hydrophobic fatty acid
113
how many peptide binding domains in SRC
2
114
how to turn on SRC
remove c term phosphate, bind sh3 domain
115
Regulatory GTP binding proteins switched on and off by what
gain and loss of phos group
116
monomeric GTPase, plays important role in cell signaling
ras
