Unit 04: Protein Structure and Function Flashcards
(102 cards)
1
Q
what are the repeating core atoms of a polypeptide backbone?
A
n-c-c
2
Q
what is the terminus that carries an amino group?
A
N terminus
3
Q
what is the terminus that carries a carboxyl group?
A
C terminus
4
Q
a polar amino acid is also _____
A
charged/neutral, reactive, hydrophilic
5
Q
a nonpolar a^2 is also _____
A
neutral, non reactive, hydrophobic
6
Q
what causes the flexibility of amino acid chains?
A
rotation around single covalent bonds
7
Q
what constrains the shape of an amino acid?
A
weak interactions within the molecules on side chains and backbone
8
Q
what are hydrophobic attractions?
A
when non polar side chains move to middle of folded protein so they don’t interact with water via weak interactions
9
Q
where can nonpolar amino acids be found on the protein?
A
ALWAYS on inside!
10
Q
where can polar amino acids be found on the protein?
A
usually on outside of protein but can also be found on inside.
11
Q
in what situation can a polar amino acid be found on the inside of a protein?
A
if hydrogen bonded to other polar amino acid, as that bond will require their charge
12
Q
what is protein confirmation?
A
the final 3D shape of the protein.
13
Q
how are protein confirmation energetically favourable?
A
minimize free energy! also are v ordered
14
Q
what is denaturation?
A
when protein confirmation falls apart due to disruption of weak interactions.
15
Q
what can denature a protein?
A
changes in pH, salinity, temperature
16
Q
what is renaturation?
A
when a protein spontaneously refolds when proper conditions are provided
17
Q
what are chaperone proteins?
A
proteins that guide a polypeptide to fold in its most energetically favourable confirmation.
18
Q
what are isolation chambers?
A
essentially a protein chamber in which we stick a polypeptide in and let it do its folding isolated so it doesn’t aggregate with other polypeptides in cytosol
19
Q
what is the average size of a polypeptide chain?
A
50-2000 a^2
20
Q
what is the size range of a polypeptide chain
A
30-10 000 a^2
21
Q
what is the backbone protein model used to showcase?
A
the polypeptide backbone
22
Q
what is the ribbon protein model used to showcase?
A
folding patterns (a-helices, beta sheets, etc)
23
Q
what is the wire protein model used to showcase?
A
shows us the r-groups attached to the backbone! can see how the r-groups are interacting!
24
Q
what is the space filling protein model used to showcase?
A
what is exposed on the surface of the protein (aka what a molecule trying to bind to it is seeing)
25
where are a-helix shapes abundant?
in proteins embedded in cell membranes
26
in an a-helix, there is an h-bond between every ____ amino acid.
fourth
27
are a-helices right or left hand coils?
right!
28
how long does it take for a full a-helix turn?
3.6 a^2
29
what is a coiled coil?
a coil of 2/3 alpha helices wrapped around each other to minimize the exposure of their hydrophobic bits
30
which proteins are made of coiled coils?
a-keratin, myosin, collagen
31
describe the structure of a-keratin briefly
dimer of two identical subunits coiling into a coiled coil
32
describe the structure of collagen briefly
three peptide chains wound into a helix with nonpolar glycine at every third position in core
33
describe elastin. why is its structure the way it is?
protein made of loose, unstructured polypeptide chains that are able to be stretched/pulled taut without breaking. are the way they are bc they are located in regions that need to be able to stretch.
34
where can elastin be found?
skin, arteries and lungs prob muscle too
35
what do beta sheets often make up?
the bulk of the base of the protein
36
how are beta sheets formed?
via hydrogen bonds between neighboring segments of polypeptides.
37
what are amyloid structures?
beta sheets stacked on top of e/o w side chains forming "zipper teeth" chain
38
can amyloid structures be good?
yes! when we want to store protein hormones or peptide for efficient packaging! (makes it compact)
39
what shape do misfolded proteins tend to form?
amyloid
40
what are amyloid proteins that infect and cause other proteins to misfold called?
prions
41
what is the human version of mad cow disease called?
creutzfeld-jakobs disease
42
how long does it usually take for symptoms of creutzfeld-jakobs disease to start showing?
5-15 years
43
what is a protein domain?
any segment of a polypeptide that can fold into a compact, stable structure
44
how long are protein domains typically?
40-350 a^2
45
what are unstructured sequences?
short polypeptide chains that link domains
46
explain how the bacterial transcription regulator works in regards to its two domains.
- large domain binds cAMP
- this binding causes a confirmational change of the protein, allowing for the small domain to bind to DNA
47
what are protein families?
groups of proteins that very closely resemble each other (aka have many similar domains) but each have their own specific function
48
what is an example of a protein family?
serine proteases
49
what is the binding site on a protein?
are of a protein where another molecule can bind via weak interactions
50
what is it called when two identical proteins are bound together?
a dimer
51
what is it called when four identical proteins are bound together?
a tetramer
52
what is it called when many non identical proteins are bound together?
no real name, just know that that is quaternary structure and that each polypeptide chain is called a subunit
53
what is an example of a protein in a chain shape?
actin filaments and microtubules
54
what is an example of a cage like protein shell
protein coats of viruses
55
which structures are made of a mix of proteins and RNA?
ribosomes and viruses
56
what are two proteins in the extracellular matrix?
collagen and elastin
57
what ties tgt amino acids from different parts of same/diff polypeptide
stable covalent cross linkages
58
what are disulfide bridges?
v stable bonds between the -SH on cysteine side chains
59
in what kind of proteins do we see disulfide bridges?
extracellular proteins
60
why do disulfide bridges occur in extracellular proteins but not intracellular proteins?
bc conditions inside cell are relatively stable so the bond is not needed, but in order to face the harsh extracellular environment, disulfide bridges are needed to provide stability
61
where can high amounts of cysteine be found? why?
in stable extracellular proteins to be able to form disulfide bridges
62
what is a ligand?
a substance that is bound by a protein
63
what is a binding site?
the region of a protein that associates with a ligand via weak bonds
64
what can a binding site do?
- regulate activity as protein often cannot function until ligand binds
- attach protein to specific part of cell
65
what type of protein do substrates bind
enzymes
66
what is a cofactor?
small inorganic molecules that aid enzymes
67
name some examples of cofactors.
- heme groups use iron
- carboxypeptidase cuts polypeptide chains a carboxyl groups with the help of zinc
68
what is a coenzyme?
small organic molecules that aid enzymes
69
name some examples of coenzymes.
- biotin aids enzymes in transferring carboxyl groups
- retinal aids rhodopsin absorb light in eyes
70
many coenzymes are _____ which we get from our diet
vitamins
71
what is a regulatory site?
site where a molecule binds to alter rate at which an enzyme functions
72
describe feedback inhibition.
when an enzyme acting early on in a reaction is inhibited by a molecule produced later on in pathway
73
what is positive regulation?
when a product in one part of a pathway stimulates the production of another product causes an enzyme to stop working
74
what is negative regulation?
when the presence of a product causes an enzyme to stop working
75
what are allosteric proteins?
proteins that have different confirmations based on what ligands are bound.
76
in an allosteric protein, it will switch _____ between active and ______ confirmations
spontaneously, inactive
77
what is phosphorylation?
the attachment of a phosphate group to an a^2 side chain
78
what amount of mammalian proteins are phosphorylated at any given time?
1/3
79
what is a protein kinase?
enzyme that transfers a phosphate group from ATP to the OH group of a serine
80
what is a protein phosphatase?
enzyme that removes phosphate group from protein
81
phosphorylation can create _____ sites for other molecules
docking
82
name some common protein modifications. where can they be found?
- addition of acetyl groups to lysine side chains. histones
- fatty acid to cysteine side chain to attach protein to cell membrane
- ubiquitin to target protein for degradation
83
describe GTP binding proteins and how they function.
- protein that binds to GTP, in this form it is active
- inactivates when GTP hydrolyzed to GDP
- reactivated due to cell signals
84
what is the function of motor proteins?
to generate energy for muscle contractions and other intra/extracellular movements (lysosomes, muscles, cillia, flagella)
85
describes the steps by which motor proteins function, using myosin specifically as an example.
1. ATP binds to myosin on actin filament
2. ATP hydrolysis creates IRREVERSIBLE step, also giving burst of free energy
3. ADP and phosphate dissociate from myosin
4. myosin proceeds in the direction needed
86
why is the irreversible step in the function of motor proteins irreversible?
it is energetically unfavourable
87
what are protein machines?
highly coordinated and linked sets of proteins
88
what causes the successive series of confirmational changes in a protein machine
hydrolysis of ATP/GTP
89
what are scaffold proteins?
large molecules that can be comprised of proteins/RNA that contain binding sites that when bound, enhances the rate of a cell process while also keeping the ligand in a specific spot in cell.
90
what is the general structure of scaffold proteins?
can be either rigid or elastic in different regions
91
what are bimolecular condensates?
collections of proteins and RNA (scaffolds) held together by weak interactions. they contain fluid, membraneless subcompartments that perform functions
92
what are clients?
molecules that get concentrated on scaffolds by weak interactions
93
do concentrates blend into their environment?
no! remains separate from surroundings
94
what is an example of a bimolecular condensate?
nucleolus
95
describe the steps of protein purification.
1. break open cells to extract contents
2. isolate class of molecules of interest by FRACTIONATION
3. CHROMATOGRAPHY separates individual components into fractions (polypeptides) based on their protein properties
4 GEL ELECTROPHORESIS allows polypeptides to migrate through gel at different speed due to their size and charge.
96
what is affinity chromatography?
a type of chromatography where polypeptides are separated based on their ability to bind to certain molecules
97
what are some ways of determining protein structure?
- direct analysis of a^2 by using proteases to break protein into smaller pieces
- mass spectroscopy
98
describe mass spectroscopy
process by which proteins are blasted by a laser and fly towards a detector to determine their mass. the time it takes each piece to get to the detector is directly related to mass and charge.
we can compare with a database
99
name some methods used to determine 3D structure of protein
- x-ray crystallography
- nuclear magnetic resonance (NMR) spectroscopy
- cryo-electron microscopy
100
what can sequence patterns signal to us?
if there are sequence patterns across varied organisms, we can assume that the domain has the same function regardless of what cell it came from
101
what is the p53 protein used for?
responding to DNA damage
102
at how many different sites can the p53 protein be modified?
at least 20
