Protein Structure and Function Flashcards
1
Q
what are the 8 types of proteins?
A
structural
enzymes
transport
storage
motor
signal
receptor
gene regulatory
2
Q
what is the function of structural proteins?
A
provides mechanical support to cells/tissues
3
Q
what is the function of enzymes
A
catalyse covalent bond breakage/formation
4
Q
what is the function of transport proteins?
A
carry small ions/molecules
5
Q
what is the function of motor proteins?
A
generate movements in cells/tissues
6
Q
what is the function of signal proteins?
A
carry signals from cell to cell and transmit through the cytoplasm
7
Q
what is the function of receptor proteins
A
detect signals and transmit them to the cells response machinery
8
Q
what is the function of gene regulatory proteins?
A
bind to DNA to switch genes on/off
9
Q
how do amino acids and protein structure link?
A
amino acid sequence dictates the properties of the protein and so the function
10
Q
what is the general structure of an amino acid?
A
amino group bonded to central carbon
central carbon bonded to H atom, R group, carboxyl group
11
Q
how are amino acids joined together?
A
joined by covalent peptide bonds in a covalent reaction
12
Q
what are oligopeptides?
A
small numbers of amino acids linked together
13
Q
what direction do amino acids link?
A
N-terminus to C-terminus
14
Q
where do the R groups go during backbone formation?
A
project out of the backbone
15
Q
what are the two ways amino acids can be grouped?
A
hydrophobic/hydrophilic
essential/non-essential
16
Q
what are essential amino acids?
A
amino acids that can’t be made by humans so have to be included in diet
17
Q
what are the properties of hydrophilic polar amino acids?
A
readily form H bonds
likely to be on the surface of water soluble proteins
participate in H bonding with water
pushed hydrophobic amino acids to protein’s centre
18
Q
what are the properties of hydrophobic amino acids?
A
cannot form H bonds with water/polar entities
located of soluble protein’s inside to be protected from water
located on the outside of membrane-embedded proteins to interacts with non-polar tails of membrane lipids
19
Q
what does pKa stand for?
A
acid dissociation constant
20
Q
what is the pKa?
A
number that described the acidity of a molecule
pH that the amino acid loses a H= molecule
dissociation of carboxyl and amino groups
21
Q
what does pI stand for?
A
isoelectric point
22
Q
what is pI?
A
the pH where the amino acid has no net charger
23
Q
how does an amino acid gain neutrality?
A
positive and negative ions counteract each other
24
Q
what are the properties of a peptide bond?
A
inflexible bond limits folding
charge asymmetry favours H bonding
rigid
planar
double bond restricts rotation so folding is identical for same amino acids
25
what are the 5 interactions between R groups?
disulfide bonds
ionic bonds
hydrogen bonds
van der Waals
hydrophobic interactions
26
what is the only R group interaction that is covalent?
disulphide bridge
27
how does a disulphide bridge form?
two cysteine molecules form a strong bond to stabilise conformation
28
why does only cysteine form a disulphide bridge?
it is the only R group that contains cysteine
29
what are ionic bonds between R groups?
strong electrostatic attraction between oppositely charged R groups
30
how can ionic bonds between R groups be disrupted?
pH changes
temperature
31
are ionic bonds weak?
no
32
what are van der Waals interactions between R groups?
attracting forces between transient positive and negative charges in non-polar molecules
33
how do van der Waals happen?
electrons in the same atom create an atom with one positive side, one negative side
34
are van der Waals strong?
no
35
how effective are van der Waals?
only effective when R groups are close together over a short distance
36
what are hydrogen bonds between R groups?
electronegative atom and H atom bound to another electronegative atom (delta positive and negative)
37
how strong are hydrogen bonds?
only strong when high in numbers
38
how do hydrophobic interactions occur?
water forces hydrophobic groups together
minimises disruptive effect on H bonded network
39
what helps proteins fold?
chaperone proteins
40
what happens when proteins fold incorrectly?
forms aggregate
41
what is the primary structure of proteins determined by?
mRNA order
42
how does a change in the amino acid affect the protein
sequence changes
order of R group changes
order of ionic, H, disulphide bonds change
43
what bonds do the primary structure of proteins include?
peptide bonds
44
how is an alpha helix generated?
hydrogen bonds form between N-H and C=O groups in polypeptide bonds
45
why do proteins with large R groups not form alpha helices?
the coil is distorted
H bonds can't form
46
why is proline known as a "helix disruptor"?
proline is connected to the backbone twice as forms a ring, taking N
causes kink as N atom can't form H bond
47
what is a coiled coil?
2 or 3 alpha helices wrapping around each other
48
how do coiled coils occur?
when a helices have most of the non-polar side chains on one side
49
what are beta pleated sheets?
extended sheets with successive atoms in polypeptide chains
50
how to beta pleated sheets form?
H bonds between segments of polypeptide chains lying side by side
51
how are amino acids presented on beta pleated sheets?
amino acid chains alternate protruding above and below the sheet
52
what are the two lay outs of beta pleated sheets?
parallel
antiparallel
53
what are parallel beta sheets?
2 interacting regions run in the same N-C direction
54
what are antiparallel beta sheets?
2 interacting regions run in the opposite direction
N-C and C-N
54
what are beta turns?
peptide chain changes direction in a sharp bend to redirect polypeptide back in interior
54
what percentage of amino acids are random turns/coils?
40%
54
what percent of amino acids are laid out as helices and sheets?
60%
54
why does proline have beta turns?
kink
allows polypeptide backbone to fold into tight U shape
55
why does glycine have beta turns?
lack of large side chain
R group is a H molecule
55
what are beta turns stabilised by?
h bonds
56
what are the two types of proteins ?
fibrous
globular
57
what are some examples of fibrous proteins?
hair
fur
nails
skin
collagen
keratin
58
what is the structure of fibrous proteins
individual alpha helices wound around each rope-like structure
extended
water insoluble
highly stable
highly ordered/repetitive structure
59
how do intermediate filaments form from fibrous proteins
2 alpha helices form coiled coil (dimer)
2 coiled coils form proto-filaments (4 helices)
8 protofilaments form intermediate filaments bundle to form hair fibres
60
what is fibroin used for?
cocoons
webs
nets
egg stalks
61
what is the structure of silk fibroin
antiparallel beta sheets whose chains extend parallel to the fibre acid
6 amino acids repeat
sheets stack to form microcrystalline array
small R groups pack well together
62
why is folding possible in globular proteins?
regions are interspersed with random coils to allow the polypeptide to loop and fold
63
how do globular proteins form a globular shape?
regions of secondary structure folded on one another to be compact
64
what interactions stabilise globular proteins?
H bonds
ionic bonds
van der Waals
hydrophobic interactions
disulphide bridges
65
how are alpha helices arranged in globular proteins?
in bundles
66
how are beta pleated sheets arranged in globular proteins?
barrel-like configurations
twisted sheets
67
what is the structure of myoglobin?
water soluble globular protein
70% alpha helical
compact
binds oxygen in muscle cells for storage/transport
68
what is tertiary structure?
further 3D folding of the polypeptide chain
69
what are protein domains?
segments of the polypeptide chain folded independently
different parts of the protein have different functions (modular)
70
what is quaternary structure?
2 or more polypeptide chains
71
what are individual polypeptides called in the quaternary structure?
subunits
72
what are multiple identical subunits called?
homomultimers
73
what are multiple different subunits called?
heteromultimers
74
what do two polypeptides form?
dimer
75
what do four polypeptides form?
tetramer
76
what does a denaturing agent do?
destroys protein conformation so they lose their function
disrupts cross-links
77
what things that cause denaturing?
heat disrupts H bonds/hydrophobic interactions
acids/bases disrupt H bonds between R groups and break ionic bonds
heavy metal ions break S-S bonds
agitations like whipping stretches the chain to disrupt crosslinks
78
what are ligands?
substance that binds to a protein
79
which bonds form when a ligand and protein bind?
non-covalent
80
what is a protein binding site?
cavity in protein surface
formed by side chain arrangement
region that binds to ligand
81
are enzymes globular or fibrous?
globular
82
what is the main function of an enzym
biological catalyst so accelerates specific reactions
83
what happens to the enzyme's state after binding to a ligand?
it remains unchanged
84
how many enzymes are needed for a reaction
required in small amounts?
85
do enzymes work by themselves?
no, often in tandem with other enzymes
one enzyme converts substrate to product that is a substrate for another enzyme
86
what type of reactions do enzymes speed up? what does this mean
energetically favourable reaction
reactions that would happen normally
87
what do enzymes do to the equilibrium of a reaction?
nothing- equilibrium remains the same
88
what is the turnover number?
how fast an enzyme produces the produce
how many molecules of reactant the enzyme can convert to product per second
89
what is the active site?
part of enzyme that binds substrate
small number of amino acids that are positively charged
90
what is Lock and Key Theory?
active site has a rigid shape so substrate must have a highly specific shape to fit
lock= enzyme, key=substrate
91
what is Induced Fit Theory?
enzyme changes chape to bind to substrate by distorting bonds to expose regions of the enzyme the substrate can bind to
92
what does a substrate binding to an enzyme produce?
enzyme-substrate complex
93
what does the ES create?
transition phase
94
what is created after the ES?
enzyme-product complex?
95
what happens after the EP is created?
product is released
96
how does an ES form in lysozymes?
sugar D forced into strained conformation
Glu35 attacks sugar-sugar bond to donate H+
Asp52 attacks C-1 of sugar D
97
what happens in the transition stage of lysozymes?
Asp52 forms covalent bond between enzyme and C-1 of sugar D
Glu35 polarises water so oxygen can attach C-1 of sugar D and displace Asp52
98
how does an EP form in lysozymes?
water molecule splits
OH and H+ donated to Glu35
hydrolysis complete
enzyme returned to normal state
product is released
99
what is Gibb's Free Energy?
potential energy that is useable
the change of this free energy during a chemical reaction
100
what is the activation energy?
minimum amount of energy needed to push reactants over the energy barrier so transition state can be reached
101
what do enzymes do to the Ea?
reduce it
102
how do enzymes lower the Ea?
binding more tightly to the transition state than reactants
stabilises the complex so decreases energy
103
what are the 3 ways enzymes can alter the physical/chemical properties of the substrate?
substrate orientation
changing substrate reactivity
induce strain in substrate
104
how do enzymes alter substrate orientation?
by lowering the substrate entropy
substrate is taken by the enzyme where collisions are more likely
105
how do enzymes induce strain on the substrate?
exerts force on certain bonds within the substrate
destabilises substrate by adopting transition state
106
how do enzymes change substrate reactivity?
rearranges electrons in the substrate to create +ve and -ve that encourage a reaction
contains cofactors
107
what are enzyme cofactors?
nonprotein components that carry out activities that amino acids aren't suited for (donating/accepting electrons) to increase substrate reactivity
108
what is a prosthetic cofactor?
associated with the enzyme even between reaction cycles
109
what are weakly bound cofactors?
cofactors that dissociate from the enzyme between reaction cycles
110
what are the first 3 stages of the catalytic cycle?
substrate binds to active site
substrate held by weak bonds to R groups at active site
substrate binding causes conformation change
111
what are the second 3 stages of the catalytic cycle?
substrate is bound more firmly
lowers free energy of transition state
substrate is converted to product
112
what are the last 3 stages of the catalytic cycle?
products are released from the active site
enzyme returns to original conformation
active site now available for another molecule of substrate
113
what are the 4 main factors that affect enzyme activity?
temperature
pH
enzyme concentration
substrate concentration
114
how does temperature affect enzyme activity?
rate increases with temperature
past temperature, enzyme denatures
115
how does pH affect enzyme activity?
extreme pH will disrupt ionic and H bonds on R groups
alters tertiary structure
pH dependence will reflect the environment the enzyme is usually active
116
how does enzyme concentration affect enzyme activity?
increases as concentration increases
more substrate can bind
117
how does substrate concentration affect enzyme activity?
increases as concentration increases
reaches max activity when all enzyme active sites are full
118
what 3 other factors affect enzyme activity?
inhibitors
activators
general ionic strength
119
why do we use the initial reaction rate when measuring enzyme kinetics?
substrate concentration not decreased enough to affect reaction rate
product levels too small for reverse reactions
120
what does [S] stand for?
substrate concentration
120
what does V stand for?
number of moles of product formed per seconds
121
what is the main principle of Michaelis-Menton kinetics?
as you increase [S], reaction velocity (v) increases
122
what is Vmax?
maximum rate of enzymatic reaction
123
when is Vmax reached in theory?
immediately after the addition of substrate
124
why is the Vmax value only theoretical?
substrate into product takes time
125
why is the Vmax value useful?
measure of potential max rate of reaction
can estimate the likely rate of reaction under cellular conditions
126
what is enzyme saturation?
all active sites are occupied
all enzymes working maximum capacity
127
what does doubling [S] do to the V value?
doubles the V value
128
what does an overall change in [S] do to product concentration and V?
increases
129
what is Km?
concentration of substrate which the enzyme operates at half of its maximum reaction velocity
affinity of an enzyme for its substrate
130
why is the Km value useful?
can estimate where along the MM plot an enzyme functions
estimate what fraction of max velocity the reaction is likely to proceed
131
what does a lower Km indicate on [S]?
lower [S] range is which the enzyme if effective
132
what is the Kcat?
turnover number- rate of efficiency of an enzyme
how many molecules of a reactant a molecule of an enzyme can convert to products per sec
133
apart from the MM plot, what other graphical determination can we use for enzyme kinetics?
Lineweaver-Burke
134
what are the 3 types of reversible inhibition?
competitive
non-competitive
uncompetitive
135
what is Ki?
indicator of how potent an inhibitor is
concentration required to produce half maximum inhibition
136
what is competitive inhibition?
directly competes with substrate by binding to the enzyme
substrate cant bind to enzyme
no product is formed
137
how is competitive inhibition overcome?
by [S] increasing
138
how does competitive inhibition affect Vmax/Km?
Vmax remains unchanged
Km changes
139
what is non-competitive inhibition?
binds to different site on enzyme
causes physical distortion to the enzyme so substrate is no longer complementary
140
how can non-competitive inhibition be overcome?
it cant
141
how does non-competitive inhibition affect Vmax and Km?
Vmax changes
Km remains unchanged
142
what is uncompetitive inhibtion?
binds to the enzyme once the substate has bound
143
what does uncompetitive inhibition do to the Vmax and Km value?
Vmax changes
Km changes
144
what is irreversible inhibition also known as? why?
suicide inhibitors
they are toxic
145
what is irreversible inhibition?
inhibitor forms covalent linkages to amino acids at the active site so modifies the enzyme permanently
146
what effect does irreversible inhibition have on the Vmax and Km values?
Vmax decrease
Km stays the same
147
what are the 4 ways enzymes regulation theirselves?
substrate level control
feedback control
allosteric enzymes
covalent modification
148
what is substrate level control of enzyme regulation?
direct interactions between substrate and product
higher substrate concentration to increase enzyme activity
product binds to active site as inhibitor if product levels get too high
149
what is feedback control of enzyme regulation?
cell controls product generation by stopping the 1st step of the pathway
involves allosteric enzymes
150
what are allosteric enzymes?
multi subunit proteins with multiple active sites
have active and allosteric site
151
what is positive cooperativity?
catalytic activity increases faster than normal as [S] increases
152
what is negative cooperativity?
catalytic activity increases slower than normal as [S] increases
153
what are allosteric activators?
enzyme is inactive when activator isn't bound
low affinity for [S]
enzyme active when activator is bound so then has a high [S] affinity
154
what is covalent modification for enzyme regulation?
adding/removing a chemical group via a covalent bond
155
what are the two ways enzymes covalently modify?
de/phosphorylation
proteolytic cleavage
156
what is enzyme regulation phosphorylation?
addition of phosphate group using kinase
can be an activator or inhibitor
reversible
removal of phosphate group using phosphatase
157
what is enzyme regulation proteolytic cleavage?
irreversible
removes polypeptide chain portion
