Exam 2 Flashcards
1
Q
Enzymes become ___ at high substrate concentration
A
Saturated
2
Q
ΔG tells us what? what does it not tell us
A
-if the reaction will occur
-nothing about the RATE
3
Q
what is a catalyst
A
something that speeds up a rxn but reamins unchanged when the rxn is over
lowers activation energy
4
Q
what does a catalyst not affect
A
ΔG, equilibrium point, add energy
5
Q
what are enzymes
A
proteins that act as biological catalysts
6
Q
what are ribozymes
A
RNA molecules that act as biological catalysts
7
Q
what is the activation energy
A
energy barrier must be overcome before a reaction can occur, even for spontaneous
8
Q
what might activation energy represent
A
- energy needed to bring substrates into transition state
-unfavorable chemical environment for rxn
-physical separation of reactants
-other factors that hinder progress of reaction
9
Q
for uncatalyzed rxns where does the activation energy come from
A
random thermal energy
10
Q
what can overcome activation energy
A
heat
11
Q
what do high temperatures do to cellular structures
A
denature them by destroying the hydrogen bonds
12
Q
how do catalysts work
A
-bringing reactants together
-altering chemical environments around reactants
-bringing substrates into transition state
-doing other things to remove obstacles to reaction progress
13
Q
what3 properties do all catalysts share
A
- increase rxn rates by lowering activation energy
- form transient, reversible complexes with substrate molecules
- change the rate at which equilibrium is achieved not position of equilibrium
14
Q
what is a coupled rxn
A
use of an exergonic rxn to provide energy for an endergonic rxn
15
Q
extracellular vs intracellular
A
extracellular matrix
-collagen in animals
cytoskeleton for intracellular
16
Q
what forms of communication do proteins use
A
receptors
antibodies (animals)
hormones
transport
17
Q
what do proteins regulation function regulate
A
- gene expression
physically by histones
physiologically by enzymes that control transcription - other proteins
-calmodulin
18
Q
why are histones positively charged
A
because DNA has phosphates which make them negative and the histones are positive- before phosphates are added
19
Q
what is one example of the adhesion function in proteins
A
glycoproteins at cell surface
-stick us together
20
Q
what is an example of storage and transport function in proteins
A
blood- transporting oxygen
storing amino acids to build new structures
21
Q
how many amino acids are used in protein synthesis
A
20
22
Q
at pH 7 what is ionized in the basic amino acid structure
A
amino(+) and carboxyl groups(-)
23
Q
nonpolar amino acids have what characteristics
A
r-group is mostly hydrocarbon- nothing charged or polar
24
Q
peptide bond characteristics
A
partial double bond characteristic - which limits rotation around the bond and how a polypeptide can fold
25
how would you describe primary structure
sequence of amino acids in a chain- from N to C terminus
26
peptides fold to achieve what
lowest free energy state
27
why does folding in protein happen
noncovalent bonds and hydrophobic exclusion
28
how would you describe secondary structure
conformation oof polypeptide strand, alpha helix and beta strand result from rotation of bonds around alpha-c in chain
29
alpha helix structure charcteristics
right handed spiral- held by v.d.w forces and hydrogen bonds- side chains point out from helix axis
30
what category of amino acids would most likely be found in a alpha helix
nonpolar group of amino acids
31
how many amino acids are needed to cross the bilayer as part of an alpha helix
3.6 on each fold or turn
5.56 turns to get across nonpolar
=20 aa needed to span the bilayer- round up
32
beta strand characteristics
-stretched chain
-no H-bonds within strand but do link neighboring strands
-side chains (R) point up and down
33
what would loops and turns on a protein be caused by
proline
charged side chains
34
why are loops and turns on a protein important
bending and folding of polypeptide
-short stretches that connect alpha helices and beta strands
35
what are intrinsically disordered proteins and what do they lack
random coils - gain structure when environment changes, abundant in cells,
-tertiary structure, hydrophobic and aromatic amino acids
36
how would IDP's be able to have a predictive function
can adapt some order if mixed with particular lipids that are membrane formers can adapt to that structure
37
what are motifs
modular
-common patterns of secondary structures
-may have functional significance
38
what are domains
stable, independently folding protein regions
-may have functional significance
39
what three things always affect noncovalent bonds
ph, temp, and salt concentration
40
how would you explain pic of motif
either a beta sheet or alpha helices anti parallel both ways but can see it in beta sheet
41
what structure does carbonic anhydrase have
beta sheets
42
when something is hydrophobic is it polar or nonpolar
nonpolar (tails in a membrane)
43
what are the 3 noncovalent bonds that help proteins fold
hydrogen bonds, van der waals attraction, electrostatic connections
44
what is denaturation and is it reversible
unfolding that disrupts function, may be reversible may not be
45
what are examples of things that would cause denaturation
heat, alcohol, acids, bases, heavy metals, reducing agents, detergent
46
in tertiary structures disulfide bridges
stabilize- must have a cysteine to do oxidation and reduction
47
proteins bind to
ligands
48
enzymes bind to
substrates to catalyze reactions
49
what does enzymes binding to substrates do
decreases activation energy and increases reaction rates
50
what does the sentence enzymes are reusable explain
they return to their initial state after releasing reaction products.
51
what does the sentence enzymes are specific in activity mean
each catalyzes one type of reaction for a single type substrate
52
how do enzymes recognize substrates
by their shape and chemical properties
53
what is the active site
where substrate binds and catalysis occurs
54
what do enzymes have that contribute to activity that are nonproteins
cofactors
55
what are the 2 types of cofactors
inorganic (metal ions)
organic
56
what is a prosthetic group
organic cofactor- molecule is tightly bound to protein and required for activity
57
what is a coenzyme
cofactor- not tightly bound to protein-, carries substrates to or products from enzymes
58
coenzymes are or are derived from
vitamins
59
what is a lysozyme
cleaves a polysaccharide chain
60
what bonds do lysozymes cleave
beta 1-4 linkages
61
enzymes become ____ at high substrate concentration
saturated
62
what is vmax
maximal velocity - how fast
63
what is km
substrate concentration when v=1/2 vmax
64
km is related to enzymes
affinity for substrate
65
if there is high affinity km will be
low
66
why would isomers have different affinity
structure between different isomers
67
can too high of a temperature or ph affect enzyme activity
yes too high of a temp can cause a huge drop in function
-each enzyme has an optimal curve for environment they have evolved
68
how does ph affect structure and function
affect the charge on basic and acidic amino acids
optimal curve, pH maximum correlates to in vivo environment of enzyme
69
what kind of environments do lysozymes operate in
acidic, so too high of a pH affects structure and function
ionic strength also affects activity
70
what 2 things regulate protein abundance
-gene expression
-proteolysis
71
what is gene expression
turns on gene to make more protein and more enzymes
72
what is proteolysis
degrade proteins in regulated manner
73
what is the main type of covalent modification in regulation of protein activity
phophorylation and dephosphorylation
-fast
74
what does the protein kinase do
phosphate added to amino acids with OH
75
what does phophotase do
removes phosphates
76
which amino acids can be targeted by protein kinases
those with OH groups-tyrosine, serine, thereonine
77
allosteric proteins can change shape when changes
its job
78
where is the allosteric site located
regulatory domain
79
what does an allosteric site bind
allosteric regulator
80
how is allostery a regulation method
the change in shape affects the active site and whether the substrate can bind or not
81
allosteric activators increase the affinity for substrate so what about the km
km decreases
82
what is a competitive inhibitor
binds to active site of enzyme and blocks substrate binding
-may be an alternative substrate, looks like one
-if binds covalently then it is a toxin
83
nonpolar side chains make the amino acids hydrophobic or hydrophillic
hydrophobic which forms the core of many proteins
84
secondary and tertiary structure difference in bonding how
secondary- bonds between hydrogens
tertiary- bonds between R groups
85
nonpolar molecules are hydrophobic or hydrophillic
hydrophobic- in membranes the tails
86
how does a competitive inhibitor affect the value of km and vmax
km- increase
vmax- no change
87
is competitive inhibition reversible
yes, add more of desired substrate to out compete then inhibitor
88
what is competing in competitive inhibition
two substrates competing for the active site
89
what is non-competitive inhibition
inhibitor binds to regulatory site and decreases enzymes ability to catalyze rxn
90
how does noncompetitive inhibition affect km and vmax
no change in km but decreases vmax
91
what are examples of noncompetitive inhibitors
toxins, heavy metals
92
is noncompetitive inhibition reversible
no- toxins affect protein structures
93
what is feedback inhibition
products of metabolic pathways act as inhibitors of enzymes
- bind to allosteric site to cause conformational change
94
calcium in calmodulin properties
calcium regulates the proteins structure
it is a motif that is part of the protein structure
-calcium affects the shape and function
95
what does the plasma membrane do and what is the labeled function
separates cell contents from outside environments
-compartmentation
96
how does compartmentation function in biological membranes
-separate different part of the cell from one another
- allows different reactions with different membranes to exist within cell
97
how does the function of metabolism work in biological membranes - 3 ways
-some rxns and pathways function in nonpolar environment, enzymes in membrane catalyze
- organization of some metabolic pathways
- enable electrochemical gradients to exist
98
what is an example of metabolism in biological membranes
mitochondria forming ATP
99
can prokes have a electrochemical gradient
yes even though no strong permeability barrier or compartments
100
what is the only membrane that prokaryotes have? why is that important?
plasma membrane and they use it to maintain electrochemical gradients
101
what are examples of communicators in biological membranes
plasma membrane, hormone signals
102
what is the structure of biological membranes
fluid mosaic model
- bilayer of hydrophillic and hydrophobic lipids forms matrix
103
where are proteins located in membranes
on and in bilayer
104
how are carbohydrates related to membranes
found on the outer surface of plasma membrane
-glycocalyx and glycoproteins (furry)
105
what is the wight vs molar ration between proteins and lipids in the membranes
weight ratio- 1:1
molar ratio -1:50
106
how would ratios of components vary in membranes
-depend on type of membrane, cell, tissue, organ, species, and environment
- highest protein content
-molar vs weight ratio
107
what are the ways that membrane proteins attach to membrane
peripheral proteins
integral membrane proteins
108
what are integral membrane proteins
tightly associated with membrane structure
109
what are peripheral proteins
are held on surface by non-covalent bonds
110
properties of hydrophobic (nonpolar) regions in the core of bilayer
-hydrophobic aa
-membrane spanning a-helices and b-barrels are common
-amphipathic a-helices and b-barrels can form channels through membranes
111
how would you calculate how many amino acids needed to span a bilayer
bilayer across divided by vertical rise
and then times 3.6
112
what is an example of a channel protein in a membrane
beta barrel filled with water molecules which is an polar structure - forms a hydrophillic core!
113
outer leaflet vs inner leaflet
outer- glycocalyx, layer of carbs- more saturated fatty acids- sphingomyelin, PC
inner- less saturated, PE, PS
114
how does protein asymmetry occur
as they are being synthesized
115
If protein asymmetry is the orientation of proteins in membranes and is specific across bilayer, how are they determined?
when proteins are made and inserted into membrane layer- different things on different sides
116
what may asymmetry be due to among different parts of cell surface
- tight junctions that seal cells together
- linkage to cytoskeleton
-membrane rafts
117
what are membrane rafts important for
cell signaling
118
what do membrane rafts often contain
lipids with lower fluidity - saturated
119
what is a membrane raft
where membrane lipids have similar physical and chemical properties aggregate
120
what physical properties allow the fluid phase to have a high degree of motional freedom
- around c-c bonds in fatty acids
-rotation of entire molecule
- lateral diffusion
121
what is the gel phase when talking about physical properties of membranes
slower movement, tightly packed lipids
122
what are the physical properties of membranes
1. the phase transitions between fluid and gel
2. fluid phase has more freedom
3. gel phase
4.fluid gel transition
5. non bilayer phases exist
123
what is the fluid-gel transition being influenced by and is it reversible?
temperature
yes
-think of butter
124
what is the importance of non bilayer phases existing
- membrane fusion
- 2 membranes next to eachother fusing, one must break out
125
membranes with less fluidity would take longer to do what
recover from bleached light
126
when talking about the fluid- gel phase transition what helps keep the membranes fluid
double bonds - wider curve
127
what does tm depend on in the fluid- gel phase
# of unsaturated c-c bonds
length of fatty acid
-position of double bond
-headgroup
-solution properties
128
the more carbon atoms more or less fluid
less
129
what are consequences of fluid-gel phase transitions
-membrane functionality
-change in permeability , 100% less permeable in gel phase
-protein function - increased or decreases, depends on interactions with lipids
130
how do sterols interfere with the gel phase
fluidity buffer, lower fluidity
131
protein diffusion is determined, in part, by lipid ____. also depends on whether protein is ____ by attachment to _____ of extracellular matrix
fluidity, anchored, cytoskeleton
131
if some proteins were anchored and bleached would it recover faster or slower
slower
132
what is homeoviscous adaptation
organisms can change membrane composition to keep them fluid as environment changes
-seasonal, homeothermic
133
as winter approaches, what type of lipid is most liely to accumulate
unsaturated fatty acids- lower boiling point, more fluid
134
what types of cells have the cytoplasmic enzyme complex and what does it make
prokaryotes and eukaryotes
-in eukaryotes it makes saturated and monosaturated fatty acids
135
what does the chloroplastic pathway make
prokaryotes -polyunsaturated fatty acids
136
where does fatty acid synthesis occur
in cytosol not a membrane
137
what leaflet is facing the cytosol
outer leaflet
138
fatty acids added to membrane lipids in where
outer leaflet of er- biogenesis
139
is the er or golgi symmetrical or asymmetrical
asymmetrical
140
what do scramblase and flippase do in membrane biogenesis
1st step- scramblase- moves fatty acids to some inner leaflet
flippase- moves some back to get correct positioning
141
what carries lipids and proteins to endomembrane system
vesicles
142
what do lipid transfer proteins do
move lipid molecules from er to organelles NOT in endomembrane system
143
what is included in the endomembrane system
er, golgi, endosomes, lysosomes, nuclear envelope
144
polypeptides are inserted into the membrane as they are
synthesized
145
vesicles with proteins in membrane bud off and move to____. more glycosylations and other _____ can occur
golgi, modifications
146
membrane lipids and proteins move to ___ ______ as vesicles
plasma membrane
147
where are proteins for membranes that are not included in the endomembrane system made and taken to
made on soluble ribosomes
taken to target membrane with chaperone proteins
148
ion concentrations are ______ inside and outside of the cell
different
149
lipid bilayer in terms of transport
permeability barrier for large, polar, and charged molecules
-semi permeable
150
what is stored in gradients
potential energy (free energy)
151
uncharged solutes make what type of gradient
chemical concentration gradients
152
what type of gradient to charged solutes make
electrochemical gradients
-free energy has voltage gradient
153
passive or active transport depends on what
change in G
154
is active transport exergonic or endergonic
endergonic
155
does diffusion require energy- what does it depend on
no, depends on random thermal energy
156
is diffusion spontaneous or nonspontaneous
spontaneous
157
as diffusion occurs is the change in G moving closer or farther from 0
closer- less negative
158
Jj=Dj x ΔG /distance - what does each part of the equation mean
-ficks 1st law of diffusion
Jj= amount of j crossing a given area per unit of time
Dj= diffusion coefficient- depends on permeability- slope
distance= thickness of barrier
159
what is simple diffusion
through the membrane= passive movement through lipid bilayer
160
a membrane that has transporter proteins and enzymes is going to have a higher or lower Dj
higher
161
what is facilitated diffusion? is it spontaneous? does it require energy? what does it require?
-passive movement of polar or charged molecules across membrane
-spontaneous
-no energy needed
-requires transmembrane protein
162
how do transporters (carriers) work?
bind solute on one side of membrane
- solute falls off and diffuses away
-undergo conformation change that opens binding site
163
how are the transporters for facilitated diffusion enzyme like (4)
- specific for specific solutes
-recognize solutes by chemical properties
-saturate at high conc.
-competitive inhibition by similar solutes
164
uniport vs cotransport
uniport- transport single solutes
cotransport- moves 2 solutes
165
channels are mainly for what type of transport and what does it not bind
ion- do not bind solute
166
porins vs aquaporins in proteins for facilitated diffusion or passive transport
porins - large channels opening 4nm
aquaporins = water channels
-bacteria, endosymbiosis theory
facilitate water diffusion when simple diffusion is not fast enough
167
an ion channel has a ____ filter that controls which ____ ions it will allow to cross the membrane
selectivity, inorganic
168
what is a gated channel
opens/shuts to control solute movement
169
what is active transport
requires input of energy to overcome unfavorable free energy gradient
170
active transport moves solutes....
against their gradient- coupled rxn
171
energy usually comes from
directly or indirectly from ATP
172
what is direct active transport
transport protein uses ATP hydrolysis to get energy
-binding site for ATP
-establishes membrane potential
173
5 characteristics for the P-type pump in direct active transport
-pump is phosphorylated by ATP
-single polypeptide with 8-10 trasnsmembrane helices
-all pump cations
-all inhibited by vandate
-located in plasma membrane and er
174
p type pumps bind what during transport cycle
phosphate of atp
175
what face does atp bind on
cytosolic
176
what is a sodium-potassium ATPase
a p type pump that pumps 3 Na+ out and 2K+ into animal cells
177
hydrolysis and binding of atp causes what
shape change
178
what is the v type pump in direct active transport
- not phosphorylated by atp- makes atp
-multi subunit proteins
-unaffected by vandate
-all pump H+ out of cytosol- into vacuole
179
characteristics of v type pump and H+-ATPase
-pumps H+ out of cytosol into organelles and vesicles
-helps regulate cystolic ph
-can acidify some vesicles
-active transporter
