bio chem midterm 2 real Flashcards

(278 cards)

1
Q

Enzymes

A

biological catalysts

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2
Q

enzymes differ from ordinary chemical catalysts in several aspects

A
  • higher rxn rates

-milder rxn conditions

-greater rxn specificity

-capacity for regulation

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3
Q

higher rxn rates

A

10^6-10^12 rate enhancement

-several orders of magnitude faster than chemical catalysts

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4
Q

milder rxn conditions

A

-temp

-pressure

-pH

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5
Q

greater rxn specifity

A

-narrow range of substate/product specificity

-stereospecificity, no side products

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6
Q

capacity for regulation

A

‘fine’ control of rxn rate

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7
Q

Enzyme catalysis

A

enzymes accelerate but are unchanged by a rxn

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8
Q

any given enzyme is extremely specific

A

-act on only one/few ligands (substrates)

-carry out limited types of chemical rxns

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9
Q

substrate

A

the molecule on which an enzyme acts

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10
Q

types of rxns

A

hydrolytic

condensation

isomerization

oxidation-reduction

group transfer

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11
Q

hydrolytic

A

-where a substrate is broken down by adding water

-often used by enzymes to break apart complex molecules into smaller usable fragments

-nucleases, proteases, phosphatases
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12
Q

condensation

A

-usually removes water and combining two molecules together to create a larger molecule
-polymerases, synthases

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13
Q

isomerization

A

-rearranges bonds often by breaking and forming covalent bonds between atoms resulting in a structurally different molecule
-isomerases

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14
Q

oxidation-reduction

A

-gain or loss of electrons (transfer of electrons between atoms or molecules)
-oxidases, reductases, dehydrogenases

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15
Q

group transfer

A

transfer of a specific functional group or atom from one molecule to another
-kinases, transferases

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16
Q

substrate binding

A

when a substrate interacts with an enzyme

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17
Q

binding sites are-

A

-an indent or cleft on the surface of the enzyme

-geometric complementarity

-electronic complementarity

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18
Q

geometric complementarity

A

when the substrate fits into the enzymes active site complementary in that it binds snugly

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19
Q

electronic complementarity

A

complementary electrostatic surface potentials to the substrate

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20
Q

how do complementary substrates, geometric and electronic, bind to an enzyme’s binding site?

A

noncovalent forces

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21
Q

what are the two major hypotheses for substrate binding models

A

-lock-and-key

-induced fit

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22
Q

lock-and-key hypothesis

A

enzyme active site has specific shape that fit the substrate perfectly

enzyme is the lock and the substrate is the key

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23
Q

induced fit hypothesis

A

enzyme active site only forms in the presence of substrate and adapts in a change in shape for the substrate to bind to.

-enhances catalytic efficiency

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24
Q

structural data suggests active sites are-

A

largely preformed with the most demonstrating at least some induced fit

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25
enzyme specificity
range of compounds utilized as substrates
26
specificity of enzymes vary widely
-a few enzymes are specific for a specific compound -most enzymes catalyze the rxns of a small range of related compounds -some enzymes are 'promiscuous', it is more appropriate to talk of preference than specificity
27
enzymes are -
stereospecific ex, glycolsis is specific for D-glucose
28
cofactors
small molecules
29
protein functional groups are not suited to all types of rxns
-proteins have evolved binding sites for cofactors that participate in catalysis -range from ions to large organic molecules known as coenzymes (transient) -referred to as prosthetics if they have a permanent association with the enzyme
30
transient
Coenzymes
31
prosthetics
Group
32
nomenclature for enzymes that bind cofactors
apoenzyme (inactive) +cofactor -><- holoenzyme (active)
33
transition state
the state corresponding to the highest energy along the rxn coordinate -colliding reactant molecules will always go on to form products
34
rxn coordinate
-representation of a rxns progress (reactants->products) -shows intermediates and transition state -progress of bond formation/breakage
35
enzyme catalysis about the transition state
- an intermediate form between the reactants and products -a transient, high energy state (unstable) -a form different from both the reactants and products
36
activiation energy
Energy must be put into the molecules (reactants) to push them to the transition state
37
The speed of a reaction is determined by what?
how difficult it is to get to the transition state
38
what do enzymes do?
makes it easier to get to the transition state (thereby, increasing the reaction rate)
39
the overall main energy remains..-
unchanged for an enzyme catalyzed reaction compared to the uncatalyzed reaction
40
Lowering activation energies mechanisms step 1
enzyme binds to 2 substrate molecules and orients them precisely to encourage a reaction to occure between them
41
Lowering activation energies mechanisms step 2
binding of substrate to enzyme rearranges electrons in the substrate, creating partial negative and postitve charges that favor a reaction
42
Lowering activation energies mechanisms step 3
enzyme strains the bound substrate molecule, forcing it toward a transtion state to favour a reaction
43
enzymes decrease-
the activation energy -makes it easier to reach transition state
44
highest affinity of enzyme is for-
the transition state, and NOT the substrate or product
45
topography of the active site is complementary to-
transition state
46
binding of the substrate pushes the enzyme towards-
the tranition state -results in a stain on the substrate
47
enzymes do not change-
equilibriums -allows equilibrium to be achieved sooner
48
How do enzymes make it so equilibrium to be achieved sooner?
-accelerates kinetics of the reaction (rate) -both forward and reverse rxns are catalzyed by an enzyme -enzymes also do not change the free energy difference between substrate and product
49
regulation
cells must regulate catalytic activity of enzymes in order to coordinante metabolic processess
50
two general approaches for regulation
-regulate activity by varying the amount of an enzyme -the activity of an enzyme may be regulated directly
51
regulate activity by varying the amount of an enzyme
-synthesis of new enzyme -degradation of exisiting enzyme -constant activity, variable amount
52
the activity of an enzyme may be regluated directly
-competitive inhibition -subtle conformation changes alter substrate affinity or catalytic activity of the enzyme -structural alterations result from either a) non-covalent binding of a regulatory molecule (effectors) b) covalent modification of the enzyme
53
competitive inhibition
resembles enzymes natural substrate but does not react (or reacts very slowly) -often used to investigate the nature of the substrate-binding site or the enzyme mechanism
54
compounds that resemble the transition state are-
-similar geometry, charge distribution -do not undergo a chemical reaction -excellent inhibitors because they bind tightly, blocking the active site -many drugs and antibiotics are enzyme inhibitors, and are most effective if they are transition state analogs
55
effectors
any molecule that regulates the binding affinity of a protein/enzyme (can be activators or inhibitors)
56
allostery
effector binds at a site away from the active site usually heterotropic effectors
57
cooperativity
-ligand binding alters affinity for same ligand at second site -always homotropic effectors
58
homotropic effectors
same as the ligand or substrate
59
heterotropic effectors
different from the ligand or substrate
60
pathway product is an-
inhibitor of the enzyme catalyzing the first committed step of a pathway
61
feedback inhibition
-at high concentraion, CTP heterotropically inhibits the enzyme -stabilizes inactive state
62
ATP activation
-ATP heterotropically activates enzyme -stabilizes active state
63
nulcleotides and their derivatives
participate in nearly all biochemical processes
64
How do nucleotides and derivatives affect biochemical processes? #1
monomeric units of nucleic acids
65
How do nucleotides and derivatives affect biochemical processes? #2
nucleoside triphosphates (ATP) are 'NRG rich' end products of most energy releasing pathways -consumed in energy requiring processess
66
How do nucleotides and derivatives affect biochemical processes? #3
regulators of metabolic pathways and processes
67
How do nucleotides and derivatives affect biochemical processes? #4
reguired component of enzymatic rxns (cofactors)
68
nucleotides
are nucleoside phosphates
69
nucleosides consist of-
a nitrogenous base covalently attached via a beta glycosidic bond the C1' of a 5 carbon sugar (pentose)
70
all nucleotides contain a-
nucleoside
71
Nitrogenous bases are-
planar, aromatic molecules that are structural derivatives of purine or pyrimidine
72
riboses are-
5 carbon sugars with an aldehyde functional group
73
phosphate
covalently attached to the D-ribose via ester bonds
74
what are phosphates typically attached to
c5'
75
In polymers the phosphate is attached to-
both the c5' and C3'
76
nucleic acid polymers have what end?
3' and 5'
77
what is more complex, purine or pyrimidine?
purine
78
what is in the purine group?
adenine and guanine
79
what is in the pyrimidine group?
uracil, thymine, and cytosine
80
what does uracil and thymine occur in? DNA or RNA
thymine = DNA uracil = RNA
81
Major groove and minor groove
major = larger minor = smaller
82
Amount of A T G C
A = T G = C due to complementary base pairing
83
Base conformations
dependent upon the glycosidic bond torsion angle
84
anti conformation
-favoured orients bulky groups away from ribose -H over ribose ring
85
syn conformation
-disfavoured places bulky groups over the ribose -6 member ring (purine) or O (pyrimidine) over ribose ring
86
A-DNA helical sense
right
87
B-DNA helical sense
right
88
Z-DNA helical sense
left
89
A-DNA major groove
Narrow and Deep
90
B-DNA major groove
WIde and deep
91
Z-DNA major groove
flat
92
A-DNA minor groove
wide and shallow
93
B-DNA minor groove
Narrow and deep
94
Z-DNA minor groove
Narrow and deep
95
A-DNA sugar pucker
C3'-endo
96
B-DNA sugar pucker
C2'- endo
97
Z-DNA sugar pucker
C2'-endo/C3'-endo
98
A-DNA glycosidic bond
anti
99
B-DNA glycosidic bond
anti
100
Z-DNA glycosidic bond
anti and syn
101
stabilizing forces
-base stacking h-bonding ionic interactions
102
base stacking
-hydrophobic interactions -significant contribution -G and C > A and T
103
H-bonding
between bases -contributes some stability - G and C ine) over ribose ring
104
ionic interactions
between phosphates and cations -cations shield negative charges -divalent cations (Mn2+, Mg2+) are far more effective than monovalent ones
105
super-coiling is
defined by the writhe and twist
106
writhe
number of helix coils about self
107
twist
length (bp)/ pitch (bp/turn)
108
DNA denaturation
temperature is most common way to denature DNA -cooperative process (hard to start but easy after it does start)
109
melting temperature (Tm)
50% disassociated changes based on the composition of the DNA
110
DNA structure is-
sequence independent
111
RNA structure is-
sequence dependent (like protiens)
112
double stranded DNA absorbs light-
differently from single strands
113
informational DNA
provide informational template for protein synthesis messenger RNA
114
messenger RNA
mRNA -carries the 'genetic message' from gene to the ribosomes
115
functional RNAS
RNA that is functional as an RNA molecule and is not translated into a protein (non-coding) Transfer RNA Ribsosomal RNA
116
transfer RNA
tRNA transport of aa to the ribosome
117
ribsomal RNA
rRNA component of the ribosome
118
mRNA transcripts includes-
upstream and downstream elements
119
ribosome binding site is-
upstream
120
termination elements are-
downstream
121
complementary to the template strand
-one DNA strand acts a template (non-coding or anti-sense) - -other strand is the non-template strand (coding or sense)
122
what is the template strand
-complamentry to the RNA strand what is read -only one strand on a double stranded DNA the other strand =non-template
123
consensus sequences
-35, -10 and +1 closer you are the higher transcription you are
124
holoenzyme
enzyme along with its cofactor has sigma 70 recognizes -35 and -10 regions (where the start of the gene is)
125
why is transcription commonly aborted?
halo enzyme and core enzymes -they are part of initiation
126
once the promoter is located and transcription is initiated; o (sigma)-
dissociates and the core enzyme binds tightly
127
transcription rates are directly proportional to the-
affinity (Kd) of RNAP for a promoter
128
transcription -termination independent
factor (protein) independent (intrinsic) (doesn't need protiens to do this) -stop point defined by RNA sequence -2 elements: hairpin loop (internal base pairing forms helical stem) and poly-u stretch following hairpin
129
core enzyme
doesnt have sigma 70 when sigma 70 leaves, there is a change in polimerize - end of antination
130
promoter binding =
prokaryote
131
transcription- termination dependent
factor (protein) dependent -less common than independednt termination -energy (ATP) dependent -p binds to RNA near RNAP -'rolls' up nascent RNA, destablilizing RNA-DNA hybrid
132
Transcription elongation
-generates localized supercoilng
133
prokaryotic mRNA
short lived (min) and is typically being translated before transcription is even complete -bacterial mRNA processing is uncommon
134
eukaryotic mRNA
-extensively processed before it is exported from the nucleus and translated by ribosomes -5'capping and 3' - polyadenylation of ends -intron removal or splicing
135
5' capping
7-methyl-guanosine is added to the 5' end of transcipt -a 'signal' for export
136
Why 5'cap?
-Recognition by the ribosome (translation) -prevents and protects 5' end from exonuclease degradation -nuclear export
137
3' polyadenylation
-endonuclease recognizes cleavage site and adds a bunch of A's -prevents exonuclease degration
138
splicing
introns, initially transcribed, are removed and exons spliced together -occurs in the nucleus before export -catalyzed by specific ribozymes and ribinucleoproteins (spliceosome)
139
Alternative splicing possible reasons:
a gene gives 1 messenger RNA molecule = gives 1 protein -many protiens are multisubnited (greater diversity of proteins) may increase likelihood of gene rearrangements producing successfully folded proteins -one gene gives 1 primary RNA molecule and we take bits out (can splice in different ways)
140
words =
codons
141
condons must be at least-
3 letters long
142
overlapping
each nt is part of more than one codon
143
non-overlapping
each nt is part of a single codon
144
a single base-pair substitution mutation only ever changes-
1 amino acid within a protein
145
are codons read in an overlapping or non-overlapping manner
non-overlappingu
146
supressor muation 1
deletes a letter (reversion)
147
supressor mutation 2
adds a letter (suppresses)
148
reading frame
a set by the start codon determines amino acid sequence
149
features of the genetic code #1
-each amino acid is specified by a group of three nuleotides, a codon, in the mRNA and is read in a specific 'frame'
150
Features of genetic code #2
degenerate
151
degenerate
1 amino acid is coded for by > 1 codon
152
features of the genetic code #3
nonrandom
153
nonrandom
-similar amino acids are encoded by similar codons -change of 1 base has little impact
154
features of the genetic code #4
nearly universal
155
nearly universal
-same in most organisms from bacteria to human with very few exceptions
156
what are the components required for translation
mRNA amino acids tRNAS ribosome protein factors
157
mRNA for translation
template for protien synthesis
158
amino acids for translation
protien building blocks
159
tRNAs for translation
-carry amino acids to the ribosome -decode mRNA information
160
ribosome for translation
-RNP complex -catalyzes peptide bond formation
161
protein factors for translation
-initiation factors (IF) - enlongation factors (EF) -release factors (RF)
162
tRNA
the adapter molecule for protien synthesis -base-pairing between tRNA and an mRNA codon specifies the amino acid to be inserted -a cell must contain at least 20 different tRNA one for each amino acid -amino acids are covalently attached to tRNA = charging
163
aminoacyl-tRNA synthetase
-activation transfer proofreading
164
aminoacyl-tRNA synthetase activation
activation of amino acid by forming aminoacyl-AMP sticking a phosphate on it
165
aminoacyl-tRNA synthetase transfer
to tRNA 3'-OH ester bond with COO- of amino acid
166
aminoacyl-tRNA synthetase proofreading
bonds to incorrect amino acids are hydrolyzed
167
charging accuracy is crucial for translation
-binds only one amino acid -binds onoly appropriate tRNAs
168
small subunits
-binds mRNA -decoding site
169
large subunits
catalyzes peptide bond formation
170
components: ribosomes
comprised of a large and small subunits
171
termination (prokayotes)
termination hydrolysis ribosome subunits dissociates
172
termination pro
requires release factors (RF1, RF2, RF3) RF1 or RF2 bind stop codon RF3 catalyzes RF1 or RF2 removal
173
hydrolysis pro
breaks bond tRNA (P-site) and PP chain
174
ribsoome subunits dissociate pro
ribosome recycling factor (RRF) and EF-G catalyze removal of tRNA and mRNA from the ribosome
175
lipids
are distinguished by their high solubility in non-polar solvents and low solubility in H2O
176
fatty acids
building block for complex lipids
177
A-site
aminoacyle site
178
P-site
peptide site
179
E-site
exit site
180
triacylglycerols
membrane precursors and energy storage
181
glycerophospholipds
membrane components
182
sphingolipids
brain lipids, membrane components
183
steroids
cholesterol, bile salts, steroid hormones
184
what are fatty acids composed of?
a carboxylic acid 'head group' and long hydrocarbon 'tail' 16 and 18 Cs most common
185
hydrocarbon tails can be -
saturated or unsaturated
186
unsaturated hydrocarbon tails contain-
one or more double bonds
187
most naturally ocurring double bonds are in the-
cis conformation
188
what does 18: 3n-3
18 carbons, 3 double bonds, omega, - point of saturation
189
what does 18: 0
18 carbons, saturated
190
where is the alpha carbon
the 2nd C
191
where is beta carbon
the 3rd C
192
where is omega carbon
the last C
193
saturated
completley saturated with hydrogen
194
trans and cis-unsaturated
not completely saturated with hydrogen cis is what is observed most under unsaturated fatty acids
195
fatty acids melting points are affected by
the length and unsaturation -longer hydrocarbon chains increase the melting point -unsaturated chains decrease the melting point
196
saturated tend to be ____ while unstaturated are____ at room temperature
soild, liquid
197
palmitate
carbons: 16 DB : 0
198
stearate
carbons: 18 DB : 0
199
palmitoleate
carbons: 16 DB : 1 IUPAC: cis-^9
200
oleate
carbons: 18 DB : 1 IUPAC: cis-^9
201
Linoleate
carbons: 18 DB : 2 IUPAC: cis-^9,12
202
linolenate
carbons: 18 DB : 3 IUPAC: cis-^9,12,15
203
fatty acid characteristics
-double bonds produce kinks in the hydrocarbon chains -decreases forces -saturated fatty acids pack closer (no kinks) -maximizes van der waals interactions
204
good fats
high in polyunsaturated fatty acids
205
bad fats
high in saturated fatty acids
206
really bad fats
trans fatty acids
207
triacylglycerols (triglycerides)
-most abundant form of fatty acids -major energy reserves -hydrophobic
208
1 fatty acid + glycerol =
monoacylglycerol
209
2 fatty acid + glycerol =
diacylglycerol
210
3 fatty acid + glycerol =
triaclyglycerol -not amphipathic (hydrophobic)
211
amphipathic
both hydrophilic and hydrophobic
212
glycerophospholipids
1,2-diacylglycerol (fatty acids) with a phosphate group at position 3 -essentail components of cell membranes and other cellular structures -parent molecule is phosphatidic acid -additional compounds can be esterified to the phosphate group
213
glycerophospholipids
-phosphatidic acid -phosphatidylethanolamine -phosphatidylcholine -phosphatidylserine -phosphatidylglycerol
214
phosphatidic acid
name of X: - formula of X: H net charge (at pH 7): -1
215
phosphatidylethanolamine
name of X: ethanolamine formula of X: -CH2-CH2-NH3+ net charge (at pH 7): 0
216
phosphatidylcholine
name of X: choline formula of X: -CH2-CH2-N(CH3)3+ net charge (at pH 7): 0
217
phosphatidylserine
name of X: Serine formula of X: -CH2-CH(-COO-)-NH3 net charge (at pH 7): -1
218
phosphatidylglycerol
name of X: Glycerol formula of X: -CH2-CH(-OH)-CH2-OH net charge (at pH 7): -1
219
sphingolipids:
sphingomyelins cerebrosides gangliosides
220
sphingomyelins
phosphocholine or phosophoethanolamine
221
cerebrosides
single sugar residue
222
gangliosides
Oligosaccharides
223
steroids
cholesterol steriod hormones vitamin D bile salts
224
cholesterol
most abundant steriod, part of membranes
225
steriod hormones
cortisol, estrogens, testosterone
226
bile salts
fat emulsofocation and metabolism regulation
227
membranes
essential components of all living cells
228
what do membranes do
-excludes toxic ions and compounds; accumulation of nutrients -reproductive processes -signal transduction -varied interactions with molecules and cells -energy transduction; cell locomotion
229
micelles
-single-tailed lipids form micelles in water (cone head-tail circle thing)
230
double-tailed lipids
form disc-shaped micelles in water
231
liposomes
phosopholipid suspensions in water can form uni and multilamellar vesicles artificial
232
fluid mosaic model
proposed membranes are a highly dynamic structures
233
bilayers are best described as-
2 dimentional fluids -fluids are highly mobile in the plane of the bilayer (lateral diffusion) -lipid transfer across the membrane is rare
234
lipids do not-
flip between 2 monolayers
235
uncatalyzed transverse (flip-flop) diffution
=very slow (flips to other side)
236
uncatalyzed lateral diffution
very fast (moves forward)
237
lipid distribution is-
asymmetrical
238
when we drop temperature the membrane becomes-
ordered (packed nice and tight) -increased van der wall interactions -(bilayers lose their fludity)
239
transition temperature-
decreases with shorter tails and more unsaturation
240
ordered state is____ by long tails sturatued hydrocarbons
favoured
241
cholesterol regulates -
membrane fluidity low temp and high temp
242
low temp for cholesterol
decreases transition temp by inhibiting the formation of the gel-like state -hinders packing of hydrocarbon tails - increases fluidity
243
high temp for cholesterol
decreases membrane fluidity -inhibits rational movement of fatty acid chains -decreases fluidity
244
cholesterol broadens the____ in which the membrane remains functional
temperature range
245
proteins membranes contain
-integral membrane proteins -peripheral membrane proteins -lipid-linked proteins
246
integral membrane proteins
-tightly bound by hydrophobic forces (core) -asymmetrically oriented -transmembrane or embedded proteins
247
peripheral membrane proteins
-loosely assocaited with membranes surface
248
lipid-linked proteins
-have covalently attached hydropohobic groups -groups act to anchor protein to the membrane
249
portions of integral proteins within the membrane bilayer must have-
hydrophibic side chains on the surface
250
nonmediated transport
simple diffusion controlled transport -small molecules are able to cross the membrane by simple diffusion
251
only thing that moves molecules
free energy high to low concentraions
252
mediated transport
transport through action and specific carrier proteins (needs something to help get passed the membrane) -passive -active
253
passive transport
(or facilitated diffusion) - concentration gradient driven -doesn't need help to move (water down dam) ionophores and porins
254
active transport
transport against a concentration gradeint (low -> high) needs energy (water coming up a dam)
255
ionophores
2 types- both are highly selective ion carriers ion channels
256
ion carriers
binds solutes (ions) and aids their diffusion -protein inbedded in membrane can bind to a specific ion
257
ion channels
forms a pore allowing selected solutes to pass through to aid diffusion
258
porins
-forms a pore, larger, less selective -H2O filled -commonly trimeric arrangement
259
transporter classifications
uniport symport antiport electroneutal electrogenic
260
uniport
single molecule transport moves one type of molecule in one way
261
symport
transports two molecule types, in the opposite direction
262
antiport
transports 2 molecule types, in the opposite direction
263
electroneutral
transport does not charge the charge seperation across the membrane -symport with oppositely charged molecules -antiport with similarly charges molecules -not changing, no net movement of charge
264
electrogenic
transport result in charge separation -changes the charge across the membrane, driven by active transport -transport of one type of ion charge produces a difference in charge, thus acting as a type of current
265
1 transporters
uses ATP as free energy source -can also use energy of oxidation
266
2 transporters
doesnt use ATP, uses ion concentration gradient to run system -makes use of the graident already present
267
Na/K pump
-used ATP to pump 3 na ions out of the cell and pumps 2 K into it at the same time -creates a na graident
268
na/glucose pump
antiporter = moves ions in oppisite directions symporter = moves ions in the same direction
269
the transition state is an unstable chemical structure that represents a -
free energy maxima on a reaction coordinate diagram
270
the larger the change in energy is the-
slower the reaction is
271
the slowest step in an overall reaction is referred to as the-
rate determining step = largest ^G = slowest step
272
how do catalysts enhance reaction rate?
by lowering the activation barrier, ^G They do NOT change the ^G of the overall reaction enhance rates of both the forwards and reverse reactions
273
^^G
the difference in activation energy between the catalyzed and uncatalyzed rxn
274
^G < 0 is -
the more favourable reaction
275
kcat
number of substrate molecules converted into product per active site per second -how many rxns in a given time we carry out
276
catalytic efficiency: kcat/km
describes rate constant at low substrate concentraions ([S]<
277
competitive inhibitors increase the-
apparent km (decrease affinity) between enzyme and substrate
278
large km =
weak binding (low affinity)