Final Review Flashcards
1
Q
equation for Kcat when given {s} and Vo
A
Vmax/ET
(Vmax is velocity at highest level of substrate)
2
Q
the biconcave shape of erythrocytes which maximizes rapid diffusion of oxygen is primarily maintained by what
A
a network of embedded spectrin that crosslink to other membrane proteins
3
Q
should hemoglobin lose its ability to cooperatively bind oxygen what would also be destroyed
A
-hemoglobin would no longer serve to accepts/donate protons for blood buffering system
4
Q
botulinum toxin(botox) prevents the release of acetylcholine ultimately needed for muscle contraction thereby softening wrinkles. the function of botox is described by how
A
botox works by inhibiting the function of SNARE proteins
5
Q
the oxyanion hole helps serine proteases preferentially bind to what
A
the tetrahedral intermediate
6
Q
a peptide comprised of over 200 residues has 10 pKa values associated with its structure would have how many inflection points
A
10
7
Q
order of steps in secretory pathway
A
-synthesis occurs with single leading peptide
-signal peptide binds to SRP and GDP is replaced with GTP
-SRP changes in conformation arresting peptide growth
-the SRP-ribosome complex binds to SRP receptor-translocon complex
-GTP hydrolysis results in disassociation of SRP and SR
-signal peptidase cleaves the protein from the signal peptide
-the nascent protein begins to fold and post-translational modification is initiated
8
Q
transistion of hemoglobin from R-state to T-state has all of the following effects except which one?
A. increase in pH enhances oxygen release
B. Promotes interactions with BPG
C. Promotes binding of CO2
D. promotes uptake of protons from blood buffering system
E. facilitated transport of CO2 as carbonic acid/bicarbonate
A
A. increase in pH enhances oxygen release
as pH increases Hb affinity for oxygen increases
9
Q
what correctly describes the usefulness of SNAREs
A
-they are effective at overcoming electrostatic repulsion between vesicle membranes
-they facilitate anchoring between vesicle membranes
-they are essential for proper post-translational processing(??)
10
Q
how to tell if a protein fragment is the C-term(end) fragment
A
it doesnt end with one of the residues the enzyme will cleave at
11
Q
what residues does trypsin cleave
A
lysine(K)
arginine(R)
12
Q
what residues does chymotrypsin cleave
A
Phe(F)
Trp(W)
Tyr(Y)
13
Q
what residues does elastase cleave
A
Ala(A)
Gly(G)
Ser(S)
Val(V)
14
Q
Bronsted Lowry acid and base definition
A
acid: proton doner
base: proton acceptor
15
Q
Henderson-Hasselbalch equation
A
pH=pKa + log(deprotonated/protonated)
16
Q
titration curve inflection point definition
A
point where enough base has been added to neutralize 50% of the acid
17
Q
titration curve equivalence point definition
A
point where enough acid has been added to neutralize all the acid
18
Q
how many inflection points will a triprotic acid have
A
3
19
Q
characteristics of non polar aliphatic AAs
A
-hydrophobic interactions
-minimize contact with water
-will not participate in H bonding or ionic/dipole interactions
20
Q
AAs with non polar aliphatic R groups
A
Gly(G)
Ala(A)
Pro(P)
Leu(L)
Ile(I)
Val(V)
Met(M)
(non player) guys always propose like its very magical
21
Q
characteristics of aromatic R groups
A
classified by bulk and polarity
-Phe and Trp are non-polar
-Tyr is polar uncharged
22
Q
AAs with aromatic R groups
A
Phe(F)
Tyr(Y)
Trp(W)
23
Q
characteristics of uncharged polar AAs
A
-uncharged at pH 7.4
-hydrophelic
-like to H bond
24
Q
AAs with uncharged polar R groups
A
Ser(S)
Gln(Q)
Thr(T)
Asn(N)
Cys(C)
(underrespected) sisters quietly trip newborn cats
25
characteristics of positively charged AAs
-like ionic interactions
-H bond donors
26
AAs with positively charged R groups
His(H)
Arg(R)
Lys(K)
(positive) his reagent king
27
characteristics of polar negatively charged AAs
-like ionic interactions
-H bond acceptors
28
AAs with negatively charged R groups
Asp(D)
Glu(E)
29
pKa of free amino and carboxyl groups
amino: 9
carboxyl: 2
30
how to read a hydropathy scale
highly hydrophobic: high and positive numbers
highly hydrophilic: high and negative numbers
31
isoelectric point
pH where molecule has no net charge(less soluble)
32
pKa of amino and carboxyl group in a polypeptide
amino: 8.5
carboxyl: 3.5
33
what does the "yl" suffix mean when attached to an AA
that AA is in the middle of a polypeptide chain
34
average molecular weight of AAs
110 daltons
35
ways to detect proteins
UV
Bradford Assay
Beer-Lambert law
36
UV detection of proteins
-works on aromatics
-260-280 nm
-not very sensitive
37
bradford assay detection of protein
-uses coomasie blue
-measure 595 nm
-highly sensitive
38
beer-lambert law
A=elc
A:absorbance
e:extinction coefficient
l:pathlenght
c:concentration
39
extinction coefficient
.02 mL mg-1 cm-1
40
typical AA pathlength
1 cm
41
protein purification steps
isolate
detect
assay activity
separate
quantitate
42
protein separation techniques
salting out
ion exchange
hydrophobic interactions
gel filtration
affinity chromatography
43
ways to quantitate protein
gel electrophoresis
isoelectric focusing
44
what AA residue prevents fragments from getting lost in solution
Cystein
45
steps of edman degradation
separate chains
cleave disulfide bonds
determine composition
end group determination
cleave into smaller fragments
repeat previous step
sequence peptide
reconstruct protein
46
how to cleave disulfide bridges
2-mercaptoethanol: reducing agent
iodoacetate: caps newly formed ends
47
how to determine the N-term end
dansyl chloride
FDNB
48
how to determine the C-term end
carboxy peptidase
49
what enzymes are used to cleave proteins in the edman degredation
Trypsin
chymotrypsin
CNBr
50
mass spectrometry to determine protein
-quick and accurate
-measure mass-to-charge(m/z) in gas phase
51
electrospray ionization
used to generate gas phase for mass spectrometry
52
protein conformation characteristics
-40% double bond character makes it rigid
-planar
-trans conformation almost always favored
-described through tosion angles(phi and psi)
53
a-helix numbers
3.6 residues per turn
1.5 rise per residues
5.4 rise per turn
54
a-helix characteristics
-right hand spiral
-net dipole: neg to N-term side
-prefer AA with +charge at N side and - charge at C side
55
B sheet characteistics
backbone H bonds with neighboring polypeptide chains, prefers AA with small R groups
-Parallel: right hand twist, L AA, >5 strands
-Antiparallel: crossover connections that have a-helices, smaller structures
56
what protein structure are prosthetic groups included
tertiary structure
57
what type of interaction occurs between subunits of quaternary protein structure
non covalent
58
globular protein structure
-highly folded and compact
-spherical with hydrophobic core
-most common
-contains many a-helices and B-sheets
59
fibrous protein structure
repeating secondary structure
60
fibrous protein examples
keratin
collagen
61
keratin structure
coiled coil
resembles a-helix
many layers
62
collagen structure
collagen triple helix
1/3 of residues are gly
30% of residues are pro and Hypro
63
T/F non standard AA are modified then added to the sequence
FALSE. the parent is added then its modified
64
what stabilizes collagen triple helix
H bonding between hydroxylated AAs
65
what stabilizes collagen
covalent crosslinks between Lys and His residues
66
what makes up 30% of the human body, provides strength, and is found in connective tissue
collagen
67
interactions of tertiary structure and what they do
-hydrophobic interactions: major determination of protein structure
-van der waals forces: dipols stabilize folded protein
-H bonds: minor contributor to protein stability
-ion pairs: minor contributor to protein stability, 75% of charged residues are in ion pairs
-disulfide bonds: "lock in" backbone folding pattern
68
where are disulfide bonds common and not common
common: proteins secreted from the cell
uncommon: intracellular proteins
69
ligand definition
any molecule that reversibly binds to a protein
70
p50
affinity
71
Y describes what for Hb and Mb
fractional saturation
72
Po2
partial pressure
73
Fe coordination
4 nitrogens
His residue
O2(acts as 6th ligand to Fe)
74
what holds the heme in place
Val E11
Phe CD1
75
Distal His Vs. proximal His in heme
distal his: binds to O2 to stabilize it
proximal his: bound directly to Fe
76
what residues can bind to the heme with higher affinity than O2
CO
NO
H2S
77
factors affecting association constant
affinity
ligand concentration
78
association constant equation
Ka = bound/free
79
what is the dissociation constant dependent on
affinity
80
dissociation constant equation
Kd = free/bound
81
where is Kd found on a binding curve, how to read it
Kd=where [L] is .5 FS
-low Kd: high affinity
-high Kd: low affinity
82
what stabilizes T state
ion pairs between protomers
83
what characteristics do ion pairs give to the T state
increased PK
less acidic
hold onto protons
84
how does the level of ion pairs in R state impact it
absent ion pairs
-low PK
-more acidic
-gives up protons
85
Po2 in venous and arterial blood
venous: 30 torr
arterial: 100 torr
86
P50 Mb vs Hb
Mb: 2.8 torr
Hb: 26 torr
87
factors affecting Hb affinity
Bohr effect
[CO2]
[BPG]
88
bohr effect of Hb affinity
as pH increases([H+] decreases) affinity increases
89
characteristics of BPG
-binds tightly to T state
-lowers affinity for O2
-helps unload O2 in tissues
-low affinity in fetal Hb
90
how does the blood buffering system keep pH stable
low pH: equalibrium shifts to H2CO3 to produce CO2 for exhalation in lungs
high pH: breathing is adjusted to increase CO2 for H2CO3 production
91
what is carbamation
CO2 binds to N-terminal groups to form carbamates
92
functions of carbamation
-aids in CO2 transport to lungs
-increases bohr effect by releasing H+
-form ion pairs to stabilize T-state
93
T/F carbamation is more likely to occur in the R state than the T state
FALSE. T binds more CO2 than R
94
allosteric effects
binding at one site affects binding at another site
95
negative allosteric effectors
bind at different location than O2
-CO2
-BPG
96
cause of sikle-cell anemia
Val replaces Glu on surface of B-chains allowing it to enter hydrophobic pockets to form long cells of proteins
97
enzyme classifications and what they do
-oxidoreductase: oxidation-reduction
-transferase: transfer functional groups
-hydrolases: hydrolysis
-lyasses: group elimination to form DB
-isomerase: isomerization (rearrangement)
-ligases: bond formation with ATP hydrolysis
98
cofactor definition
functional groups of proteins that facilitate acid-base reactions, transient covalent bonds, and charge-charge interactions
99
types of cofactors
metal ions
coenzymes
100
types of coenzymes
cosubstrate: transiently attached
prosthetic groups: permanently attached
101
holoenzyme definition
catalytically active enzyme with cofactor complex
102
apoenzyme
enzyme without cofactor
103
2 assumptions of michaelis menten equation
equilibrium assumption
assumption of steady state
104
equilibrium assumption
-E + S reversibly bind to form ES
-this association is at rapid equilibrium
-Ks = k-1/k1
105
assumption of steady state
[ES] can be treated as a constant
106
michaelis menton equation when [S] = km
1/2 vmax
107
michaelis menton equation when [S] >> km
vmax
108
michaelis menton equation when [S] << km
(vmax/km) x [S]
109
where is km found on a michaelis menten plot
at [S] when Vo = 1/2 vmax
110
Kcat equation
vmax/[ET]
111
what does Kcat/km describe
substrate specificity(you want a high number)
112
Kcat/km of catalytically perfect enzymes
10^9 M-1 s-1
113
characteristics of competitive inhibition
-competes with substrate for binding site
-can be overcome by high [S]
affects binding not chemistry
114
pattern for lineweaver burk plot of competitive inhibition
intersecting pattern
115
parameters and how they are effected on a lineweaver burk polot for competitive inhibition
-km/vmax(slope-binding): increases with inhibitor(binding decreased)
-vmax:(y-int-chemistry): no effect
-km(x-int-affinity): larger km with inhibitor(apparent affinity decrease)
116
characteristics of uncompetitive inhibition
-binds to enzyme substrate complex
-can not be overcome by high [S]
-affects chemistry not bonding
117
parameters and how they are effected on a lineweaver burk polot for uncompetitive inhibition
-km/vmax(slope-binding): no effect
-vmax:(y-int-chemistry): chemistry decreases with inhibitor
-km(x-int-affinity): larger km with inhibitor(apparent affinity decrease)
118
characteristics of mixed/non-competitive inhibition
-inhibitor does not bind to active site
-only partially overcome by high [S]
-can bind to either E or ES
-all parameters are effected/binding, chemistry, and affinity decresed
119
pattern for LWBP for uncompetitive inhibition
parallel pattern
120
where do the lines intersect on a LWBP for mixed inhibition favoring E binding
above the X-axis
121
where do the lines intersect on a LWBP for mixed inhibition favoring ES binding
below the X-axis
122
what parameter is most effected on the LWBP for mixed inhibition favoring E binding
kcat/km
(binding)
123
what parameter is most effected on the LWBP for mixed inhibition favoring ES binding
vmax
(chemistry)
124
characteristics of pure noncompetitive inhibition
-equal affinity for E and ES
-very rare
125
where do the lines meet on the LWBP for pure noncompetitive inhibition
on the X-axis
126
how do irreversible inhibitors bind to enzyme
covalent bonds permanently modify enzyme
127
how to distinguish irreversible inhibitors from pure noncompetitive
flood system with buffer to see if inhibitor comes off
128
kinetic parameters and how they are effected for sequential reactions
increased B increases binding(vmax/km), chemistry(vmax), and affinity(km) of A
129
types of sequential reactions
ordered sequential
random sequential
130
characteristics of ordered sequential reactions
-compulsory order of substrate addition
-substrate B cannot bind without substrate A bound
-all substrates must bind before chemistry can occur
131
example of ordered sequential reaction
lactate dehydrogenase
132
characteristics of random sequential reactions
-no preferred order of substrates
-no leading substrate
-all substrates must bind before chemistry can occur
133
example of random sequential reaction
creatine kinase
134
kinetic parameters and how they are effected for ping pong reactions
vmax/km(slope-binding) is unaffected)
chemistry and affinity are affected
135
characteristics of ping pong reactions
-one or more products may release before all substrates have bound
-alternate enzyme form (F) is produced at half reaction
- binding of A and B are not related(each substrate binds to different enzyme form)
136
example of ping pong reaction
aspartate transaminase
137
characteristics of transition state analogues
-chemically and structurally similar to transition state
-effective enzyme inhibitors
-bind more strongly than substrate or inhibitor
137
uses for transition state analogues
study binding
138
specific vs general acid base catalysis
specific: H+ or OH- diffuse from solution
general: proton transferred in transition state
138
covalent catalysis
accelerates reaction through catalyst-substrate covalent bond
(enzyme as nucleophile, substrate as electrophile)
139
example of acid-base catalysis? whats the base? whats the acid?
RNase
Base: His 12
Acid: His 119
140
uses for metal ion catalysis
-orient substrates
-mediate redox rxns by changing oxidation state
-stabilize/shield negative charge
141
metalloenzyme vs. metal activated enzymes
metalloenzyme: bind tightly
metal activated: bind loosely
142
what causes the oxyanion hole
conformation distortions from formation of tetrahedral intermediate forcing the carbonyl carbon deeper into the active site
143
T/F serine proteases preferentially bind the transition state
TRUE
144
how does affinity for the transition state impact rxn rates
the more tightly it binds the transition state the greater the rate of rxn
145
characteristics of aspartic protease
-2 active site aspartic acid residues
-active in acidic pH
-important in digestion and blood pressure regulation
146
functions of aspartic acid residues in aspartic proteas
-asp 32 with carbonyl acts as nucleophile to extract proton
-asp 215 donates proton
147
example of aspartic protease
HIV-1 protease
148
what are protease inhibitors
transition analogues
149
methods of enzyme regulation
-availability (synthesis/degradation)
-proteolysis
-allosteric regulation
-covalent modification
150
problem with synthesizing/degrading enzymes as needed
too slow
requires energy
151
proteolysis definition
producing enzyme in inactive form and activating when needed
152
characteristics of allosteric regulation
-local
-rapid
-can be negative or positive feedback effectors
153
characteristics of covalent modification
-global
-reversibly convert enzyme between active and inactive form
154
example of allosteric regulation? what are its effectors?
aspartate transcarbamoylase
positive: ATP(stabilize R state)
negative: CTP(stabilize T state)
155
example of covalent modification? what are its effectors?
glycogen phosphorylase
positive: AMP
negative: ATP
156
isoenzymes
enzy,mes with similar but not identical AA sequences that catalyze the same biochemical rxns
157
where do isoenzymes differ
kinetic parameters
regulation methods
158
example of isoenzymes
hexokinase and glucokinase
159
enantiomers
mirror images
160
epimers
differ at 1 carbon
161
pyran
5 carbon ring
162
furan
4 carbon ring
163
anomeric carbon
carbonyl carbon used for cyclic formation
164
anomers
carbohydrates that differ only at anomeric carbon
165
how does cyclization happen
hydroxyl end reacts with carbonyl carbon
166
sugar derivatives
-oxidation of aldehydes to carboxylic acids
-oxidation of primary alcohols to uronic acids
-reduction of aldoses and ketoses to ribitols
-amination
167
uses for aminated sugars
enzymes
transport proteins
receptors
hormones
structural proteins
168
what are aminated sugars important for
glycoproteins and glycolipids
169
lactose makeup
glucose and galactose
B (1-->4)
170
sucrose makeup
glucose and fructose
a (1-->2)
171
cellulose makeup
glucose
B (1-->4)
172
chitan makeup
N-acetlyglucosamine
B (1-->4)
173
starch makeup
glucose
amylose: a (1-->4)
amylopectin: a (1-->4) & a (1-->6)
174
characteristics of glycogen
-used for storage
-mainly in skeletal muscle and liver
-highly branched in amylopectin
175
glycosaminoglycans
-components of connective tissue and synovial fluid
-often found in joint supplements
176
how are sugars attached to proteins to form glycoproteins
through either O-glycosidic or N-glycosidic bonds
177
proteoglycans
made of proteins + glycosaminoglycans
178
what acts as a secondary energy reserve after glycogen
triacylglycerides
179
what lipid types make up membranes
glycerophospholipids
sphingolipids
180
common classes of glycerophospholipids
ethanolamine
choline
serine
myo-inositen
glycerol
phophatidylglycerol
181
ethanolamine structure
-CH2CH2NH3+
182
choline structure
-CH2CH2N(CH3)3+
183
serine structure
-CH2CH(NH3+)COO-
184
myo-inositen structure
cyclic pyranose
185
glycerol structure(for glycerophospholipids)
CH2CH(OH)ch2OH
186
phosphatidylglycerol structure
glycerol with phosphate and 2 R groups attached
187
what makes up myelin sheath for axons
sphingolipids
188
basic unit of sphingolipids
ceraminde
189
what happens if sphingolipids dont degrade properly
development of fatal neurological diseases
190
cerebrosides
sphingolipid with 1 sugar head groups
191
gangliosides makeup
sphingolipid with 3 or more sugars, at least one is sialic acid
192
function of gangliosides
-primary componant for brain lipids
-pituitary receptors for hormones that regulate physiological function
193
what steroid is the precursor for almost all other steroids
cholesterol
194
what are cholesterol esters? why are they bad?
FA chain added to cholesterol, makes it more hydrophobic leading to it thickening the artery wall
195
how are steroid hormones classified
based on the physiological response they evoke
196
types of steroid hormones
glucocorticoids
mineralcorticoids
androgens/estrogens
197
what type of steroids are synthesized by the adrenal gland
glucocorticoids
mineralcorticoids
198
function of glucocorticoids
carbohydrate, protein, and lipid metabolism
199
function of mineralcorticoids
regulate excretion of salt by kidneys
200
T/F steroid hormones must bind to a protein for transport
TRUE. bc they are water insoluble
201
function of vitamin D
regulate calcium metabolism
202
function of vitamin A
forms retinol(defficiency leads to blindness)
203
function of vitamin K
blood clotting
204
what vitamins daily requirement is 1/2 supplied by intestinal bacteria
K
205
function of vitamin E
antioxidant
206
characteristics of isoprenoids
-soluble in lipid bilayer
-5C skeleton
207
non membrane functions of isoprenoids
-signaling lipids(ex. eicosonoids)
-lipid cofactors
-pigments/antioxidants
208
what isoprenoid functions as electron transport within the ETC
ubiquinone/coenzyme Q
209
why are glycerophospholipids used for the lipid bilayer but not FAs
glycerophospholipids have 2 tails that prevent water pockets
210
what structure is commonly used for drug delivery
liposomes
211
transverse diffusion of lipids
transfer of lipids across bilayer
212
lateral diffusion
lipids are highly mobile in plane of bilayer
213
T/F lipid bilayers are relatively symmetrical
FALSE. sugars on the outside, proteins of the inside
214
how to increase transition temp
increase chain length
increase saturation of FAs
215
peripheral proteins
-bind to surface of lipids and easily dissociate
216
example of peripheral protein
phospholipase
217
integral proteins
-embed in one side of bilayer
-amphiphiles
218
example of integral protein
bacteriorhodopsin(used in retina)
219
structure of rhodopsin
7 helical segments
220
T/F hydropathy plots can show how many segments are in a protein
TRUE
221
lipid linked protein types
prenylated
fatty-acid linked
glycosylphosphatidylnositol
222
characteristics of glycosylphosphatidylnositol
-most elaborate lipid linked protein
-always attached to the C-term end
223
characteristics of prenylated lipid linked proteins
covalently attached proteins made of isopren units
224
proteins within membrane skeleton
ankyrin
spectrin
225
characteristics of spectrin
-makeup 75% of membrane skeleton
-composed of repeating segments that fold into triple stranded helix
226
proteins that associate with lipid rafts
GPI-linked
TM signaling
Various viruses
227
caveolae
specialized form of lipid raft that participates in endocytosis
228
where do partially processed TM proteins appear
golgi apparatus
229
post translational modification in golgi apparatus
-antiretrograde: cis-to-trans transport
-retrograde: trans-to-cis transport
230
coated vesicles and their functions
COP1: return escaped ER proteins from golgi
COP2: transport from ER to golgi
Clatherin: transport from golgi to plasma membrane
231
clathrin cages
flexible 3 legged proteins(triskelions) that form a vertex
232
R-SNARE vs. Q-SNARE
R-SNARE: Arg residue, vesicle membrane
Q-SNARE: Gln residue, target membrane
233
function of SNAREs
-link vesicles to plasma membranes for diffusion
dissociation mediated via ATpase and SNAP protein
234
equation for membrane potential
inside potential-outside potential
235
what is commonly referred to as the inside of the membrane
cytosol
236
T/F the overall membrane potential is most often positive
FALSE. it is more often negative
237
ionophore passive transport
bacterial molecules that carry ions across membrane
238
carrier ionophores vs. channel forming ionophores
carrier: bind to ion for diffusion
channel forming: from transmembrane channels
239
example of carrier ionophore
valinomyecine (transports K+)
240
porin ion transport characteristics
-B barrels
-simple
-always open
-located in outer membrane
-selective
241
example of selectivity in porins
TYR 118 acts as steric barrier only allowing planar molecules through
242
example of porin
maltodextrin: degradation of starch
243
characteristics of ion channels
-rapid passage
-ion concentrations must be maintained in cell
244
functions of ion channels
-signal transduction
-change membrane potential(neurotransmission)
-maintain osmotic balance
245
why do K+ ion channels dehydrate the K+
to keep water in cytosol
246
T/F gated ion channels are continuously open
FALSE. they remain closed unless acted upon by stimuli
247
aquaporins
-water transports
-prevent proton jumping
-made of 8 a-helices
248
connexins
form channels known as gap junctions for transport proteins
249
example of transport protein using connexins
GLUT1
250
types of transport proteins
uniport
symport
antiport
251
symport vs antiport
symport: two molecules transported in the same direction
antiport: two molecules transported in different directions
252
primary vs secondary active transport
primary: energy directly related to moving substrate
secondary: energy produced from movent of another substrate brings desired substrate with it
253
P-type active transporters
Na/K ATPase
Ca ATPase
254
F-type active transporters
ATP-dependant proton transport
F1-Fo ATPase
255
function of Na/K ATPase
antiport
3 Na out
2 K in
256
structure of Ca ATPase
4 unique domains
257
function of F1-Fo
proton transported by Fo
Formation of ATP by F1
