biochem Flashcards
(576 cards)
1
Q
what two groups do AA contain
A
amino and carboxyl
2
Q
amino group
A
NH2
3
Q
the α-carbon of most AA is a chiral center. what is the exception?
A
glycine, it has a H as R
4
Q
all chiral AA in us are ____-amino acids
A
L
5
Q
in a Fischer of L-AA, what group is drawn on the left?
A
NH2
6
Q
all AA have a S configuration except ________
A
cysteine
7
Q
non polar, non-aromatic AA (7)
A
glycine, alanine, valine, leucine, isoleucine, methionine, proline
GAVLIMP
8
Q
which AA forms a cyclic structure
A
proline
9
Q
aromatic AA (3)
A
TPT
tryptophan, pheynalanine, tyrosine
10
Q
which AA has a double ring structure?
A
tryptophan
11
Q
what is phenylalanine side chain
A
benzyl ring + CH2
12
Q
adding ____ to phenylalanine makes tyrosine
A
OH
13
Q
which aromatic AA is polar
A
tyrosine
14
Q
polar, non-aromatic AA (5)
A
serine, threonine, asparagine, glutamine, cysteine
STAGC
stage with a C
15
Q
serine and threonine have _____ in their R
A
-OH
16
Q
asparagine and glutamine have ______ side chains
A
amide
17
Q
amide
A
NH2 - C = O
18
Q
what is cysteine’s side group
A
thiol, -SH
19
Q
which AA is particularly prone to oxidation? why
A
cysteine, thiol is weaker than OH
20
Q
negative, acidic AA (2)
A
aspartate and glutamate
21
Q
rather than amides of asparagine/glutamine, aspartate/glutamate have ______ group
A
COO-
22
Q
aspartate/glutamate is the _________ form of aspartic/glutamic acid
A
deprotonated
23
Q
positive, basic AA (3)
A
lysine, arginine, histidine
LAH
24
Q
which AA has an imidazole
A
histidine
25
which AA are hydrophobic
long side chain AA
alanine, leucine, isoleucine, valine, phenylalanine
26
which AA are hydrophilic
charged
LAH + aspartate + glutamate
27
pKa
pH at which half of the molecules are protonated
| [HA] = [A-]
28
if pH < pKa, most will be
protonated
29
all AA have at least _____ pKa values
2
30
which pKa is first
2, carboxyl
31
which pKa is usually second
9-10, amino
32
when pH is close to pKa, the solution acts as a
buffer
33
pH = isoelectric point (pI) when
every molecule in the solution is a zwitterion (neutral)
34
how do you find the pI of an uncharged AA
average of pKa of amino & pKa of carboxyl
| ~6
35
how do you find pI of a negatively charged (acidic) AA
average of pKa of side group + pKa of carboxyl
36
how do you find pI of positively charged (basic) AA
average of pKa of amino + pKa of R group
37
basic AA have ______ pI
high, > 6
38
acidic AA have ___ pI
low, < 6
39
amino acid subunits make up a
peptide
40
what type of reaction is a peptide bond formation
condensation/dehydration
41
how do trypsin and chymotrypsin break the peptide bond
add H to amide N and OH to carbonyl, add H2O
42
where does trypsin clave
C-terminus of arginine and lysine
43
where does chymotrypsin cleave
C-terminus of non polar aromatic AA (phenyl, tryptophan, tyro)
44
what stabilizes primary structure
covalent peptide bonds between AA
45
what stabilizes secondary structure
hydrogen bonding between AA
46
what stabilizes an α-helix
hydrogen bond between = O and and an amide H from four AA away
47
in an α-helix, the side chains point
away from core
48
what is the α-helix important in
keratin
49
what stabilizes a β-sheet
hydrogen bond between = O of one chain and amide H of the adjacent chain
50
in a β-pleated sheet, the side chains point
above and blow the plane
51
what is the β-sheet important in
fibroin, silk fibers
52
what AA is not found in α-helices? why?
proline, it can make it kink
53
where is proline found in secondary structures
turns of a β-sheet or start of an α-helix
54
proteins that resemble sheets or strands are _______
fibrous
55
proteins that are spherical are ______
globular
56
what stabilizes tertiary structure
hydrophilic and hydrophobic interactions between R groups
57
what type of bond is important in tertiary structure
disulfide bonds
58
cysteine + cysteine =
cystine
59
what do disulfide bonds do
create loops in the chain
60
there is a _____ change in entropy when a hydrophobic solute is in water
negative, water surrounds in to maximize hydrogen bonding
61
what makes solvation more favorable after a solute is initially dropped
the hydrophilic move towards water, hydrophobic move to anterior
this allows water to spread out and increases entropy
62
quaternary structure only exists for proteins with
more than one chain
63
conjugated proteins
get some function from covalently attached prosthetic groups
64
oxidoreductase
catalyze oxidation-reduction reactions
65
oxidoreductaases often have
cofactors that carry electrons (NAD+, NADP+)
66
reductant
molecule that gives electrion
67
oxidant
molecule that receives electron
68
ΔG and ΔH _________ by catalysts
stay the same
69
enzymes active site is in appropriate conformation for substrate to bind, no alteration occurs. this is the __________ theory
lock and key
70
the shape of the active state becomes a good fit after the substrate begins to bind. this is the _________ theory
induced fit
71
apoenzymes
enzyme without their cofactor
72
holoenzymes
enzymes with their cofactor
73
cofactors
inorganic molecules or metal ions
74
coenzymes
organic groups
75
water-soluble enzymes (2)
vitamin B and ascorbic acid (vitamin C)
76
fat-soluble enzymes
A, D, E, K
77
vitamins and derivates are co__________
enzymes
78
thiamine
B1
79
riboflavin
B2
80
niacin
B3
81
pantothenic acid
B5
82
pyridoxal phosphate
B6
83
biotin
B7
84
folic acid
B9
85
cyanocobalamin
B12
86
Vmax = __________ of enzyme
saturation
87
how do you increase Vmax at saturation
increase concentration of enzyme
88
write the Michaelis-Menten equation
K1 Kcat
E + S ES --> E + P
K-1
89
velocity of MM equation
v = Vmax * [S]
__________
Km + [S]
90
when at 1/2 Vmax, Km =
[S]
91
what is Km
Michaelis constant, the concentration where half of the active sites are full
92
a higher Km = _________ affinity
lower
93
you ______ change Km
cannot
94
Vmax equation
Vmax = [E]kcat
95
kcat
of substrates converted to product per enzyme in a second
96
catalytic efficiency
Kcat / Km
97
an efficient enzyme will have a ____ Kcat and ____ Km
large, small
98
when will a enzyme show a sigmoidal curve on MM plot
when it has cooperativity
99
Hill's coefficient > 1
positive cooperative binding
100
Hill's coefficient < 1
negative cooperative binding
101
Hill's coefficient = 1
no cooperative binding
102
feedback regulation
enzymes regulated by products produced later in the pathway
103
feedforward regulation
enzymes regulated by intermediates preceding the enzyme in a pathway
104
four types of reversible inhibition
competitive, noncompetitive, uncompetitive, mixed
105
competitive inhibition
substrate cant bind if something is blocking the site
106
how do you overcome competitive inhibition
add more substrate to outcompete
107
competitive inhibition
Vmax ____________
Km _____________
Vmax stays the same - there is enough enzymes
| Km increases - need more substrate to outcompete
108
noncompetitive inhibition
inhibitor binds to an allosteric site, which induces an unfavorable change in conformation
inhibitor can bind the enzyme or enzyme-substrate complex, but binds them both equally
109
noncompetitive inhibition
Vmax ____________
Km _____________
Vmax decreases - less enzyme available
| Km stays the same - affinity doesn't change
110
mixed inhibition
inhibitor can bind to either enzyme or enzyme-substrate complex, but prefers one or the other
111
if a mixed inhibitor prefers the enzyme
Vmax ____________
Km _____________
Vmax decreases - less enzyme available
| Km increases - makes the enzyme not want substrate
112
if a mixed inhibitor prefers the enzyme-substrate
Vmax ____________
Km _____________
Vmax decreases - less enzyme
| Km decreases - makes the enzyme want substrate so it can bind
113
uncompetitive inhibition
bind only to enzyme-substrate complex and prevents release of substrate
114
uncompetitive inhibition
Vmax ____________
Km _____________
Vmax decreases - less enzyme free
| Km decreases - want substrate there
115
motif
repetitive organization of secondary structures
116
collagen structure
trihelical, three left-handed helices forming a secondary right-handed helix
117
collagen function
strength and flexibility
118
elastin function
restores shape of connective tissue, acts like a spring
119
keratin function
mechanical integrity of cell
regulatory protein
primary protein in hair and nails
120
actin function
make up microfilaments
121
actin structure
positive and negative side, polarity allows motor proteins to travel unidirectionally
122
tubulin function
makes up MT
123
tubulin structure
negative end next to nucleus, positive end in periphery
124
motor protein involved with actin
myosin
125
motor proteins involved with tubulin
kinesin and dynein
126
kinesin function
align chromosomes during metaphase
| depolarize MT during anaphasa
127
dynein function
sliding movement of cilia and flagellaa
128
kinesin & dynein also play a role in vesicle transport. how?
kinesin bring vesicle towards + end of MT
| dynein bring vesicle towards - end of MT
129
CAMS are all ________ membrane proteins
integral
130
CAMs
bind cell to ECM or other cells
131
three families of CAMs
cadherins, integrals, selectins
132
cadherin
glycoprotein groups mediating calcium-dependent cell adhesion
133
caherins usually hold
similar cells together
134
integrin structure
β and α chains
135
integrin function
```
bind to/communicate with ECM
cellular signaling (apoptosis, division)
```
136
selectin structure
bind to carbs that project from other cells
137
weakest adhesion molecule bond
selectin bond
138
which two CAM families play a role in defense
selectin and aherin
139
what hold the chains of Ig together
disulfide linkages and noncovalent interactions
140
how do you isolate proteins and biomolecules from tissue
lysis or homogenization
141
how do you isolate proteins from smaller molecules
centrifugation
142
how do you isolate proteins from other proteins
electrophoresis and chromatography
143
migration velocity equation
v = Ez / f
```
z = net charge of molecule
f = frictional coefficient
```
144
a small, highly charged molecule in a strong E will have a _____ migration velocity
larger
145
in electrophoresis, anions will move towards the ______
anode
146
in electrophoresis, cations will mov towards the ______
cathode
147
anode is ___ charged
positive +
148
cathode is ___ charged
- negatively
149
PAGE analyzes proteins in ________ state
native
150
what is the limitation of PAGE
you should know their size to be able to compare their charge
since a small positive molecule can move the same distance as a large negative
151
how does SDS-PAGE improve on PAGE
it adds sodium dodecyl sulfate, a detergent
it adds net negative chains to the protein
so, they move only based on size! not charge.
152
isoelectric focusing separates proteins based on ______
pI
153
PAGE separates proteins based on ______
size and charge
154
SDS-PAGE separates proteins based on ______
size
155
how does isoelectric focusing work
the gel is a pH gradient
| the protein stops moving at its pI
156
when is chromatography preferred
when large amounts of protein are present
157
components with high affinity for absorbent/stationary phase will move _____
very little
158
retention time
amount of time a component spends in the stationary phas
159
column chromatography uses
silica or aluminum beads
160
column chromatography separates proteins based on ______
size and polarity
161
less polar = _________ retention time
short
| if non polar, it moves really fast
162
ion-exchange chromatography separates proteins based on ______
charge
163
ion-exchange chromatography uses
charged beads, attracts opposite charge
164
size-exclusion chromatography uses
beads with pores of different sizes, small compounds get stuck in beads
165
affinity chromatography uses
beads with a receptor that has affinity for a protein
166
affinity chromatography can be followed by washing the column with (2)
a free receptor, outcompetes beads and binds protein
| pH or salinity fluid
167
how to determine protein structure
XR crystallography or NMR spectroscopy
168
how to determine AA composition
hydrolysis then chromatography
169
how to determine AA sequence
sequential digestion
170
how to determine AA of a small protein (50-70 AA)
edman degradation
171
edman degradation
removes N-terminal AA of the protein
172
what follows Edman degradation
mass spectroscopy
173
how to determine AA sequence of a large AA (>70 AA)
chymotrypsin, trypsin, cyanogen bromide
| selectively clave at specific Acs to create smaller fragments
174
what follows digestion of large proteins
Edman or electrophoresis
175
how to determine concentration of a protein
spectroscopy
176
UV spectroscopy can analyze
proteins with aromatic side chains
177
what is UV spectroscopy sensitive to
contamination
178
how to determine concentration of a single protein
assays, specific color changes in reactions
179
Bradford protein assay
mixes a protein with Coomassie blue
180
coomassie blue is
protonated, green-brown in color
181
in Bradford assay, the more blue = the more
protein
182
how does Coomaassie blue turn blue
gives H+ to AA of protein
183
aldoses
carbs that contain an aldehyde as their most oxidized functional group
184
ketoses
carbs that contain a ketone as their most oxidized functional group
185
glucose aldehyde substituted with a ketone makes
fructose
186
stereoisomer
compounds with same formula different arrangement of atoms
187
enantiomers
mirror image stereoisomers
188
any molecule with ________ and no plane of symmetry has _______
chiral carbons
| an enantiomer
189
of stereoisomers =
2^n
| n = # of chiral centers
190
how to determine D or L
look at chiral center furthest from carbonyl
if OH is on the right - D
if OH is on the left - L
191
diastereomers
two sugars with same # of carbons but aren't identical or mirror images
192
epimers
a type of diastereomer that differs at one chiral center
193
five-membered rings of carbs
pyranose
194
six-membered rings of carbs
furanose
195
anomeric carbon
carbonyl carbon that forms a ring
196
anomers
two molecules that differ at the anomeric carbon
197
α-anomer
-OH of C1 trans to CH2OH
198
β-anomer
-OH group of C1 cis to CH2OH
199
mutarotation
interconversion between α and β anomie's via ring opening and closing
occurs in water, faster if acid or base is present
200
aldonic acid
oxidized aldoses
201
reducing sugar
any sugar with a hemiacetal ring (aldehyde)
202
oxidation of an aldose yields
a lactone
203
lactone
looks like sugar but with = O instead of CHOH
204
what reagents test for reducing sugars
Tollen's and Benedict's
205
[Ag(NH3)2]+
Tollen's reagent
206
what does Tollen's reagent do in the presence of aldoses
produces a silvery mirror
207
Cu(OH)2
Benedict's reagent
208
what does Benedict's reagent do in the presence of aldoses
form a red Cu2O
209
glucose oxidase
can be used to test presence of just glucose, only oxidizes it
210
nitric acid
oxidizes aldehyde and the primary OH on C6
211
tautomerization
rearrangement of bonds in a compound
212
do ketoses react with Tollen's/Benedict
yes, they tautomerize to aldehydes
213
carbohydrates can react with carboxylic acids through
esterification
214
hemiacetal + alcohol =
acetal/glycosides
215
glycosidic bonds
C - O bond at the anomeric carbon of an acetal
216
glycoside formation is a _________ reaction
dehydration
217
maltose
glucose-α-1,4-glucose
218
lactose
galactose-β-1,4-glucose
219
sucrose
glucose-α-1,2-fructose
220
cellulose structure
homopolysaccharide
| β-1,4 bonds
221
cellulose function
fiber, draws water into our gut because we cannot digest it
222
starch (amylose) structure
homopolysaccharide
| linear α-1,2
223
amylopectin structure
homopolysaccharide
linear α-1,2
+ branches of α-1,6 (1/25)
224
what detects the presence of starch
iodine
225
β-amylase
cleaves amylase at nonreducing end (acetal)
226
amylose + β-amylase -->
maltose
227
α-amylase
cleaves randomly along amylose
228
amylose + α-amylase -->
glucose and maltose
229
glycogen structure
homopolysaccharide
linear α-1,2
+ branches of α-1,6 (1/10, a lot more)
230
glycogen phosphorylase
cleaves glucose from acetal end of a glycogen and phosphorylates it to make glucose 1-phosphate
231
branching of glycogen benefits
makes it energy efficient, stored in body more
| allows enzymes cleaving glucose to work at a lot of sites
232
fully saturated fatty acid
has only single bonds
| strong van Der Waals, very stable
233
saturated FA form _______ at room temperature
solids, ex: butter
234
unsaturated FA
has one or more double bonds
| introduce kinks
235
unsaturated FA are ________ at room temperature
liquids, ex: olive oil
236
glycerophospholipids/phosphoglycerols
have a glycerol backbone
237
what do the phospholipids of a phosphoglycerol bind to
ester linkage to two FA
| phosphodiester linkage to a head
238
what kind of lipids are cell-surface antigens
sphingolipids
239
ceramide
sphingolipid with H as head group
240
sphingomyelin
sphingophospholipids
| phosphocholine or phosphoethanolamine as head group
241
what are sphingomyelins involved in
plasma membranes of myelin producing cells
242
sphingomyelin head groups are ______ charged
0
243
glycosphingolipids
sphingolipids with sugar as had group
244
are glycosphingolipids phospholipids
no, there is no phosphodiester linkage
245
cerebrosides
glycosphingolipids with a single sugar
246
globosides
glycosphingolipids with two or more sugaars
247
gangliosides
glycosplingolipids with polar head groups of oligosaccharides + NANA (sialic acid)
248
what do gangliosides play a role in
cell interaction, recognition, and transduction
249
waxes
esters of long-chain FA with long-chain OH
250
in plants, waxes
are secreted to prevent excessive evaporation and to protect from parasites
251
in animals, waxes
prevent dehydration and act as a lubricant
252
terpenes
lipid built from isoprene (C5H8)
253
terpenes are mostly produced from
plants, protection and smell
254
monoterpenes contain ____ isoprenes
2
255
sequiterterpenes contain ____ isoprenes
3
256
diterpenes contain ____ isoprenes
4
257
vitamin A is a ___________ from which retinal is derived
diterpene
258
triterpenes can become
cholesterol and steroids
259
tetraterpenes can become
carotenoids
260
terpenoids
terpenes that have undergone oxygenation or rearrangement
261
steroids
metabolic derivatives of terpenes
262
steroid structure
four cycloalkane rings fused together
263
steroid has ___ cyclohexane + _____ cyclopentane
3 + 1
264
what determines function of steroid
oxidation and functional groups of rings
265
cholesterol
a steroid responsible for mediating membrane fluidity
266
at high temperatures, cholesterol prevents the membrane from
becoming too permeable
267
at low temperatures, cholesterol prevents the membrane from
solidifying
268
prostaglandin structure
20-carbons, unsaturated carboxylic acids
derived from arachidonic acid
contain one 5-carbon ring
269
what do prostaglandins do
act was paracrine or autocrine signals
270
vitamin A = ___________
carotene
271
vitamin A functions
vision, growth, immune
272
vitamin A produces _______ metabolite. what does it do
retinal, it senses light in the eye
273
vitamin A is stored as _________. what does it do?
retinol, it oxidizes to retinoid acid that regulates gene expression during epithelial development
274
vitamin D = ___________
cholecalciferol
275
in liver/kidneys, vitamin D becomes _________. what does it do?
calcitriol, it increases calcium and phosphate uptake to promote bone production
276
rickets
underdeveloped, curved long bones due to impeded growth
277
vitamin E structure
aromatic ring with a long isoprenoid side chain
278
vitamin E = ____________
tocopherols and tocotorienols
279
what do tocopherols do
antioxidants, prevent oxidative damage
280
vitamin K = ________
phylloquinone and menaquinone
281
what does vitamin K do
post translational modification to form prothrombin
| introduces calcium-binding sites on several proteins
282
animals store large amounts of fat in
adipocytes
283
plants store large amounts of fat in
seeds
284
how do free FA move around
bound to albumin
285
saponification
ester hydrolysis of triacylglycerols using a strong base
286
lye
Na/KOH
287
triacylglycerol + lye =
glycerol + soap (FA salt)
288
flippass
assist flipping of lipids in the membrane
289
what transports FA from diet
chylomicrons
290
which fats are more unhealthy
saturated
291
tight junctions
prevent paracellular transport of water and solutes
292
where are tight junctions found
epithelial cells
293
desmosomes
bind adjacent cells by anchoring their cytoskeleton
294
hemidesmosomes
attach cells to underlying structure (epithelial to basement membrane)
295
which mitochondrial membrane is more permeable
outer
296
what does the inner mitochondrial membrane have a lot of? what does it not have?
a lot of cardiolipin
| no cholesterol
297
how are nucleotides joined
3'-5' phosphodiester bonds
298
DNA and RNA are overall ____ ly charged
negative
299
which nitrogenous base has two rings
purine
300
purines
adenine and guanine
301
which nitrogenous base has one ring
pyrimidines
302
pyrimidines
cytosine, thymine, uracil
303
four roles of aromaticity
1. cyclic
2. planar
3. conjugating
4. 4n+2 pi electrons (Huckels rule)
304
Watson and Crick model describes
DNA structure
305
Adenine:Thymine by ____ hydrogen bonds
2
306
Guanine:Cytosine by ___ hydrogen bonds
3
307
what provides stability for the double helix
hydrogen bonds and hydrophobic interactions btwn bases
308
B-DNA structure
right-handed
| turns every 3.4nm, 10 bases in turn
309
Z-DNA structure
zigzag, left-handed
| turns every 4.6nm, 12 bases in turn
310
what do the major and minor grooves of DNA do
provide binding sites for regulatory proteins
311
what breaks in DNA denaturation? what doesn't?
hydrogen bonds do
| phosphodiester bonds do not
312
5 histone proteins
H2A x2, H2B, H3, H4
313
H1
seals off DNA as it enter/leaves nucleosome, stabilizes
314
DNA + histones =
nucleosome
315
heterochromatin
compacted chromatin, often repetitive sequences
| does not get transcribed
316
euchromatin
dispersed chromatin, genetically active DNA
317
TTAGGG
telomere sequence
318
telomere contributions
aging
| knots off end to prevent unraveling
319
what kind of DNA makes up centromeres
heterochromatin
320
replisome
set of proteins helping DNA polymerase
321
origins of replication
where DNA unwinds
322
helicase
unwinds DNA
323
single-stranded DNA binding proteins
bind to the unraveled strands to prevent them from binding back together
324
nucleases
degrade DNA
325
DNA topoisomerase
reduces torsional stress but introducing negative supercoils
| break and reseal strand
326
semiconservative model
one parental strand, one daughter strand
327
DNA polymerase III (α, δ, ϵ - eukaryotes)
read the parent and make the daughter
328
DNA polymerase reads __' to ____' and makes ___' to ____'
reads 3' to 5'
| makes 5' to 3'
329
Okazaki fragments
small strands made on the lagoon strand
330
primase
makes a short RNA primer in the 5' to 3' direction to start replication
331
DNA polymerase I (RNAase H - eukaryotes)
removes RNA primers
332
DNA polymerase I (δ - eukaryotes)
adds DNA where RNA primer was
333
DNA ligas
seals DNA fragments into a complete strand
334
DNA polymerase γ
replicates mitochondrial DNA
335
DNA polymerase δ and ϵ
forms a sliding clamp with PCNA, strengthens interaction between polymerases and template
336
DNA polymerase β and ϵ
DNA repair
337
DNA gyrase
removals supercoils to reduce torsional stress in PROKARYOTES
338
which strand has is more methylated
parent, been there longer
339
what proofreads DNA
DNA polymerase, checks for unstable bonds between bases
| matches the more methylated strand
340
mismatch repair occurs
during G2
341
what do mismatch repair enzymes do
(MSH2 and MLH1)
| detect errors missed during S phase
342
whaat does nucleotide excision repair remove
thymine dimers
343
steps of nucleotide excision repair
1. proteins scan DNA and notice a bulge
2. excision endonuclease cuts pieces of the phosphodiester backbone on bond sides of the thymine dimer
3. it removes the messed up nucleotide
4. DNA polymerase replaces it
5. DNA ligase seals it
344
what causes thymine dimers
UV light
345
what causes cytosine deamination
heat
346
what happens when cytosine is deaminated
it becomes uracil
347
steps of base excision repair
1. cytosine is recognized as uracil
2. the base is removed by glycosylase enzyme
3. apurinic/apyrimidic (abasic) site is left
4. AP endonuclease recognizes site
5. it removes the sequence of DNA
6. DNA polymerase and ligase refill it
348
recombinant DNA
DNA multiplied by gene cloning or PCR
349
restriction endonucleases
enzymes that recognize specific dsDNA sequences
350
palindromic
two strands are identical
351
how are restriction enzymes used
cut at palindromic sequences to take sticky ends that can be used to recombine with a vector
352
what must DNA vectors have (3)
1. a sequence recognized by restriction enzyme
2. origin of replication
3. gene for antibiotic resistance - allows selection of colonies
353
DNA vs cDNA
DNA has introns and exons
| cDNA is made from mRNA so only has exons
354
hybridization
combining complementary sequences (DNA-DNA or DNA-RNA)
355
PCR can clone DNA without
bacteria amplification
356
Southern blot
detects presence and quantity of DNA strands
357
mRNA
carries AA sequence to the ribosome
358
mRNA is transcribed from _________ by _________
from a template DNA strand
| by RNA polymerase
359
what occurs in the nucleus before mRNA leaves
transcribed from DNA --> mRNA
| + posttranscriptional modifications
360
monocistromic
mRNA translates to one protein
361
polycistromic
mRNA translates to different proteins, depending where it starts
362
tRNA
converts nucleic acid sequence to amino acids
363
anticodon
pairs with specific codon on mRNA in the ribosome
364
where is mature tRNA found
cytoplasm
365
what sequence does AA bind to tRNA at
CCA
366
aminoacyl-tRNA synthetase
binds AA to 3' end of tRNA, requires ATP be broken down twice into AMP
367
what supplies the energy to create a peptide bond during translation
aminoacyl-tRNA (it has a lot of energy)
368
rRNA
part of ribosomal machinery, made in nucleolus
| help catalyze formation of peptide bonds & splices its own introns
369
each codon represents ____ AA
one
370
the codon of mRNA is recognized by
an anticodon on tRNA
371
what is the start AA
methionine
372
start codon
AUG
373
three stop codons
UAA u are annoying
UGA u go away
UAG u are gay
374
degenerate
an AA can be coded for by more than one codon
375
what does degeneracy allow
for mutations in DNA that are silent, mutation in wobble position codes for same AA
376
what strand does mRNA copy from
template strand of DNA (antisense)
377
what enzymes transcribes mRNA
RNA polymerase II
378
what must RNA polymerase II recognize
promotor regions
379
what part of the promoter region does RNA polymerase bind
TATA box, lots of thymine and adenine
380
transcription factors
help RNA polymerase find the TATAA and bind
381
RNA polymerase I
synthesizes rRNA
382
RNA polymerase II
synthesizes hnRNA (preprocessed) and snRNA (small nuclear)
383
what strand matches the mRNA strand
coding/sense DNA strand, the one not being copied from
| it will just have T instead of U
384
what number is the TATA box
about -25
385
DNA --> __________ --> mRNA
hnRNA
386
RNA polymerase III
synthesizes tRNA and rRNA
387
what are the three post transcription processes that must occur for hnRNA to become mRNA
1. intron/exon splicing
2. 5' cap
3. 3' poly-A tail
388
spliceosome
snRNA + snRNP, cuts 5' and 3' ends of introns
389
how are introns excised
as a lariat
390
7-methylguanylate triphosphate cap
added to 5' end of hnRNA
391
what does the 5' cap do
serves as binding site to ribosome
| protects mRNA from degradation when it leaves
392
polyadenosyl tail
added to the 3' end of hRNA
393
what does the 3' polyA tail do
protects mRNA against degradation, adds a ton of As that are like a ticking bomb
assists export from nucleus
394
three subunit sizes of prokaryotic ribosome
30S + 50S = 70S
395
three subunit sizes of eukaryotic ribosome
40S + 60S = 80S
396
where does the small ribosome bind in prokaryotes
shine-delgarno
397
where does the small subunit bind in eukaryotes
5' cap
398
where does the initiator tRNA bind
AUG, start codon
399
what part of the ribosome does tRNA bind to mRNA
P
400
after the small unit binds to mRNA, what happens
the large subunit binds to the small subunit
401
what helps the small and large subunits bind
initiation factors
402
order of sites in the ribosome
APE
403
A site
holds incoming amino-tRNA
| next AA being added, determined by codon in the A site
404
P site
holds tRNA carrying the chain
| where Met binds
405
what site does a peptide bond form
when a polypeptide is moving from P to A
406
what forms the peptide bond in ribosome
peptidyl transferase, requires GTP
407
E site
inactivated tRNA passes before exiting
408
what helps locate and recruit amino-tRNA and GTP
| and remove GDP
elongation factors
409
release factor
binds to termination codon, causing a water to be added to the polypeptide chain
410
what hydrolyzes the peptide chain from tRNA
peptidyl transferase and termination factors
| once water is bound
411
chaperones
assist folding of protein
412
operon
a cluster of genes that are transcribed together in bacteria
413
Jacob-Monod model
operons contain structural genes + operator + promotor + regulator
414
structural gene
codes for protein
415
operator
non transcribable region of DNA that binds a repressor protein
416
promotor
provides a place for RNA polymerase to bind
417
regulator
codes for repressor
418
operons offer
an on and off switch for gene control in prokaryotes
419
inducible system
repressor is bound to operator and blocks RNA polymerase from binding to the promotor region
OFF but can be turned ON
420
how do you remove repressors
add an inducer to remove it
421
how does the lac operon work
1. drop in glucose
2. increase in cAMP
3. cAMP binds to CAP
4. CAP binds to promotor of operon
5. transcription increases
422
lac operon is __________
inducible, it is off unless lactose levels are higher than glucose
423
repressible systems allow
constant production of a gene
424
in a repressible system, how does the repressor act
it is not bound to the operator site unless bound to a corepressor
425
trp operan is __________
repressible, tryptophan acts as a corepressor and causes the cell to stop making more tryptophan
426
enhancer
response elements outside the promotor regions, fear away so DNA must bend
427
histone acetylase
acetylate lysine on the amino terminal of histone proteins
428
what does histone acetylation do
decreases positive charge of histones, make them bind less strongly to DNA
this opens chromatin to allow for transcription of DNA
429
DNA methylation
add methyl to cytosine and adenine, silences gene
430
GLUT2 is located
in liver and pancreatic cells
431
GLUT2 function
captures excess glucose traveling through hepatic portal vein when levels are HIGH
432
Km of GLUT2 is _______
high, so liver/pancreatic cells have low affinity for glucose
433
GLUT4 location
fat tissue and muscle
434
GLUT4 reaches the membrane when
insulin is released
435
Km of GLUT4 is __________
close to glucose, so really sensitive to glucose
436
how can cells increase glucose reuptake with GLUT4
increase the # of GLUT4 on the membrane
| by releasing insulin
437
_____ cells carry out glycolysis
ALL, doesn't require mitochondria
438
GLUT transporters are specific to
glucose alone, not glucose-6-phosphate
439
hexokinase located in
tissues, inhibited by Glu6Phosphate
440
glucokinase located in
liver and pancreatic B cells, induced by insulin
441
what inhibits PFKI
ATP and citrate
442
what activates PFK1
AMP
443
insulin activates _______, which will indirectly activate PFK1
PFK2, which makes Fru6BisP --> Fru26BisP which activates PFK1
444
glucagon _____ PFK2, which inhibits PFK1
glucagon lowers P26BisP which inhibits PFK1
445
where is PFK2 mostly found
liver
446
substrate level phosphorylation
ADP phosphorylated to ATP by a high-energy intermediate
447
what activates pyruvate kinase
Fructose16BisP
448
what does lactate DH do
prevents the cell from running our of NAD+ for glycolysis
449
in yeast, what does pyruvate become
ethanol and CO2
450
in animals without oxygen, whaat does pyruvate become
lactate
451
____ --> Fru1,6BisP --> glycerol 3P --> glycerol
DHAP
452
what three enzymes catalyze irreversible reactions
hexo/glucokinase
PFK1
pyruvate kinase
453
net ATP for glycolysis
2
454
BPG mutase
makes 1,3BPG -> 2,3BPG
2,3BPG binds to Hgb and decreases affinity for oxygen (right shift)
allows oxygen to be unloaded at tissues, so increase this when oxygen levels are low
455
epimerase
catalyze conversion of one sugar epimer to another
456
what activates pyruvate DH
insulin
457
three fates of pyruvate
1. lactate by lactate DH
2. acetyl coA by pyruvate DH
3. oxaloacetate by pyruvate carboxylase
458
what factors does pyruvate DH require
thiamine pyrophosphate, lipoid acid, CoA, FAD, NAD+
459
what inhibits pyruvate DH
acetyl CoA
460
how is glycogen stored
in granules in the cytoplasm
461
glycogen granules of liner chairs have highest density of glucose
near the protein core
462
glycogen granules that are branched have highest density of glucose at
periphery, allows rapid release
463
glycogen in liver is for
release of glucose when insulin levels are low
464
glycogen in muscle is for
release of glucose when muscles are exercised
465
glycogenesis
synthesis of glycogen granules
466
glycogenin
core protein of glycogen granule
467
what stimulates glycogen synthase
insulin and Glu6P
468
what inhibits glycogen synthase
glucagon and epinephrine
469
what introduces the α-1,6 branches to the granule
branching enzyme
470
what bonds does glycogen phosphorylase braak
α-1,4
| cannot break 1,6 so stops at branches
471
what activates glycogen phosphorylase
glucagon, epinephrine, AMP
472
what inhibits glycogen phosphorylase
AMP
473
how does debranching enzyme work
one enzyme moves the branch point chain to the end of another chain
one enzyme breaks the single glucose from the branch
474
what process increases after 12 hours of fasting
gluconeogenesis, glycogen stores have depleted
475
gluconeogenesis
making glucose from things other than glucose/glycogen
476
glucogenic AA
can be converted into intermediates that can enter gluconeogenesis
all AA except leucine and lysine
477
ketogenic AA
converted into ketone bodies, used as alternative fuel
478
three substrates for gluconeogenesis
glycerol 3 phosphate from fats
lactate from glycolysis
glycogenic AA from muscle proteins
479
acetyl coA from ________ activates ___________ to convert pyruvate to OAA
lipids
| pyruvate carboxylase
480
what induces PEPCK
glucagon and cortisol
481
OAA --> PEP by
PEPCK
482
pyruvate --> PEP by
pyruvate carboxylase and PEPCK
483
what is the rate limiting step of gluconeogenesis
F-1,6-bisphosphatase
484
where is glucose 6 phosphatase found
ER
485
Glu6P --> ER --> glucose --> _____
cytoplasm
486
what does gluconeogenesis depend on
Beta oxidation of FA to produce acetyl-coA
487
what are the two functions of the PPP
to make NADPH
| to make ribose 5-phosphate for nucleotide synthesis
488
Glucose6P --> 6phosphogluconate by
glucose6P dehydrogenase
| NADP --> NAPH
489
fructose6P / GAP -> ribose 5P by
rtanektolaase and transaldolase
490
where does the TCA cycle occur
mitochondria
491
how does pyruvate enter the mitochondria
active transport
492
activation
thioester bond formation between carboxyl of FA to CoA-SH
493
carnitine
FA-carnitine, allows fatty acyl to cross inner membrane
494
in the matrix, ______ can convert FA-carnitine to
FA-CoA, which can be oxidized to Acetyl CoA
495
alcohol is converted to acetyl coA by
alcohol dehydrogenase and acetaldehyde dehydrogenaase
496
when alcohol produces acetyl coA
it builds up NADH, which inhibits Krebs
497
how many ATP does NADH make`
2.5
498
how many ATP does FADH2 make
1.5
499
new ATP per glucose
30-32, 7 from glycolysis & 25 from citric acid
500
net ATP per pyruvate
12.5
501
what inhibits citrate synthase
ATP, NADH, succinylcoA, citratae
502
what inhibits citrate synthase
ATP, NADH, succinylcoA, citratae
503
what inhibits pyruvate DH
acetylCoA, ATP, NADH
504
what inhibits isocitrate DH
ATP and NADH
505
what inhibits AKGDH
NADH ATP and succinylcoA
506
what does succinylcoA Inhibit
AKGDH and citrate synthase
507
what stimulates AKGDH
ADP and calcium
508
when do lipids start being digested
in the duodenum
509
triacylglycerol --> 2-monoacylglycerol by
emulsification by bile and pancreatic lipase
510
free FA, 2-monoacylglycerol, and bile salts form
micelles
511
how are bile salts reabsorbed
active transport
512
triacylglycerol is reformed in
the mucosal cells
513
phospholipids, cholesterol, fat-soluble vitamins, and triacylglycerol make up
chylomicrons
514
chylomicrons leave the intestine via
lacteals
515
chylomicrons enter the blood via
thoracic duct
516
water-soluble short-chain FA reabsorption
just diffuse simply into blood
517
glucagon effect on fat tissue
none
518
insulin effect on fat tissue
low insulin activates hormone-sensitive lipase that breaks down triacylglycerols
519
what activates HSL
epinephrine, cortisol, and low insulin levels
520
in VLDL and chylomicrons, how are triacylglycerols broken down
lipoprotein lipase (LPL)
521
how are free FA transported in blood
with albumin
522
how are triacylglycerols and cholesterol transported in blood
as lipoproteins
523
chylomicrons are the least dense meaning
high fat, low protein
524
chylomicrons and VLDL carry
triacylglycerols and cholesteryl esters
525
LDL and HDL carry
cholesterol
526
chylomicron carries from _____ to _______
intestine
| tissue
527
VLDL carries from ______ to ________
liver
| tissues
528
IDL picks up
cholesteryl esters from HDL in liver to become LDL
529
LDL delivers
cholesterol
530
HDL picks up
cholesterol from blood, delivers to liver and steroidogenic tissues
531
IDL lacks
triacylglycerols
532
HDL helps
clean up cholesterol from blood for excretion
533
where does de novo synthesis of cholesterol occur
liver
534
citrate shuttle
carries acetylCoa from mitochondria into cytoplasm, uses NADPH from PPP
535
rate limiting step of cholesterol synthesis
HMG-CoA reductase, produces mevalonic acid in SER
536
insulin promotes cholesterol _______
synthesis
537
LCAT is found
in blood
538
LCAT is activated by
HDL apoproteins
539
LCAT function
adds FA to cholesterol, producing cholesteryl esters
540
CETP
transfers cholesteryl esters to other lipoproteins (IDL)
541
acetyl-CoA shuttling
1. Krebs inhibited by too much citrate
2. citrate accumulates
3. citrate crosses into cytosol
4. in cytosol, it is broken into acetyl-CoA and OAA by citrate lyase
542
acetyl-CoA --> malonyl coA by __________
acetyl-CoA carboxylase (biotin)
543
malonyl CoA --> FA palmitic acid by
fatty acid synthase
544
rate limiting step of FA synthesis
acetyl-coA carboxylase
545
what activates acetyl-CoA carboxylase
citrate and insulin
546
what vitamin is required for FA synthase
B5
547
what energy carrier Is required for FA synthase
NADPH
548
rate limiting step of FA oxidation
carnitine acyltransferase I
549
ΔU =
Q - W
heat - work (W is change in pressure/volume)
in closed systems, W is constant
ΔU = Q
550
enthalpy
change in heat
551
at constant pressure and volume, ΔH =
ΔQ
| enthalpy = heat
552
entropy
measure of disorder
553
units of entropy
J/K
554
Gibbs free energy
ΔG = ΔH - TΔS
555
standard free energy
ΔG = ΔGo + RTln(Q)
556
ΔGo' means
it has been adjusted for pH = 7
557
ATP hydrolysis
breaking down ATP
558
ATP cleavage
transfer of P from ATP to something else
559
spontaneous redox reactions have ΔG ___ and E ___
- and +
560
flavoproteins
contain riboflavin, B2
561
postprandial state
after eating
more anabolism and fuel storage
lasts 3-5 hours
562
what cells are insensitive to insulin
nervous and RBC
563
how dose nervous tissue derive energy
breaking glucose into CO2 and H2O
564
how do RBC derive energy
glycolysis
565
what levels are elevated during starvation
glucagon and epinephrine
566
insulin increase (3)
1. glucose and triacylglycerol uptake by fat cells
2. lipoprotein lipase activity, clears VLDL and chylomicrons from blood
3. lipogenesis in fat tissue
566
insulin increase (3)
1. glucose and triacylglycerol uptake by fat cells
2. lipoprotein lipase activity, clears VLDL and chylomicrons from blood
3. lipogenesis in fat tissue
567
insulin decreases (2)
1. lipolysis
| 2. formation of ketone bodies
568
glucagon increases (4)
1. glycogenolysis
2. gluconeogenesis
3. ketogenesis, less lipogenesis
4. lipolysis
569
glucagon is activated by
low glucose levels and high protein levels
570
cortisol functions (3)
1. inhibits glucose uptake by cells
2. increases liver output of glucose by gluconeogenesis
3. enhances glucagon, epinephrine, and catecholamines
571
catecholamines promote
glycogenolysis and lipolysis
572
T4 effect on metabolic rate
latent over several hours, last days
573
T3 effects on metabolic rate
rapid increase, shorter duration
574
Respiratory quotient =
CO2 produced / O2 consumed
575
BMI =
mass / height ^2
