full review - biochem mcat Flashcards
(547 cards)
1
Q
four groups on AAs
A
carboxylic acid
R group
H atom
amino group
2
Q
R group on AA determines
A
functions
3
Q
amino acids with long alkyl chains are
A
hydrophobic
4
Q
AAs with charges are
A
hydrophilic
5
Q
stereochemistry of alpha-carbon is (answer) for all chiral AAs
A
L configuration
6
Q
carbohydrates are (answer) configuration
A
D config
7
Q
all chiral AAs except (what) have S configuration
A
cysteine
8
Q
all amino acids are chiral except
A
glycine
9
Q
lower pH means
A
AA is FULLY protonated
10
Q
when the pH is around the same value of the pI, that means the AA is a
A
neutral zwitterion
11
Q
increased pH means that the AA is
A
FULLY deprotonated
12
Q
what is pI?
A
pH at which AA is in zwitterion form
charges cancel out to make a neutral molecule
13
Q
titration midpoint
A
pH = pKa
14
Q
equivalence pt for a titration
A
pH = pI
15
Q
dipeptide = how many residues
A
2
16
Q
tripeptide =
A
3 residues
17
Q
oligopeptides has less than
A
20 residues
18
Q
polypeptides have greater than
A
20 residues
19
Q
how to form a peptide bond
A
dehydration rxn
20
Q
in a dehydration rxn, nucleophilic amino group of one AA attacks the
A
electrophilic carbonyl group of another AA
21
Q
amide bonds
A
C-N bond of a peptide bond
RIGID due to resonance
22
Q
breaking a peptide bond is a
A
hydrolysis rxn
23
Q
primary structure of a protein
A
linear sequence of an AA in a peptide
24
Q
what stabilizes primary structure
A
peptide bonds
25
AA sequence in primary structure is written
N-terminus to C-terminus
N-terminus is POSITIVELY charged due to -NH3+
26
secondary structure is the local structure of
neighboring AA
27
what stabilizes secondary structure
H-bonding between amino groups and nonadjacent carboxyl groups
28
alpha helices are found in what protein structure
secondary structure
clockwise coils around a central axis
29
beta-plated sheets are found in
2ndary structure
rippled strand that can be parallel or antiparallel
30
which AA can interrupt 2ndary structure
proline b/c of its rigid cyclic structure
31
what is denaturing
protein (or nucleic acid) loses quarternary/tertiary/2ndary structures
non-covalent interactions break
32
what non-covalent interactions break during denaturing
h-bonds
hydrophobic interactions
dipole-dipole interactions
33
tertiary structure is the
3d shape of a single polypeptide chain
34
what stabilizes tertiary structure
hydrophobic interactions
acid-base interactions
h bonds
disulfide bonds
35
hydrophobic interactions push r groups to the
interior of a protein
increases entropy of surrounding water molecules
negative gibbs free E created
36
disulfide bonds occur when two cystein molecules…
oxidize and create a covalent bond b/w thiol groups
37
when two cystein molecules are oxidized and create a covalet bond b/w thiol groups, what is formed
cystine
38
quarternary structure is the interaction between
peptides in proteins that contain multiple subunits
39
conjugated proteins are proteins with
covalently attached molecules
40
what is the attached molecule in a conjugated protein?
prosthetic group
41
what can a prosthetic group be?
metal ion
vitamin
lipid
carbohydrate
nucleic acid
42
what can cause denaturation
heat or solute concentration
43
monosaccharides are single carbohydrate units with...
glucose as the most commonly observed monomer
44
monosaccharides can undergo
oxidation/reduction
esterification
glycoside formation
45
aldoses oxidized into
aldonic acids
reduced to alditols
46
sugar that can be oxidized are
reducing agents
47
sugar that are reducing agents can be detected by
reacting with Tollen's or Benedict's reagents
48
in deoxy sugars, what replaces what
-H replaces -OH
49
in esterification, sugars react with...
carboxylic acids and their derivatives
forming esters
50
phosphorylation is a phosphate ester formed by....
transferring a phosphate group from ATP onto sugar
51
glycoside formation is the basis for building....
complex carbohydrates and requires anomeric carbon to link to another sugar
52
cyclization describes ring formation of
carbohydrates from straight-chain forms
53
anomeric carbon is the new chiral center formed in
ring closure
54
alpha-anomers have the -OH on the
anomeric carbon trans to the free -CH2OH group
55
beta-anomers have the --OH on the
anomeric carbon cis to the free CH2OH group
56
what represents 3D structure of a monosaccharide?
hawthorn projections
57
mutarotation is the spontaneous shift from one
anomeric form to another w/ the straight-chain form as an intermediate
58
disaccharides form as a result of
glycosidic bonding b/w two monosaccharide subunits
59
dissacharide examples
sucrose, lactose, maltose
60
polysaccharides are formed by repeated...
monosaccharide or polysaccharide glycosidic bonding
61
cellulose is the main structure component for
plant cell walls
62
cellulose is the main source of
fiber in a human diet
63
starches are the main energy storage form for
plants
64
amylose is unbranched or branched?
unbranched
65
amylopectin is branched or unbranched?
branched
66
lipids are insolube in
water
67
lipids are soluble in
nonpolar organic solvents
68
phospholipids are
amphipathic and form the bilayer of membranes
69
phospholipids contain a
polar head and nonpolar tails
70
polar head is attached by
phosphodiester linkage which determines the phospholipid function
71
saturation of the fatty acid tails determines
membrane fluidity
72
saturated fatty acid is less or more fluid than unsaturated
less
73
glycerophospholipids contain a
glycerol backbone
74
spingolopids contain a
spingosine backbone
75
many spingolipids are also phospholipids with a
phosphodiester bond
76
spingomyelines are the major class of
spingophospholipids
part of myelin sheath
77
glycosphingolipids are attached to sugar moieties instead of
a phosphate group
78
cerebrodies have how many sugars connected to the spingosine
1 sugar
79
globosides have how many sugars
2 connected to spingosine
80
gangliosides contain oligosaccharides with....
at least 1 terminal acetylneuraminic acid
81
waxes contain long-chain fatty acids...
esterified to long chain alcohols
protection against evaporation/parasites in plants and animals
82
terpenes are
steroid precursors
83
terpenoids are derived from terpenes via
oxygenation or backbone rearrangement
odorous characteristics
84
steroids contain...
3 cyclohexane rings
1 cyclopentane
3 rooms and 1 basement
85
steroid hormones have high-affinity receptors, work at low...
concentrations
affect gene expression/metabolism
86
cholesterol is a steroid important to
membrane fluidity and stability
serves as a precursor to many other molecules
87
prostaglandins are what kind of signalling molecules
autocrine and paracrine signalling molecules
88
prostaglandins regulate
cAMP levels
89
prostaglandins affect
smooth muscle contraction
body temp
sleep-wake cycle
fever
pain
90
fat soluble vitamins
vitamins A, D, E, K
91
vitamin A
carotene
vision
92
vit D
cholecalciferol
bone formation
93
vit E
tocopherols
antioxidants
94
vit K
forms prothrombin (clotting factor)
phylloquinone and menaquinone
95
triacylglycerols are a storage form of
fatty acids
96
1 glycerol attached to 3 fatty acids by ester bonds is
triacylglycerols (very hydrophobic!)
97
adipocytes are animals cells used for
triacyglycerol storage
98
free fatty acids are unesterified fatty acids that
travel in bloodstream
salts of free fatty acids = soaps
99
saponification is the ester hydrolysis of
triacylglycerols using a strong base like sodium or KOH
100
micelle can dissolve a lipid-solube molecule in
its fatty acid core
washes away with water b/c of shell with carboxylate head groups
101
cerebroside is a type of
glycolipids
102
a glycolipid is a
lipid linked to any sugar
103
2ndary structure are interactions between bases within
the same molecule
104
2ndary structure in DNA, bases are held together by
h bonds
105
2ndary structure is responsible for the
shape of nucleic acid
106
quarternary structure is the interactions of
nucleic acids with other molecules
e.g. chromatin interacting w/ histones
107
nucleic acids are
polymers of nucleotides
108
DNA replication is the process of producing an
identical replica of a DNA molecule
occurs during S phase of cell cycle
109
oncogenes develop from mutations of
proto-oncogenes and promote cell cycling
may lead to cancer
110
oncogenes =
stepping on gas pedal
111
tumor suppressor genes code for
proteins that REDUCE cell cycling
promote DNA repair
112
mutated tumor suppressor genes =
cutting the brakes
113
proofreading is when DNA polymerase
proofreads its work and excises incorrectly matched bases
114
daughter strand is identified by its
lack of methylation and corrected accordingly
115
mismatch repair occurs during
G2 phase using MSH2 and MLH1 genes
116
nucleotide excision repair fixes helix-deforming lesions of
DNA such a thymine dimers
cut-and-patch process
excision endonuclease
117
base excision fixes nondeforming lesions of the
DNA helix such as the cytosine deamination by removing base
leaving AP site
118
AP endonuclease removes the
damaged sequence which can be filled in with the correct bases
119
what is DNA
macromolecule that stores genetic info in all living organisms
120
nucleoside is a 5-carbon sugar and
nitrogenous base
NO PHOSPHATE groups
121
nucleotides are
a nucleoside with 1 to 3 phosphate groups added
122
nucleotides in DNA contain
deoxyribose
123
nucleotides in RNA contain
ribose
124
name the nucleotides
adenine (A)
thymine (T)
guanine (G)
cytosine (C)
uracil (U)
125
in RNA, what replaces T
U replaces T
A paired with U via 2 H-bonds
126
watson-crick model is the backbone of
alternating sugar/phosphate groups
127
watson-crick model is always read
5' to 3'
128
two strands with antiparallel polarity wind into a
double helix
129
nitrogenous bases
purines: adenine and guanine (2 rings)
pyrimidines: cytosine, thymine, uracil (1 ring)
130
chargaff's rule states that
number of purines = number of pyrimidines
A = T
C = G
131
B-DNA means
a right-handed helix is formed
DNA is B-DNA
132
low concentrations of Z-DNA has what shape
zigzag shape
has a high GC content or high salt concentration
133
denatured DNA gets
pulled aparted
134
reannealed DNA gets
brought back together
135
how many chromosomes in human cells
46
136
DNA is wound around (what) to form...
histones to form nucleosomes
137
nucleosomes can be stabilized by
another histone protein
138
as a whole, DNA and its associated histones make up
chromatin in the nucleus
139
chromatin types
heterochromatin
euchromatin
140
heterochromatin is
dark, dense, silent
141
euchromatin is
light, uncondensed, expressed
142
where are telomeres
end of chromosomes
143
telomeres contain high GC-content to prevent
DNA unravelling
144
during replication, telomeres are
shortened
145
telomeres shortening can be partially...
reversed by telomerase
146
where are centromeres
middle of chromosomes
147
centromeres hold
sister chromatids together until separation during anaphase in mitosis
148
high GC-content maintains what between chromatids
a strong bond
149
acrocentric chromosomes is located near one end of the
chromosome and not in the middle
150
recombinant DNA is DNA composed of
nucleotides from 2 different sources
151
hybridization is the joining of
complementary base pair sequences
152
what is the central dogma
statement that DNA is transcribed to DNA which is translated to protein
153
degenerate code allows for multiple codons to
encode for the same AA
154
start and stop codons
start codon: AUG
stop codons: UAA, UGA, UAG
155
start codon
AUG
156
stop codons
UAA
UGA
UAG
157
wobble is the
3rd base in the codon
allows for mutations to occur w/o effects in protein
158
wobble base pairings are less
stable
159
silent point mutations are...
mutations with no effect on protein synthesis
160
silent point mutations are usually found in the
3rd base of a codon
161
nonsense point mutations are...
mutations that produce a premature STOP codon
162
missense point mutations produce a codon that...
codes for a different AA
163
frameshift mutations result from a
nucleotide addition or deletion
164
frameshift mutations change the
reading frame of subsequent codons
165
RNA is similar to DNA except that
ribose sugar instead of deoxyribose
uracil instead of thymine
single stranded not double
166
3 types of RNA
mRNA
tRNA
rRNA
167
mRNA is transcribed from
DNA in nucleus
168
mRNA travels into
cytoplasm for translation
169
tRNA brings in AAs and...
recognizes the codon on mRNA using its anticodon
170
rRNA makes up the
ribosome and is enzymatically active
171
tRNA translates the...
codon into the correct AA
172
ribosomes are factories where
translation (protein synthesis) occurs
173
eukaryotes have which ribosomes
80s
174
prokaryotes have which ribosomes
70s
175
initiation in prokaryotes is when the
30S ribosome attaches to the Shine-Delgarno sequences
scans for a start codon
lays down N-formylmethionine in P side of ribosome
176
eukaryote initiation
when 40S ribosome attaches to 5' cap
scans for start codon
lays down methionine in P site of ribosome
177
elongation is the addition of a new
aminoacyl-tRNA into the A site of ribosome
transfer of growing polypeptide chain from tRNA in P site --> tRNA in A site
uncharged tRNA pauses in E site before exiting ribosome
A site tRNA moves to P site
178
termination occurs when the codon in the
A site is a stop codon
179
release factors places a water molecule on the
polypeptide chain and thus releases the protein during termination
180
posttranslation modifications:
folding by chaperones
quarternary structure formation
cleavage of protein/signal sequences
covalent addition of other biomolecules (phosphorylation, carboxylation, glycosylation, prenylation)
181
DNA ligase fuses what together to create...
fuses DNA strands to create one strand
182
helicase function
unwinds DNA double helix
183
RNA polymerase II function
binds to TATA box within promoter region of gene
25 base pairs upstream from first transcribed base
184
hnRNA is the collective term for
the unprocessed mRNA in nucleus
185
posttranscriptional modification is the process in which the
eukaryotic cells where primary transcript RNA is converted into mature RNA
introns cut out
186
exons exit the
nucleus and form mRNA
187
introns spliced out so they
stay in nucleus
188
introns also enable
alternative splicing
189
alternative splicing is when
introns cut away and exons remain
but in alternative splicing, a certain exon may be cut out or an intro may stay
190
alternative splicing allows for the
RNA segment to code for more than one gene
191
what are added to the mRNA
5' cap and poly-A tail
192
what do the 5' cap and poly-A tail do
stabilizes mRNA for translation
193
prokaryotic cells can increase variability of gene products from
one transcript through polycistronic genes
194
multiple translation sites within the gene which leads to
different gene products
195
jacob-monod model explains how
operons work
196
operons are inducible or repressible
clusters of genes transcribed as a single mRNA
197
inducible systems
under normal condition, IS bonded to a repressor
turned on when an inducer pulls the repressor off
e.g. Lac operon
198
repressible systems
transcribed under normal conditions
can be turned off by a corepressor coupling w/ the repressor
binding of complex to operator site
e.g. Trp operon
199
transcription factors search for promoter and enhancer
regions in DNA
bind to DNA and recruit RNA polymerase
200
promoters are within
25 base pairs of transcription start site
201
enhancers are more than
25 base pairs away from the transcription start site
202
modification of chromatin structure affects the ability of transcriptional enzymes to....
access the DNA thru histone acetylation (+ access)
or DNA methylation (- access)
203
what does the fluid mosaic model account for?
presence of lipids, proteins and carbohydrates in a dynamic, semisolid plasma membrane that surrounds cells
204
in the phospholipid bilayer, each phosphlipid has a
hydrophilic head + hydrophobic tail
205
heads of phospholipids are arranged so that they are
facing outward and the tails make up in the inside of the membrane
206
proteins are embedded in the
phospholipid bilayer
207
lipid rafts are made of
lipids moving freely in the plane of the membrane
208
flippases are specific membrane proteins that maintain the...
bidirectional transport of lipids b/w layers of the phospholipid bilayer in cells
209
proteins and carbohydrates may also move within the
membrane but are slowed by their large size
210
all transmembrane movement is based on
concentration gradients
211
concentration gradient tells us whether the process is
passive or active
212
osmotic pressure is what kind of property
colligative
213
osmotic pressure is the pressure applied to a
pure solvent to prevent osmosis
used to express solution's concentration
214
what characterizes osmotic pressure
"sucking" pressure in which a solution is drawing water in
proportional to its concentration
215
passive transport does not require
energy b/c the molecule is moving down its concentration gradient
216
simple diffusion is a type of
passive transport
217
in simple diffusion, small nonpolar molecules move...
passively from an area of high to low concentration until equilibrium is achieved
218
osmosis is a type of
passive transport
219
osmosis describes diffusion of water across
a selectively permeable membrane
220
facilitated diffusion is a form of
passive transport
221
facilitated diffusion uses what to move...
transport proteins to move impermeable solute across the cell membrane
222
active transport requires
energy (ATP)
223
primary active transport uses what to...
ATP to power transport of molecules across a membrane
224
secondary active transport is known as
coupled transport
225
2ndary active transport harnesses energy released by
one particle going down electrochemical gradient to drive a different particle up its gradient
226
symport is when
both particles flow in same direction
part of 2ndary active transport
227
antiport is when
particles flow in opp direction
part of secondary active transport
228
endocytosis and exocytosis are the methods of
engulfing material into the cells or releasing material out of the cell
229
pinocytosis is the ingestion of
liquids aka vesicles
230
phagocytosis is the ingestion of
larger solid materials
231
lipids are the primary...
membrane component
both by mass and mole fraction
232
triaglycerols and fatty acids act as
phospholipid precursors and are found in low levels in the membrane
233
glycerophospholipids replace one fatty acid with a
phosphate group (often linked to other hydrophilic groups)
234
cholesterol is present in
large amounts in the membrane
235
cholesterol contributes to
membrane fluidity and stability
lower temp = decrease fluidity
increase temp = increase fluidity
236
waxes are present in very
small amounts
237
what are waxes most prevalent in?
in plants
function: waterproofing and defense
238
transmembrane proteins are a type of integral protein that...
spans the entire membrane
often glycoproteins
239
embedded proteins are most likely part of
catalytic complex or involved in cellular communication
240
membrane-associated proteins may act as
recognition molecules or enzymes
241
carbohydrates can form a
protective glycoprotein and also function in cell recognition
242
extracellular ligands can bind to
membrane receptors which function as channels/enzymes in second messenger pathways
243
gap functions allow for rapid exchange of
ions and other small molecules b/w adjacent cells
244
tight junctions prevent solutes from leaking into
the space b/w cells via a paracellular route
do NOT provide intercellular transport
245
desmosomes bind adjacent cells by
anchoring to cytoskeletons
246
hemidesmosomes are similar to desmosomes but
their main function is to attach epithelial cells to underlying structures
247
GLUT-2 is found in
liver for glucose storage and pancretic b-islet cells (as a part of the glucose sensor)
INCREASED Km
248
GLUT-4 is found in
adipose tissue and muscle
stimulated by insulin
LOWERED Km
249
mechanical digestion of lipids occurs...
primarily in the mouth and stomach
250
chemical digestion of lipids occurs in the
small intenstine
251
chemical digestion is facilitated by
bile, pancreatic lipase, colipase, cholesterol esterase
252
upon entry into the duodenum, what occurs
emulsification which is the mixing two liquids don't mix usually (fat + water)
253
emulsification increases the
surface area of the lipid
254
increasing surface of the lipid via emulsification permits
greater enzymatic interaction and processing
255
what aids emulsification?
bile salts
256
micelles are
water-soluble spheres w/ a lipid soluble interior
257
digested lipids may form micelles to be carried to
the intestinal epithelium where they are absorbed across the PM
258
short chain fatty acids are absorbed across
the intestine into the blood
259
long chain fatty acids are absorbed as
micelles and assembled into CHYLOMICRONS for release into lymphatic system
260
fatty acids are
carboxylic acids w/ a long chain
261
saturated fatty acids have
NO double bonds
262
unsaturated fatty acids have
one or more double bonds
263
five steps of fatty acid synthesis
activation
bond formation
reduction
dehydration
second reduction
264
where are fatty acids formed
cytoplasm from acetyl-COA that is transported out of the mitochondria
265
arachidonate is the precursor to
eicosanoid signalling mollecules
leukotrienes
266
eicosanoid signalling molecules:
prostaglandins
prostacyclins
thromboxanes
267
fatty acid oxidation occurs in the
mitochondria following transport by the carnitine shuttle
268
beta-oxidation uses cycle of
oxidation, hydration, thiolysis cleavage
269
fatty acid chain is shortened by
two carbon atoms in fatty acid oxidation
270
in fatty acid oxidation, what is generated
FADH2
NADH
acetyl CoA
271
ketogenesis is the process by which
ketone bodies form due to excess acetyl-CoA in liver (during prolonged starvation)
272
ketolysis regenerated
acetyl-CoA for energy use in peripheral tissues
273
brain can derive up to
2/3 of its energy from ketone bodies during starvation
274
where does protein digestion usually occur
small intestine
275
catabolism of cellular proteins occurs ONLY under
conditions of starvation
276
amino acids released from proteins usually...
lose their amino group through deamination
277
in protein catabolism, remaining carbon skeleton can be used for
energy
278
glucogenic AAs can be converted into
glucose through gluconeogenesis
279
all amino acids except (which ones) can be converted into glucose via gluconeogenesis
leucine and lysine
280
ketogenic can be converted into
acetyl-CoA and ketone bodies
281
which AAs are the only ones that are solely ketogenic?
leucine and lysine
282
cholesterol may be obtained through
dietary sources or through de novo synthesis in liver
283
HMG-CoA reductase synthesizes
mevalonate
rate limiting step of cholesterol synthesis
284
LCAT catalyzes formation of
cholesteryl esters for transport with HDL
285
CETP catalyzes transition of LDL by
transferring cholesteryl esters from HDL
286
open system is where matter and E can be
exchanged with the environment
287
closed system is where
ONLY energy can be exchanged w/ the environment
288
no work is performed during a closed system because
pressure and volume remain constant
289
entropy is the measure of
energy dispersion in a system
290
chain in free energy
delta G that occurs at 1 M concentration, 1 atm, 25 C
291
ATP is a
mid level energy molecules
292
ATP contains high energy phosphate bonds that are
stabilized via hydrolysis by resonance, ionization, loss of charge repulsion
293
ATP provides energy through
hydrolysis and coupling to energetically unfavorable reactions
294
ATP can donate a
phosphate group to other molecules
295
in glycolysis, ATP donates a
phosphate group to glucose = G6P
296
bio oxidation and reduction reactions can be broken down into
component half-reactions
297
half-reactions provide useful info about
stoichiometry and thermodynamics
298
high energy electron carriers may be
soluble or membrane-bound
299
high energy electron carriers include
NADH2
NADPH
FADH2
ubiquinone
cytochromes
glutathione
300
flavoproteins is a subclass of electrons carriers...
dervied from riboflavin (vit B2)
e.g. FAD and FMN
301
insulin is secreted by
pancreatic b-cells
302
insulin is regulated by
glucose
303
insulin decreases
blood glucose by increasing cellular uptake
304
insulin increases rate of
anabolic metabolism
305
what secretes glucagon
pancreate a-cells
306
glucagon is stimulated by
low glucose and high AA levels
307
glucose increases
blood glucose by promoting gluconeogensis and glycogenolysis in liver
308
glucocorticoids increase blood glucose in response to...
stress by mobilizing fat stores and inhibiting glucose uptake
309
glucocorticoids increase impact of...
glucagon and catecholamines
e.g. cortisol
310
catecholamines promote glycogenolysis and....
increases basal metabolic rate through sympathetic NS activity
"adrenaline rush"
e.g. epinephrine and noriepinephine
311
thyroid hormones increase
basal metabolic rate
due to increased oxygen consumption and heat production when thyroid hormones are secreted
312
T3 is more potent than
T4 b/c i.t. has a shorter half-life
t3 is available in lower concentrations in the blood
313
T4 is converted to
t3 at tissues
314
thyroid hormones are what-based
tyrosine
315
equilibrium is a (what) state for most biochemical rxns
undesirable state for biochemicals rxns b/c organisms need free energy to survive
316
postprandial state is when body is
well-fed + absorptive
insulin increases
anabolism prevails
317
postabsorptive state is when body is
fasting
lowered insulin
increased glucagon and catecholamine
transition to catabolism
318
starvation leads to increased
glucagon and catecholamine
319
most tissues rely on
fatty acids
320
calorimetry measures
metabolic rates
321
respiratory quotient estimates
composition of fuel actively consumed by body
322
RQ =
Co2 produced / O2 consumed
323
ghrelin increases
appetite
regulatory hormone
324
orexin increases
appetite
regulatory hormone
325
leptin decreases
appetite by suppressing orexin production
326
BMI =
mass / height^2
327
liver is the most
metabolically diverse tissue
328
hepatocytes are responsible for the maintenance of blood glucose levels...
by glycogenolysis and gluconeogenesis to pancreatic hormone stimulation
329
liver process what materials
lipids, cholesterol, bile, urea, toxins
330
adipose tissue stores lipids under the influences of...
insulin and releases them under the influence of epinephrine
331
skeletal muscle metabolism will differ depending on
current activity level and fiber type
332
resting muscle conserve carbohydrates in...
glycogen stores and uses free fatty acids from bloodstream
333
active muscle may use anaerobic metabolism and...
glucose phosphorylation
direct phosphorylation from creatine phosphate
or
fatty acid oxidation
depending on fiber type + exercise duration
334
cardiac muscle uses fatty acid oxidation in...
both the well-fed and fasting states
335
brain and nervous tissue consume only glucose in
all metabolic states except for prolonged fasts (where 2/3 of brain's fuel will come from ketone bodies)
336
name the branched alkyl side chains
leucine
isoleucine
valine
337
protein domains are
distinct regions in a polypeptide chain that fold independently
338
each protein domain carries out
a separate function (may assist another domain in performing its function)
339
one of the most common functions of a protein domain is to
bind a ligand (small molecule)
340
what does Kd measure
Kd = dissociation constant / affinity of a protein
341
small Kd =
high binding affinity (low tendency of complex to dissociate)
342
what does DNA determine?
sequence of AA in proteins
blueprint for living organisms passed from one gen to the next
343
main difference b/w prok or euk cells?
NUCLEUS
344
which of the following is found in prokaryotes:
mitochondria
nucleus
chloroplasts
ribosomes
more than 1 of these
ribosomes
345
where are ribosomes found?
rough ER
346
smooth ER does what?
makes lipids
347
rough ER does what?
makes ribosomes from mRNA
348
what can capture light energy and turn it to sugar?
chloroplast
349
what does the golgi apparatus involved in
sorting and modifying
350
spontaneous reaction is exer or endergonic?
exergonic
351
speed of spontaneous process?
FAST
352
heat of reaction at constant pressure is marked by
its change in enthalpy
353
hydrolysis of ATP involves
release of energy
354
monomers of proteins are
amino acids
355
what kind of compounds are more likely to dissolve in nonpolar solvents?
covalent compounds
356
ionic compounds and polar covalent compounds tend to dissolve in water because of
on-dipole and dipole-dipole interactions
357
hydrogen bonds can only form within a single molecule. T or F?
false
358
max number of H bonds a single water molecule can form?
4
359
what makes for a good H bond acceptor?
high electronegativity
nonbonding pair of electrons
360
h bonds explain which of the following properties of water?
water is a good solvent for ionic/polar molecules
water has a high melting pt and boiling pts for its small size
ice expands when frozen
361
bases are
proton acceptors
362
what has a greater Ka: weak or strong acid?
strong acid
363
small pkA means
strong acid
364
dissociation cosntant (Ka) for an acid with a pKa value of 6.0 is
1 x 10^-6
365
how to calculate pH from H+ ion concentration
pH = -log[H+|
366
how to calculate H+ concentration
[H+] = 10^ -pH
367
buffering capacity refers to the
extent to which a buffer solution can counteract the effect of added base or acid
368
main intracellular buffer system
H2PO4- / HPO4
369
stereoisomers are
nonsuperimposable mirror-image molecules
370
which AA takes on a negative charge when the R group loses a proton?
glutamic acid
371
true or false: Thr and Ser have hydroxyls as side chains
true
372
Asn has a polar or nonpolar side chain?
polar
373
pKa values of the amino groups of common AAs are around
pH 9
374
alpha-helices only use
intrachain H bonds
375
beta-sheets can use
intrachain or interchain H bonds
376
in the alpha-helix, there are
h bonds parallel to the helix axis
377
which forces are important in tertiary structure
disulfide bonds
h bonds
hydrophobic interactions
378
bonds involved in disulfide bonding
covalent bonds w/ R groups
379
what can cause protein denaturation?
heat
extreme pH
detergents
380
what maintains quarternary structure of a protein?
h bonds
ionic interactions
hydrophobic interactions
381
what does catalyst do to deltaG?
catalyst lowers deltaG
382
what does increased temperature do to enzyme-catalyzed reactions?
rate of enzyme rxns increases until heat denatures enzymes
383
true or false: all catalysts work by lowering the activation energy for a rxn
TRUE
384
active sit of an enzyme
substrate binds via noncovalent forces
substrate binding site
reactive group catalyze rxn here
385
sigmoidal curve suggests that
the characteristics of a multi-subunit enzyme
386
what type of enzyme display sigmoidal kinetics
ALLOSTERIC
387
allosteric enzymes have what curve shape
sigmoidal
e.g. hemoglobin
388
mechanism of an enzyme-catalyzed reaction makes which assumption about the conversion of production into substrate
product is not converted to substrate to any appreciable extent
389
lineweaver burk plot is useful for
seeing whether points deviate from a straight line than from a curve
390
lineweaver burk plot is not affected by
presence of inhibitors
391
lineweaver-burk plot can be used whether or not
the enzyme displays michaelis-menten kinetics
392
what does the michaelis constant determine
Km
393
michaelis constant describes the
affinity between enzyme and substrate
394
dimension (units) for the michaelis constant is
concentration such as molarity
395
Km is the substrate concentration necessary to
reach 1/2 vmax
396
lower Km =
HIGHER affinity
397
which inhibitor binds to the enzyme at a site other than the active site?
noncompetitive inhibitor
398
what inhibitor has an unchanged Vmax?
competitive inhibitor
399
what happens to the vmax with noncompetitive inhibitor?
vmax is altered
400
behavior of allosteric enzymes depends on
changes in quaternary structure upon binding of substrate or effectors
401
according to the concerted model of allosteric behavior, an allosteric activator favors the
relaxed form of the enzyme
402
main distinguishing feature of the concerted model for the behavior of allosteric enzyme is the
conformation of all subunits changes simultaneously
403
phosphorylation and allosteric control of enzymes can be combined to
afford a high degree of control over enzymatic reactions
404
in zymogen activation, an inactive protein is converted to
an active one by bond cleavage
405
how are cofactors bound to their enzymes
either covalently or non-covalently
406
examples of coenzymes
NAD+
FAD
biotin
407
what often functions as coenzymes in redox reactions?
NAD+ and FAD (nicotinamide adenine dinucleotides)
408
what does amphipathic mean?
there are hydrophilic and hydrophobic regions
409
fatty acids in both (x and y) vary
triacylglycerols and phospoacylglycerols
410
cholesterol has some degree of what nature
amphipathic
411
true or false: lipids differ from most biomolecules b/c they are defined on basis of solubility rather than chemical structure
TRUE
412
what does cholesterol do for membrane fluidity?
prevents extremes (too fluid or too firm)
413
association of integral membrane proteins w/ lipids in the membrane bilayer always involves
hydrophobic interactions
414
plants oils have more unsaturated or saturated fats?
UNSATURATED (less cholesterol)
415
distribution of lipids in membrane is
uneven w/ bulkier molecules on exterior
416
where can membrane proteins be located?
entirely within membrane
on surface of membrane
417
properties of membrane proteins
transport of substances into and out of cell
catalysis (enzymatic activity)
acting as a receptor
418
is energy storage part of the functions for membrane proteins?
no
419
lipid vitamins found in membranes
vitamins A and E
420
vitamin needed for blood coagulation
vitamin K
421
if a single strand of DNA contains 2100 A residues and 1800 T residues, what will be on the complementary strand?
2100 T (threonine) residues and 1800 A residues (alanine)
422
supercoiled helix can be untwisted by
helicase
423
production RNA from a DNA template is
transcription
424
mRNA base sequence directs AA sequence of a protein is called
translation
425
DNA replication in a prokaryote begins at a
unique site and proceeds in one direction all the way around a typically circular chromosome
426
when the synthesis of new DNA is directed by an original template DNA molecule...
two DNA molecules are formed
each w/ one new strand and the other from original DNA
427
functions of DNA polymerase III
polymerization
clamping on to the DNA template
proofreading
428
what activity of DNA polymerase I is most important in removing the primer?
3' to 5' exonuclease activity
429
strands in double helix are
anti-parallel
have their 3' to 5' directions opposed
430
DNA synthesis direction
5' to 3' end on one strand and 3' to 5' end on the other strand
431
which enzyme is responsible for bulk of DNA synthesis during replication
DNA polymerase I
432
okazaki fragments are
short DNA pieces that explain how DNA is synthesized on lagging strand
433
why is a primer strand needed in DNA replication
DNA polymerases require a preexisting strand w/ a nucleotide having a 3'-OH
434
why is telomerase needed
one major difficulty in replicating linear DNA molecules is replacing DNA segment that is occupied by the RNA primer on telomeres at DNA ends
435
hydrolysis of a nucleoside triphosphate drives the
reaction
436
direction of RNA synthesis
5' to 3' end
437
RNA base pairing includes
A to U
G to C
438
promote site is
site on DNA at which RNA polymerase bind to start transcription
439
which RNA has a cloverleaf structure
tRNA
440
ends of eukaryotic mRNA protected from degradation
3' end only (polyA tail)
441
5' end of mRNA is the
5' cap
442
which ends of prokaryotic mRNA are protected from degradation
neither end
443
TRUE OR FALSE: single codon can coded for more than one AA
false
444
best linkage describes covalent bond b/w an AA and its tRNA
carboxyl group fo AA linked to 3' --OH of tRNA
445
codons known for each AA?
depends on AA
446
TRUE OR FALSE: in bacterial, each mRNA will bind to only one ribosome at a time?
TRUE
447
necessary step after peptide bond formation takes place to continue protein synthesis
dissociation of ribosomal subunits
448
in protein synthesis formation of new peptide bonds is catalyzed by
peptidyl transferase
449
translation of mRNA in bacteria begins
during transcription of mRNA
450
first tRNA (bearing fmet) binds to
"P" site on the ribosome
451
production of larger to smaller molecules is called
catabolism
452
what kind of process is catabolism
oxidative
453
what kind of process is anabolism
reduction
454
smaller to larger molecules is
anabolism
455
oxidation refers to the
loss of electrons
456
reduction refers to the
gain of electrons
457
TRUE OR FALSE: molecular oxygen is always the substrate in oxidation rxns
true
458
TRUE OR FALSE: oxidation of food molecules supplies energy used to separate ATP
TRUE
459
to drive the synthesis of ATP, hydrolysis of an organic phosphate substrate must
have a HIGHER free energy than ADP + Pi --> ATP
460
TRUE OR FALSE: in order to initiate a metabolic pathway it is sometimes necessary to activate the starting materials
TRUE
461
mechanisms used to activate substrates for further metabolism
making an isomer that is more reactive
addition of a phosphate group
combination with a vitamin (i.e. coenzyme A)
462
metabolism takes place in stages to:
- allow for efficient production and use of E and regulation of process
- b/c large free energy changes cannot occur in living organisms
463
in the absence of oxygen, pyruvate can be converted to
lactate IN HUMANS
464
in glycolysis, how many actual steps involve electron transfer
1 step
465
enzyme glucokinase does what?
phosphorylates a number of different sugars:
glucose, fructose, mannose
466
which molecule allosterically control the enzyme phosphofructokinase?
ATP
467
isomerization of dihydroxyacetone phosphate (DHAP) to G3P is favored because
G3P is being continuously drained off subsequent rxn in glycolytic pathway
468
ATP is synthesize by what in glycolysis
both substrate-level and oxidative phosphorylation
469
can the citric acid cycle be used as both an anabolic and catabolic pathway?
NO
470
which enzyme uses coenzyme FAD as an e- acceptor?
succinate dehydrogenase
471
conversion of malate to oxaloacetate has a high/pos gibbs free E yet it can take place b/c
the oxaloacetate product is used up in the subsequent rxn
472
when mitochondria are actively carrying out aerobic respiration...
the pH of the matrix is greater than the pH of the intermembrane space
473
TRUE OR FALSE: synthesis of ATP in mitochondria is driven by a proton/pH gradient
true
474
ultimate electron acceptor in ETC is
oxygen
475
what is an advantage of the multiple steps in electron transport?
more E can be captured to synthesize ATP by using small steps
476
ATP is more efficiently generated through
substrate level phosrylation than oxphos
477
main purpose of TCA
generate reduced coenzymes NADH and FADH2 to be used in ETC = ATP
478
net yield of ATP per glucose molecule during aerobic respiration
max 28
479
reduction of pyruvate to lactate
allows for recycling of NAD+
lactate fermentation
480
alcohol dehydrogenase resembles lactate dehydrogenase in that it
uses NADH as a coenzyme
481
does fermentation make any ATP?
no - it uses NAD+ when oxygen is not present
482
an uncompetitive inhibitor binds only with the
enzyme-substrate complex
483
allosteric effector binds at (where) and does what
allosteric site
induces a chance in enzyme shape so substrate can no longer bind to the active site
484
what happens with positive effectors
activity goes up
485
negative effectors
activity goes down
486
secondary structure of nucleic acids is made up of
interactions between bases within same molecule
487
secondary structure is responsible for the
shape that the nucleic acid assumes
488
RNA secondary structure has 4 basic elemetns
loops
helices
bulges
junctions
489
what fixes helix-deforming lesions of DNA such as thymine dimers
nucleotide excision repair
cut and patch process
490
oncogenes develop from
mutations of proto-oncogenes and promote cell cycling
may lead to cancer
491
DNA ligase function
joins DNA strands by catalyzing formation of phosphodiester bonds
492
pyrimidines
C, T, U
493
purines
A and G
494
during replication, telomeres are shortened and this can
be partially reversed by telomerase
495
recombinant DNA is composed of
nucleotides from two different sources
created only in labs
496
base excision repair fixes
nondeforming lesions of DNA helix by removing base and leaving an AP site
497
AP endonuclease then removes the
damaged sequence which can be filled in w/ the correct bases
498
bonds between nucleotide bases
h bonds
499
DNA backbone is held together by
phosphodiester bonds
form b/w sugar and phosphate groups
500
saturated fatty acid has how many double bonds in its tail and is more/less fluid
NO double bonds
less fluid
501
prostaglandins are
lipid compounds that are signalling molecules and regulae cAMP levels
502
prostaglandins affect the following functions
smooth muscle contraction
body temp
sleep-wake cycle
fever
pain
503
3 parts of a nucleotide
phosphate group, nitrogenous base, pentose sugar
504
irreversible inhibitor is any inhibitor that
covalently binds to the active site of some enzyme (eliminates any activity)
505
vmax and Km in noncompetitive inhibition
vmax goes down
Km has no change
506
vmax and Km in uncompetitive inhibition
vmax and Km go down
507
vmax and Km in competitive inhibition
vmax - no change
Km goes up
508
feedback inhibition of an enzyme is when
an enzyme is inhibited by high levels of a production from later in the same pathway
509
translation occurs in the
cytoplasm at the ribosomes
510
translation steps
initiation
elongation
termination
511
in prokaryotic translation, the 30S ribosome subunit attaches to the
Shine-Delgarno sequence and scans for a start codon
512
in translation elongation, the new tRNA enters ribosome at
A site
513
in elogation, the polypeptide chain is transferred from the
P site to A site to meet the new tRNA
514
in elogation, before leaving the ribosome, the tRNA stops in the
E site
515
order of sites for tRNA is
A P E
516
in translation, termination will occur when the
codon in the A site is a stop codon
517
release factor places a water molecule on the
polypeptide chain and thus releases the protein
518
post-translational modification can happen at
any time of protein's lifespan
commonly phosphorylation
519
what are operons
found in prok DNA
contain groups of genes regulated together
520
operons contain
activators
inducers
repressors
521
advantage of operons
group of genes whose products are all needed for a common function can be transcribed together
522
operon promoter is the
binding site for RNA polymerase (enzyme that performs transcription)
523
operon operation is a
short region of DNA that lies partially within the promoter
interacts w/ a repressor that controls transcription of the operon
524
operation repressor does what
turns operon off
525
repressor binds to the
operator
blocks movement of RNA polymerase down DNA
526
when lactose is absent, the lac repressor
binds tightly to the operator
gets in RNA polymerase's way
prevents transcription
527
with lactose, the lac repressor
is bound to allolactose and operator is released
RNA polymerase can now transcribe operon
528
operon activator does what
turns operon on
529
lac operon uses
catabolite activation protein (CAP)
530
when glucose levels are low, what is produced
cAMP
cAMP attaches to CAP --> binding DNA
RNA polymerase binds to promoter --> high levels of transcription
531
when glucose levels are high,
no cAMP is made
CAP cannot bind DNA w/o cAMP --> low levels of transcription
532
operon inducer
small molecule that triggers gene or operon expression
533
lac operon is considered an
inducible operon b/c its default state is to be turned off/repressed
but can be turned on w/ allolactose
534
inducible operon under normal conditions is
bonded to a repressor
535
inducible operons are turned on when an inducer
pulls the repressor from the operator site
e.g. lac operon is an inducible operon
536
repressible operon under normal conditions will
proceed w/ transcription
537
repressible operons can be turned off by a
corepressor coupling w/ the repressor and
the binding of this complex to the operator site
e.g. Trp operon
538
in the absence of tryptophan, the trp repressor
dissociated from operator and RNA synthesis proceeds
539
when trp is present, the trp repressor binds the operator and
RNA synthesis is blocked
540
transcription factors are proteins that
help turn specific genes "on" or "off" by binding to nearby DNA
541
enhancers are sequences of DNA that function
to enhance transcription
more than 25 base pairs away from transcription start site
542
histone acetylation increases accessibility of chromatin and allows
DNA binding proteins to interact
activates transcription
543
DNA methylation decreases the
accessibility of chromatin and stops DNA binding proteins from interacting
inhibits transcription
544
lac operon contains genes that code for proteins in
charge of transporting lactose into the cytosol and digesting into glucose
glucose used to make energy
INDUCIBLE operon
545
genes in the lac operon will be expressed if
lactose is available
glucose is low
546
when lactose is available, the inducer
binds to the repressor and the repressor detaches from the DNA
547
