mcat rev Flashcards
1
Q
amino acids have four groups attached to a
A
central alpha carbon
2
Q
the four groups that make up an AA?
A
carboxylic acid group, H atom, amino group, R group
3
Q
R group function
A
chemistry and function of AA
4
Q
how many AAs appear in eukaryotic organisms’ proteins?
A
20
5
Q
ALL AAs are chiral except
A
glycine
6
Q
ALL chiral AAs except cysteine have
A
S configuration
7
Q
nonpolar/nonaromatic side chains:
A
glycine, alanine, valine, leucine, isoleucine, methionine, proline
8
Q
aromatic side chains:
A
tryptophan, phenylalanine, tyrosine
9
Q
polar side chains:
A
serine, threonine, asparagine, glutamine, cysteine
10
Q
negative charged (acidic) side chains:
A
aspartate, glutamate
11
Q
positively charged (basic) side chains:
A
lysine, arginine, histidine
12
Q
amino acids w/ long alkyl chains are
A
hydrophobic
13
Q
amino acids with short alkyl chains are
A
hydrophilic
14
Q
amphoteric:
A
means AAs can accept or donate protons
15
Q
pKa of a group is the
A
pH at which half the species is deprotonated
[HA] = [A-]
16
Q
AAs exist in different forms at
A
different pH values
17
Q
at low (acidic) pH, AA is
A
fully protonated
18
Q
at pH near the isoelectric pt (pI) of the AA,
A
the AA is a neutral zwitterion
19
Q
at high (alkaline) pH, AA is
A
fully deprotonated
20
Q
isoelectric point (pI) is
A
calculated for an AA without charged side chains by averaging two pKa values
21
Q
can AAs be titrated?
A
yes
22
Q
titration curve is nearly flat at
A
pKa values of AA
23
Q
titration curve is nearly vertical at the
A
pI of the AA
24
Q
AAs with charged side chains have additional
A
pKa value
pI is calculated by averaging the two pKa values that correspond to the protonation and deprotonation of zwitterion
25
AAs w/o charged side chains have a
pI around 6
26
acidic AAs have a pI
below 6
27
basic AAs have a pI
above 6
28
dipeptides have two
AA residues
29
tripeptides have three
AA residues
30
oligopeptides have a (x) AA residues
FEW (less than 20)
31
polypeptides have
MANY AA residues
32
forming a peptide bond is a
condensation or dehydration rxn
33
nucleophilic amino group of one AA attacks
the electrophilic carbonyl group of another AA
34
amide bonds are rigid because of
resonance
35
breaking a peptide bond is a
hydrolysis reaction
36
primary structure of a protein is the
linear sequence of AAs in a peptide and is stabilized by peptide bonds
37
secondary structure of a protein is the
local structure of nearby AAs
stabilized by H-bonding b/w amino groups and nonadjacent carboxyl groups
38
alpha-helices are
clockwise coils around a central axis
39
beta-pleated sheets are
rippled strands that can be parallel or antiparallel
40
proline can interrupt
secondary structure b/c of its rigid cycle structure
41
tertiary structure is the
3D shape of a single polypeptide chain
42
what stabilizes tertiary structure?
hydrophobic interactions
acid-base interactions (salt bridges)
h-bonding
disulfide bonds
43
hydrophobic interactions
push hydrophobic R groups to the interior of a protein
increases entropy of the surrounding water molecules and creates a negative gibbs free E
44
disulfide bonds occur when
two cysteine molecules are oxidized and create a covalent bond to form cystine
45
quaternary structure is the interaction
between peptides in proteins that contain multiple subunits
46
conjugated proteins
proteins with covalently attached molecules
47
attached molecules on conjugated proteins is called
prosthetic group
48
what can the prosthetic group be?
metal ion
vitamin
lipid
carbohydrate
nucleic acid
49
denaturation is
when heat and increasing solute concentration can lead to loss of 3D protein structure
50
what do enzymes do?
lower activation energy
increase reaction rate
51
enzyme specificity states that a given enzyme will ONLY catalyze....
a single rxn / class of rxns with these substrates
52
substrates
molecules upon which an enzyme acts
53
six types of enzymes
oxidoreductase, transferase, hydrolase, lyase, isomerase, ligase
54
oxidoreductases catalyze
oxidation-reduction reactions
- transfer of electrons bw bio molecules
- often have a cofactor that acts as an electron carrier (NAD+ or NADP+)
55
in reactions catalyzed by oxidoreductases, the electron donor is the
REDUCTANT
56
in reactions catalyzed by oxidoreductases, the electron acceptor is the
OXIDANT
57
enzymes in which oxygen is the final electron acceptor
often includes oxidase in their names
58
transferases catalyze the movement of
a functional group from one molecule to another
59
kinases catalyze the transfer of a
phosphate group generally from ATP to another molecule
60
hydrolases catalyze the breaking of
a compound into two molecules using the addition of water
61
lysases catalyze the
cleavage of a single molecule intwo two products
62
lysases do not require
water as a substrate and do not act as oxidoreductases
63
because most enzymes can also catalyze the reverse of their specific reactions,
the synthesis of two molecules into a single molecule may also be catalyzed by a lyase
64
isomerase catalyze the rearrangement of
bonds within a molecule
65
isomerases catalyze rxns b/w
stereoisomers as well as constitutional isomers
66
some isomerases can also be classified as
oxidoreductases, transferases, lyases
67
ligases catalyze
addition or synthesis reactions (generally b/w large similar reactions) and often require atp
68
synthesis rxns with smaller molecules are generally done by
lyases
69
ligases are most likely to be involved in
nucleic acid synthesis and repair
70
what do lineweaver-burk plots display?
enzyme kinetic data in linear form
inverse of rxn velocity on y axis and inverse of substrate concentration on x axis
71
vmax is
the max possible rxn rate
72
km is the
concentration of substrate at which 1/2 vmax is achieved
73
y intercept of a lineweaver-burk plot is
1/vmax
74
x intercept of lineweaver-burk plot is
-1/Km
75
allosteric effectors are molecules that bind to
enzymes at a site other than the active site and either increase/decrease activity
76
allosteric effectors that increase activity
activators
77
allosteric effectors that decrease activity
inhibitors
78
lineweaver-burk plots created in the presence and absence of an allosteric effector can be compared to find out how
the effector alters Km and Vmax
79
x and y intercepts are related to the
inverse of Km and vmax
80
when presence of allosteric effector show y intercept increasing
vmax decreases, making effector an inhibtor
81
when x-int on lineweaver-burk plot is negative...
this shift moves intercept away from origin --> mag increases
82
(+) sign on lineweaver-burk plot means
allosteric effector is present
83
increasing y intercept =
decreased vmax
84
(-) means allosteric effector
is absent
85
left shifted x intercept means
decreased Km
86
which deoxyribonucleotides would move most slowly down an alkaline agarose gel during electrophoresis?
dGMP (pruine deoxyguanosine phosphate) would move the slowest as it's the biggest
87
gel electrophoresis separates
molecules by molecular weight
88
DNA is composed of four
deoxyribonucleotides (dNMPs)
89
dGMP
purine deoxyguanosine phosphate is the largest
90
2nd largest deoxyribonucleotides (dNMPs)
deoxyadenosine monophosphate (dAMP)
91
3rd larges dNMP
deoxythymidine monophospate (dTMP)
92
smallest dNMP
deoxycytidine monophosphate (dCMPs)
93
oligonucleotide is a short strand of
DNA and its molecular weight is determined by its composition of dNMPs
94
metabolic pathways consist of both
reversible and irreversible reactions
95
opposing metabolic processes usually
use the same enzymes for reversible rxns (going in opp directions)
96
opposing metabolic processes must use
different enzymes to catalyze distinct rxns for the irreversible steps
97
many metabolic pathways are regulated by
allosteric effectors
98
allosteric effectors are
small molecules that bind to enzymes at sites other than the active site
99
upon binding, allosteric effectors induce
conformational changes in enzymes that alter enzyme activity
100
an effector that activates one metabolic pathways often
inhibits the opposing pathways
e.g. F2,6BP in glycolysis and gluconeogenesis
101
how many ntp produced during glycolysis
2 NTP
102
catabolic pathways degrade complex molecules into
simpler molecules to product high energy nucleotide triphosphates (NTPs such as ATP or GTP)
103
anabolic pathways use
simple molecules to synthesize more complex molecules (e.g. proteins, polysaccharides)
104
NTPs provide
energy for many bio processes
105
anabolism requires
energy input from NTPs
106
most catabolic processes are paired
with an opposing anabolic process
107
net ntp production or consumption refers to
the difference bw the numbers of NTPs produced and consumed in a process
108
ntp used in glycolysis
consumed 2 atps
produces 4 atps per glucose molecules
net production of 2 atps per glucose
109
glycolysis is what kind of process
catabolic
110
gluconeogenesis is what kind of process
anabolic
111
gluconeogenesis - ntps/atps
consumes a net total of 6 ntps (4 atps and 2 gtps) to produce one glucose molecule
112
glycolysis in the muscles is connected to
gluconeogenesis in the liver by the cori cycle
113
2 net ntps are produced when glucose becomes
pyruvate (glycolysis) partially offset the 6 net that are consumed later when pyruvate becomes glucose through gluconeogenesis
114
net number of ntps consumed by the first round of the cori cycle
6 - 2 = 4 net ntps consumed
115
ntps consumed in glycolysis/gluconeogensis
2 in glycolysis, 6 in gluconeogenesis = 8 total ntps consumes
4 ntps produced (glycolysis only)
8-4 = 4 new ntps consumed
116
catabolic processes lead to
energy production typically in the form of atp equivalents
117
anabolic processes consume
energy
118
glycolysis (catabolic) and gluconeogensis (anabolic) are connected by
the cori cycle
119
what metabolic process provides E necessary for sustained gluconeogenesis?
fatty acid oxidation
120
fatty acid oxidation produces
atp equivalents
121
fatty acid degradation to acetyl-CoA yields
NADH and FADH2 (both enter ETC = ATP)
122
resulting acetyl-CoA can enter the
citrtic acid cycle to produce more NADH and FADH2 as well as gtp (atp equivalent)
123
glycogenesis produces
glucose
124
when glycogen is present, gluconeogenesis is
not required
125
gluconeogenesis generally occurs
after glycogen stores have been depleted
126
fermentation is the conversion of
pyrute to lactate
127
resulting lactate from fermentation can enter gluconeogenesis after
being converted back to pyruvate
128
pentose phosphate pathway converts g
glucose and glycolysis intermediates to ribose-5-phosphate
process doesn't consume/produce ATP
129
gluconeogenesis is an
anabolic process that requires energy from atp equivalents
130
necessary E for gluconeogenesis is provided by
catabolic processes such as fatty acid oxidation
131
blood glucose levels are primarily controlled by
peptide hormones insulin and glucagon
132
when blood glucose levels are high...
pancreas releases insulting --> induces glucose uptake into cells
133
insulin also induces
glycolysis and glycogen synthesis
helps remove glucose from bloodstream
134
when blood glucose is low...
pancreas releases glucagon
135
when glucagon binds to receptors on liver cells...
i.t. induces an intracellular response that ends up upregulating glycogenolysis and gluconeogenesis
releases glucose into blood
136
glucagon decreases
rate of glycolysis
increases gluconeogenesis
137
histones are nuclear proteins that...
help in the organization of eukaryotic DNA
serve as structural support for DNA to wind tightly around
allows genomic DNA to be condensed into the nucleus
138
histones can also help...
regular gene expression
depending on strength of the binding interaction bw histone and its associated DNA
139
strong interactions inhibit the
DNA's accessibility and prevent transcription/gene expression
140
weaker binding interactions bw histone and its DNA
promote transcription and gene expression
141
lysine residues are charged...
positively
play an important role in histones due to their electrostatic interaction w/ neg charged phosphate groups on sugar-phosphate backbone
142
rxn with BHB neutralizes the...
lysine side chain
replaced charged amine w/ a neutral and non-ionizable amide
DNA-histone interaction weakens --> upregulation of gene expression
143
protein function is related to
structure and affected by temp
144
primary protein structure
linear AA sequence
145
secondary structure
results from H bonding in polypeptide backbone
146
quaternary structure
28 C
results from assembly of 1+ polypeptide chain
147
tertiary structure
37 C
results from AA side chain (R group) interactions
148
protein in quarternary structure binds...
DNA at lower temp
blocks transcription
149
protein in tertiary structure does not bind...
DNA at higher temp so transcription occurs
150
what links AAs?
peptide bonds link AAs
form proteins
151
sequence in which AAs are linked defines a
protein's primary structure
chem characteristics (e.g. side-chain charge) of AAs in sequence
protein structure
function
152
environmental factors can change
protein structure (denaturation) and protein function
153
at lower temperatures, less protein was...
produced
transcription was repressed
allow dimerization
154
at higher temps, dimerization does...
not occur
transcription increases
155
mRNA is translated
into protein by ribosomes
CODING RNA
156
rRNA associates with
specific proteins to form ribosomes
NONCODING RNA
157
tRNA pairs
mRNA codons w/ specific AAs during translation
NONCODING RNA
158
snRNA associates with
specific proteins to form small nuclear ribonucleoproteins (snRNPs)
building block of spliceosomes
NONCODING RNA
159
siRNA (small interfering RNA)
functions in RNA interference
binds complementary mRNA and signals for its degradation
NONCODING RNA
160
miRNA (microRNA)
functions in RNA interference
binds target complementary sequence on mRNA molecule to silence gene expression
161
microRNAs bind
complementary sequences on target mRNA
inhibit expression at translational level
162
following binding, miRNA-mediated silencing occurs either by
promoting endonuclease activation
subsequent cleavage of target mRNA
or prevents target mRNA from binding to ribosomes (blocking translation)
163
rRNA pairs with specific proteins to form
ribosome, a molecular complex that brings mRNA and tRNA together
enzymatically manufacture polypeptides during translations
164
polymerase chain reaction (PCR) measures
DNA amplification after all the thermal cycles are complete
165
real time PCR quantifies
product amplification as rxn progresses in real time
166
oncogene is a
mutated/overexpressed gene that induces uncontrolled cell growth
promote cell cycle progression + inhibition of apoptosis
167
key feature of a tumor suppressor gene
inhibition of cell cycle progression
168
tumor suppressor genes regulate DNA repair by
rrepressing/pausing cell cycle to ensure that only normal cells proceed to divise stage
programmed cell death induced if repair fails
169
nucleic acid structures with more (x) pairs are more stable
G-C
170
A-U have how many H-bonds?
2
171
G-C bonds have how many H-bonds?
3
172
173
as beta-sheets form, the R groups
become aligned
174
glutamine is a
polar uncharged AA w/ an amide side chain
175
amides contain both a
carbonyl oxygen and an amide -NH2 group
176
amide -NH2 group can act as a
h-bond donor
177
carbonyl oxygen can act as a
h-bond acceptor
178
because side chains are aligned in beta-sheet and because glutamine side chain can simultaneously act as an acceptor and donor,
polyQ beta-sheets can form networks of H-bonds
179
in addition to the h-bonds b/w peptide backbone amide groups, glutamine-mediated h-bond networks...
further strengthen and stabilize beta-sheet conformation
having a stronger effect as polyQ length increases
180
stacking interactions stabilize which protein structure
secondary
occur between aromatic side chains such as Phe, Tyr, Tryp
181
which is more flexible: glutamine or glycine?
glycine
flexibility is favorable for beta-turns
182
proline's ridigity is
conducive to tight turns
183
is glutamine rigid?
no
184
hydrophobic effect drives
protein folding
185
hydrophobic effect causes proteins to
adopt a conformation that hides as many hydrophobic residues in protein's interior
186
changes that cause a protein to misfold often expose...
hydrophobic residues to the aqueous environment
187
misfolded proteins often
aggregate (group togther) to hide exposed residues
188
aggregation often results in a significant decrease in
protein's solubility
189
glutamine has an uncharged
polar side chain
no ionic interactions to disrupt
190
interaction of glutamine side chains with each does not...
prevent interaction w/ water
191
h-bonds b/w side chains can transiently...
break to bond w/ water and vice versa
192
peptide backbones are not very hydrophobic because
they have both a carbonyl and an amino group that can form h-bonds
193
proteins that adopt non-native conformations are generally forced to...
more hydrophobic residues to the aqueous environment
194
hydrophobic residues cannot interact with water and therefore tend to
aggregate to minimize exposure due to hydrophobic effect
195
inability to interact with water results in
precipitation out of solute
196
how can beta-sheets be oriented?
parallel or antiparallel manner
197
parallel strands run in the same direction so the N-terminal of one strand aligns....
with the N-terminal portions of the others
198
in antiparallel sheets, the individual strand run in directions opposite each other so the...
N-terminal portion of one strand lines up w/ C-terminal portion of neighboring strands
199
secondary structure always includes
H-bonds b/w amide carbonyls and NH groups in the polypeptide backbone
200
parallel and antiparallel sheets differ in their
hydrogen bond geometries with bond pairs directly aligned in antiparallel sheets and slightly offset in parallel sheets
201
antiparallel strands run in
opposite directions
202
antiparallel strands may be linked by a
short sequence of AAs called a beta-turn
induces 180 degree bend in polypeptide chain
203
parallel beta strands do not reverse
directionality
204
neighboring strands must be linked instead by
longer loops that makes 360 degree turns to align N-terminal regions of neighboring strands
205
parallel strand can never be liked by
beta turns
206
beta-turns are
a short sequence of amino acids that induce a 180 degree bend in the polypeptide chain
207
molecular chapterones are proteins that
facilitate the proper folding of other proteins
208
chaperones ensure protein folds properly by binding
hydrophobic regions of nascent/misfolded/aggregated proteins
exposure to aqueous solvent is prevented
209
chaperons prevent or reverse
aggregation by blocking interactions b/w hydrophobic regions of separate polypeptides
210
disruption of interactions b/w beta-sheets could help disaggregate
amyloid fibers which may increase solubility and reduce toxicity
211
where are globular domains found?
oxidizing environment of the Golgi apparatus and its vesicles
212
bonds that most likely form between cysteine residues?
disulfide bonds
stabilizes tertiary structure
213
peptide bonds are covalent bonds formed between
amino acids to make proteins and peptides
contribute to a protein's primary structure but not its tertiary structure
214
electrostatic interactions are frequently involved in
tertiary protein structure
DO NOT involve shared electrons and covalent bonds
215
thioester bonds form between a
sulfur atom and a carbonyl carbon
216
what are thioester bonds important for
coenzymes and metabolites such as acetyl-CoA and succinyl-CoA
do not participate in tertiary protein structure
217
3D folded form of a protein includes
secondary and tertiary structure
DETERMINED BY primary structure (AA sequence)
218
proteins with similar AA sequences often...
fold similarly
AAs with similar folds have similar AA sequences
219
proteins with different sequences are likely
to adopt distinct folds
220
domains with a protein behave as
individual units and typically fold indepedently from each other
221
low Kd means
few ligands required for binding
HIGH AFFINITY of a protein
222
high Kd means
many ligands required for binding
LOW AFFINITY
223
3rd base in a codon can
wobble and break standard Watson-Crick rules but STILL code for intended protein
224
wobble is caused by
redundancy found in genetic code
225
are wobble base pairings stable?
LESS STABLE
226
what mutation results from a nucleotide addition/deletion that changes reading frame of subsequent codons?
frameshift mutation
227
where are silent mutations usually found?
3rd base of a codon
228
missense mutation produces a
codon that codes for a different AA
229
nonsense mutation produces a
premature stop codon
230
first step of gene expression
transcription
231
transcription is the when
segment of DNA is copied into RNA by enzyme RNA polymerase
232
tRNA brings AAs to the ribosome and recognizes the
codon on the mRNA using its own anticodon
233
rRNA makes up the
ribosome and is enzymatically active
234
what is a segment of DNA wound in sequence around 8 histone protein cores
nucleosome
235
introns are
segments of DNA/RNA molecule that does NOT code for protein
236
introns stay in the
nucleus since they are cut out and not included in mRNA
237
exons exit the
nucleus and form mRNA
238
what process in eukaryotic cells have primary transcript RNA converted into mature RNA?
post-transcriptional modification
introns are cut out
239
alternative splicing is a
regulated process during gene expression resulting in a single gene coding for multiple proteins
240
in normal gene expression, introns are
cut away and exons remain in sequence
241
in alternative splicing, a certain exon may be
cut out or an intron may stay
242
alternative splicing allows for the
RNA segment to code for more than one gene
243
chromatin packages DNA into a
smaller volume to fit in the cell
244
heterochromatin is
dark, dense and silent
245
euchromatin is
light, uncondensed, expressed
246
segment of prokaryotic mRNA that encodes several proteins
polycistronic gene
247
purpose of 5' cap and poly-A tail on mRNA is that they
protect mRNA for translation
248
start codon also codes for
methionine
249
in translation, a succession of tRNAs add their
AAs to the polypeptide chain as mRNA is moved through ribosome one codon at a time
250
acrocentric chromosome is one in which the
centromere is located near one end of the chromosome and not in the middle
251
what is transcribed from DNA in nucleus?
mRNA
252
mRNA travels into
cytoplasm for translation
253
