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biochem > mcat rev > Flashcards

mcat rev Flashcards

1
Q

amino acids have four groups attached to a

A

central alpha carbon

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2
Q

the four groups that make up an AA?

A

carboxylic acid group, H atom, amino group, R group

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3
Q

R group function

A

chemistry and function of AA

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4
Q

how many AAs appear in eukaryotic organisms’ proteins?

A

20

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5
Q

ALL AAs are chiral except

A

glycine

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6
Q

ALL chiral AAs except cysteine have

A

S configuration

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7
Q

nonpolar/nonaromatic side chains:

A

glycine, alanine, valine, leucine, isoleucine, methionine, proline

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8
Q

aromatic side chains:

A

tryptophan, phenylalanine, tyrosine

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9
Q

polar side chains:

A

serine, threonine, asparagine, glutamine, cysteine

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10
Q

negative charged (acidic) side chains:

A

aspartate, glutamate

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11
Q

positively charged (basic) side chains:

A

lysine, arginine, histidine

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12
Q

amino acids w/ long alkyl chains are

A

hydrophobic

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13
Q

amino acids with short alkyl chains are

A

hydrophilic

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14
Q

amphoteric:

A

means AAs can accept or donate protons

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15
Q

pKa of a group is the

A

pH at which half the species is deprotonated

[HA] = [A-]

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16
Q

AAs exist in different forms at

A

different pH values

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17
Q

at low (acidic) pH, AA is

A

fully protonated

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18
Q

at pH near the isoelectric pt (pI) of the AA,

A

the AA is a neutral zwitterion

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19
Q

at high (alkaline) pH, AA is

A

fully deprotonated

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20
Q

isoelectric point (pI) is

A

calculated for an AA without charged side chains by averaging two pKa values

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21
Q

can AAs be titrated?

A

yes

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22
Q

titration curve is nearly flat at

A

pKa values of AA

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23
Q

titration curve is nearly vertical at the

A

pI of the AA

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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

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25
Q

AAs w/o charged side chains have a

A

pI around 6

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26
Q

acidic AAs have a pI

A

below 6

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27
Q

basic AAs have a pI

A

above 6

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28
Q

dipeptides have two

A

AA residues

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29
Q

tripeptides have three

A

AA residues

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30
Q

oligopeptides have a (x) AA residues

A

FEW (less than 20)

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31
Q

polypeptides have

A

MANY AA residues

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32
Q

forming a peptide bond is a

A

condensation or dehydration rxn

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33
Q

nucleophilic amino group of one AA attacks

A

the electrophilic carbonyl group of another AA

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34
Q

amide bonds are rigid because of

A

resonance

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35
Q

breaking a peptide bond is a

A

hydrolysis reaction

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36
Q

primary structure of a protein is the

A

linear sequence of AAs in a peptide and is stabilized by peptide bonds

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37
Q

secondary structure of a protein is the

A

local structure of nearby AAs

stabilized by H-bonding b/w amino groups and nonadjacent carboxyl groups

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38
Q

alpha-helices are

A

clockwise coils around a central axis

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39
Q

beta-pleated sheets are

A

rippled strands that can be parallel or antiparallel

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40
Q

proline can interrupt

A

secondary structure b/c of its rigid cycle structure

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41
Q

tertiary structure is the

A

3D shape of a single polypeptide chain

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42
Q

what stabilizes tertiary structure?

A

hydrophobic interactions
acid-base interactions (salt bridges)
h-bonding
disulfide bonds

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43
Q

hydrophobic interactions

A

push hydrophobic R groups to the interior of a protein

increases entropy of the surrounding water molecules and creates a negative gibbs free E

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44
Q

disulfide bonds occur when

A

two cysteine molecules are oxidized and create a covalent bond to form cystine

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45
Q

quaternary structure is the interaction

A

between peptides in proteins that contain multiple subunits

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46
Q

conjugated proteins

A

proteins with covalently attached molecules

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47
Q

attached molecules on conjugated proteins is called

A

prosthetic group

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48
Q

what can the prosthetic group be?

A

metal ion
vitamin
lipid
carbohydrate
nucleic acid

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49
Q

denaturation is

A

when heat and increasing solute concentration can lead to loss of 3D protein structure

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50
Q

what do enzymes do?

A

lower activation energy

increase reaction rate

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51
Q

enzyme specificity states that a given enzyme will ONLY catalyze….

A

a single rxn / class of rxns with these substrates

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52
Q

substrates

A

molecules upon which an enzyme acts

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53
Q

six types of enzymes

A

oxidoreductase, transferase, hydrolase, lyase, isomerase, ligase

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54
Q

oxidoreductases catalyze

A

oxidation-reduction reactions

  • transfer of electrons bw bio molecules
  • often have a cofactor that acts as an electron carrier (NAD+ or NADP+)
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55
Q

in reactions catalyzed by oxidoreductases, the electron donor is the

A

REDUCTANT

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56
Q

in reactions catalyzed by oxidoreductases, the electron acceptor is the

A

OXIDANT

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57
Q

enzymes in which oxygen is the final electron acceptor

A

often includes oxidase in their names

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58
Q

transferases catalyze the movement of

A

a functional group from one molecule to another

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59
Q

kinases catalyze the transfer of a

A

phosphate group generally from ATP to another molecule

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60
Q

hydrolases catalyze the breaking of

A

a compound into two molecules using the addition of water

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61
Q

lysases catalyze the

A

cleavage of a single molecule intwo two products

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62
Q

lysases do not require

A

water as a substrate and do not act as oxidoreductases

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63
Q

because most enzymes can also catalyze the reverse of their specific reactions,

A

the synthesis of two molecules into a single molecule may also be catalyzed by a lyase

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64
Q

isomerase catalyze the rearrangement of

A

bonds within a molecule

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65
Q

isomerases catalyze rxns b/w

A

stereoisomers as well as constitutional isomers

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66
Q

some isomerases can also be classified as

A

oxidoreductases, transferases, lyases

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67
Q

ligases catalyze

A

addition or synthesis reactions (generally b/w large similar reactions) and often require atp

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68
Q

synthesis rxns with smaller molecules are generally done by

A

lyases

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69
Q

ligases are most likely to be involved in

A

nucleic acid synthesis and repair

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70
Q

what do lineweaver-burk plots display?

A

enzyme kinetic data in linear form

inverse of rxn velocity on y axis and inverse of substrate concentration on x axis

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71
Q

vmax is

A

the max possible rxn rate

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72
Q

km is the

A

concentration of substrate at which 1/2 vmax is achieved

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73
Q

y intercept of a lineweaver-burk plot is

A

1/vmax

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74
Q

x intercept of lineweaver-burk plot is

A

-1/Km

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75
Q

allosteric effectors are molecules that bind to

A

enzymes at a site other than the active site and either increase/decrease activity

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76
Q

allosteric effectors that increase activity

A

activators

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77
Q

allosteric effectors that decrease activity

A

inhibitors

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78
Q

lineweaver-burk plots created in the presence and absence of an allosteric effector can be compared to find out how

A

the effector alters Km and Vmax

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79
Q

x and y intercepts are related to the

A

inverse of Km and vmax

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80
Q

when presence of allosteric effector show y intercept increasing

A

vmax decreases, making effector an inhibtor

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81
Q

when x-int on lineweaver-burk plot is negative…

A

this shift moves intercept away from origin –> mag increases

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82
Q

(+) sign on lineweaver-burk plot means

A

allosteric effector is present

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83
Q

increasing y intercept =

A

decreased vmax

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84
Q

(-) means allosteric effector

A

is absent

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85
Q

left shifted x intercept means

A

decreased Km

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86
Q

which deoxyribonucleotides would move most slowly down an alkaline agarose gel during electrophoresis?

A

dGMP (pruine deoxyguanosine phosphate) would move the slowest as it’s the biggest

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87
Q

gel electrophoresis separates

A

molecules by molecular weight

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88
Q

DNA is composed of four

A

deoxyribonucleotides (dNMPs)

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89
Q

dGMP

A

purine deoxyguanosine phosphate is the largest

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90
Q

2nd largest deoxyribonucleotides (dNMPs)

A

deoxyadenosine monophosphate (dAMP)

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91
Q

3rd larges dNMP

A

deoxythymidine monophospate (dTMP)

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92
Q

smallest dNMP

A

deoxycytidine monophosphate (dCMPs)

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93
Q

oligonucleotide is a short strand of

A

DNA and its molecular weight is determined by its composition of dNMPs

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94
Q

metabolic pathways consist of both

A

reversible and irreversible reactions

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95
Q

opposing metabolic processes usually

A

use the same enzymes for reversible rxns (going in opp directions)

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96
Q

opposing metabolic processes must use

A

different enzymes to catalyze distinct rxns for the irreversible steps

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97
Q

many metabolic pathways are regulated by

A

allosteric effectors

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98
Q

allosteric effectors are

A

small molecules that bind to enzymes at sites other than the active site

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99
Q

upon binding, allosteric effectors induce

A

conformational changes in enzymes that alter enzyme activity

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100
Q

an effector that activates one metabolic pathways often

A

inhibits the opposing pathways

e.g. F2,6BP in glycolysis and gluconeogenesis

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101
Q

how many ntp produced during glycolysis

A

2 NTP

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102
Q

catabolic pathways degrade complex molecules into

A

simpler molecules to product high energy nucleotide triphosphates (NTPs such as ATP or GTP)

103
Q

anabolic pathways use

A

simple molecules to synthesize more complex molecules (e.g. proteins, polysaccharides)

104
Q

NTPs provide

A

energy for many bio processes

105
Q

anabolism requires

A

energy input from NTPs

106
Q

most catabolic processes are paired

A

with an opposing anabolic process

107
Q

net ntp production or consumption refers to

A

the difference bw the numbers of NTPs produced and consumed in a process

108
Q

ntp used in glycolysis

A

consumed 2 atps
produces 4 atps per glucose molecules

net production of 2 atps per glucose

109
Q

glycolysis is what kind of process

A

catabolic

110
Q

gluconeogenesis is what kind of process

A

anabolic

111
Q

gluconeogenesis - ntps/atps

A

consumes a net total of 6 ntps (4 atps and 2 gtps) to produce one glucose molecule

112
Q

glycolysis in the muscles is connected to

A

gluconeogenesis in the liver by the cori cycle

113
Q

2 net ntps are produced when glucose becomes

A

pyruvate (glycolysis) partially offset the 6 net that are consumed later when pyruvate becomes glucose through gluconeogenesis

114
Q

net number of ntps consumed by the first round of the cori cycle

A

6 - 2 = 4 net ntps consumed

115
Q

ntps consumed in glycolysis/gluconeogensis

A

2 in glycolysis, 6 in gluconeogenesis = 8 total ntps consumes

4 ntps produced (glycolysis only)

8-4 = 4 new ntps consumed

116
Q

catabolic processes lead to

A

energy production typically in the form of atp equivalents

117
Q

anabolic processes consume

A

energy

118
Q

glycolysis (catabolic) and gluconeogensis (anabolic) are connected by

A

the cori cycle

119
Q

what metabolic process provides E necessary for sustained gluconeogenesis?

A

fatty acid oxidation

120
Q

fatty acid oxidation produces

A

atp equivalents

121
Q

fatty acid degradation to acetyl-CoA yields

A

NADH and FADH2 (both enter ETC = ATP)

122
Q

resulting acetyl-CoA can enter the

A

citrtic acid cycle to produce more NADH and FADH2 as well as gtp (atp equivalent)

123
Q

glycogenesis produces

A

glucose

124
Q

when glycogen is present, gluconeogenesis is

A

not required

125
Q

gluconeogenesis generally occurs

A

after glycogen stores have been depleted

126
Q

fermentation is the conversion of

A

pyrute to lactate

127
Q

resulting lactate from fermentation can enter gluconeogenesis after

A

being converted back to pyruvate

128
Q

pentose phosphate pathway converts g

A

glucose and glycolysis intermediates to ribose-5-phosphate

process doesn’t consume/produce ATP

129
Q

gluconeogenesis is an

A

anabolic process that requires energy from atp equivalents

130
Q

necessary E for gluconeogenesis is provided by

A

catabolic processes such as fatty acid oxidation

131
Q

blood glucose levels are primarily controlled by

A

peptide hormones insulin and glucagon

132
Q

when blood glucose levels are high…

A

pancreas releases insulting –> induces glucose uptake into cells

133
Q

insulin also induces

A

glycolysis and glycogen synthesis

helps remove glucose from bloodstream

134
Q

when blood glucose is low…

A

pancreas releases glucagon

135
Q

when glucagon binds to receptors on liver cells…

A

i.t. induces an intracellular response that ends up upregulating glycogenolysis and gluconeogenesis

releases glucose into blood

136
Q

glucagon decreases

A

rate of glycolysis

increases gluconeogenesis

137
Q

histones are nuclear proteins that…

A

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
Q

histones can also help…

A

regular gene expression

depending on strength of the binding interaction bw histone and its associated DNA

139
Q

strong interactions inhibit the

A

DNA’s accessibility and prevent transcription/gene expression

140
Q

weaker binding interactions bw histone and its DNA

A

promote transcription and gene expression

141
Q

lysine residues are charged…

A

positively

play an important role in histones due to their electrostatic interaction w/ neg charged phosphate groups on sugar-phosphate backbone

142
Q

rxn with BHB neutralizes the…

A

lysine side chain

replaced charged amine w/ a neutral and non-ionizable amide

DNA-histone interaction weakens –> upregulation of gene expression

143
Q

protein function is related to

A

structure and affected by temp

144
Q

primary protein structure

A

linear AA sequence

145
Q

secondary structure

A

results from H bonding in polypeptide backbone

146
Q

quaternary structure

A

28 C

results from assembly of 1+ polypeptide chain

147
Q

tertiary structure

A

37 C

results from AA side chain (R group) interactions

148
Q

protein in quarternary structure binds…

A

DNA at lower temp

blocks transcription

149
Q

protein in tertiary structure does not bind…

A

DNA at higher temp so transcription occurs

150
Q

what links AAs?

A

peptide bonds link AAs

form proteins

151
Q

sequence in which AAs are linked defines a

A

protein’s primary structure

chem characteristics (e.g. side-chain charge) of AAs in sequence

protein structure

function

152
Q

environmental factors can change

A

protein structure (denaturation) and protein function

153
Q

at lower temperatures, less protein was…

A

produced

transcription was repressed

allow dimerization

154
Q

at higher temps, dimerization does…

A

not occur

transcription increases

155
Q

mRNA is translated

A

into protein by ribosomes

CODING RNA

156
Q

rRNA associates with

A

specific proteins to form ribosomes

NONCODING RNA

157
Q

tRNA pairs

A

mRNA codons w/ specific AAs during translation

NONCODING RNA

158
Q

snRNA associates with

A

specific proteins to form small nuclear ribonucleoproteins (snRNPs)

building block of spliceosomes

NONCODING RNA

159
Q

siRNA (small interfering RNA)

A

functions in RNA interference

binds complementary mRNA and signals for its degradation

NONCODING RNA

160
Q

miRNA (microRNA)

A

functions in RNA interference

binds target complementary sequence on mRNA molecule to silence gene expression

161
Q

microRNAs bind

A

complementary sequences on target mRNA

inhibit expression at translational level

162
Q

following binding, miRNA-mediated silencing occurs either by

A

promoting endonuclease activation

subsequent cleavage of target mRNA

or prevents target mRNA from binding to ribosomes (blocking translation)

163
Q

rRNA pairs with specific proteins to form

A

ribosome, a molecular complex that brings mRNA and tRNA together

enzymatically manufacture polypeptides during translations

164
Q

polymerase chain reaction (PCR) measures

A

DNA amplification after all the thermal cycles are complete

165
Q

real time PCR quantifies

A

product amplification as rxn progresses in real time

166
Q

oncogene is a

A

mutated/overexpressed gene that induces uncontrolled cell growth

promote cell cycle progression + inhibition of apoptosis

167
Q

key feature of a tumor suppressor gene

A

inhibition of cell cycle progression

168
Q

tumor suppressor genes regulate DNA repair by

A

rrepressing/pausing cell cycle to ensure that only normal cells proceed to divise stage

programmed cell death induced if repair fails

169
Q

nucleic acid structures with more (x) pairs are more stable

A

G-C

170
Q

A-U have how many H-bonds?

A

2

171
Q

G-C bonds have how many H-bonds?

A

3

172
Q
A
173
Q

as beta-sheets form, the R groups

A

become aligned

174
Q

glutamine is a

A

polar uncharged AA w/ an amide side chain

175
Q

amides contain both a

A

carbonyl oxygen and an amide -NH2 group

176
Q

amide -NH2 group can act as a

A

h-bond donor

177
Q

carbonyl oxygen can act as a

A

h-bond acceptor

178
Q

because side chains are aligned in beta-sheet and because glutamine side chain can simultaneously act as an acceptor and donor,

A

polyQ beta-sheets can form networks of H-bonds

179
Q

in addition to the h-bonds b/w peptide backbone amide groups, glutamine-mediated h-bond networks…

A

further strengthen and stabilize beta-sheet conformation

having a stronger effect as polyQ length increases

180
Q

stacking interactions stabilize which protein structure

A

secondary

occur between aromatic side chains such as Phe, Tyr, Tryp

181
Q

which is more flexible: glutamine or glycine?

A

glycine

flexibility is favorable for beta-turns

182
Q

proline’s ridigity is

A

conducive to tight turns

183
Q

is glutamine rigid?

A

no

184
Q

hydrophobic effect drives

A

protein folding

185
Q

hydrophobic effect causes proteins to

A

adopt a conformation that hides as many hydrophobic residues in protein’s interior

186
Q

changes that cause a protein to misfold often expose…

A

hydrophobic residues to the aqueous environment

187
Q

misfolded proteins often

A

aggregate (group togther) to hide exposed residues

188
Q

aggregation often results in a significant decrease in

A

protein’s solubility

189
Q

glutamine has an uncharged

A

polar side chain

no ionic interactions to disrupt

190
Q

interaction of glutamine side chains with each does not…

A

prevent interaction w/ water

191
Q

h-bonds b/w side chains can transiently…

A

break to bond w/ water and vice versa

192
Q

peptide backbones are not very hydrophobic because

A

they have both a carbonyl and an amino group that can form h-bonds

193
Q

proteins that adopt non-native conformations are generally forced to…

A

more hydrophobic residues to the aqueous environment

194
Q

hydrophobic residues cannot interact with water and therefore tend to

A

aggregate to minimize exposure due to hydrophobic effect

195
Q

inability to interact with water results in

A

precipitation out of solute

196
Q

how can beta-sheets be oriented?

A

parallel or antiparallel manner

197
Q

parallel strands run in the same direction so the N-terminal of one strand aligns….

A

with the N-terminal portions of the others

198
Q

in antiparallel sheets, the individual strand run in directions opposite each other so the…

A

N-terminal portion of one strand lines up w/ C-terminal portion of neighboring strands

199
Q

secondary structure always includes

A

H-bonds b/w amide carbonyls and NH groups in the polypeptide backbone

200
Q

parallel and antiparallel sheets differ in their

A

hydrogen bond geometries with bond pairs directly aligned in antiparallel sheets and slightly offset in parallel sheets

201
Q

antiparallel strands run in

A

opposite directions

202
Q

antiparallel strands may be linked by a

A

short sequence of AAs called a beta-turn

induces 180 degree bend in polypeptide chain

203
Q

parallel beta strands do not reverse

A

directionality

204
Q

neighboring strands must be linked instead by

A

longer loops that makes 360 degree turns to align N-terminal regions of neighboring strands

205
Q

parallel strand can never be liked by

A

beta turns

206
Q

beta-turns are

A

a short sequence of amino acids that induce a 180 degree bend in the polypeptide chain

207
Q

molecular chapterones are proteins that

A

facilitate the proper folding of other proteins

208
Q

chaperones ensure protein folds properly by binding

A

hydrophobic regions of nascent/misfolded/aggregated proteins

exposure to aqueous solvent is prevented

209
Q

chaperons prevent or reverse

A

aggregation by blocking interactions b/w hydrophobic regions of separate polypeptides

210
Q

disruption of interactions b/w beta-sheets could help disaggregate

A

amyloid fibers which may increase solubility and reduce toxicity

211
Q

where are globular domains found?

A

oxidizing environment of the Golgi apparatus and its vesicles

212
Q

bonds that most likely form between cysteine residues?

A

disulfide bonds

stabilizes tertiary structure

213
Q

peptide bonds are covalent bonds formed between

A

amino acids to make proteins and peptides

contribute to a protein’s primary structure but not its tertiary structure

214
Q

electrostatic interactions are frequently involved in

A

tertiary protein structure

DO NOT involve shared electrons and covalent bonds

215
Q

thioester bonds form between a

A

sulfur atom and a carbonyl carbon

216
Q

what are thioester bonds important for

A

coenzymes and metabolites such as acetyl-CoA and succinyl-CoA

do not participate in tertiary protein structure

217
Q

3D folded form of a protein includes

A

secondary and tertiary structure

DETERMINED BY primary structure (AA sequence)

218
Q

proteins with similar AA sequences often…

A

fold similarly

AAs with similar folds have similar AA sequences

219
Q

proteins with different sequences are likely

A

to adopt distinct folds

220
Q

domains with a protein behave as

A

individual units and typically fold indepedently from each other

221
Q

low Kd means

A

few ligands required for binding

HIGH AFFINITY of a protein

222
Q

high Kd means

A

many ligands required for binding

LOW AFFINITY

223
Q

3rd base in a codon can

A

wobble and break standard Watson-Crick rules but STILL code for intended protein

224
Q

wobble is caused by

A

redundancy found in genetic code

225
Q

are wobble base pairings stable?

A

LESS STABLE

226
Q

what mutation results from a nucleotide addition/deletion that changes reading frame of subsequent codons?

A

frameshift mutation

227
Q

where are silent mutations usually found?

A

3rd base of a codon

228
Q

missense mutation produces a

A

codon that codes for a different AA

229
Q

nonsense mutation produces a

A

premature stop codon

230
Q

first step of gene expression

A

transcription

231
Q

transcription is the when

A

segment of DNA is copied into RNA by enzyme RNA polymerase

232
Q

tRNA brings AAs to the ribosome and recognizes the

A

codon on the mRNA using its own anticodon

233
Q

rRNA makes up the

A

ribosome and is enzymatically active

234
Q

what is a segment of DNA wound in sequence around 8 histone protein cores

A

nucleosome

235
Q

introns are

A

segments of DNA/RNA molecule that does NOT code for protein

236
Q

introns stay in the

A

nucleus since they are cut out and not included in mRNA

237
Q

exons exit the

A

nucleus and form mRNA

238
Q

what process in eukaryotic cells have primary transcript RNA converted into mature RNA?

A

post-transcriptional modification

introns are cut out

239
Q

alternative splicing is a

A

regulated process during gene expression resulting in a single gene coding for multiple proteins

240
Q

in normal gene expression, introns are

A

cut away and exons remain in sequence

241
Q

in alternative splicing, a certain exon may be

A

cut out or an intron may stay

242
Q

alternative splicing allows for the

A

RNA segment to code for more than one gene

243
Q

chromatin packages DNA into a

A

smaller volume to fit in the cell

244
Q

heterochromatin is

A

dark, dense and silent

245
Q

euchromatin is

A

light, uncondensed, expressed

246
Q

segment of prokaryotic mRNA that encodes several proteins

A

polycistronic gene

247
Q

purpose of 5’ cap and poly-A tail on mRNA is that they

A

protect mRNA for translation

248
Q

start codon also codes for

A

methionine

249
Q

in translation, a succession of tRNAs add their

A

AAs to the polypeptide chain as mRNA is moved through ribosome one codon at a time

250
Q

acrocentric chromosome is one in which the

A

centromere is located near one end of the chromosome and not in the middle

251
Q

what is transcribed from DNA in nucleus?

A

mRNA

252
Q

mRNA travels into

A

cytoplasm for translation

253
Q
A

biochem (11 decks)

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