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CMM > Study Guide Questions Section 1 > Flashcards

Study Guide Questions Section 1 Flashcards

1
Q

non-polar amino acids?

A

glycine, valine, leucine, isoleucine, alanine, proline

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2
Q

hydrophobic amino acids?

A

leucine, isoleucine, proline, methionine, tryptophan, phenylalanine, tyrosine

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3
Q

hydrophilic amino acids?

A

serine, threonine, asparagine, glutamine, cysteine

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4
Q

very hydrophilic amino acids?

A

glutamate, aspartate, histidine, arginine, lysine

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5
Q

pKa of lysine, arginine, aspartate, and glutamate?

A

lysine: 10.5
arginine: 12
asp: 4
glu: 4

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6
Q

henderson-hasselbach?

A

pH = pKa +log[base]/[acid]

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7
Q

definition of pKa?

A

the pH when the concentration of acid and its conjugate base are the same

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8
Q

what is pI?

A

the pH when the positive and negative charges are balanced

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9
Q

what is the pKa of bicarbonate?

A

6.1

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10
Q

six differences between DNA and RNA?

A

DNA: double-stranded, has thymine instead of uracil
RNA: has an OH at 2’ of ribose, has no repair mechanism, more fragile, has more errors

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11
Q

what is the direction of activity of DNA polymerase’s exonuclease?

A

3’–5’ usually and 5’–3’ for primer removal

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12
Q

why is codon preference useful?

A

it helps to conserve energy for microorganisms

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13
Q

what is a synonymous SNP?

A

a point mutation that leads to the codon for the same amino acid (silent mutation)

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14
Q

what is a non-synonymous SNP?

A

a point mutation in which the codon leads to a different amino acid being selected (missense mutation)

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15
Q

what is read-through SNP?

A

a point mutation that changes a stop codon into a codon that codes for an amino acid

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16
Q

what type of process is peptide formation?

A

dehydration

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17
Q

how many genes and polyproteins does HIV have? how does it carry out its function with this number of genes?

A

it has three genes and two polyproteins

protease cleaves the polyproteins into smaller proteins that have different functions

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18
Q

what is the structure of collagen?

A

rope-like helix

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19
Q

what is the structure of a peptide bond?

A

planar like a double bond

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20
Q

what stabilizes secondary structures?

A

hydrogen bonds

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21
Q

what stabilizes tertiary and quaternary structures?

A

hydrogen bonds, ionic interactions, hydrophobic interactions, van der waals, and sometimes disulfide linkages

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22
Q

name three compounds that have disulfide bonds:

A

insulin, immunoglobulins, ribonuclease

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23
Q

what is protein folding driven by?

A

entropy

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24
Q

another name for chaperones and what do they do?

A

heat shock protein

they prevent collection of newly-synthesized proteins to facilitate in the formation of secondary structure

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25
Q

name two processes that proteases are important for:

A

food digestion and blood clotting

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26
Q

which amino acids form salt bridges?

A

aspartate, glutamate, arginine, lysine, histidine

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27
Q

what is the charge of a protein above its pI?

A

negative

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28
Q

what is the charge of a protein below its pI?

A

positive

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29
Q

how does vCJD get to the brain of its new host?

A

it gets through intestinal epithelium via transcytosis and gets transmitted to the brain through macrophages or dendrites

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30
Q

what is different in the structure of normal and abnormal PrP?

A

normal PrP are helical
abnormal are beta sheets
amino acid sequence is the same

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31
Q

how did people get Kuru?

A

from eating brains of humans in a traditional ceremony

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32
Q

what does vCJD look like under a microscope?

A

like a sponge around the plaque

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33
Q

what is proteopathy?

A

disease from protein misfolding

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34
Q

what are the two prospective causes of Alzheimer’s?

A

amyloid plaques from ABeta proteins and neurofibrillary tangles

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35
Q

what do reticulocytes makes?

A

hemoglobin and red blood cells

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36
Q

neutrophils last how long and have what degradative enzymes?

A 
one to two days
contain proteases (elastase) nd myeloperoxidase
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37
Q

what are foam cells?

A

when macrophages engulf LDL with cholesterol

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38
Q

what do eosinophils do?

A

defend against parasitic infection

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39
Q

what is plasma and what is serum?

A 
plasma = liquid portion of blood that contains salts, vitamins, amino acids, proteins, fats 
serum = plasma that is spin down to remove the coagulation factors
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40
Q

what does albumin do?

A

consists of up to 50% of the plasma proteins
stabilizes osmotic pressure, aids in the transport of water-insoluble compounds such as bilirubin
negatively charged to bind to positively charged compounds

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41
Q

what do the alpha1, alpha2, beta, and gamma peaks signify?

A

alpha1: alpha 1 antitrypsin = SERPIN that inhibits elastase; defects in this protease will cause emphysema; tobacco smoke oxidizes the methionine and inhibits the function of this enzyme
alpha2: haptoglobulin = binds hemoglobin; GC globulin = transports Vit D; ceruloplasmin = transports copper; prothrombin = precursor to thrombin; antithrombin III = a SERPIN that inhibits the formation of thrombin in the presence of heparin
beta: transferrin = transports 2 Fe 3+; hemopexin = binds heme
gamma: immunoglobulins (majority A, M, and G)

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42
Q

why is CRP called acute phase protein?

A

inflammatory response due to infection, cancer, and inflammation
can increase 50,000 times when triggered

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43
Q

what does fibrinogen do and how?

A

zymogen

cleaved by thrombin to form fibrin which aids in the formation of a clot

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44
Q

what two things that were in the notes counteract the effects of histamine and how?

A

epinephrine narrows the blood vessels to increase blood pressure
antihistamines (Benadryl) block histamine surface receptors

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45
Q

what is humira?

A

a monoclonal antibody drug

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46
Q

what is hematocrit?

A

the percentage of red blood cells in the blood

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47
Q

what is heme made out of?

A

protoporphyrin IX and Fe2+

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48
Q

what is the difference in structure between hemoglobin and myoglobin and their curves on the chart?

A

hemoglobin has four subunits and myoglobin is a monomer

hemoglobin curve is sigmoidal and the myoglobin curve is hyperbolic

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49
Q

what is an allosteric effect?

A

cooperativity of hemoglobin subunits

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50
Q

what is the bohr effect?

A

curve of hemoglobin shifting to the right for increases in pCO2, acid, BPG

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51
Q

what is Restriction Fragment Length Polymerization (RFLP)?

A

southern blot that targets a specific mutation sequence

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52
Q

what is a southern blot?

A

detects specific DNA sequences by hybridizing with the sequence and is illuminated using a radioactive probe or tag

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53
Q

what is a northern blot?

A

detects for specific RNA sequences

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54
Q

what is a western blot?

A

detects for specific proteins

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55
Q

SDS separates proteins based on what property?

A

size

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56
Q

what is TAQ and what is it used for?

A

thermus aquaticus and it is used for PCRs

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57
Q

name the different types of enzymes?

A

lyase, oxidoreductase, transferase, hydrolate, isomerase, ligase

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58
Q

what is a holoenzyme?

A

enzyme plus prosthetic group

[prosthetic group = tightly bound cofactor]

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59
Q

what is an apoenzyme?

A

enzyme without prosthetic group

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60
Q

what is a metalloenzyme and give example:

A

enzyme that uses a metal as a cofactor

vitamin-derived molecules

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61
Q

what is the change in free energy for spontaneous reaction?

A

negative

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62
Q

what do enzymes do to the transition state of a reaction?

A

stabilize transition state

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63
Q

where does chymotrypsin cleave?

A

phenylalanine, tyrosine, leucine (hydrophobic AA)

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64
Q

where does elastase cleave?

A

alanine, isoleucine, methionine (small aliphatic AA)

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65
Q

where does thrombin cleave?

A

arginine residues

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66
Q

where does trypsin cleave?

A

lysine and arginine

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67
Q

what is Km?

A

substrate concentration at 1/2 the maximum velocity of the reaction

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68
Q

what is Kcat?

A

reaction rate

number of substrate reacting per second

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69
Q

what is Kcat/Km?

A

catalytic efficiency

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70
Q

why do some enzymes have sigmoidal curves?

A

binding of one substrate molecule enhances the binding of another substrate molecule

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71
Q

enzymes that follow MM kinetics have what type of graph?

A

hyperbolic

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72
Q

what is PLP, what is it derived from, and what does it do?

A

pyridoxal phosphate
derived from vitamin B6 (pyridoxine)
it is a coenzyme used with aminotransferases

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73
Q

give an example of metalloenzyme:

what metal is its cofactor?

A

carbonic anhydrase uses Zn2+

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74
Q

what are statins?

A

competitive inhibitors that reduce cholesterol by binding to HMG CoA reductase (used in cholesterol synthesis)

75
Q

what is an ACE inhibitor?

A

Angiotensin Converting Inhibitor

competitive inhibitor of ACE and lowers blood pressure

76
Q

what is the effect of competitive inhibition on Km and Vmax?

A

Vmax unchanged

Km increases

77
Q

what is the effect of noncompetitive inhibition on Km and Vmax?

A

Vmax decreases

Km unchanged

78
Q

give example of noncompetitive inhibitor:

A

ferrochelatase

79
Q

irreversible inhibitors form what type of bond with enzymes?

A

covalent bonds in the enzyme’s active site

80
Q

what is an isoenzyme and give examples:

A

catalyze the same reaction
COX-1
COX-2

81
Q

give examples of irreversible inhibitors:

A

aspirin
penicillin
SERPINs

82
Q

what do ibuprofen and naproxen sodium do?

A

reversibly inhibit COX-1 and COX-2

83
Q

how do irreversible inhibitors affect Km and Vmax?

A

same as noncompetitive inhibitor

84
Q

what is a homotropic effector and a heterotropic effector?

A 
homotropic = the substrate
heterotropic = not the substrate [as in feedback inhibition]
85
Q

why are enzymes and substrates contained in organelles?

A

an increase in proximity increases metabolic efficiency

86
Q

how is muscle glycogen activated?

A

covalently bonding with phosphate or allosterically by binding to AMP

87
Q

which amino acid can be phosphorylated?

A

serine, threonine, tyrosine

88
Q

what amino acid does ubiquitin attach to?

A

lysine

89
Q

what makes cancer cells immortal with respect to proteasome?

A

pro-apoptotic factors that signal cell death are degraded by the proteasome

90
Q

how does velcade work?

A

inhibits proteasome degradation of pro-apoptotic factors

91
Q

what form are most proteases in?

A

inactive zymogen form

92
Q

where is trypsinogen made, and what does its active form do?

A

made in the pancreas and participates in protein degradation in the duodenum

93
Q

where are blood coagulation proteins made?

A

liver

94
Q

when heart muscle is damaged, what other protein increases?

A

muscle troponin

95
Q

how do the Vmax and Km of isoenzymes compare?

A

they are different depending on the demands of the cell

96
Q

what does alanine amino transferase in the blood indicate?

A

liver damage

97
Q

what are the primary, secondary, tertiary, and quaternary structures of DNA?

A

nucleotide sequence of one strand, helix with complementary strand, supercoiling of duplex helix, and supercoiled structure with histones or RNA

98
Q

what form does DNA exist inside cells?

A

Right-handed helix

99
Q

what is a quinolone?

A

a drug that inhibits bacterial DNA gyrase

100
Q

what are examples of nucleotide analogs? what do they do?

A

AZT, araA, araC, dideoxyinosine

used as antitumors or antivirals

101
Q

what is telomerase?

A

a reverse transcriptase mainly in germ and stem cells that copy RNA into DNA at their ends

102
Q

what are DNA polymerase alpha, beta, gamma, delta, and epsilon?

A 
initiation 
DNA repair 
mitochondrial DNA synthesis 
lagging strand synthesis 
leading strand synthesis
103
Q

what are DNA polymerase I, II, and III?

A

removal of primers and fill in
DNA repair
leading strand synthesis

104
Q

what is a transition?

A

a DNA polymorphism that changes a purine to a purine or a pyrimidine to a pyrimidine

105
Q

what is a transversion?

A

a DNA polymorphism that changes a purine to a pyrimidine or a pyrimidine to a purine

106
Q

name the causes of spontaneous mutation

A

deamination (loss of amido group of a base)
depurination (hydrolysis of the glycosidic bond)
oxidations (additions of an O group to a base)

107
Q

name the causes of induced mutation and examples

A

alkylating agents, x-rays induces single and dsDNA breaks, dietary carcinogens, UV light, smoking

108
Q

what biological processes lead to mutation

A

viral and transposon insertion, errors of replication, mutation in DNA repair enzymes

109
Q

what decreases the effects of mutation?

A

only 2-3% of the DNA is coded, introns where mutations occur are removed, the code is degenerate (mutation changes the codon but codes for the same amino acid)

110
Q

how can mutations be inherited?

A

if they are mitochondrial or in germ line cells

111
Q

name the types of excision repair mechanisms and how they do it

A

base excision repair - uses N-glycosylase to remove the damaged base and an AP endonuclease removes the rest of the nucleotide creating an AP site
nucleotide excision repair - uses endonucleases to remove ~30 nucleotides

112
Q

breast, colon, and ovarian cancer have gene mutation in what set of enzymes?

A

repair enzymes

113
Q

what are suicidal proteins?

A

alkyl-transferases - removes alkyl groups and dies

114
Q

what is Xeroderma pigmentosum?

A

disease due to mutations in repair enzymes [NER]

115
Q

how does recombination repair work?

A

DNA from undamaged chromosome is used to repair the damage

116
Q

where are the predominant sites that homologous recombination occurs?

A

in germ line cells to allow for diversity

117
Q

what type of gene is often in transposable elements?

A

resistance genes

118
Q

what percent of our DNA are transposable?

A

40%

119
Q

what is a complex transposon?

A

associated genes that move with the element

120
Q

what sign shows that transposition has occured?

A

direct repeat

121
Q

what do RNA polymerase I, II, and III transcribe?

A

I - rRNA
II - mRNA
III - 5S rRNA and tRNA

122
Q

where on the DNA does transcription begin?

A

promoter region

123
Q

how is DNA polymerase II unique?

A

it has a site for phosphorylation to control transcription

124
Q

what are basal transcription factors?

A

they identify the promoter region and stimulate RNA polymerase binding

125
Q

name the types of termination and mechanism

A

factor (rho) dependent that uses ATP and forms a hairpin structure
factor independent where an AU rich region is followed by a GC rich stem loop

126
Q

name the prokaryotic and eukaryotic inhibitors of RNA polymerase

A

rifampicin and amanitin (mushrooms)

127
Q

what are dihydrouridine, pseudouridine, and ribothymine examples of?

A

post-transcriptional alterations commonly found in tRNA

128
Q

why does mRNA need alterations and what are they?

A

it needs 5’ methyl guanine cap and a 3’ poly A tail in order to leave the nucleus

129
Q

what do ribonucleases do?

A

process tRNA and rRNA that change the size of RNA’s primary structure

130
Q

what is transesterification used in?

A

splicing out introns

131
Q

what is the purpose of exon shuffling?

A

creating genetic diversity

132
Q

what do enzyme cascades do to reactions?

A

amplify the reaction

133
Q

what does COX-1 do?

A

produces thromboxane that is a vasoconstrictor and activates more platelets

134
Q

what is required for platelet aggregation?

A

ADP

135
Q

what serine proteases does ATIII inhibit?

A

factors IXa, Xa, XIa, XIIa, VIIa, IIa

136
Q

what molecule on endothelial cells prevents unnecessary clotting?

A

heparin-like molecules are expressed to maintain low levels of ATIII

137
Q

what does nitric oxide do?

A

made by endothelial cells which inhibit platelet aggregation

138
Q

what is tissue plasminogen activator?

A

made by endothelial cells that activates plasminogen to degrade fibrin

139
Q

what does plasmin do?

A

breaks down fibrin

140
Q

what is ferrochelatase and why is it significant?

A

it binds to lead and can be noncompetitively inhibited by lead

141
Q

where on the tRNA are amino acids attached?

A

the 2’ or 3’ OH of the adenine with the carboxyl group of the amino acid

142
Q

what enzyme adds an amino acid to a tRNA?

A

amino acyl tRNA synthetase

143
Q

what allows for less than 61 tRNAs to be used for a cell?

A

wobble or non watson-crick base pairing

144
Q

what step in charging a tRNA is irreversible and drives the reaction forward?

A

the amino acid being added to the amino acyl tRNA using ATP catalyzed by pyrophosphatase

145
Q

what do all tRNAs have in common in relation to their structure?

A

similar secondary structures and 3D structures

146
Q

where does wobble base pairing usually occur on the mRNA and the tRNA?

A

the 3’ nucleotide on the mRNA and the 5’ nucleotide on the tRNA

147
Q

what is inosine and what is it used for?

A

adenosine deaminated and is often found at the 5’ position of tRNAs to allow for wobble
it binds with C, A, U eliminating the need of 2 tRNA molecules

148
Q

what is the most energetically expensive process in a cell?

A

translation

149
Q

what is the energy source used for translation

A

GTP and ATP in eukaryotes but just ATP in prokaryotes

150
Q

what are the different sites in the ribosome for tRNA

A

A site - where the new tRNA enter
P site - contains the tRNA with the peptide chain
E site - where the tRNA sit before they are kicked out

151
Q

what determines lifespan of an mRNA molecule

A

how rapidly it loses its poly A tail

152
Q

what is the most important target for antibiotics

A

ribosomes

153
Q

post translational modifications change which structures of proteins

A

primary and secondary

154
Q

chaperones are particularly useful for folding what type of proteins

A

large ones

155
Q

what happens to proteins that need to be secreted

A

they have signal recognition peptide that is recognized by a signal recognition particle and cleaved by a signal peptidase

156
Q

what determines the amount of transcription of most genes

A

how often RNA polymerase binds and initiates synthesis

157
Q

name the other types of control of gene expression that affect mRNA turnover

A

mRNA processing and splicing, transport from the nucleus, translational control and ribonucleases

158
Q

what is the TATA box and what binds there

A

an AT rich region where RNA polymerase binds along with basal transcription factors

159
Q

what is a repressor and what is an activator

A

gene specific transcription factors that bind to specific DNA sequences to increase or decrease RNA polymerase activity

160
Q

what are enhancer binding proteins

A

they bind at enhancer region away from promoter and enhance transcriptional activity by bending the DNA to recruit RNA polymerase

161
Q

what does it mean when a gene is constitutive or inducible?

A

constitutive is always expressed

induced is expressed when needed

162
Q

where are enhancer sequences located?

A

either upstream or downstream several thousand sequences away from the promoter

163
Q

what are mediator proteins?

A

the link enhancer sites with basal transcription factors

164
Q

what are regulatory genes?

A

genes that code for proteins that control gene expression

165
Q

what does hyperacetylation of histones do?

A

allows TF access to DNA which activates gene expression

166
Q

what does acetylation do to lysine?

A

reduces the positive charge of lysines on histones which reduces the interaction between it and negative PO4 group of DNA

167
Q

what are CpG islands

A

can have cytosine methylated which turns off the gene

transcriptionally active genes are here

168
Q

what is imprinting

A

a differential degree of methylation from mom and dad that is inherited

169
Q

heterochromatin vs euchromatin

A

hetero - inactive/supercoiled up

eu - active

170
Q

what are VDRE, TRE, and RARE? what do they have in common?

A

they are vitamine D, thyroxine, and retinoic acid binding proteins
they bind these hormones in the nucleus and function as heterodimers with a common receptor monomer and recognize direct repeats

171
Q

what are GRE and ERE

A

they are glucocorticoid and estrogen binding proteins and bind these hormones in the cytoplasm and function in the nucleus as homodimers after releasing heat shock proteins and recognize inverted repeats

172
Q

recessive mutations affect the activity of

A

enzymes

173
Q

dominant mutations affect the

A

structural proteins

174
Q

what is haploinsufficiency

A

when the heterozygote of a recessive mutation has a phenotypic effect

175
Q

what is thalassemia

A

autosomal recessive mutation that leads to decreased production of hemoglobin subunits

176
Q

what is muscular dystrophy

A

affects dystrophin and causes muscle weakness

x linked

177
Q

what is tay-sachs

A

autosomal recessive mutation that leads to a lysosomal storage disease due to a defect in enzyme processing

178
Q

nucleotide triplet repeat expansion is due to what and usually leads to what type of disease

A

slipped mispairing during DNA replication and leads to neurological disorders

179
Q

name the nucleotide repeat expansion diseases we talked about

A

huntington’s
fragile x
myotonic dystrophy
friedreich ataxia

180
Q

what is huntington’s

A

autosomal dominant

binds CBP transcription factors and affects neuronal cell transcription

181
Q

what is fragile x

A

a CpG island is in the promoter of FMR1 gene leads to down regulation of transcription by hypermethylation
no translational regulation
x linked

182
Q

what is myotonic dystropy

A

autosomal dominant mutation that interferes with polyadenylation or mRNA splicing of protein kinase mRNA that keeps it in the nucleus

183
Q

what is friedreich ataxia

A

autosomal recessive mutation resulting in splicing alteration of an intron in mRNA for mitochondrial frataxin protein used in iron metabolism

CMM (3 decks)

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