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First Aid Biochem > FA Biochem I > Flashcards

FA Biochem I Flashcards

1
Q

In the chromatin structure, which histones form the octamer, and which ties the nucleosome beads together in a string?

A

octamer = 2 sets of H2A, H2B, H3, H4 - tie =H1

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2
Q

What amino acid makes up most of the histone octamer?

A

lysine and arginine

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3
Q

Which type of chromatin is condensed, transcriptionally inactive, sterically inaccessible?

A

heterochromatin = HighlyCondensed

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4
Q

Which type of chromatin is less condensed, transcriptionally active, sterically accesible

A

euchromatin

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5
Q

What does PURe As Gold and CUT The Py stand for

A

purines= A, G pyrimidine = C, T (U)

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6
Q

How many rings do purines have

A

2 rings

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7
Q

How many rings do pyrimidines have

A

1 ring

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8
Q

How does cytosine become uracil

A

deamination

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9
Q

What polar group does guanine have, and what non polar group does thymine have

A

ketone, methyl

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10
Q

Which bond is stronger AT or CG and why? What is the laboratory consequence of this?

A

CG- 3 > AT-2 - More CG content, melting point goes up

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11
Q

What 3 amino acids are necessary for purine synthesis

A

glycine, aspartate, glutamine

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12
Q

What makes up a nucleoside

A

base + ribose

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13
Q

What makes up a nucleotide

A

base + ribose + phosphate (3’ -5’) phosphodiester bond

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14
Q

What are purines made from

A

IMP precursor

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15
Q

What are pyrimidines made from

A

orotate precursor, with PRPP added later

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16
Q

What is made fir rNucleotides or deoxyrNucleotides and what enzyme is necessary to convert one to the next

A

ribos first then deoxyribos with ribonucleotide reductase

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17
Q

What two pathways is carbomoyl phosphate involved in, and what enzyme deficiency leads to a build of carbamoyl phosphate leading to what element in pyrimidine synthesis

A

de novo pyrimidine synthesis and urea, ornithine transcarbamoyl def in the urea cycle leads to a build of CP, then converted to orotic acid in pyrimidine synthesis pathway

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18
Q

Name 5 drugs that interfere with nucleotide synthesis

A

hydroxyurea - inhibits ribonucleotide reductase, 6 MP - blocks de novo purine synthesis, 5 FU inhibits thymidilate synthase, MTX - inhibits DHFR, Trimethroprin inhibits bacterial DHFR

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19
Q

Inhibition of thymidilate synthase and and DHFR lead to decrease in what substance

A

dTMP

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20
Q

Which step in the de novo purine and pyrimidine synthesis pathway requires just aspartate

A

orotic acid to UMP

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21
Q

Which step in the de novo purine and pyrimidine synthesis pathway requires aspartate, glycine, glutamine and THF

A

Ribose 5-P to PRPP

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22
Q

An inability to convert orotic acid to UMP would be caused by a deficiency either of which two enzymes

A

orotic acid phosphoribosyltransferase or orotidine 5’-phosphate decarboxylase

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23
Q

How is orotic aciduria inherited

A

AR

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24
Q

What are the findings in orotic aciduria

A

inc orotic acid in urine, megaloblastic anemia (does not correct with B12 or folate), failure to thrive

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25
Q

What lab value can distinguish orotic aciduria from ornithine transcarbamoylase def?

A

OTC has hyperammonemia, orotic aciduira does not

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26
Q

What is the treatment for orotic aciduria

A

oral uridine administration

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27
Q

What does Adenosine deaminase deficiency cause a build up of, and what does that lead to?

A

excess ATP, dATP, feeback inhibits ribonucleotide reductase, no DNA synthesis

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28
Q

Adenosine deaminase deficiency is an important cause of what immunodeficiency?

A

dec DNA, dec lymphos leads to SCID

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29
Q

Leysh-Nyhan syndrome is a defect in which enzyme and what are the biochemical results

A

HGPRT, defective purine salvage, excess uric acid production

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30
Q

What are the findings in Lesch-Nyhan

A

retardation, self mutilation, aggression, hyperuricemia, gout, choreoathetosis

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31
Q

How is Lesch Neyhan inherited

A

X-linked recessive

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32
Q

What enzyme converts adenine to AMP

A

APRT + PRPP

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33
Q

What step of uric acid synthesis does xanthine oxidase catalyze

A

hypoxanthine to xanthing and xanthine to uric acid

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34
Q

What reaction does adenosine deaminase normally catalyze

A

adenosine to inosine

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35
Q

What does an umabiguous genetic code refer to

A

each codon specifies only 1 amino acid

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36
Q

What does degenerate/rundant genetic code refer to

A

more than 1 codon may code for the same amino acid

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37
Q

What is the exception to genetic redundancy

A

methionine encode by only 1 codon (AUG)

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38
Q

What does commaless, nonoverlapping genetic code refer to

A

read from a fixed starting point as a continuous sequence of bases

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39
Q

What does universal genetic code refer to and what are some exception

A

genetic code is conserved throughout evolution, except for mito, archaebacteria, mycoplasma, and some yeast

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40
Q

What is a silent mutation

A

same AA, often base change in 3rd position of codon (tRNA wobble)

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41
Q

What is a missense mutation

A

changed AA (convservative - new AA is similar in chemical structure)

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42
Q

What is a nonsense mutation

A

change resulting in early stop codon

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43
Q

What is a frame shift

A

change resulting in misreading of all nucleotides downstream, usually resulting in a truncated nonfxnal protein

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44
Q

What is the order of severity for the different types of mutations

A

nonsense > missense > silent

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45
Q

Eukaryotic and prokaryotic DNA synthesis is blank and involves both blank and blank strands

A

semiconservative, continuous and discontinuous strands (okazaki fragments)

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46
Q

For eukaryotes, where does replication begin?

A

consesus sequenec of base pairs

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47
Q

What is the origin of replication

A

particular sequence of DNA where replicatino begins - may be single of multiple

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48
Q

Describe the replication fork

A

Y shaped region along the DNA template where leading nad lagging strands are synthesized

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49
Q

What does helicase do

A

unwinds DNA template at replcation fork

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50
Q

What do the single stranded binding proteins do

A

prevent strands from reannealing

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51
Q

What do DNA topoisomerases do

A

creat a nick in the helix to relieave supercoils created during replication

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52
Q

What does primase do

A

makes RNA primer on which DNA poly III can initiate replication

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53
Q

What does DNA poly III do?

A

prokaryotic only - elongates leading strand by adding deoxnucTIDE to the 3’ end. Elongates lagging strand until it reaches primer of preceeding fragment. 3’ to 5’ exonuclease activity “proofreads” each added nucTIDE

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54
Q

What does DNA poly I do?

A

prokaryotic only - degrades RNA primer and fills in the gap with DNA

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55
Q

What does DNA ligase do

A

seals.

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56
Q

How do fluoroquinolones work

A

inhibit DNA gyrase specific for prokaryotic topoisomerase

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57
Q

In which single strand DNA repair mechanism do specific endonucleases release the oligonucTIDE containing bases and DNA poly and ligase fill and reseal, and what disease occures when this is mutated

A

nucleotide excision repair - xeroderma pigmentosum; unable to repair thymidine dimers caused by UV light

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58
Q

In base excision repaire, what recognizes and removes damaged bases and what cuts the DNA to remove the empty sugar

A

specific glycosylases, AP endonuclease

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59
Q

In mismatch repair, which strand is recognized and in what hereditary syndrome is this defective

A

unmethylated, newly synthesized, HNPCC

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60
Q

Is there any requirement for homology in NHEJ

A

no - its non homologous

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61
Q

In what direction are DNA and RNA synthesized

A

5’ to 3’

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62
Q

Which carbon bears the triphosphate and the energy source for bond formation

A

5’ of the incoming nucleotide

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63
Q

What is the target of the 3’ hydroxyl attack

A

The triphosphate bond

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64
Q

In which direction is protein synthesized

A

N to C

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65
Q

What is the most abundant type of RNA

A

rRNA

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66
Q

What is the longest time of RNA and shortest

A

mRNA, tRNA

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67
Q

What does the start codon code for in eukaryotes and prokaryotes

A

eu - methionine, pro - formyl-methionine

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68
Q

What are the mRNA stop codons

A

UGA, UAA and UAG

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69
Q

Which part of the DNA binds RNA polymerase and multiple other TFs upstream from gene locus

A

promotor - TATA box, and CAAT box, AT rich

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70
Q

What stretch of DNA that alters gene expression by binding of transcription factors

A

enhancers

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71
Q

This is the site where negative regulators bind

A

silencers

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72
Q

In eukaryotes, what does RNA poly I make

A

rRNA

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73
Q

In eukaryotes, what does RNA poly II make

A

mRNA

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74
Q

In eukaryotes, what does RNA poly III make

A

tRNA

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75
Q

Which RNA poly opens DNA at promotor site

A

RNA poly II

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76
Q

RNA poly can’t proofread, but what can it do

A

initiate chains

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77
Q

In prokaryotes, what does makes the different types of RNA

A

1 kind with multiple subunits

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78
Q

Why does alpha amanitin cause liver failure and where is it found

A

inhibits RNA polymerase II, found in death cap mushrooms

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79
Q

What 3 steps in RNA processing occur after transcription

A

1- capping on 5’ (7-methyguanosine) 2 - polyadenylation on 3’ end 3 - splicing out of introns

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80
Q

What is the initial transcript called and what is the capped and tailed transcript called

A

initial is heterogenous nuclear RNA, the capped and tailed is called mRNA

81
Q

Which enzyme involved in RNA synthesis does not require a template

A

poly A polymerase - signal is AAUAA

82
Q

What kind of RNA is transported out of the nucleus

A

only processed RNA

83
Q

What does the primary transcript combine with to form the spliceosome

A

snRNPs and other proteins

84
Q

What shape does the RNA generate during splicing and why?

A

lariat shape in order and remove intron precisely and join 2 exons

85
Q

Which aspect of the spliceosome do patients with lupus make antibodies against

A

snRNPs

86
Q

What part of the pre mRNA contains the actual genetic information coding for protein

A

exons

87
Q

How many nucTIDEs is a tRNA and what does the secondary sturcture form

A

75 to 90, cloverleaf

88
Q

Which end of the tRNA is the amino acid bound to

A

3’ end (with CCA)

89
Q

What does aminoacyl tRNA synthetase do the AA before and after it binds to tRNA, and what happens if it’s the wrong the match

A

scrutinizes, hydrolyzes the bond

90
Q

What does a mischarge tRNA do

A

reads usual codon but inserts wrong AA

91
Q

How do tetracyclines work

A

bind 30s subunit preventing attachment of aminoacyl-tRNA

92
Q

Accurate base pairing is required only in the first two nucleotide positions of an mRNA codon, so conds differeing in the 3rd position may code for the same tRNA/AA due to degenerate genetic code

A

wobble

93
Q

What initiates protein synthesis

A

GTP hydrolysis, initiation factors assemble 40S ribosomal subunit with initiator tRNA and are released with mRNA and ribosomal subunit assemble with the complex

94
Q

What happens in elongation of protein synthesis

A

Aminoacyl-tRNA binds A site, ribosomal rRNA catalyzes peptide bond formation, transfers growing peptide to AA in A site, ribosome advances 3 nucTIDE toward 3’ end of RNA, moving peptidyl RNA to P side

95
Q

What happens in termination of proteins synthesis

A

stop codon is recognized by release factor, and completed protein is released from ribosome

96
Q

What ribosomes do eukaryotes have

A

40, 60, 80

97
Q

What ribosomes do prokaryotes have

A

30, 50, 70

98
Q

What is the energy source for tRNA actication (charging)

A

ATP

99
Q

What is the energy source for translocation

A

GTP

100
Q

How do aminoglycosides work

A

by inhibiting formation of the initiation complex and cause misreading of mRNA

101
Q

How does chloramphenicol work

A

inhibits 50S peptidyltransferase

102
Q

How do macrolides and clindamycin work

A

binds 50S, blocking translocation

103
Q

What is trimming

A

removal of N or C termal propeptides from zymogens to generate mature proteins

104
Q

What are covalent alterations

A

phosphorylation, glycosylation, hydroxylation

105
Q

What is proteasomal degredation

A

attachment of ubiquitin to defective proteins tag them for breakdown

106
Q

What are CDKs

A

cyclin dependent kinases;constitutive and inactive

107
Q

What are cyclins

A

regulatory proteins that control cell cycle events; phase specific; activate CDKs

108
Q

What are cyclin-CDK complexes

A

must be both activated and inactivated for cell cycle to progress

109
Q

Which tumor suppresors inhibit G1 to S progression, where mutations result in unrestrained growth

A

Rb and p53

110
Q

How do permanent cells grow and regenerate and what are examples of permanent cells

A

remain in G0, regenerate from stem cells, neurons, skeletal/cardiac muscle, RBCs

111
Q

How do stable (quiescent) cells grow and regenerate and what are examples

A

enter G1 from G0 when stimulated, hepatocytes and lymphocytes

112
Q

How do labile celss grow and regenerate and what are examples

A

never go to G0, divide rapidly with a short G1, bone marrow, gut epi, skin, hair follicles

113
Q

Where are the secretory proteins made and N-linked oligosaccharide addtions put on proteins

A

RER

114
Q

Where are cytosolic and organellar proteins made

A

free ribosomes

115
Q

What is the RER called in neurons and what is made there

A

Nissl body, enzyme and NTs

116
Q

What two cells are particularly rich in RER

A

mucus secreting globlet cells and antibody secreting plasma cells

117
Q

What happens at the smooth ER

A

site of steroid synthesis and detoxification of drugs and poisons

118
Q

Which cells are rich in smooth ER

A

liver hepatocytes and steroid producing cells of the adrenal cortex

119
Q

The golgi apparatus fxns as a distribution center between what organelles in the cell and what does it process

A

for proteins and lipids from ER to plasma membrane, lysosomes and secretory vesicles

120
Q

What does the golgi apparatus do on asparagine

A

modifies N-oligosaccharides

121
Q

What does the golgi add to serine and threonine residues

A

O-oligosaccharaides

122
Q

What does the addition of mannose-6 phosphate do

A

targets the proteins for lysosome

123
Q

What does the golgi assemble proteoglycans from

A

core proteins

124
Q

what does the golgi do to sugars in proteoglycans and of selected tyrosine on proteins

A

sulfation

125
Q

What is I cell disease

A

inherited lysosomal storage disorder; failure of addition of mannose 6 phosphate to lysosomal proteins, enzymes secreted outside of cell instead of lysosomes

126
Q

What are the clinical features of I cell diesase

A

coarse facial features, clouded corneas, restricted joint movements, high plasma levels of lysosomal enzymes, often fatal in childhood

127
Q

What two proteins make up microtubules and how are they arranged

A

alpha and beta tubulin, dimers have two GTP bound

128
Q

In which structures do you find microtubules

A

flagella, cilia, mitotic spindles

129
Q

How do microtubules grow and collapse

A

grows slowly, collapses quickly

130
Q

Which direction does dynein go

A

post to neg

131
Q

Which direction does kinesin go

A

neg to pos

132
Q

Which antihelminthe drugs work on microtubules

A

mebendazole/thiabendazole

133
Q

Which antifungal drugs work on microtubules

A

griseofulvin

134
Q

Which anticancer drugs work on microtubules

A

vincritsine/vinblastine

135
Q

Which anti breast cancer drugs work on micortubules

A

paclitaxel

136
Q

Which anti gout drugs work on microtubules

A

colchicine

137
Q

What is chediak higashi

A

microtuble polymerization defect causing a dec in phagocytosis results in recurrent pyogenic infections, partial albinism, and peripheral neuropathy

138
Q

Describe the structure of cilia

A

9+2 arrangement of microtubules

139
Q

What is axonemal dynein

A

ATPase that links peripheral 9 doublets and causes bending of cilium by differential sliding of doublets

140
Q

What is kartageners syndrome

A

immotile cilia due to dynein arm defect, male and femail infertile, bronchiectasis, recurrent sinusitis, associated with situs inversus

141
Q

cytoskeletal elements in micorvilli, muscle contracting fibers, cytokenesis, adherens jxns

A

actin and myosin

142
Q

cytoskeletal elements associated with cilia, flagella, mitotic spindle, neurones and centrioles

A

microtubules

143
Q

cytoskeletal elements associated with vimenentin, desmin, cytokeratin, glial fibrillary acid protiens (GFAP), neurofilaments

A

intermediate filaments

144
Q

What does high cholesterol or long saturated fatty acid content do to the melting temperature and fluidity

A

inc melt, dec fluidity

145
Q

What does the vimentin stain for

A

connective tissue

146
Q

What does desmin stain for

A

muscle

147
Q

What does cytokeratin stain for

A

epithelial cells

148
Q

what does GFAP stain for

A

neuralgia

149
Q

What do neurofilaments stain for

A

neurons

150
Q

Describe the location and fxn of the Na/K ATPase

A

plasma membrane, 3Na out, 2K in, ATP on cytoplasmic side

151
Q

How does ouabain work

A

inhibits the Na/K pump by binding the K side

152
Q

How do cardia glycosides work

A

directly inhibit the Na/K pump which leads to indirect inhibition of Na/Ca exchange, inc calcium inside the cell, inc cardiac contractility

153
Q

What is the most abundant protein in the body

A

collagen

154
Q

Type I collagen

A

Bone, skin, tendon, dentin, fascia, cornea, late wound repair

155
Q

Type II collagen

A

cartilage, hyaline, vitreous body, nucleus pulposus

156
Q

Type III collagen

A

reticulin - skin, blood vessels, uterus, fetal tissue, granulation tissue

157
Q

Type IV collagen

A

basement membrane or basal lamina

158
Q

Type I bone

A

bONE

159
Q

Type II cartilage

A

carTWOlage

160
Q

Type IV BM

A

4 under the floor

161
Q

What happens in the first stage of collagen synthesis, and where does it happen

A

RER - translation of alpha chains, usually Gly-X-Y polypeptide (preprocollagen)

162
Q

What residues are hydroxylated in step 2 of collagen synthesis, and what does this require

A

proline and lysine, vit C

163
Q

What does glycosylation of pro alpha chian yield and what is the structure

A

procollagen, triple helix of 3 alpha collagen chains

164
Q

In what cell is collagen synthesis initiated

A

fibroblast

165
Q

Outside the fibroblast what part of procollagen is cleaved and what is it transformed into

A

terminal regions, tropocollagen

166
Q

How are the many staggered tropocollagen molecules reinforced

A

covalent cross-linking by lysyl oxidase to make collagen fibrils

167
Q

What does Ehlers Danlos cause and why

A

faulty collagen synthesis, hyperextensible skin, tendency to bleed, easy bruising, hypermobile joints

168
Q

What collagen type is most frequently affected in ehlers danlos and what are common complications

A

III, joint dislocation, anuerysms, organ rupture

169
Q

What does osteogenesis imperfecta causes and why

A

brittle bone disease, most commonly lead AD with abnl type I collagen causing multiple fractures with minimal trauma, blue sclerae due to translucency of connective tissue over the choroid, hearing loss, dental imperfections due to lack of dentin

170
Q

Which kind of osteogenesis imperfecta is fata in utero or in neonatal period

A

type II

171
Q

What does Alports syndrome cause and why

A

progressive hreditary nephritis and deafness, associated with occular disturbances - due to abnl type IV collagen, usually x-linked recessive

172
Q

Type IV collagen is an important structural componenet of the BM for which 3 organs

A

kidney, ears, eyes

173
Q

Where do you find elastin and what does it do

A

lungs, large arteries, elastic ligaments, vocal cords, ligamenta flava - stretch.

174
Q

Which amino acids are elastin rich in

A

proline and glycine (non glycosylated forms)

175
Q

Why enzyme breaks down elastin and what enzyme inhibits it

A

elastase, inhibited by alpha1 antitrypsin

176
Q

What is the structure of elastin

A

tropoelastin with fibrillin scafolding

177
Q

What causes Marfan syndrome

A

defect in fibrillin

178
Q

What enzyme def can cause emphysema

A

alpha1 antitrypsin

179
Q

What lab procedure is used to amplify desired fragment of DNA and what are the 3 steps

A

PCR, denaturation, annealing, elongation

180
Q

What does a southern blot use as its sample

A

DNA

181
Q

What does a northern blot use as its sample

A

RNA

182
Q

What does a western blot use for its sample

A

protein

183
Q

What lab technique is use to profile gene expression levels of thousands of genes simultaneously to study certain diseases and treatments

A

microarrays

184
Q

What is the smallest mutation a mircoarray can detect

A

SNP

185
Q

What does the ELISA test for

A

antigen - antibody reactivity - can look for antigen or antibody in patients blood

186
Q

Fluorescent DNA or RNA probe binds to specific gene of interest - used for specific localization of genes and direct visualization of anomalies, like microdeletions, at molecular level

A

FISH

187
Q

What is DNA cloning and how do you do it?

A

production of a recombinant DNA molecule that is self perpetuating, plasmids, selection, restriction enzyme cleavage, tissue mRNA with reverse transcriptase to make cDNA

188
Q

What are the two transgenic strategies in mice

A

constitutive - random insertion of gene into mouse genome and conditional - targeted insertion or deletion of gene through homologous recombination with mouse gene

189
Q

antbiotic controlled promoter to induciblly manipulate genes at specific developmental points

A

cre-lox system

190
Q

What is RNAi used for

A

dsRNA promotes degradation of target mRNA knocking down gene expression

191
Q

metaphse chromosomes are stained, ordered and numbered according to morphology, size, arm length ratio, banding pattern

A

karyotyping

192
Q

What tissue samples are used for karyotyping

A

blood, bone marrown, amniotic fluid, placental tissue

193
Q

What is codominance and give an example

A

neither of 2 alleles is dominant, blood groups

194
Q

What is variable expression and what is an example

A

nature and severity of phenotype vary from 1 individual to another, NF type 1

195
Q

What is incomplete penetrence and give an example

A

not all individuals with a mutant genotype show the mutant phenotype

196
Q

What is pleiotropy and given an example

A

1 gene had >1 effect on an individuals phenotype, PKU causes many seemingly unrelated symptoms ranging from mental retardation to hair/skin changes

197
Q

What is imprinting and give an example

A

differences in phenotype depend on whether the mutation is of maternal or paternal origin, prader-willi and angelman’s syndrome

198
Q

What is anticipation and give an example

A

severity of disease worsens or age of onset of disease is earlier in succeeding generations, huntingtons

199
Q

What is loss of heterozygosity and give an example

A

if pt inherits or develops a mutation in a tumor suppresor gene, the complementary allele must be deleted/mutated before cancer develops- not true of oncogenes, retinoblastoma

First Aid Biochem (3 decks)

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