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USMLE Step 1-2015 > Bicohem > Flashcards

Bicohem Flashcards

1
Q

Histones are rich in what two amino acids making it positively charged?

A

lysine and arginine

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2
Q

What phase do DNA and histone synthesis occur in?

A

S phase

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3
Q

Inactive DNA and histone morphology?

A

Heterochromatin. Deacetylated and methylated histones allows for tight association and transcriptionally inactive)

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4
Q

Active DNA and histone morphology?

A

Euchromatin. Acetylated and non-methylated histones allow for loose association and transcriptionally active)

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5
Q

What is methylated in promoter region that can lead to silencing and decreased transcription?

A

CpG island

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6
Q

What is methylated in prokaryotic DNA replication to allow for mismatch repair enzymes to distinguish between old and new prokaryotic strands?

A

Cytosine and Adenine

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7
Q

5 parts needed for purine synthesis

A

Glycine, aspartate, glutamine (“PURe girls still gag”), THF, CO2

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8
Q

2 parts needed for pyrimidine synthesis

A

Carbomyl phosphate, aspartate

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9
Q

What is carbomoyl phosphate derived from?

A

Glutamine + CO2

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10
Q

Nucleoside vs Nucleotide?

A

Nucleoside-base + (deoxy)ribose

Nucleotide-base + (deoxy)ribose + phosphate; linked by 3’–>5’ phosphodiester bond

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11
Q

Cytosine deamination–>

A

Uracil

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12
Q

Thymine has a ______

A

Methyl group

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13
Q

Guanine vs. Adenine?

A

Guanine has a =O and can be thought of as “OG”

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14
Q

Rings in purines?

A

2 rings

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15
Q

Rings in pyrimidines?

A

1 ring

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16
Q

Rate limiting step for pyrimidine production

A

Glutamine+ CO2–>Carbomyl phosphate (via CPS II)

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17
Q

Leflunomide inhibits…

A

Dihydroorotate dehydrogenase

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18
Q

Mycophenolate and ribavirin inhibit..

A

IMP dehydrogenase

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19
Q

Hydroxyurea inhibits..

A

ribonucleotide reductase

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20
Q

6 MP and its prodrug azothioprine inhibits…

A

de novo purine synthesis

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21
Q

5 FU inhibits

A

Thymidilate synthase

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22
Q

Metotrexate, Trimethoprim, and pyrimethamine inhibit…

A

DHF reductase

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23
Q

How are ribonuclotides converted to deoxyribonucleotides?

A

ribonucleotide reductase

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24
Q

Draw the purine/pyrimidine synthesis pathway

A

p. 63 FA

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25
Q

What is the salvage pathway for thymidylate synthase inhibition?

A

Thymidine kinase requires thymidine supplementation and normally accounts for 5-10% of dTMP synthesis

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26
Q

Draw the purine salvage pathway

A

p. 64 FA

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27
Q

Inheritance of adenosine deaminase deficiency?

A

Auto recessive

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28
Q

Inheritanc of Lesch nyhan syndrome?

A

X-linked recessive

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29
Q

symptoms of HGPRT deficiency

A

Hyperuricemia, Gout, Pissed off (aggression, self mutilation) Retardation, DysTonia

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30
Q

Treatment for HGPRT?

A

Can’t treat other symptoms but can treat hyperuricemia/gout with allopurinol and febuxostat

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31
Q

Each codon specifies only 1 amino acid

A

Unambiguous

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32
Q

Most amino acids are coded by multiple codons?

A

Degenerate/redundant

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33
Q

What are the exceptions to AA being coded by multiple codons?

A

Methionine (AUG)

Tryptophan (UGG)

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34
Q

What is commaless, nonoverlappying genetic code?

A

Read from a fixed starting point as a continuous sequence of bases (exception: viruses)

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35
Q

What is a universal genetic code?

A

genetic code convserved throughout evolution (exception: mitochondria)

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36
Q

2 enzymes that increase activity of de novo purine synthesis?

A

PRPP synthetase (Ribose 5-Phosphate–>PRPP) and PRPP amidotransferase (PRPP–>5-phosphoribosylamine)

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37
Q

Rate limiting enzyme of purine synthesis

A

Glutamine PRPP amidotransferase

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38
Q

Carbon sources in purine synthesis?

A

Glycine, THF, CO2 (Aspartate, glutamine nitrogen sourceS)

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39
Q

Consensus sequence of base pairs in genome where DNA replication begins. Difference in prokaryotes and eukaryotes?

A

Origin of replication

Multiple (eukaryotes), single (prokaryotes)

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40
Q

Y-shaped region along dna template where leading and lagging strands are synthesized

A

Replication fork

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41
Q

Unwinds DNA template at replication fork

A

Helicase

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42
Q

Prevents strands from reannealing after unwinding

A

Single-stranded binding proteins

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43
Q

Create a single-or double-stranded break in the helix to add or remove supercoils

A

DNA topoisomerases

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44
Q

How do replication forks travel?

A

Travel bidirectionally away from origin of replication as DNA polymerase synthesizes complementary daughter DNA strands

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45
Q

Makes an RNA primer on which DNA pol III can initiate replication

A

Primase

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46
Q

What is ori identified and bound by that locally allows it do dissociate from dsDNA into ssDNA?

A

DNA A protein. SSB proteins then bind to ssDNA and stabilize and prevent premature reannealing. Helicase then binds ssDNA at ori, moves into rep fork and proceeds to seperate and unwind DNA

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47
Q

What protein triggers DNA replication in bacteria?

A

DNA A

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48
Q

5’–>3’ synthesis on leading and lagging strand (until reaches primer of preceeding fragment) and proofreads with 3’–>5’ exonuclease

A

DNA polymerase III

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49
Q

5’–>3’ synthesis of leading and lagging strand with 3’–>5’ exonuclease and also excises RNA primer with 5’–>3’ exonuclease+repair of damaged parent DNA

A

DNA polymerase I

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50
Q

Catalyzes formation of phosphodiester bond within a strand of dsDNA (ie. joins Okazaki fragments)–>seals

A

DNA ligase

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51
Q

RNA dependent DNA polymerase (reverse transcriptase) that adds DNA to 3’ ends of chromosomes to avoid loss of genetic material with every duplication?

A

Telomerase

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52
Q

Inhibit prokaryotic enzyme topoisomerase II (DNA gyrase) and topoisomerase IV

A

Fluoroquinolones

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53
Q

Makes up DNA helicase and primase complex

A

Primosomes

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54
Q

Coes for tRNA and rRNA and resembles bacterial (prokaryotic) chromosome

A

Mitochondrial DNA (small circular chromosome similar to bacterial chromosome)

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55
Q

What is an exonuclease?

A

Removes nucleotides at the end of DNA molecule so it has a particular direction

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56
Q

Sequence added to 3’ DNA ends of chromosomes

A

TTAGGG

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57
Q

Telomeres are expressed in what 3 types of cells

A

Stem cells-long telomeres and act ve telomerase, telomeres shorten with each cell division
Cancer cells-upregulate telomerase activity, preventing cell death by maintaining length of telomeres. Cancer cells immportal b/c cells continue to divide w/o aging and shortening of telomeres
Somatic cells-terminally differentiated and

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58
Q

Transversion and transition apply to which type of mutations?

A

Point mutations (silent, missence, nonsence)

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59
Q

Transition mutation

A

purine to purine or pyrimidine to pyrimidine “same”

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60
Q

Transversion mutation

A

purine to pyrimidine or pyrimidine to purine

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61
Q

Sickle cell disease is a type of what mutation and what happens?

A

Point mutation that is missence (GAG (glutamic acid) substitution with GTG (valine))

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62
Q

Where is the base change in a silent mutation?

A

Often base change in the 3rd position of codon (tRNA wobble)

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63
Q

What is it called if new AA is similar in structure to old in missence mutation?

A

Conservative

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64
Q

Duchenne muscular dystrophy is what type of mutation?

A

Frameshift mutation (deletion of dystrophin gene)

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65
Q

Slapped strand mispairing can lead to what?

A

Insertion and frameshift mutation

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66
Q

What causes the formation of a larger nonfunctional protein, but usually the immunoreactivity of normal proteins (i.e.binding to antibodies?

A

Splice site mutations (type of point mutation) where mutation of splice sites (not removing all introns from hnRNA in formation of mature mRNA). This is a type of point mutation

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67
Q

Eukaryotic lagging strand building

A

DNA pol. alpha

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68
Q

Eukaryotic leading strand building

A

DNA pol. delta

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69
Q

Eukaryotic DNA repair (specifically base excision repair)

A

DNA pol. beta

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70
Q

replicates mitochondrial DNA

A

DNA pol. gamma

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71
Q

Mechanism defective in xeroderma pigmentosum

A

nucleotide excision repair

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72
Q

Repair important in spontaneous/toxic deamination

A

base excision repair

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73
Q

Mechanism defective in HNPCC

A

Mismatch repair

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74
Q

Mechanism defective in ataxia telangiectasia; fanconi anemia

A

Nonhomologous end joining

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75
Q

What is an endonuclease?

A

Cut DNA specific DNA sequences within the molecules with no particular direction

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76
Q

When does nucleotide excision repair occur and when does base excision repair occur and when does mismatch repair occur?

A

G1 phase-NER
Throughout cell cycle-BER
G2 phase-Mismatch repair

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77
Q

Steps in nucleotide excision repair

A

Specific endonucleases release oligonucleotides by creating a nick on either side. DNA polymerase and ligase fill and reseal gap respectively.

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78
Q

Steps in base excision repair

A

Base-specific glycosylase (specific endo nuclease) removes base creating an AP site. Following that, one or more nucleotides are removed via AP endonuclease on 5’ end and lyase and 3’ end. After that DNA polymerase beta adds DNA and is sealed via ligase.

79
Q

Steps in mismatch repair

A

Newly synthesized strand is recognized. Mismatched nucleotides are removed. Gap is filled and resealed.

80
Q

Cause and symptoms of xeroderma pigmentousm?

A

Most commonly due to absence of UV-specific endonuclease. This is responsible for normally excising thymine dimers by nicking the strand at the thymine dimer.
Symptoms include photosensitivity, poilkiloderma, and hyperpigmentation in sun exposed areas–> increase risk of skin cancer

81
Q

What brings together 2 ends of DNA fragments to repair ds breaks?

A

Nonhomologous end joining

82
Q

DNA and RNA is synthesized in what direction?
mRNA is read in what direction?
Protein synthesis?

A

5’–>3’
5–>3’
N terminus–>C terminus

83
Q

What is the mechanism behind drugs that block DNA replication?

A

modified 3’ OH, preventing addition of next nucleotide (i.e. cant attach 5’ end triphosphate)–> “chain termination”

84
Q

Mutations in what 2 genes account for 90% of lynch syndrome?

A

MSH2 and MLH1 genes code for MutS and Mut L homologs. Normally, mismatch repair beings with MutS homolog detecting a mis-match on new daughter strand, which is distinguished from parent strand with occasional nicks in phosphodiester bonds. Mut L recruited slides along complex until nick is recgonized. Exonuclease I loaded onto and activated by repair complex. Daughter strand degraded. DNA pol. delta creates new strand and ligase seals

85
Q

mRNA start codons (eukaryotes vs. prokaryotes)

A

Eukaryotes-codes for methionine, which may be removed before translation is completed
Prokaryotes-codes for N-formylmethionine (fMet). fMet stimulates neutrophil chemotaxis.

86
Q

RNA pol binding?

A

Promoter region

87
Q

CAP binding in lac operon (prokaryotic)

A

At CAP site upstream of promoter

88
Q

lac l transcribes?

A

Repressor protein (known as regulatory gene)

89
Q

lac z codes for?

A

B-galactosidase (responsible for hydrolysis of lactose into glucose and galactose)

90
Q

lac y codes for?

A

Permease (allowing lactose to enter bacterium)

91
Q

lac A encodes?

A

B galactosidease transacetylase

92
Q

Repressor protein binds to (prokaryotic)?

A

operator region

93
Q

Toxin Inhibits RNA pol II and side effect?

A 
a-amanitin (found in amanita phalloides death cap mushrooms)
Severe hepatotoxicity (increase ALT, AST, bilirubin)
94
Q

Inhibits RNA pol in prokaryotes

95
Q

Inhibits RNA pol in eukaryotes and prokaryotes

A

Actinomycin D

96
Q

What opens DNA at promoter site?

A

RNA pol II

97
Q

What are specific foci involved in mRNA regulation/turnover in the cytoplasm?

98
Q

Antibodies to spliceosomal snRNPs

A

Anti-smith antibodies in SLE

99
Q

Anti-U1 RNP antibodies

100
Q

Single gene coding for multiple proteins when same gene is organized differently in different tissues

A

Alternative splicing

101
Q

Abnormal splicing variants implicated in what?

A

Oncogenesis, genetic disorders (B-thalassemia)

102
Q

3’ end of tRNA

103
Q

D arm (dihydrouracil residues)

A

Recognizes specific aminoacyl tRNA synthetase for each AA

104
Q

T arm (thymine, psuedouracil, cytosine)

A

Recognizes sequence necessary for tRNA-ribosome binding

105
Q

Hsp60 in yeast is example of a?

A

Chaperone protein (facilitating and/or maintaining protein folding)

106
Q

What helps incoming tRNA bind to A site?

A

elongation factors

107
Q

What catalyzes peptide bond formation, transferring growing peptide to AA in A site?

A

rRNA (“ribozyme”) mediates peptidyl transferase activity

108
Q

How does prokaryotic protein synthesis begin and what is first step for initiation?

A

mRNA (Shane-Dalgarno sequence) binds to complementary to 16S rRNA (part of 30S ribosomal subunit) and this is necessary for initiation of protein translation.

109
Q

AA linked by covalent peptide bonds

A

Primary structure

110
Q

alpha helix, B-sheet

A

Secondary structure

111
Q

Compact folding of secondary structure with ionic hdyrophobic hydrogen disulfide stabilizing

A

Tertiary structure

112
Q

Arrangement of multiple folded protein into a multi-subunit complex

A

Quarternary structure

113
Q

Constitutive and inactive regulation of cell cycle

114
Q

Regulatory proteins that control cell cycle events; phase specific

115
Q

Phosphorylate other proteins to coordinate cell cycle progression; must be activated and inactivated at appropriate times for cell cycle to progress

A

Cyclin-CDK complexes

116
Q

2 cells rich in RER

A

Mucus-secreting goblet cells of small intestine and antibody-secreting plasma cells

117
Q

3 cells rich in SER

A

Liver hepatocytes, steroid hormone producting cells of adrenal cortex, gonads

118
Q

Functions in lipid synthesis and carbohydrate metabolism

119
Q

Functions in synthesis of proteins (exported)

120
Q

Two subunits of ribosomes?

A

Small unit-binds mRNA (template for protein synthesis) and tRNA (carry amino acids)
Large unit-contains peptidyl transferase (catalyzes peptide bond formation in AA)

121
Q

Membrane enclosed organelle involved in catabolism of very-long chain fatty acids, branched-chain fatty acids, and amino acids

A

Peroxisomes

122
Q

Degrades damaged or uibiquitin-tagged proteins.

A

proteosome

123
Q

Defects of ubiquitin proteoasome system in what disease?

A

Parkinson disease

124
Q

N-oligosaccharides on what in post translational modification?

A

Asparagine amino group

125
Q

O-oligosaccharides on what in post translational modification?

A

serine and threonine hydroxyl group

126
Q

Mechanism for coarse facial features, clouded corneas, restricted joint movement, and high plasma levels of lysosomal enzymes

A

Failure of golgi to phosphorylate mannose residues on glyocoprotins so proteins are not delivered to lysososomes.

127
Q

COP I

A

Golgi–>Golgi (Retrograde); cis golgi–>ER

128
Q

COP II

A

ER–>cis-golgi (anterograde)

129
Q

Clathrin

A

trans golgi–>lysosomes; plamsa membrane–>endosomes

130
Q

Which AA can be modified by the golgi apparatus?

A

Asparagine, serine, threonine

131
Q

Cyclin D binds to what?

A

CDK4–>phosphorylation of Rb protein–>Rb protein is released from transcription factor E2F–>w/ E2F unbound, cell is free to transcribe/synthesize components needed for progressing THROUGH S phase (DHF, cyclin E, thymidilate synthase, DNA polymerase)

132
Q

Cyclin E binds to what?

A

CDK2–>allows progression INTO S phase.

133
Q

Cyclin A binds to what?

A

CDK2 to allow progression from G2–>M (mitotic prophase)

134
Q

Cyclin B binds to what?

A

CDK1 complex activated by Cdc 25–>breakdown of nuclear lamnins (skeletal framework) and initiation of mitosis

135
Q

Nuclear localization signals rich in what AA?

A

Proline, Arginine, Lysine (PAL). Makes sense b/c histones are in nucleus and rich and lysine and arginine

136
Q

What are the sorting centers of the cell?

A

Endosomes. For material from outside of cell or from Goligi, sending it to lysosomes for destruction or back to membrane/golgi for further use.

137
Q

Stain: Vimentin

Cell type: ?

A

Connective tissue (stain used to identify sarcoma)

138
Q

Stain: Desmin

Cell type?

A

Muscle (stain used to identify rhabdomyosarcoma for example)

139
Q

Stain: Cytokeratin

Cell type?

A

Epithelial cell (cell used to identify carcinoma)

140
Q

Stain: GFAP

Cell type?

A

Neuroglia (Astrocytoma)

141
Q

Stain: Neurofilaments

Cell type?

A

Neurons (specifically axons. used to identify neuroblastoma)

142
Q

Predominant function of microfilaments?

A

Muscle contraction, cytokinesis

143
Q

Predominant function of intermediate filaments?

A

cell structure

144
Q

Predominant function of microtubules?

A

Cell division, movement

145
Q

Drugs that act on microtubules?

A

Mebendazole, Griseofulvin, Colchicine, Vincristine/Vinblastine, Paclitaxel (Microtubules Get Constructed Very Poorly)

146
Q

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

A

Axonemal dynein

147
Q

MOA of Ouabain?

A

Inhibits Na+ K+ ATPase by binding to K+ site.

148
Q

Most abundant protein in human body

149
Q

Inhibited by scurvy?

A

hydroxylation of specific proline and lysine residues

150
Q

OI has problems forming what?

A

problems forming triple helix (procollagen)

151
Q

Ehlers danlos, menkes disease has problems with what?

A

Cross-linking tropocollagen molecules to make collagen fibrils (secondary to lysyl oxidase covalently linking lysine-hydroxylysine cross-linkage)

152
Q

Mature collagen is synthetized in what cells?

A

Fibroblasts, osteoblasts, and chondroblasts

153
Q

Most abundant AA in collagen?

154
Q

What catalyzes cleavage of disulfide rich terminal regions of procollagen?

A

Extracellular precollagen peptidases

155
Q

2 components of bone matrix

A

Inorganic hydroxyapatite crystals and organic type I collagen

156
Q

Common mutations leading to ehlers danlos phenotypes include deficiencies in what two enzymes?

A

Lysyl hydroxylase (characteristic of kyphoscoliosis and ocular fragility) and pro-collagen peptidase (joint laxity, loos skin, and easy bruising)

157
Q

3 major differences between collagen and elastin?

A

1) Very few proline, lysine residues hydroxylated in elastin (thought of as rich in nonhydroxylated proline, glycine, and lysine
2) Triple helix in collagen. No triple helix in elastin
3) Triple helix formation in collagen is initiated by hydroxylation, glycosylation, and inter-chain disulfide bridges @ C-terminus of procollagen. These modifications not happen in elastin molecules

158
Q

Enzyme catalyzing elastin b linking vs collagen cross linking

A

Lysyl hydroxylase vs lysyl oxidase

159
Q

What is unique about elastin crosslinking?

A

Unique form of desmosine crosslinking between 4 lysine residues between 4 different elastin chains.

160
Q

Southern blot

A

DNA sample cleaved into smaller pieces (restriction endonuclease). Electrophoresed on gel. Transferred to filter and filter soaked in denaturant, which is than labeled by DNA probe that recognizes and anneals to complementary strand

161
Q

Northern blot

A

Similar to Southern blot except RNA sample is electrophoresed and recognized by DNA probe

162
Q

Western blot

A

Sample protein via gel electrophoresis and labeled antibody used to bind relevant protein

163
Q

Southwestern blot

A

DNA binding proteins (TF, histones, nucleases) used labeled oligonucleotide probes

164
Q

Describe HIV confirmatory test

A

Western blot. Antibodies to gp41, gp120/160, p24. Two positive necessary for confirmed positive diagnosis

165
Q

Direct ELISA used for?

A

Test for antigen in patient blood

166
Q

Indirect ELISA used for?

A

Test for antibody in patient blood

167
Q

Constitutive insertion

A

Random insertion of gene into mouse genome

168
Q

Conditional insertion

A

Targeted insertion or deletion of gene thorugh recombination with mouse gene

169
Q

Inducibly manipulate genes at specific developmental points

A

Cre-lox system

170
Q

dsRNA is synthesized that is complementary to the mRNA sequence of interest. When transfected into human cells., dsRNA seperates and promotes degradation of traget mRNA, “knocking down” gene expression

A

RNA interference.

171
Q

What explains variable expression in mitochondrially inherited disease

A

Heteroplasmy due to presence of both normal and mutated mtDNA.

172
Q

Mccune albright syndrome is an example of

A

somatic mosaicims that arises from mitotic errors after fertilization and propagates through multiple tissues or organs

173
Q

4 assumptions of hardy weinberg

A

No net migration, no mutation at locus, completely random mating, natural selection is not occuring

174
Q

X-linked recessive diseases:

A

“Oblivious female will give her boys x-linked disorders”

Ocular albinism, fabry disease, wiskott-aldrich, g6pd deficiency, hunter syndrome, bruton agammaglobulinemia, hemophilia A+B, lesch nyhan, duchenne muscular dystrophy

175
Q

Hypophosphatemic rickets inheritance

A

x-linked dominant

176
Q

Lifraumeni syndrome commonly causes:

A

SBLA cancer: sarcoma, brain/breast, leukemia, adrenal gland cancers

177
Q

Deletion of what 3 nucleotides in cystic fibrosis coding for what?

A

Phe at position 508

178
Q

Quad screen Downs, Edwards, Patau?

A

Down: Increase B-hCG, Decrease afp, decrease estriol, increase inhibin A
Edwards: Decrease b-hCG, decrease afp, decrease estriol, decrease or normal inhibin A
Patau: decrease bCG decrease PAPPA and increase nuchal translucency in 1st trimester screening (not quad screen)

179
Q

Chromosome 3 disorders

A

VHL, renal cell carcinoma

180
Q

Chromosome 4 disorders

A

ADPKD with PKD2 defect, Huntington disease

181
Q

Chromosome 5 disorder

A

Cri-du-chat syndrome, FAP

182
Q

Chromosome 7 disorders

A

williams syndrome, cystic fibrosis

183
Q

Chromosome 9 disorder

A

Fredreich ataxia

184
Q

Chromosme 11 disorder

A

Wilms tumor

185
Q

Chromosome 13 disorder

A

Patau syndrome, wilson disease

186
Q

Chromosome 15 disorder

A

Prader-willi, angelman

187
Q

Chromosome 16 disorder

A

ADPKD with PKD1 defect

188
Q

Chromosome 17 disorder

189
Q

Chromsome 18 disorder

190
Q

Chromsome 21 disorder

191
Q

Chromsome 22

A

nf2, digeorge

192
Q

X chromosome

A

Fragil x, klinefelter, x-linked agammaglobulinemia

193
Q

what 5 chromosome pairs do robertsonian translocation occur in?

A

13,14,15,21,22

194
Q 
Trinucleotide expanision
Fragile X
Fredreich ataxia
Hungtinton 
Myotonic dystrohy
A

CGG
GAA
CAG
CTG

USMLE Step 1-2015 (18 decks)

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