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Exam 1 > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

Campothecin

A

targets Topo I

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2
Q

m-AMSA

A

targets Topo II (like Doxorubin)

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3
Q

Doxorubin

A

targets Topo II (like m-AMSA)

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4
Q

DNA methylation

A

Adds methyl onto A or C.

Represses transcription.

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5
Q

histone acetylation

A

Adds acetyl onto Lys residue.
Neutralizes Lys.
Opens DNA for transcription

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6
Q

helicase

A

uses ATP to break H bonds of bases

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7
Q

DNA ligase

A

seals DNA nicks with ATP

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8
Q

Bloom’s Syndrome

A

Deficient DNA helicase.

Causes malignancies.

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9
Q

Werner’s Syndrome

A 
Associated with a mutation in the gene that encodes helicase.
Premature ageing (cataracts, balding, dwarfism).
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10
Q

DNA Pol a (alpha) primase

A

forms RNA/DNA primer

equivalent to Pol I in prokaryotes

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11
Q

DNA Pol d (delta)

A

Synthesizes lagging strand of DNA.
High processivity.
Needs PCNA clamp.
Equivalent to Pol III in prokaryotes.

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12
Q

DNA Pol e (epsilon)

A

Synthesizes leading strand of DNA.
High processivity.
Needs PCNA clamp.

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13
Q

DNA Pol y (gamma)

A

mtDNA

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14
Q

DNA Pol B (beta)

A

repairs DNA synthesis mutations

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15
Q

Zidovudine (AZT)

A

Nucleotide analogue.Inhibits reverse transcriptase in HIV.
Limitations: 1) high toxicity (inhibits Pol Y, mtDNA)
2) mutant forms arise with low affinity for AZT

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16
Q

Acyclovir

A

Nucleotide analogue.

Inhibits Herpes DNA polymerase.

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17
Q

Li-Fraumeni Syndrome

A

Mutated p53.
Tumors at multiple sites.
All cells carry the mutation.

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18
Q

mismatch repair in proks

A

Mut S recognizes mismatch.
Mut H recognizes methylation and makes incision.
Mut L links Mut S and Mut H

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19
Q

mismatch repair in euks

A

Human Mut S/L homologues (hMSH, hMLH) have been isolated.
Mut H homologue has not.
Defects associated with HNPCC.
Defects usually due to a Trinucleotide Repeat Expansion.

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20
Q

Hereditary Non-Polypsis Colon Cancer (HNPCC)

A

Caused by defects in hMSH and hMLH.

Usually due to Nucleotide Repeat Expansion.

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21
Q

excision repair

A

For bulkier DNA adducts.
uvrABC complex recognizes thymine dimers, then cuts on both sides of damage.
Faulty DNA excises, filled, sealed.

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22
Q

Xeroderma Pigmentosum

A

skin cancer associated with faulty excision repair.

specifically, the nuclease is faulty

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23
Q

uracil removal

A

Uracil-DNA glycosidase recognizes uracil and hydrolyzes the glycosidic bond.
Creates an AP site.
Endonuclease cuts backbone.
Excise, fill, seal.
Cytosine spontaneously deaminates to uracil.

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24
Q

nitrous oxide (HNO2)

A

Causes deamination.
C to U.
A to Hypoxanthine.

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25
Q

adenylation of guanine

A

N-7 methylation causes alkaline amine.
Breaks glycosidic bond.

carcinogen

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26
Q

intercalators

A

Polycyclic hydrocarbons.
Cause insertions/deletions.
Ethidium bromide, proflavin.

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27
Q

radiation

A

alters DNA structure

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28
Q

pulsed field gel electrophoresis

A

can separate whole chromosomes

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29
Q

Southern Blot

A

Detects DNA of interest.

1) cut DNA with restriction endonuclease
2) run on a gel to separate fragments
3) expose to NaOH to make ssDNA
4) transfer to nitrocellulose membrane
5) expose to a labeled probe.

Can detect large deletions/additions and trinucleotide repeat expansions

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30
Q

DNA fingerprinting

A

Humans have different restriction sites.

Treating with restriction endonuclease results in a barcode-like result that is fairly unique

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31
Q

Restriction Fragment Length Polymorphism (RFLP)

A

Restriction enzyme sites are highly polymorphic.
Can detect the presence of a mutation if RE sites is altered (compares RE sites from different cells of same individual).

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32
Q

Fluorescence in Situ Hybridization (FISH)

A

Determines presence, absence, or copy of a chromosome.

ex: monosomy, trisomy

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33
Q

Northern Blot

A

RNA detection

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34
Q

Western Blot

A

Protein detection.
SDS page eliminates charge differences so it separates by size.
Labeled antibody probe.

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35
Q

DNA band shift

A

Electrophoretic mobile shift assay.

If there is an interaction between DNA and protein, it will move slower, creating a band shift.

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36
Q

RT-PCR

A

Used to determine cancer reoccurrence.

Measures expression of cancer genes.

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37
Q

Single Strand Conformation Polymorphism (SSCP)

A

PCR products are run/separated on gel.

If mutated, the band pattern will differ from normal PCR product.

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38
Q

RNA Polymerase I

A 
Transcribes rRNA.
RESISTANT to a-amanitin.
Nucleolus.
***FACTOR B and S help it bind to promoter.***
Upstream promoter.18S, 5.8S, 28S rRNA
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39
Q

RNA Polymerase II

A

Transcribes mRNA.
SENSITIVE to a-amanitin.
Upstream promoter.

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40
Q

RNA Polymerase III

A

Transcribes 5S rRNA, tRNA, miRNA (small RNA).
Promoter is WITHIN the gene.

TFIIIA and TFIIIC facilitate binding of TFIIIB, which recruits RNAPIII to initiate transcription.

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41
Q

Transcription initiation

A

TFIID binds to TATA box, recruits TFIIB.
TFIIB recruits other TFs.
TFIIB binds RNAP II and directs it to the promoter.
TFIIF/E/H bind.
TFIIH phosphorylates RNAP II to initiate transcription.

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42
Q

prokaryotic promoter features

A

Pribnow box.

35 bp TTGACA

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43
Q

poly-A tail is added ______

A

where the internal signal occurs (not at very end of transcript)

CPSF binds to signal, recruits poly A polymerase (PAP)

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44
Q

splicing mechanism

A

u1 snRNP recognizes 5’ GU of intron.
u2 snRNP recognizes 3’ AG of intron.
u1 and u2 recruit other snRNPs for the spliceosome (u4, u5, u6).
5’ intron/exon junction is cleaved, lariat forms.3’ junction is cleaved, exon ligated.

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45
Q

thalassemias

A

Hereditary abnormalities of hemoglobin production.
Lack of either alpha or beta chains.
Due to faulty splicing.

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46
Q

actinomycin D

A

Binds to DNA and distorts it so it cannot be used as a template.
Inhibits transcription.

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47
Q

rifampicin

A

blocks initiation of RNA synthesis in bacteria

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48
Q

in DNA, deoxyribonucleotides are linked via:

A

3’ to 5’ phosphodiester linkages

49
Q

Alu repeat

A
  • SINE
  • 280 bp long
  • occurs every 5,000 bp
50
Q

LI

A
  • LINE

* >500 kb long

51
Q

Simple sequence repeats constitute about __% of the human genome

A

3%

52
Q

microsatellite

A

2-5 bp repeats.
Array size of ~10.
Highly polymorphic.

53
Q

telomeres

A

Example of satellite sequence.
TTAGGG repeats.
Shorten with age.
Cancer cells turn then on.

54
Q

Simian Virus 40

A

Initially used to study human DNA replication.

Only requires 1 viral protein, T-ag (all others are supplied by host cell).

55
Q

T-ag

A

From SV40.
Multifunctional protein.
Binds origin of replication and acts as DNA helicase.

56
Q

restriction endomucleases

A

Cleave at palindromic sites.
Protection against foreign pathogenic bacteriophage.
Bacterial DNA protected by methylation.

57
Q

sickle cell anemia (method of diagnosis)

A

Southern Blot.

Restriction endonuclease site is altered, leading to a longer restriction fragment.

58
Q

large ribosomal subunit is composed of…

A

5 s, 5.8 s, 28 s rRNA (and proteins)

59
Q

small ribosomal subunit is composed of…

A

18 s rRNA (and proteins)

60
Q

B and S factors

A

help with initiation of RNAP I

61
Q

TFIIH

A

Has protein kinase activity.

Phosphorylates RNAP II –> initiates transcription.

62
Q

5’ cap (what is added, what type of linkage)

A

7-methylguanosine.

5’-5’ triphosphate linkage.

63
Q

Examples of alternative splicing

A

Antibodies.

a-tropomyosin.

64
Q

locus control regions

A

regulate chromatin regulation over chromosomal domains (ex: all globin genes)

65
Q

SWI-SNF protein complex

A

Alter chromatin structure

66
Q

CpG methylation

A

associated with repression/X-inactivation

67
Q

CpG dinucleotides are hotspots for mutations because…

A

deamination of 5-methyl cytosine forms thymine

68
Q

CpG islands

A

Long CpG rich regions in promoter regions.
Almost always lack methylation.
Usually near genes that are always turned on.

69
Q

PDX1 protein

A

Regulates the insulin made in the pancreas.

Triggered by glucose.

70
Q

DNA microarrays

A

Determine differences in mRNA population of two cell types.
mRNA is isolated.
Glass slides with ssDNA of interest are prepared.
mRNA is converted to cDNA and labeled with a fluorescent probe.
cDNA is hybridized to DNA on microarrays.
If relatively same amount of mRNA from each cell is present, then it will be a blend of two colors.
If one cell has much more expression of mRNA then it will be a primary color.

71
Q

RNA-seq

A

Alternative to microarrays.
NExt gen sequencing determines composition and quantity of RNA in cell.
The more sequence that appears, the more RNA that is present.

72
Q

siRNA

A

Double stranded.
Forms a ribonucleotide complex (RISC) that binds to target mRNA via complementary base pairing.
Destroys the bound mRNA.
“Knocks down” the expression (not completely gone)

73
Q

CRISPR-Cas

A

Used to “knock out” specific genes.

Cas9 is a programmable nuclease that can be guided to certain sites.

74
Q

tRNA structure

A

Clover leaf.
Anti-codon loop.
CCA terminus (AA binds here).
Modifications/unusual bases.

75
Q

addition of AA onto tRNA

A

Carboxy end of AA to 3’ end of tRNA.
“Activates” the AA by creating a high energy covalent bond.
Different synthetase for each AA.

AA + ATP –> aminoacyl-AMP —binds with tRNA—> aminoacyl tRNA (AMP leaves)

76
Q

initiation of protein synthesis

A 
Small subunit, eIF4, and eIF2-GTP-Met-tRNA bind to 5' cap.
eIF4 positions mRNA on small subunit.
Scans for AUG start codon.
eIF2-GDP and other eIFs leave.
Large subunit joins.
77
Q

eEF1

A

Catalyzes the GTP-dependent binding of new aminoacyl-tRNAs in the A site.
Regulates fidelity and rate of polypeptide elongation.

78
Q

peptidyl transferase

A

Part of 28S subunit.

Forms peptide bond.

79
Q

eEF2

A

Needed for translocation.

80
Q

elongation of peptide chain

A

eEF1 catalyzes GTP-dependent binding of tRNA in A site.
Peptidyl transferase forms peptide bond.
eEF2 is required for translocation of tRNA

81
Q

phosphorylation of eIF2

A

Inactivates eIF2.
Represses translation and conserves energy.
Usually in times of stress.

82
Q

polyribosome

A

multiple ribosomes moving along the same mRNA, functioning independently of each other.

83
Q

missense mutation

A

single base substitution leads to a different amino acid

84
Q

nonsense mutation

A

single base substitution leads to a premature stop codon

85
Q

IRES

A

Internal Ribosome Entry Sites.
Specialized sequences used by viruses.
Recruits pre-initiation complex without involving the cap or scanning process.
Allows virus to take over protein synthesis machinery.

86
Q

miRNA

A

Endogenous.
Recruit RISC complex.
If it is completely homologous to the target mRNA, then RISC degrades the mRNA.
If it is not 100% homologous to the target mRNA, then it stalls the machinery, blocking translation (but does not degrade it)

87
Q

glioblastoma

A

Tumor of the brain or spine.
Difficult to surgically remove.
Gene sequencing can be used instead to guide treatment.

88
Q

bisulfite sequencing

A

Used to determine if DNA is methylated (repressed).
Methylation of MGMT is used as a guide for chemotherapy.
Can only use chemo if MGMT is silenced by methylation.

89
Q

proline

A

fits poorly into a-helices

90
Q

amino acids that absorb UV light

A

tyrosine, tryptophan

91
Q

glycine

A

small amino acid that allows close approaches

92
Q

CFTR

A

Transmembrane protein.
Transports CL- out of the cell.
To transport, the R domain must be phosphorylated, and ATP must be bound/hydrolyzed.

93
Q

Elastin

A

Fibrous, unstructured protein.
Desmosine: lysine linkages.
In elastic tissues (lungs).

94
Q

Keratin

A

Fibrous protein with tight a-helices.

In hair, nails, skin.

95
Q

maximum buffering occurs when…

A

[base] = [acid]

at the pKa

96
Q

bicarbonate buffer

A

In the blood.
pKa slightly lower than neutral.
Exhalation increases pH.
CO2 + H20 H2CO3 H+ + HCO3-

97
Q

phosphate buffer

A

Inside cells.

Neutral.

98
Q

protein buffer

A

Side chains help buffer.

In blood/cells.

99
Q

Myoglobin (structure, function, Hill Coeff.)

A

Monomeric, helical protein.
Heme prosthetic group.
Transports oxygen in muscle.
Hill coefficient = 1 (no cooperativity).

100
Q

oxygenated heme // oxidized heme // deoxygenated heme

A

OXYGENATED:
Bright red. (+2)

OXIDIZED:
Brownish. (+3), still bound to O2.

DEOXYGENATED:
Blue/purple. No O2.

101
Q

functions of histidines in myoglobin and hemoglobin.\

A

1) form a ligand with the iron that moves upon oxygenation.

2) provide a steric hindrance to reduce CO binding

102
Q

hemoglobin structure, Hill coeff.

A

2 alpha subunits.
2 beta subunits.
1 heme per subunit (4 total).

Hill coefficient > 1 (cooperative binding)

103
Q

conformations of hemoglobin

A

T form - TAUT
Binds oxygen poorly.

R form - RELAXED
Binds oxygen with higher affinity.

104
Q

negative allosteric inhibitors of hemoglobin

A

CO2, H+, BPG

actively metabolizing tissue releases CO2 and H+, causing O2 to be released from hemoglobin and delivered to tissues.

105
Q

where does BPG bind?

A

in the pocket formed between the two B subunits

106
Q

fetal hemoglobin (subunits, affinity)

A

2 alpha subunits, 2 gamma subunits.
BPG binds less well.
Higher affinity for oxygen.

107
Q

HbS (sickle)

A

Substitution in Beta subunit.
Sickles under low oxygen conditions.
Substitution adds a hydrophobic surface knob, which fits into the hydrophobic pocket that forms under low oxygen conditions.

Few symptoms under highly oxygenated conditions (no hydrophobic pocket).

108
Q

Methemoglobin

A

Carries Fe3+ (cannot carry O2)
Due to mutation, or ingestion of oxidizing agents (fertilizer).
Vitamin C can reduce iron to active Fe2+ state for carrying O2.

109
Q

treatment of sickle cell anemia

A

1) Hydroxyurea: produces small amount of HbF.
2) Antibiotics to treat secondary infections.
3) Bone marrow transplant: replaces HbS with HbA.
4) Gene therapy.

110
Q

cysteine forms disulfide bonds in a(n) ___________ environment

A

oxidizing environment (in ER, outside cell)

111
Q

maturation of insulin

A

PREPROINSULIN
Inside the cell, reduced.

PROINSULIN
In ER, oxidized.
Disulfide bonds form.
N-terminal peptide sequence removed.

INSULIN
Secreted, oxidized.
Internal peptide removed.

112
Q

type 1 collagen

A

bone, skin, tendons

113
Q

type III collagen

A

reticulin (skin repair)

114
Q

Collagen Biosynthesis

A

1) Polypeptide chain synthesis (repeats of Gly, Pro, Hydroxy Pro)
2) Hydroxylation of Pro and Lys (requires prolyl/lysyl hydroxylase, with Vitamin C cofactor).
3) Glycosylation
4) Disulfide bond formation at C-terminus
5) Triple helix formation (from C-terminal to N terminal)
6) Secretion.
7) Hydrolysis of peptides (cleaved by precollagen peptidases), forms alpha-collagen chains.
8) Assembly into fibril.
9) Formation of crosslinks (lysyl oxidase forms allysine from lysine.

115
Q

Osteogenesis Imperfecta

A

Mutation in collagen type I.

Changes Glycine to Cysteine, messing up helical structure.

116
Q

Ehlers-Danlos syndromes (when dominant/recessive)

A

Mutation in collagen type I or III.
Stretchy skin, hyperextensive joints.
Dominant if a structural protein.
Recessive if a processing enzyme.

117
Q

Prion diseases

A

Protein “gone bad.”

Less of the helical form, more of the aggregated form.

118
Q

how prion diseases are acquired

A

1) missense mutation (acquired or inherited) [classical]

2) contact with “bad form” [new]

Exam 1 (3 decks)

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