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Biochemistry - Victor > Sandmeyer Insanity > Flashcards

Sandmeyer Insanity Flashcards

0
Q

Pyrimidines contain a _____ ring. Purines contain a ______ ring.

A

Double, single.

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1
Q

What does a nucleotide have that a nucleoside doesn’t?

A

Phosphate.

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2
Q

Which pairing is stronger, AT or CG?

A

CG

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3
Q

Do proteins regularly interact with the minor or major groove of DNA?

A

Major.

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4
Q

T or F. Positive supercoiling occurs ahead of the DNA polymerase, and negative supercoiling compensates for the unwound backbone.

A

True. Also, DNA of most organisms is negatively supercoiled (wikipedia).

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5
Q

T or F. Gyrase is involved in both positive and negative supercoiling.

A

True? lol i hate topoisomerases.

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6
Q

Quinolones and novobiocin inhibit bacterial ______.

A

Topoisomerase 2, gyrase.

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7
Q

T or F. RNA typically exists as single stranded, but can also be duplex.

A

True.

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8
Q

Denaturing temperature of DNA can be highly dependent on the DNA’s _______ content.

A

GC

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9
Q

Nucleotides are added to the ____ end (5 or 3’) in DNA synthesis.

A

3’

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10
Q

RNA polymerase moves from the _____ end to the _____ end of the template strand.

A

3’ to 5’

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11
Q

T or F. Termination of prokaryotic transcription requires the rho protein.

A

False. Rho independent termination involves hairpin RNA.

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12
Q

T or F. mRNAs outnumber all other types of RNAs.

A

False. mRNAs only 2%, ribosomal RNAs are 80%.

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13
Q

What happens in the lac operon in the absence of lactose?

A

Lactose doesn’t bind the repressor, allowing the repressor to bind to the operator region of the lac operon. RNA pol gets stuck.

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14
Q

What happens to the lac operon in the presence of lactose?

A

Lactose binds the repressor, preventing it from binding to the operator regions. RNA pol does work.

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15
Q

What happens to the lac operon in the presence of glucose?

A

Glucose leads to low cAMP. This means CRP is inactive and can’t be a part of the RNA pol complex. low lac expression.

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16
Q

What happens to the lac operon in the absence of glucose?

A

Low glucose means high cAMP. cAMP + CRP associates with RNA pol and stimulates transx of lac.

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17
Q

What is a silent, missense and nonsense mutation?

A

silent: no change in aa
missense: change in aa
nonsense: termination

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18
Q

T or F. Insertions and deletions in the intron or exons of a gene may result in frameshift mutation.

A

False. Only insertions/deletions in ORF.

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19
Q

How can you test if a chemical is a DNA mutagen?

A

Spray that shit over histidine deficient bacteria and grow it in histidine deficient medium. Colonies will grow if your chemical is a mutagen.

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20
Q

Name two characteristics of transposons.

A

Encodes enzymes that move it around. Usually have good selection quality (eg antibiotic resistance).

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21
Q

T or F. Bacteria can independently take up DNA from the environment.

A

True.

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22
Q

What is the difference between F plasmid and Hfr conjugation?

A

F plasmid replicates plasmid, gives plasmid copy to recipient.
Hfr has F integrated into chromosome, gives F copy to recipient which replaces portion of recipient DNA.

23
Q

What is transduction?

A

DNA transfer from one bacteria to another by a virus.

24
Q

T or F. Nearly half of the genome in humans can be mobilized by retrotransposons/homologous recombination.

A

True. LINES, SINES, LTR retrotransposons, DNA retrotransposons, simple sequence repeats.

25
Q

What is the difference between G light bands and G dark bands?

A

G light bands: GC rich, expressed genes, SINES

G dark bands: AT rich, L1 repeats

26
Q

What’s the difference between LINEs and SINEs?

A

SINEs don’t encode reverse transcriptase.

27
Q

Give an example of de novo spontaneous mutation?

A

LCR1 and LCR2 recombine when it shouldnt, causes duplication on one allele and deletion on another.

28
Q

What does acetylation do to DNA?

A

makes it accessible for transcription. acetylation attaches to glycine tail of histone, reduces positive charge of histone. DNA thus binds less tightly to histone, promotes transx.

29
Q

Describe non allelic homologous recombination.

A

Recombination between part of a gene with another gene on the same strand, inverting and splitting the gene.

30
Q

What does each eukaryotic pol make?

A

pol 1 : ribosomal RNA
pol 2 : mRNA, miRNAs
pol 3 : tRNAs, splicing RNAs, small noncoding RNAs

31
Q

What does the 5’ UTR and 3’ UTR (untranslated region) regulate?

A

5’ UTR regulates translation efficiency, 3’ UTR affects localization after nuclear export.

32
Q

What is the initiator codon?

A

Met

33
Q

What does phosphorylated CTD of RNA pol involved in?

A

Unphosphorylated CTD: initiation. Phosphorylated CTD: elongation.

34
Q

Describe the process of splicing.

A

snRNPS form spliceosome on intron, two step transesterification turns intron into branched lariat.

35
Q

Can unspliced RNA generally leave the nucleus? What is nonsense mediated decay?

A

Not exported from nucleus. Nonsense mediated decay: internal stops of unspliced RNA recognized, degraded.

36
Q

What does methylation of cytosine at the 5 position do?

A

Its an epigenetic modification which can target additional repressive modifications and is retained through replication. What this means, I do not know.

37
Q

T or F. Transcription factors can be directly regulated by changes in conformation from binding to small molecules.

A

True.

38
Q

Zinc fingers, leucine zippers, homeobox and helix turn helix are all examples of _______ domains.

A

DNA binding domains.

39
Q

T or F. Most methylation is removed in germ cells and is replaced in the egg and sperm.

A

True. Methylation at specific sites is paternal maternal dependent.

40
Q

What is genomic imprinting?

A

Epigenetic process involving methylation and histone modulation resulting in monoallelic gene expression without altering genetic sequence. Deletion of imprinted sequences between repeated sequences can cause genetic syndromes (Prader willis (paternal), Angelman syndrome (maternal))

41
Q

Inactivation of one of the two female chromosomes occurs by _______.

A

DNA methylation.

42
Q

Deamination of C to U is an example of _______ editing.

A

RNA editing. Responsible for making apoB 48.

43
Q

Low iron allows IRP to bind IRE, protecting the 3’ end from _______. Tfr is made as a result.

A

degradation. This is an example of regulation of RNA by degradation. High iron binds IRP, so the IRE hairpins causes degradation.

44
Q

T or F. Splicing is cotranscriptional.

A

True.

45
Q

What are the main difference between siRNAs and miRNAs?

A

siRNAs require perfect match to target specifc mRNA. miRNAs dont need perfect match. srRNAs cleave mRNAs, miRNAs degrade mRNAs

46
Q

What are some eukaryotic promoter features?

A

TATA element, activator factor binding sites, enhancer sequences (CpG islands near housekeeping genes)

47
Q

In Prader Willi, which parental chromosome is methylated? deleted?

A

Paternal is deleted, maternal usually methylated.

48
Q

In Angelman syndrome, which parental chromosome is methylated? deleted?

A

Maternal is deleted, paternal usually methylated.

49
Q

_________ of C to U helps create apoB.

A

Deamination.

50
Q

In regards to ELISA, describe a direct assay, indirect assay and capture assay.

A

Direct Assay: Ag on plate, Ab-enzyme applied to Ag. Add substrate for visualization.
Indirect Assay: Ag on plate, Ab applied to Ag. Ab-enzyme added to Ab. Substrate added for visualization.
Capture Assay: Ab1 to Ag on plate. Add Ag. Add another Ab2 to Ag. Add Ab3 to Ab2.

51
Q

What are a few methods commonly used to detect hemoglobinopaties (eg sickle cell) in people?

A

Southern blot (mutation deletes restriction site)
PCR assay the mutated region, sequence that region.
Microarray with probes for several mutant alleles.

52
Q

T or F. Variable number tandem repeat alleles are polymorphic regions that help distinguish normal individuals.

A

True.

53
Q

Sanger sequencing uses fluorescent __________ to terminate elongation.

A

dideoxy NTPs.

54
Q

SNPs can be detected using what methods?

A

microarray, bead array, next generation sequencing

55
Q

Southern blot detects_____
Northern _______
Western ______

A

DNA, RNA, Protein

Biochemistry - Victor (17 decks)

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