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biochem: molecular Flashcards

1
Q

heterochromatic

A

condensed, darker on EM, inactive, inaccessible. e.g. Barr bodies

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2
Q

euchromatin

A

less condensed, lighter on EM. active, accessible.

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3
Q

DNA methylation

A

template strand cytosine and adenine are methylated in DNA replication, allowing repair enzymes to distinguish old and new strands. methylation at CpG islands represses transcription

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4
Q

histone methylation

A

usually reversibly represses transcription, but sometimes activates it (depending on location).

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5
Q

histone acetylation

A

relaxes DNA coiling, allowing for transcription

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6
Q

purines

A

2 rings. A, G. PURe As Gold

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7
Q

pyrimidines

A

1 ring. C, T, U. CUT the PY

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8
Q

thymine

A

THYmine has a meTHYl

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9
Q

deamination of cystosine makes

A

uracil

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10
Q

G-C bond

A

= 3 H bonds = stronger than A-T bond (2 H bonds). so more G-Cs -> higher melting temp

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11
Q

AAs necessary for purine synthesis

A

GAG = gylcine, aspartate, glutamine

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12
Q

adenosine deaminase deficiency

A

autosomal recessive cause of SCID. excess ATP and dATP imbalances nucleotide pool via feedback inhibition of ribonucleotide reductase -? prevents DNA synthesis, so decreases lymphocyte count

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13
Q

lesch-nyhan syndrome

A

defective purine salvage due to avsent HGPRT, which concerts hypoxanthine to IMP and guanine to GMP. results in excess uric acid production and de novo purine synthesis. x-linked recessive. HGPRT: hyperuricemia, gout, pissed off (aggression, self-mutilation), retardation, dysTonia. Tx w/allopurinol or febuxostat

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14
Q

origin of replication

A

particular consensus sequence of base pairs in genome where DNA replication begins. may be single (prokaryotes) or multiple (eukaryotes)

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15
Q

replication fork

A

y-shaped region along DNA template where leading and lagging strands are synthesized

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16
Q

helicase

A

unwinds DNA template at replication fork

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17
Q

single-stranded binding proteins

A

prevent strands from reannealing

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18
Q

DNA topoisomerases

A

create a single- or double-stranded break in the helix to add or remove supercoils. fluoroquinolones inhibit prokaryotic topoisomerase II (DNA gyrase) and topoisomerase IV

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19
Q

primase

A

makes an RNA primer on which DNA polymerase II can initiate replication

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20
Q

DNA polymerase III

A

prokaryotic only. elongates leading strand by adding deoxynucleotides to the 3’ end. elongates lagging strand until it reaches primer of preceding fragment. 3’->5’ exonuclease activity “proofreads” each added nucleotide. 5’->3’ synthesis, 3’->5’ proofreading.

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21
Q

DNA polymerase I

A

prokaryotic only. degrades RNA primer, replaces it w/DNA. similar to DNA polymerase II but also excises RNA primer w/5’->3’ exonuclease

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22
Q

DNA ligase

A

seals = catalyzes the formation of a phosphodiester bond w/in a strand of double-stranded DNA (i.e. joins Okazaki fragments).

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23
Q

telomerase

A

RNA-dependent DNA polymerase that adds DNA to 3’ ends to avoid loss of genetic material w/every duplication. eukaryotes only.

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24
Q

DNA damage mutations severity

A

silent«frameshift

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25
Q

SS mutation

A

missense (glu-valine)

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26
Q

duchenne muscular dystrophy mutation

A

frameshift

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27
Q

lac operon

A

activated in low glucose conditions when lactose is present, allowing lactose metabolism instead

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28
Q

nucleotide excision repair

A

single strand. specific endonucleases release the oligonucleotides containing damages bases. DNA polymerase fills the gap, DNA ligase reseals it. repairs bulky, helix-distorting lesions. occurs in G1 phase of cell cycle

29
Q

xeroderma pigmentosum error

A

= error of nucleotide excision repair, pyrimidine dimers are damaged by UV exposure

30
Q

base excision repair

A

single strand. base-specific glycosylase removes altered base and creates AP site. one or more nucleotides are removed by AP-endonuclease, which cleaves the 5’ end. lyase cleaves the 3’ end. DNA polymerase-beta fills the gap, DNA ligase seals it. occurs throughout cell cycle

31
Q

repair of spontaneous/toxic deamination

A

base excision repair

32
Q

mismatch repair

A

single strand. newly synthesized strand is recognizes, mismatched nucleotides are removed, and the gap is filled and resealed. orrus mostly in G2 phase

33
Q

hereditary nonpolyposis colorectal cancer (HNPCC) error

A

mismatch repair

34
Q

nonhomologous end joining

A

double strand. brings together 2 ends of DNA fragments to repair double-stranded breaks. no reuirement for homology. some DNA may be lost

35
Q

ataxia telangiectasia and fanconi anemia error

A

nonhomologous end joining

36
Q

DNA/RNA/protein synthesis direction

A

both are synthesized 5’->3’. 5’ end of incoming nucleotide bears triphosphate, which is the energy source for the bond. protein synthesis occurs from N-terminus to C-terminus

37
Q

chain termination

A

caused by drugs that blocking DNA replication. modified 3’OH targets triphosphate bond, preventing addition of the next nucleotide

38
Q

mRNA start codons

A

AUG (or GUG, rarely). AUG inAURGurates protein synthesis

39
Q

mRNA start codon in eukaryotes

A

codes for methionine, which may be removed before translation is completed

40
Q

mRNA start codon in prokaryotes

A

codes for N-formylmethionine (fMet), which stimulates neutrophil chemotaxis.

41
Q

mRNA stop codons

A

UGA, UAA, UAG. UGA = U Go Away. UAA = U Are Away. UAG = U Are Gone

42
Q

promoter

A

site where RNA polymerase II and multiple other transcription factors bind to DNA upstream from gene locus (AT-rich upstream sequence w/TATA and CAAT boxes).

43
Q

promoter mutation

A

commonly results in dramatic decrease in level of gene transcription

44
Q

enhancer

A

stretch of DNA that alters gene expression by binding transcription factors. can be located close to, far from, or even w/in (in an intron) the gene whose expression it regulates.

45
Q

silencer

A

site where negative regulators (repressors) bind. can be located close to, far from, or even w/in (in an intron) the gene whose expression it regulates.

46
Q

RNA polymerase in eukaryotes

A

numbered as their products are used in protein synthesis. No proofreading fxn but can initiate chains.

47
Q

RNA polymerase I

A

makes rRNA. most numerous RNA, rampant.

48
Q

RNA polymerase II

A

makes mFRNA. largest RNA, massive

49
Q

RNA polymerase III

A

makes tRNA. smallest RNA, tiny

50
Q

alpha-amanitin MoA

A

found in amanita phalloides (death cap mushrooms). inhibits RNA polymerase II. causes severe hepatotoxicity.

51
Q

rifampin MoA

A

inhibits RNA polymerase in prokaryotes

52
Q

Actinomycin D MoA

A

inhibits RNA polymerase in both prokaryotes and eukaryotes

53
Q

RNA polymerases in prokaryotes

A

1 RNA polymerase (multisubunit complex) makes all 3 kinds of RNA

54
Q

mRNA

A

= capped, tailed, and spliced transcript of heterogeneous nuclear RNA (hnRNA). transported out of nucleus into cytoplasm, where it is translated.

55
Q

cytoplasmic P-bodies

A

contain exonucleases, decapping enzymes, and microRNAs, providing quality control for mRNA. mRNA can be stored inside for future translation.

56
Q

poly-A polymerase

A

does not require a template.

57
Q

polyadenylation signal

A

= AAUAAA. polyadenylation occurs at 3’ end (~200 As), forming tail.

58
Q

splicing of pre-mRNA

A

1: primary transcript combines w/small nuclear ribonucleoproteins (sRNPs) and other proteins to form spliceosome. 2: lariat-shaped (looped) intermediate is generated. 3: lariat is released to precisely remove intron and join 2 exons

59
Q

tRNA

A

serves as the physical link between the nucleotide sequence of nucleic acids and the amino acid sequence of proteins

60
Q

protein synthesis: initiation

A

GTP hydrolysis. initiation factors help assemble the 40s ribosomal subunit with the initiator tRNA and are released when the mRNA and the ribosomal 60S subunit assemble with the complex

61
Q

protein synthesis: elongation

A

1: aminoacyl-tRNA binds to A site (except for initiator methionine). 2: rRNA (“ribozyme”) catalyzes peptide bond formation, transfers growing polypeptide to AA in A site. 3: ribosome advances 3 nucleotides toward 3’ end of mRNA, moving peptidyl tRNA to P side (translocation)

62
Q

protein synthesis: termination

A

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

63
Q

eukaryotic ribosome

A

40S + 60S -> 80S = Even

64
Q

prOkaryotic ribosome

A

30S + 50 -> 70S = Odd

65
Q

E, P, and A sites

A

going APE: A site = incoming Aminoacyl-tRNA. P site = accommodates growing Peptide. E site = holds Empty tRNA as it Exits

66
Q

trimming

A

removal of N- or C-terminal propeptides from zymogen to generate mature protein (e.g. trypsingen to trypsin)

67
Q

covalent alterations

A

phosphorylation, glycosylation, hydroxylation, methylation, acetylation, and ubiquitination

68
Q

chaperone protein

A

intracellular protein involved in facilitating and/or maintaining protein folding. for example, in yeast, heat shock proteins are expressed at high temperatures to prevent protein denaturing/misfolding

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