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Flashcards in biochem: molecular Deck (68):
1

heterochromatic

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

2

euchromatin

less condensed, lighter on EM. active, accessible.

3

DNA methylation

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

4

histone methylation

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

5

histone acetylation

relaxes DNA coiling, allowing for transcription

6

purines

2 rings. A, G. PURe As Gold

7

pyrimidines

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

8

thymine

THYmine has a meTHYl

9

deamination of cystosine makes

uracil

10

G-C bond

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

11

AAs necessary for purine synthesis

GAG = gylcine, aspartate, glutamine

12

adenosine deaminase deficiency

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

13

lesch-nyhan syndrome

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

14

origin of replication

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

15

replication fork

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

16

helicase

unwinds DNA template at replication fork

17

single-stranded binding proteins

prevent strands from reannealing

18

DNA topoisomerases

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

19

primase

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

20

DNA polymerase III

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.

21

DNA polymerase I

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

22

DNA ligase

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

23

telomerase

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

24

DNA damage mutations severity

silent<

25

SS mutation

missense (glu-valine)

26

duchenne muscular dystrophy mutation

frameshift

27

lac operon

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

28

nucleotide excision repair

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

xeroderma pigmentosum error

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

30

base excision repair

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

repair of spontaneous/toxic deamination

base excision repair

32

mismatch repair

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

33

hereditary nonpolyposis colorectal cancer (HNPCC) error

mismatch repair

34

nonhomologous end joining

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

35

ataxia telangiectasia and fanconi anemia error

nonhomologous end joining

36

DNA/RNA/protein synthesis direction

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

chain termination

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

38

mRNA start codons

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

39

mRNA start codon in eukaryotes

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

40

mRNA start codon in prokaryotes

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

41

mRNA stop codons

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

42

promoter

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

promoter mutation

commonly results in dramatic decrease in level of gene transcription

44

enhancer

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

silencer

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

RNA polymerase in eukaryotes

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

47

RNA polymerase I

makes rRNA. most numerous RNA, rampant.

48

RNA polymerase II

makes mFRNA. largest RNA, massive

49

RNA polymerase III

makes tRNA. smallest RNA, tiny

50

alpha-amanitin MoA

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

51

rifampin MoA

inhibits RNA polymerase in prokaryotes

52

Actinomycin D MoA

inhibits RNA polymerase in both prokaryotes and eukaryotes

53

RNA polymerases in prokaryotes

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

54

mRNA

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

55

cytoplasmic P-bodies

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

56

poly-A polymerase

does not require a template.

57

polyadenylation signal

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

58

splicing of pre-mRNA

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

tRNA

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

60

protein synthesis: initiation

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

protein synthesis: elongation

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

protein synthesis: termination

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

63

eukaryotic ribosome

40S + 60S -> 80S = Even

64

prOkaryotic ribosome

30S + 50 -> 70S = Odd

65

E, P, and A sites

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

66

trimming

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

67

covalent alterations

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

68

chaperone protein

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