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Molecular Cell Bio > IR WEEK 2 > Flashcards

IR WEEK 2 Flashcards

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Biology 101 flashcards
1
Q

what is the spontaneous loss of ~500 purine (A,G) bases lost per cell per day because of hydrolysis of the glycosal linkage to deoxyribose

A

depurination

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2
Q

when does depurination occur?

A

when the bond connecting a purine to its deoxyribose sugar is broken by a molecule of water (hydrolysis) resulting in a purine free nucleotide that can’t act as a template during DNA replication (results in a deletion)

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3
Q

what is the spontaneous removal of the amine (NH2) group from ~100 cytosines per cell per day to form uracil

A

deamination

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4
Q

when does deamination occur?

A

when hydrolysis wipes away the NH2 from cytosine and replaces it with an oxygen to form uracil and an ammonium ion (results in a substitution

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5
Q

List the spontaneous DNA mutations that require DNA repair

A
  1. depurination
  2. deamination
  3. spontaneous oxidative destruction
  4. uncontrolled methylation
  5. hydrolytic attack
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6
Q

reactive oxygen radical or chemical exposure causes base damage

A

spontaneous oxidative destruction

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7
Q

forms pyrimidine dimers via covalent linkage between 2 bases

A

UV damage

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8
Q

DNA glycosylases are specific for altered DNA bases. it is detected by the glycosylase enzyme “flipping out” each nucleotide so it can be checked by the endonuclease and repaired if necessary

A

base excision repair

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9
Q

recognition of dimer begins with this repair

A

delete

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10
Q

BRCA1

A

breast and ovarian cancer; repair by homologous recombination is affected

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11
Q

Ataxia Telangiectasia (AT)

A

leukemia, lymphoma, gamma ray sensitivity, genome instability; ATM protein is affected

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12
Q

cockayne syndrome

A

UV sensitivity, developmental abnormalities; coupling of nucleotide excision repair to transcription process is affected

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13
Q

xeoderma pigmentosum

A

skin cancer, UV sensitivity, neurological abnormalities; nucleotide excision repair is affected

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14
Q

DNA is transcribed into RNA

A

transcription

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15
Q

a sequence of DNA nucleotides that signal the starting point for RNA synthesis

A

promoter

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16
Q

comparing many sequences with the same basic function and tallying up the most common nucleotides found at each position. it serves as a summary or “average” of a large number of individual nucleotide sequences

A

consensus nucleotide sequences

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17
Q

genes carried in a cells DNA, specify the amino acid sequence of proteins, and the RNAs that are copied from these genes (which ultimately direct the synthesis of proteins)

A

mRNAs

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18
Q

do not code for a protein

A

non coding RNAs

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19
Q

will form to compensate for each 10 nucleotide pairs that are open (unwound). the formation of this is energetically favorable because it restores a normal helical twist to the base paired regions that remain

A

DNA supercoiling

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20
Q

state the central dogma

A

dna to mrna to protein

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21
Q

transcribes the genes 5.8S, 18S, 28S rRNA genes

A

RNA Polymerase I

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22
Q

transcribed all protein coding genes, plus snoRNA genes, miRNA genes, siRNA genes, incRNA genes and most snRNA genes

A

RNA Polymerase II

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23
Q

transcribes tRNA genes, 5S rRNA genes, some snRNA genes and genes for other small RNAs

A

RNA Polymerase III

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24
Q

function in a variety of nuclear processes, including the splicing of pre-mRNA

A

snRNA (small nuclear RNA)

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25
Q

help to process and chemically modify rRNAs

A

snoRNA (small nucleolar RNA)

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26
Q

regulate gene expression by blocking translation of specific mRNAs and causing their degredation

A

miRNA (micro RNAs)

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27
Q

a transcribed segment of DNA; information in just one gene for just one RNA molecule or single protein (or group of mRNAs if there is splicing)

A

transcription unit

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28
Q

a sequence of DNA Ts and As located ~30 nucleotides upstream from the transcription start site.

A

TATA box

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29
Q

form the basic structure of the ribosome and catalyze protein synthesis

A

rRNA

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30
Q

joins together different portions of an RNA transcript to eliminate the intron sequences; also provides eukaryotes with the ability to synthesize several related but different proteins from the same gene

A

RNA splicing

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31
Q

allows activator proteins to communicate properly with the RNA polymerase II and with the general transcription factors

A

mediator

32
Q

the large assembly of RNA and protein molecules that performs pre-mRNA splicing in the cell, snRPs form the core

A

spliceosomes

33
Q

the nucleotide sequence of a gene, through intermediary of mRNA, is instead translated into the amino acid sequence of a protein by rules

A

genetic code

34
Q

each group of three consecutive nucleotides in mRNA is called (this) and each (this) specifies either one amino acid or a stop to the translation process

A

codon

35
Q

allows an RNA sequence to be translated in anyone of 3 different frames

A

reading frame

36
Q

a set of three consecutive nucleotides that pairs with the complementary codon in an mRNA molecule

A

anticodon

37
Q

mismatch at the third position, can base pair with any nucleotide listed in the shown column; explains why so many of the alternative codons for an amino acid differ only in their third nucleotide

A

wobble

38
Q

a complex catalytic machine made from more than 50 proteins and several RNA molecules

A

ribsomes

39
Q

RNA molecules that posses catalytic activity

A

ribozymes

40
Q

small set of RNA molecules that allow the binding to both the codon and the amino acid

A

tRNAs

41
Q

sugar group is ribose, uracil replaces thymine (loses methyl group), sometimes there are unique base pairings G wit U

A

RNA

42
Q

how does tRNA become attached to the appropriate amino acid?

A

tRNA requires aminoacyl-tRNA synthetase for recognition and attachment of the correct amino acid to the 3’ end

43
Q

what direction are proteins synthesized in

A

N-terminal end to C-terminal end

44
Q

this ribosomal subunit is important for matching tRNA to codon on mRNA

A

small subunit

45
Q

this ribosomal subunit catalyzes the formation of peptide bonds between amino acids

A

large subunit

46
Q

Four major steps to chain elongation

A

tRNA binding
peptide bond formation
large subunit translocation
small subunit translocation

47
Q

what speeds up eukaryotic translation process?

A

elongation factors EF1 and EF2

48
Q

how is codon-anticodon match checked?

A

small rRNA subunit forms hydrogen bonds between codon and anticodon; if match is correct, GTP hydrolysis occurs which moves the translation process along

49
Q

what does the mRNA 5’ cap do?

A

marker to cell that this is an mRNA
essential for translation
binds a protein complex as a recognition factor: cap binding complex

50
Q

this is considered a molecular mimic, similar in 3D conformation to tRNA which helps it bind to the A site

A

release factor

51
Q

allows more than one protein to be synthesized from a single mRNA by changing reading frame by ignoring a start or stop codon

A

translational frameshifting

52
Q

21st amino acid can be inserted directly into a growing polypeptide using

A

translation recoding

53
Q

produced from serine tRNA that is enzymatically altered, binds to stop codon

A

selenocysteine

54
Q

misplaced STOP codon

A

nonsense mediated mRNA Decay

55
Q

a collection of rare disorders involving impaired ribosome biogenesis and function; mutations affect translation and protein synthesis

A

ribosomopathies

56
Q

caused by truncated protein bc STOP codon is misplaced (Nonsense mutations)

A

CF mutations
Duchennes MD
betathalassemia
hurlers syndrome

57
Q

Disorders of missense mutation

A

sickle cell
certain types of CF mutations
certain cancers

58
Q

Have specific functions in altering a misfolded protein hsp60 and hsp70 are examples

A

chaperones

59
Q

initiates early protein folding; looks for stretches of hydrophobic amino acids which trigger ATP hydrolysis

A

HSP70

60
Q

aids in helping incorrectly or incompletely unfolded proteins fold completely

A

HSP60

61
Q

contains proteases for digestion of proteins

A

proteasomes

62
Q

serve as a recognition marker for proteasomes when it is bound to misfolded proteins

A

ubiquitin

63
Q

histone regulation

A

monoubiquiliation

64
Q

endocytosis

A

multiubiquitylation

65
Q

proteasomal degradation and DNA repair

A

polyubiquitylation

66
Q

surface amino acid sequences recognized by a set of enzymes

A

degrons

67
Q

brain/spinal cord are sensitive to protein aggregates. protein aggregates can cause

A

alzheimers
huntingtions
ALS
parkinsons

68
Q

RNA polymerase is part of the repair process by stalling at DNA alterations (specifically NER) during transcription and calls fourth coupling proteins which direct excision repair machinery to these sites

A

transcription-coupled repair

69
Q

this syndrome is caused by a defect in transcription coupled repair

A

cockayne syndrome

70
Q

methods for repairing double stranded DNA breaks

A

non-homologous end joining and homologous recombination

71
Q

involves removing a set of nucleotides, then ligating the strands back together

A

non-homologous end joining

72
Q

occurs after replication (S and G2 phases) when nearby daughter DNA duplex and serve
as template for repair

A

homologous recombination

73
Q

group of enzymes that form phosphodiester bonds between ribonulceotides

A

RNA polymerases

74
Q

unwinds DNA at the transcription start point, phosphorylates Ser5 of the RNA polymerase CTD; releases RNA polymerase from the promoter

A

TFIIH

75
Q

RNA polymerase I transcribes……

A

rRNAs

Molecular Cell Bio (11 decks)

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