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PR - Big book > 11.1-11.7 DNA replication, translation > Flashcards

11.1-11.7 DNA replication, translation Flashcards

1
Q

intergenic space

A

noncoding DNA

human has 3.2 billion BPs, 21,000 genes, and long stretches of intergenic regions (noncoding DNA) which may direct chromatin structure / regulate genes / no known function

include TANDEM REPEATS and TRANSPOSONS

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2
Q

gene

A

codes for gene product

includes REGULATORY sites (promoters, transcription stop sites), and “ACTIVE” site (codes for protein or non-coding RNA)

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3
Q

single nucleotide polymorphism

A

ALLELE - 1 nucleotide change once every 1000 bp’s, “snips” are essentially mutations

  • > sickle-cell anemia, beta-thalassemia, cystic fibrosis
  • > see picture
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4
Q

copy number variation

A

structural variations in genome (large regions of genome 10^3-10^6 can be duplicated)

DUPLICATION OF DNA, or DELETED

5-10% of human genome

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5
Q

Tandem repeats

A

short sequence of nucleotides repeat right after each other, 3-100 times

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6
Q

Transposons

A

genes code for tranposase (“cut and paste” activity)

“jumping” around the genome; very mischievous

CAUSES or REVERSES mutations

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7
Q

Hershey and Chase

A

proved DNA is the genetic material

Watch video

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8
Q

ribosome

A

very large, rRNA and protein

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9
Q

UGA

A

university of georgia at atlanta (stop codon)

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10
Q

topoisomerase

A

cuts strand and unwraps helix, releasing excess TENSION

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11
Q

single-strand binding protein

A

proteins DNA that has been de-doubled-stranded (much less stable), leads to the OPEN COMPLEX (ready to begin replication)

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12
Q

Initiation-open complex

A

an RNA primer MUST be synthesized for each template strand – primosome (contains RNA polymerase primase)

DNA pol CANNOT START a DNA chain from scratch. The RNA primer is 8-12 nucleotides long, later replaced by DNA

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13
Q

DNA Pol

A

part of a larger complex of proteins called the REPLISOME

prokaryote - 13 components
eukaryote - 27 proteins

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14
Q

thermo of DNA replication

A

removal and hydrolysis of pryophosphate (two phosphates) from each dTNP (dTNP is the nucleotide with 3 phosphates)

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15
Q

Okazaki fragments are joined by

A

DNA ligase

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16
Q

prokaryotic DNA polymerases (III and I)

A

I, II, III, and IV

III - elongation of leading strand; has 5-3 polymerase and 3-5 exonuclease activity; FAST

I - adds nucleotides at the RNA primer, 5-3 polymerase activity, only adds 15-20 nucleotides a second, taken over by pol III 400 bps downstream; capable of 3-5 exonuclease activity; removes the primer via 5-3 exonuclease activity; important for excision repair

II - backup for III

IV and V - error-prone in 5-3 polymerase activity , function to stall other polymerase enzymes at replication forks

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17
Q

telomerase

A

RIBONUCLEOPROTEIN: adds repetitive nucleotides to ends of chromosomes

expressed only in germ line, stem cells, and some white blood cells

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18
Q

transition/transversion

A

substitute pyrimidines for a pyrimidine, purine for a purine

transversion is more severe

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19
Q

translocation

A

common in cancers

two regions swap locations

occurs in genetic recombination

produces a new gene product

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20
Q

loss of heterozygosity

A

one allele of a certain gene is lost, due to deletion or recombination

hemizygous - only 1 gene copy.

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21
Q

direct reversal of dna repair

A

bacteria and plants can repair UV-induced pyrimidine photodimers DIRECTLY

nucleotide excision repair is the next step

main mechanism of repair in humans, but can introduce a mutation

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22
Q

homology-dependency repair

A

DNA is redundant (two copies)

excision repair (before DNA replication) and post-replication repair (after DNA replication)

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23
Q

excision repair

A

BEFORE dna replication; removes defective base and replaces them

24
Q

post-replication repair

A

MMR - mismatch repair pathway - targets mistakes not repaired by DNA polymerase proofreading

DURING dna replication; methylation helps determine which is wrong (A or G)

during replication, the free 3’ end and Okazaki fragments are found

25
Q

homologous recombination to repair DS breaks (see illustration p. 222)

A

nuclease and helicase generate single-stranded DNA

they find complementary sister chromatid

dna pol and ligase build new DNA

26
Q

non-homologous recombination repair of DS break

A

not perfect

27
Q

Open-reading frame (ORF)

A

after the 5-3 UTR (untranslated region - initiation and regulation), ORF is start to stop codon (coding region)

28
Q

monocistronic v. polycistronic

A

“one mRNA, one protein” - eukaryotes

polycistronic - one mRNA, multiple proteins - prokaryotes; translation can start in multiple places! termination and initiation sequences between each ORF

NOTE; PROKARYOTES DON’T PROCESS mRNA, only eukaryotes have hnRNA (which are modified: addition of cap and tail, splicing)

29
Q

rRNA (4 types)

A

18S, 5.8S, 28S, and 5S

serve in ribosome - along with polypeptide chains (proteins), 1 rRNA provides catalytic function of the ribosome (a RIBOZYME)

30
Q

Driving force of replication/transcription

A

removal and hydrolysis of pyrophosphate from each nucleotide added

31
Q

promotor (transcription) versus start site

A

the area of DNA that ACTIVATES transcription (origin is where DNA is replicated)

START site is called the “START SITE”

32
Q

antisense and sense strands

A

the DNA template is the antisense (because it’s the ANTI of the mRNA)

coding strand (“sense”); +1 is the first nucleotide transcribed

mRNA grows on the 3’ end -> proceeds downstream

33
Q

RNA polymerase

A

pribnow box (-10) and -35 sequence forms a CLOSED COMPLEX

RNA pol must unwind DNA

RNA pol HOLOenzyme bound at promotor with a region of single-stranded DNA is termed the OPEN COMPLEX (difference is that the DNA is unwound)

34
Q

bacteria transcription

A

All RNA is made of the same RNA pol

a large enzyme - 5 subunits

Core enzyme - rapid elongation
Subunit sigma factor (forms the HOLO-enzyme) - responsible for initiation

Initiation -> elongation -> termination

35
Q

sigma factor

A

helps prokaryotes find promoters

36
Q

processive elogation

A

core enzyme moves along the DNA downstream, a bubble forms when the DNA is unwound

rho helps determine when to end, polymerase falls off and bubble is closed

37
Q

eukaryotes location of transcription

A

nucleus

modify in the nucleus, transport to cytoplasm where it is translated

38
Q

prokaryotes translate…

A

…while transcribing, no post-processing involved

39
Q

eukaryotic splicing

A

extensive modification after transcription - splicing

these non-coding regions (introns) may code for proteins, contain ENHANCERS or REGULATORY sequences

40
Q

spliceosome (and snRNA)

A

mediates eukaryotic mRNA splicing

100 proteins and 5 small nuclear RNA molecules

the snRNA “detects” the intron (see image p. 227)

ALTERNATIVE splicing - multiple ways of splicing hnRNA

cap and tails must be added (5’ cap, and 3’ poly-A tail)

41
Q

RNA polymerases

A

I - rRNa
II - hnRNA, most snRNA
III - tRNA

42
Q

tRNA, the protein bonds to

A

the 3’ end

43
Q

wobble hypothesis

A

of anticodon: 3rd position is more flexible than 1 and 2

5’ base anticodon (tRNA) - 3’ base in codon (mRNA)

G -> C or U
U -> A or G
I -> A, U, C

44
Q

Amino Acid Activation p. 231

A

Need help understanding this…

  1. amino acid attaches to AMP to form aminoacyl AMP
  2. pyrophosphate leaving group is hydrolyzed to 2 orthophosphates (delta_G &laquo_space;0)
  3. tRNA loading (deltaG&raquo_space; 0) - driven by the destruction of the aminoacyl-AMP bond (basically AMP is released fro aminoacyl amp, leading to the aminoacyl-tRNA)

Final product: Aminoacyl-tRNA

Requires: 2 atp equivalents

45
Q

aminoacyl-tRNA synthetase anzyme

A

family of enzymes that recognizes the tRNA and amino acid , puts them together – HIGHLY SPECIFIC

46
Q

prokaryotic ribosome

A

30S and 50S => 70S

30S -> 16S rRNA and 21 peptides
50S -> 23S and 5S and 31 peptides

47
Q

eukaryotic ribosome

A

80S ribosome

large -> 60S -> 5S, 5.8S, 28S and 46 peptides

small -> 40S -> 18S, 33 peptides

48
Q

the 5’ end ORF

A

upstream regulatory sequence is essential for initiation, we have a ribosome binding site (Shine-Dalgarno sequence) located at -10. SD sequence is complementary to a pyrimidine rich region on the small subunit

49
Q

translation has three distinct stages

A

initiation, elongation, termination

50
Q

initiation

A

30S binds two initiation proteins called IF1 and IF3, which binds to the mRNA transcript, then aminoacyl-tRNA joins, then IF2, which is bound to 1 GTP.

50S completes the complex

Powered by hydrolysis of 1 GTP molecule

first aminoacyl-tRNA is called the initiator tRNA (fMet-tRNA) - sits in P site of 70S ribosome, hydrogen-bonded with the start codon

51
Q

elongation

A

three-steps

  1. second aminoacyl-tRNA enters the A site, h-bonds with the second codon (1 GTP)
  2. peptidyl transferase activity of large ribosomal subunit (23S) catalyzes formation of a peptide bond between fMet and the second amino acid (driven by hydrolysis of tRNA and amino acid p. 231)
  3. translocation - tRNA #1 moves to E site, tRNA #2 (holding the growing peptide) moves to the P site, and next codon moves into the A site. (1 GTP)
52
Q

termination

A

when stop codon appears in the A site

a release factor enters the A site, causes peptidyl transferase to hydrolyze the bond between the last tRNA and completed polypeptide

53
Q

5’ UTR

A

untranslated region - common in eukaryotes (e.g. Kozak sequence), located several nucleotides before start codon

54
Q

eukaryotic transcription begins…

A

…with formation of initiation complex

43S small ribosomal subunit forms + Met-tRNA_Met + several proteins called eukaryotic initiation factors (eIFs);

this is recruited to 5’ capped end of transcript, by initiation complex of proteins; additional proteins recruited (polyA tail binding protein)

Initiation complex starts scanning the 5’ end, looking for a start codon

Once found, the large ribosomal subunit (60S) is recruited and translation begins

55
Q

eukaryotes have *** elongation factors

A

2

56
Q

cap-dependent translation

A

the mRNA cap, 5’ end, is so important for translation

but cap-independent translation was discovered

site has IRES (ribosome entry site) -> helps apoptosis or deal with stress

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