information flow/transcription

Question 1

central dogma

Answer 1

dna -> transcription -> translation -> protein (or other things, some RNA not translated into protein)

Question 2

rRNA

Answer 2

ribosomal RNA, integrated with ribosomal proteins

Question 3

tRNA

Answer 3

transfer RNA, folded into a fancy structure, helps link codons to correct amino acid with amino-acyl synthase

Question 4

mRNA

Answer 4

translated into protein (polypeptide chain) in protein synthesis

Question 5

which RNAs are stable and why?

Answer 5

rRNA and tRNA are more stable, r is integrated w/ ribosomal proteins which protects and t is folded into a 2d structure which protects the RNA from degredation

Question 5

genes in molecular biology

Answer 5

transcription unit

sequence of nucleotides in DNA that codes for a single RNA molecule as well as sequences needed for it’s transcription (generally promoter, RNA-coding sequence, terminator)

Question 6

template strand

Answer 6

read 3’ to 5’, 3’ promoter 5’ terminator.

rna polymerase reads this and matches the opposite bases, so mRNA sequence will be the 5’ opposite of template 3’

Question 7

coding strand

Answer 7

shows the sequence of the mRNA just with T rather than U, 5’ ->3’ in the direction of transcription

Question 8

coding strand

Answer 8

shows the sequence of the mRNA just with T rather than U, 5’ ->3’ in the direction of transcription

Question 9

convergent genes

Answer 9

RNA polymerase for two genes on a strand of DNA move towards each other in expressed at the same time

Question 10

divergent genes

Answer 10

on same DNA strand, if expressed at the same time RNA pol would move away from each other

Question 11

transcription in bacteria/prokaryotes vs eukaryotes

Answer 11

bac - transcription and translation both occur in the cytoplasm (same time an place), RNA is not processed

euk - transcription happens in the nucleus. RNA is processed then exported to the cytoplasm

Question 12

general process of transcription

Answer 12

1. initiation - rna polymerase binds to the promoter
2. extension - transcription starts at the +1 site and continues along dna strand synth mRNA 5’ to 3’
3. termination - transcription stops after the rna pol has passed the termination sequence

Question 13

direction of synthesis of RNA

Answer 13

reads template strand 3’ to 5’, synthesizes RNA 5’ to 3’

Question 14

promoter in bacteria vs eukaryotes

Answer 14

eukaryotes, TATA box which is roughly 25 base pairs upstream from +1 site

bacteria, -10 and -35 boxes upstream from +1 site

Question 15

what binds before rna polymerase?

Answer 15

sigma factor binds to -10 and -35 box

Question 16

what binds before rna polymerase?

Answer 16

sigma factor binds to -10 and -35 box

Question 17

what sort of enzyme is made by the binding of rna pol and something?

Answer 17

RNA pol and sigma factor protein make the holoenzyme

Question 18

orientation of holoenzyme on dna strand

Answer 18

is downstream direction is too the right, sigma/rna pol would be on the bottom side, moves from -10 box to +1 site

Question 19

binding of RNA pol to promoter in eukaryotes

Answer 19

TBP (tata binding protein) and general transcription factors bind to the promotor and recruit RNA POL

Question 20

whats the name of the whole protein complex including RNA pol in eukaryotes

Answer 20

basal transcription complex

Question 21

what is the name of the transcription start site called bacteria vs eukaryotes

Answer 21

bacteria generally +1 site, eukaryotes generally called the transcription start site, mostly just +1 for both

Question 22

termination of transcription bacteria vs eukaryotes

Answer 22

in bacteria, a hairpin loop forms terminating transcription

eukaryotes, could involve binding of multiple termination factors to the dna to disturb rna polymerase

Question 23

NTPs

dNTPs

rNTPs

Answer 23

nucleotide triphosphates (A, C, G, T, U)

DNA monomers - dATP, dGTP, dCTP, dTTP

RNA monomers - rATP, rGTP, rCTP, rUTP

Question 24

signs of change in G and S ATP hydrolysis/ spontenaety

Answer 24

atp hydrolysis is spontaneous and energetically favorable

NEGATIVE change in G

POSITIVE change in S (enetropy

Question 25

how do DNA binding proteins bind??

Answer 25

bind in the major and minor grooves of DNA

recognize specific sequences of bases, bind by H-bonds and other NC interactions (amino acid side chains interact with the bases)

Question 26

in what ways can transcription of a gene be regulated?

Answer 26

1. how often RNA POL bind to the promotor
2. how tightly rna pol and sigma and other transcription factors bind to the promoter

Question 27

dna packaging as a control in transcription

Answer 27

bacteria dnas alwasy s unpackaged so accessile to rna pol therefore default state is always on

eukaryotic, dna is tightly package/ condensed so must be unpackaged for rna to start transcription

Question 28

3 ways mrna is modified before leaving the nucleus

Answer 28

1. addition of a 5’ cap
2. polyadenylation (forming a poly (A) tail) on the 3’ end
3. splicing of introns/exons

Question 29

benefits of adding a 5’ cap and 3’ tail

Answer 29

increases the stability of the mature rna and protects from degredation

helps regulate it’s translation

helps mature RNA leave the nucleus

Question 30

spliceosomes

Answer 30

protein complexes in the nucleus, recognize splice junctions, cut, and link exons

Question 31

is eukaryotic mRNA always spliced the same?

Answer 31

depends on the cell

Question 32

ribosomal binding site in relation to start codon and +1 site (bacterial)

ribosomal binding site on eukaryotic RNA

Answer 32

just downstream of the +1 site, but before the start codon

in eukaryotes, the ribosomal binding site is located on the 5’ cap, so added after

Question 33

redundancy

Answer 33

more than one codon for a single amino acid