Protein Transcription

Question 1

do all cells have the same genomic DNA, and if so, why?

Answer 1

in a single organism, all cells carry the same genomic DNA; it serves as a blueprint for cellular activity

Question 2

how are there so many different cell types if all cells have the same genomic DNA?

Answer 2

even though all cells have the same blueprint of DNA, it is regulated in how it is expressed/when it is in order to differentiate it

Question 3

define regulation of gene expression

Answer 3

an efficient way to utilize genes; genes turned on/off as they are needed

Question 4

in which direction are mrna molecules created?

Answer 4

in the 5’ to 3’, just like in DNA synthesis

Question 5

define rna polymerase

Answer 5

enzyme that synthesizes rna from a dna template

Question 6

define the sigma subunit (factor)

Answer 6

positions the rna polymerase at the site of initiation and controls the steps of transcription

Question 7

why are the -10 and -35 elements important?

Answer 7

these elements act as recognition sites upstream of the start site for the rna polymerase to bind to and initiate transcription
-10 = TATAAT
-35 = TTGACA
transcription start site = +1

Question 8

define promoter

Answer 8

region of dna where transcription is initiated via the binding of rna polymerase (-10 and -35 is an example)

Question 9

what is the closed-promoter complex?

Answer 9

initial binding of rna polymerase to a region where DNA is not unwound

Question 10

what is the open-promoter complex?

Answer 10

it’s formed when the closed complex isomerizes, which opens DNA into transcription bubble; essential for rna polymerase to access DNA template

Question 11

describe the process of initiation

Answer 11

atleast 5 GTFs needed to begin
1.) a GTF will bind to promoter
2.) recruits another GTF
3.) rna polymerase II will bind WITH an additional GTF
4.) two more GTFs will come in, forming preinitiation complex
this allows initiation IN VITRO; if IN VIVO, there is a need for more factors

Question 12

describe the process of elongation

Answer 12

rna polymerase will unwind the dna strand in the 3’ direction while also winding it in the 5’

Question 13

describe the process of termination

Answer 13

phosphorylation on the C-terminal domain will create a binding site for a rna endonuclease
endonuclease will recognize and cleave non-coding sequence after mrna, freeing it
exonuclease will degrade remaining rna sequence and cause rna polymerase II to dislodge

Question 14

what is a termination signal?

Answer 14

a sequence that signals the end of transcription or translation

Question 15

what is messenger rna?

Answer 15

type of rna associated with protein-coding genes

Question 16

what is ribosomal rna?

Answer 16

non-coding rna that forms part of the ribosome

Question 17

what is transfer rna?

Answer 17

an adaptor rna that assists in decoding mrna; has anticodon that matches to mrna codon

Question 18

what is rna polymerase II?

Answer 18

complex that transcribes dna into precursors of mrna

Question 19

describe general transcription factors

Answer 19

dna binding proteins that control the rate of transcription; needed for transcription of all genes

Question 20

what is the purpose of a promoter element?

Answer 20

it allows for the binding of transcription factors in order to begin initiation

Question 21

when is a mediator used and why?

Answer 21

complex required by rna polymerase II; used as a coactivator with GTFs and rna polymerase II

Question 22

describe the c-terminal domain

Answer 22

end of the polypeptide chain with a free carboxyl group; phosphorylation releases active rna polymerase II

Question 23

describe the difference between an endonuclease and an exonuclease

Answer 23

endo = within; cleaves phosphodiester bonds within nucleotide chain
exo = outside; cleaves phosphodiester bonds at the 3’ or 5’ ends

Question 24

how many polymerases do prokaryotes have vs how many do eukaryotes have?

Answer 24

prokaryotes = rna polymerase I - V
eukaryotes = rna polymerase I-III

Question 25

what is the TATA box?

Answer 25

an upstream dna sequence from the transcription start site that allows for factors to bind and initiate the reading

Question 26

describe bacterial transcription

Answer 26

requires rna polymerase + dna with a promoter
utilizes open/closed complexes
does not require sigma factor, but it’s helpful

Question 27

describe eukaryotic transcription

Answer 27

requires rna polymerase + additional proteins
requires transcription factors
has endo/exonucleases

Question 28

what modifications occur to pre-mrna and why?

Answer 28

1.) addition of a 5’cap to protect the mrna from degradation
2.) polyadenylation (poly-a tail) to the 3’ end to allow for termination
3.) intron/exon splicing to create a continuous code

Question 29

why are spliceosomes necessary?

Answer 29

introns must be cut out of the coding sequence in order to allow for the synthesis of a functional protein