Transcription

Question 1

coding strand vs non coding strand

Answer 1

coding is identical to RNA. non coding is the template.

Question 2

what are the stop and start codons?

Answer 2

start- AUG; stop: UAA, UAG, GUA

Question 3

operon

Answer 3

a group of genes that code for proteins with related functions and are regulated by the same promoter

Question 4

polycistronic

Answer 4

found in prokaryotes only, when 1 transcription unit codes for multiple proteins

Question 5

intron

Answer 5

non-coding piece of the transcription unit that will eventually be spliced out of mRNA

Question 6

exon

Answer 6

coding sequence transcribed in mRNA

Question 7

what are 3 types of cis-acting sequences?

Answer 7

core promoter elements, promoter proximal elements, and enchancers`

Question 8

describe core promoter elements

Answer 8

very close to the start of transcription which start and direct RNA polymerase assembly/transciption factors necessary for initiation (TATA box in eukaryotes/prinbow box in prokaryotes)

Question 9

give an example of a core promoter element

Answer 9

TATA box. Prinbow box. -35 sequence

Question 10

describe promoter proximal sequences

Answer 10

further upstream of core elements, ~200 bp, positive regulators for assembling transcription complex

Question 11

enhancers

Answer 11

can be introns or extremely far upsteam- serve as binding sites for transcription factors that can either activate or repress transcription

Question 12

how genetic material is coding in eukaryotes?

Answer 12

1.2%

Question 13

what is a gene family

Answer 13

genes with closely related functions. not necessarily on the same chromosome.

Question 14

Describe transcription initiation in prokaryotes

Answer 14

bacterial RNA polymerase consists of a core enzyme with 4 units (2 alpha and 2 similar but not identical beta units). The sigma unit binds creating the holoenzyme. the sigma unit recognizes the -35 and -10 promoter elements, forming H-bonds. The core enzyme then binds the promoter, the sigma element disassociates, and transcription begins

Question 15

how many types of RNA polymerase exist in eukaryotes? which one is important?

Answer 15

4 types. RNA 2 is important.

Question 16

what elements are preserved across DNA in eukaryotes?

Answer 16

TATA box/ initiator/ downstream promoter elements

Question 17

describe transcription initiation in eukaryotes

Answer 17

5 complexes and RNA Pol2 form together to make the preinitiation complex at the promoter. The TATA binding protein (TFB) from TFIID recognizes and binds the TATA box. Helicases from TFIIH unwind the DNA. RNA Pol2 disassociates and begins transcribing. The remainder of the initiation complex remains so multiple copies can be made

Question 18

What are the 3 stabilizing factors of mRNA processing?

Answer 18

5’ cap/intron splicing/poly A tail

Question 19

describe the 5’ cap

Answer 19

a 5’-5’ bond is made between the first base and 7-methylguanasine. this occurs while transcription is occuring and stabilizes the growing mRNA

Question 20

describe intron splicing

Answer 20

requires a splice donor (GU) and splice acceptor (AG) site which mark where cuts will be made. The branchpoint is also important. it is a key A nucleotide that forms the H-bond for the eventual Lariat shape of the intron

Question 21

describe the poly-A tail

Answer 21

the pre-mRNA is cleaved at a specific squence (AAUAAA) and a poly A tail is added (30-50) by poly(A) polymerase

Question 22

what 3 genes are coded for by the lac operon

Answer 22

beta-galactosidase- cleaves lactose into glucose and galactase (Z)
permease- increases amount of lactose into cell (Y)
transactylase- unknown mechanism (A)

Question 23

Describe the functionality of the lac operon

Answer 23

codes for X,Y,A. within the promoter there is a operator. usually, this operator is bound by an inhibitor (I) which prevents RNA Pol2 from transcribing. The inhibitor is a trans acting factor coded for upstream. Lactose can bind the inhibitor, changing it so it cannot bind the promoter, allowing transcription. Additionally, glucose regulates the system. A lack of glucose produces an increase in cAMP. cAMP forms a complex with CAP which binds at the promoter and encourages RNA Pol to bind, increasing transcription efficacy

Question 24

describe how enhancers work

Answer 24

they are sequences that help regulate transcription. they serve as binding sites for transcription factors. Transcription factors usually have a binding subunit and a loosely connected binding site for repressors or coactivators

Question 25

describe different co-activators/repressor systems

Answer 25

mediators- bind to general transcription factors and regulate initiation complex assembly
histone modifying factors- acetylation/methylation on N-Terminus promotes histone unwinding- easier to transcribe
ATP dependent chromatin remodeling- SWI/SNF or RSC- unwinds histones

Question 26

Describe nuclear hormone receptors

Answer 26

some transcription factors bind repressors at certain times and coactivators at others. they also bind steroid hormones. when a steroid is unbound, the TFs bind repressors. When the steroid is bound, it changes the active site and causes it to bind activators. the best example is tamoxifen

Question 27

describe how tamoxifen is an effective treatment for breast cancer

Answer 27

it binds in place of estrogen in estrogen present breast cancer. normally, estrogen would cause a transcription factor to recruit coactivators for tumor growth. tamoxifen binding prevents this

Question 28

transcription unit

Answer 28

part of the gene that is transcribed into RNA