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Biochem 2 > Transcription > Flashcards

Flashcards in Transcription Deck (28):
1

coding strand vs non coding strand

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

2

what are the stop and start codons?

start- AUG; stop: UAA, UAG, GUA

3

operon

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

4

polycistronic

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

5

intron

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

6

exon

coding sequence transcribed in mRNA

7

what are 3 types of cis-acting sequences?

core promoter elements, promoter proximal elements, and enchancers`

8

describe core promoter elements

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)

9

give an example of a core promoter element

TATA box. Prinbow box. -35 sequence

10

describe promoter proximal sequences

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

11

enhancers

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

12

how genetic material is coding in eukaryotes?

1.2%

13

what is a gene family

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

14

Describe transcription initiation in prokaryotes

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

15

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

4 types. RNA 2 is important.

16

what elements are preserved across DNA in eukaryotes?

TATA box/ initiator/ downstream promoter elements

17

describe transcription initiation in eukaryotes

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

18

What are the 3 stabilizing factors of mRNA processing?

5' cap/intron splicing/poly A tail

19

describe the 5' cap

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

20

describe intron splicing

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

21

describe the poly-A tail

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

22

what 3 genes are coded for by the lac operon

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

23

Describe the functionality of the lac operon

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

24

describe how enhancers work

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

25

describe different co-activators/repressor systems

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

26

Describe nuclear hormone receptors

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

27

describe how tamoxifen is an effective treatment for breast cancer

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

28

transcription unit

part of the gene that is transcribed into RNA