Transcription I

Question 1

regulatory component of gene

Answer 1

controls rate/efficiency of transcription

Question 2

strucutral component of gene

Answer 2

contains necesary information to make product

Question 3

operon

Answer 3

multiple genes and corresponding regulatory sequences that work toward a specific biological function under the control of a single promoter

Question 4

viral transcription

Answer 4

both strands of dsDNA can serve as templates for transcription; top template strand has is initially transcribed as a single large transcript and then processed to give different products

Question 5

polycistronic mRNA

Answer 5

one RNA transcript codes for multiple gene products, not in eurkaryotes

Question 6

monocistronic mRNA

Answer 6

one promoter and one gene product, seen in eukaryotes

Question 7

eukaryotic RNA polymerase II

Answer 7

makes mRNA, requires Mg2+

Question 8

eukaryotic RNA polymerase I

Answer 8

makes precursor products for the 5.8S, 18S and 28S rRNAs, requires Mg2+

Question 9

eukaryotic RNA polymerase III

Answer 9

makes tRNA and precursor products for the 5S rRNA, requires Mg2+

Question 10

conventions for transcriptions

Answer 10

reads template/noncoding/negative strand in the 3’ to 5’ direction to create an RNA transcript in the 5’ to 3’ direction; RNA transcript will read the same as the non-template/coding/positive strand (except T’s replaced with U’s)

Question 11

prokaryotic RNA polymerase (holoenzyme)

Answer 11

2 alpha, 1 beta and 1 beta prime subunits synthesize RNA, an omega subunit, and sigma subunit binds to DNA

beta sites are believed to be the catalytically active regions, the omega unit is not required in vitro

Question 12

sigma RNA polymerase subunit

Answer 12

varible region that binds to DNA first, aligns polymerase into the correct orientation, sigma units dissociates once transcription starts, sigma 70 is the most common sigma unit

Question 13

Step 1: prokaryotic transcription–binding

Answer 13

1. ) sigma 70 subunit of RNA polymerase recognizes the -35 to -10 region and forms the closed complex
2. ) unwinds DNA in this area forming open complex, DNA fed through RNA polymerase at a 90 degree angle, which forces dsDNA to open
3. ) sigma subunit release once transcription proceeds beyond the promoter region

Question 14

Step 2: prokaryotic transcription–initiation

Answer 14

1. ) purine usually added first
2. ) subsequent nucleotides added and PPi released

**PPi NOT cleaved from initial purine**

Question 15

Step 3: prokaryotic transcription–elongation

Answer 15

1. ) occurs in the transcription bubble, RNA polymerase covers 35bps and has melted 18bp, and there is an 8bp DNA/RNA hybrid region
2. ) region ahead of polymerase has positive supercoils and the region behind has negative supercoils, which can be relieved by topoisomerases

Question 16

rho independent trancript termination

Answer 16

string of adenines after hairpin structure, only two hydrogen bonds between A and U so mRNA weakly hybridized to DNA; polymerase falls off

Question 17

rho dependent transcript termination

Answer 17

hairpin structure causes polymerase to pause, rho protein then causes dissociation

Question 18

sigma 70 subunit

Answer 18

has a specific consensus sequence in the -35 to -10 region, changes in this promoter sequence decrease polymerase affinity and thus rate of transcription

Question 19

using different sigma factors

Answer 19

example is under heat stress, polymerase dissociates from sigma 70 and instead binds to sigma 32–binds to a different -10 to -35 consensus sequence

Question 20

operator site (repressor bidning site)

Answer 20

downstream of promoter, repressor proteins bind here and either block polymerase movement or block the promoter

Question 21

activator site

Answer 21

just upstream of the promoter, enhancer proteins can recruit polymerases and increase transcription

Question 22

negative transcription regulation

Answer 22

bound repressor inhibits transcription; 1.) small signal moleclar binds to the repressor, causes conformation change in affinity of repressor for DNA, falls off and transcription starts OR 2.) signal molecular always bound to repressor, when concentation of signal molecule drops, repressor falls off, transcription starts

Question 23

postive transcriptional regulation

Answer 23

bound activator facilitates transcription, same two scenarios as negative transcriptional regulation

Question 24

lactose metabolsim

Answer 24

1. ) lactose enters cells through galactosidase permease
2. ) lactose broken down by beta galactosidase into galactose and glucose

OR

3.) isomerized into allolactose

Question 25

lac repressor gene

Answer 25

located just upstream of lac operon has own promoter (P1) and contains O3 coding sequence, when no repressor, it is producted and binds to O1 and sequently O2 or O3–causes homodimerization, DNA looping and cessation of transcription

Question 26

allolactose

Answer 26

binds to lac repressor, causes conformation change, and repressor disscociates from operator, NOT sufficient enough to cause transcription of the lac genes

Question 27

cyclic AMP receptor protein (CRP)

Answer 27

bacteria only use alternative fuel source if glucose not available, when glucose low, cAMP high, cAMP binds to CRP, CRP goes to CRP activator site–acts as enhancer, increases the binding affinity for sigma 70 and RNA polymerase to allow transcription to start

Question 28

ara operon

Answer 28

encodes genes B, A and D necessary to metabolize arabinose and under the control of the BAD promoter

two operons (araO1 and araO2) and an inhibitor site (araI)

inhibitor that binds to araI is araC; encoded upstream of the operon and has its own promoter (promoter C)

Question 29

how does the ara operon function?

Answer 29

no repressor–promoter C recruits RNA polymerase and makes araC—>araC binds to araI—>other molecules of araC bind to araO and the molecules dimerize, preventing transcription

when arabinose is present, it binds to araC and converts it into an ACTIVATOR, araC dimerizes with arabinose rather than ara I

requires CRP to initiate transcription

Question 30

trp operon

Answer 30

contains all enzymes necessary to synthesize tryptophan, regulated by trp attenuation and trp repression

Question 31

trp operon mechanism of action

Answer 31

SUFFICIENT TRYPTOPHAN: ribosome translate sequence one, which contains (two Trp codons) and then sits on sequence two and blocks it before sequence 3 is transcribed

sequences 3 and 4 transcribed and they form hairpin structure, terminating transcription

INSUFFICIENT TRYPTOPHAN: ribosome pauses at sequence 1, sequences 2 and 3 form hairpin structure but this does NOT cease transcription

Question 32

-10 promoter region sequence

Answer 32

TATAAT

Question 33

-35 promoter region sequence

Answer 33

TTGACA