Mod 4 - From DNA to RNA

Question 1

what is a gene?

Answer 1

a genetic unit containing information to make a functional product

Question 2

what are the 4 levels of information that a gene contains?

Answer 2

• structural
• temporal
• positional
• inducible

Question 3

what is the function of the promoter region?

Answer 3

defines transcriptional start site and it’s direction

Question 4

what is the leader / spacer region in prokaryotic genes?

Answer 4

section of DNA which is nontranslated

Question 5

what is a cistron in prokaryotic genes?

Answer 5

a segment of DNA that corresponds to one polypeptide (protein)

Question 6

what is the function of enhancer region in eukaryotic class II (mRNA-encoding) genes?

Answer 6

contain transcription factor binding sites

Question 7

what are introns?

Answer 7

nucleotide sequences that are present in the primary transcript but are removed in the mature transcript

Question 8

what are exons?

Answer 8

nucleotide sequences that are present in both primary and mature transcript

Question 9

what is the coding (sense) strand?

Answer 9

• 5’ -> 3’
• has same sequence as RNA product

Question 10

what is the template (antisense) strand?

Answer 10

• 3’ -> 5’
• sequence is complementary to RNA product

Question 11

what are the different subunits in prokaryotic RNA polymerase used for?

Answer 11

sigma - promotor recognition
alpha - assembly + activation
beta - catalysis + termination
omega - assembly, folding

Question 12

what subunits does prokaryotic RNA polymerase consist of?

Answer 12

• 1 sigma
• 2 alpha
• 2 beta (B + B’)
• 1 omega

Question 13

what subunits does the core enzyme in prokaryotic RNA polymerase consist of?

Answer 13

• 2 alpha
• 2 beta (B + B’)

Question 14

how many RNA polymerases do prokaryotic cells have?

Answer 14

one

Question 15

how many RNA polymerases do eukaryotic cells have?

Answer 15

three
Pol I
- ribosomal RNA (rRNA)
Pol II
- protein coding genes (mRNA)
- small nuclear RNA (snRNA)
Pol III
- transfer RNA (tRNA)
- rRNA
-snRNA

Question 16

What is TFIID?

Answer 16

a complex formed from the TATA binding protien (TBP) and the TBP-associated factors (TAF’s)

Question 17

what are the functions of subunits TFIIE, F, H, J, K in RNA polymerase II ?

Answer 17

• interaction with D-A-B complex and recruitment of Pol II
• blocks non-specific binding of polymerase II to DNA
• promotor clearance

Question 18

how is transcription initiated with RNA Polymerase I ?

Answer 18

• upstream binding factor (UBF) binds to UCE and core elements in DNA
• this acts as a binding site for SL1 (TBP + pol I - specific TAF’s)
• this complex then allows RNA polymerase I to bind, initiating transcription

end complex contains UCE, core, and SL1

Question 19

what is the mode of action of RNA polymerase III ?

Answer 19

• Firstly, TFIIC is recruited to the B box (promotor)
• then, TFIIB is recruited upstream of TFIIC
• TFIIB consists of TBP + 2 pol III - specific TAF’s
• once TFIIB is recruited, TFIIC is dispensable
• RNA polymerase recruited by TFIIB - transcription can begin

Question 20

what is the difference in the mode of action of RNA Pol III between 5S rRNA genes and tRNA genes?

Answer 20

• 5S rRNA requires an additional TFIIIA to be recruited before TFIIC can be recruited, which is a precursor to the rest of the process.

Question 21

what is an operon?

Answer 21

a cluster of genes transcribed by the same promotor that gives rise to a polycistronic mRNA

Question 22

describe the function of the Lac Operon

Answer 22

• no lactose = repression of lac operon, due to repressor protein binding to operator region. prevents RNA polymerase from binding to promotor.
• allolactose binds to repressor - dissociates repressor from operator
• RNA polymerase can now move down the molecule and transcribe

kind of like a lock

Question 23

how is the lac operon under negative feedback control?

Answer 23

LacZ transcribes galactosidase, an enzyme that hydrolyses lactose to galactose + glucose
- gets rid of lactose

Question 24

what is the difference between a cis-acting and a trans-acting factor?

Answer 24

cis - will only regulate DNA to which it is directly joined (dominant)
trans - will regulate genes anywhere - mostly protein transcription factors - recessive (mostly)

Question 25

what is catabolite repression?

Answer 25

the process by which several operons are repressed by glucose and only become active when all the glucose is used up
- preferential use of glucose

Question 26

how does catabolite repression work in the lac operon?

Answer 26

• RNA polymerase requires CRP (catabolite repressor protein)
• this is because cAMP binds to CRP, which allows DNA binding
• high glucose = low cAMP, so lac operon is always off, even if lactose is available
• low glucose = high cAMP, so lac operon is on if lactose is available

Question 27

what is the Trp operon responsible for?

Answer 27

contains genes for synthesis of amino acid tryptophan

Question 28

how does the Trp operon function?

Answer 28

• Trp operon codes for trp repression (inactive)
• genes downstream of leader code for tryptophan
• active trp repressor formed by recruitment of tryptophan into trp repressor
• binds to operator region - stops transcription.

Question 29

What do the different mutations of the lac operon do?

Answer 29

• LacOc - mutated operator doesn’t allow repressor to bind
• cis-dominant (mutation cannot be corrected)
• LacI- - mutated repressor cannot bind to the operator
• trans-recessive - mutation can be corrected by introducing I+, which forms healthy repressor