Module 4 - From DNA to RNA

Question 1

Genes; what are they?

Answer 1

A genetic unit containing information to make a functional product (RNA and/or Protein)

Question 2

What information does a gene contain?

Answer 2

Structural (coding)

Temporal (developmental)

Positional (target a specific organ/cell)

Inducible (nutrients/hormones/stress)

Question 3

Prokaryote gene organisation

Answer 3

Promoter - signals where transcription should start

Cistrons - code for one polypeptide

Leaders (spacers) - non-coding, separates the coding sequences for two cistrons

Question 4

Eukaryote gene organisation

Answer 4

Enchancer - distal from promoter, contains transcription binding sites

Protomer - signals where transcriptions should start

Introns - removed before translation, as splicing occurs

Exons - Used during translation to create the new polypeptide

UTR - Untranslated region

Question 5

Introns: what is the purpose?

Answer 5

Allow for alternative splicing, making it possible to generate multiple proteins from a single gene

Question 6

Comparison of sizes between prokaryotic and eukaryotic genes

Answer 6

Eukaryotic genes can be quite large (~50kB) and most is non-coding

Lower eukaryotic and prokaryotic genes are small and equate more to the size of polypeptides they produce

Question 7

Sense strand

Answer 7

Coding strand - has the same base sequence as the RNA that will be produced in transcription

Is in the 5’ to 3’ direction

Question 8

Antisense strand

Answer 8

Template strand - has a complementary base sequence to the RNA product

Is in the 3’ to 5’ directions

Question 9

Transcription of prokaryotic RNA polymerase (in more detail)

Answer 9

RNA Polymerase holoenzyme involves several things: sigma (σ), 2 alpha (a), 2 betas (b+b’), omega (ω)

Question 10

The sigma in RNA polymerase

Answer 10

Acts as a promoter recognition region

Question 11

The 2 alphas in RNA polymerase

Answer 11

Involved in the assembly and activation of the RNA polymerase

Question 12

The 2 betas in RNA polymerase

Answer 12

Catalysis and termination (essentially do the transcribing and are the central unit to the polymerase)

Question 13

The omega in RNA polymerase

Answer 13

Not alwyas required, involved in folding and assembly of the polymerase

Question 14

What occurs after initiation in prokaryotic transcription

Answer 14

During elongation, the sigma part of the polymerase is released and the two alphas and betas are suitable for elongation

Question 15

RNA polymerases in prokaryotes and eukaryotes

Answer 15

Prokaryotes: only one

Eukaryotes:
RNA pol I - ribosomal (rRNA)

RNA pol II - protein-coding (mRNA, snRNA)

RNA pol III - transfer (tRNA, snRNA)

Question 16

Assembly of RNA pol II: the 4 main parts

Answer 16

Transcription factors IID (TFIID), IIA (TFIIA), and IIB (TFIIB), and TATA-binding proteins (TBP), as well as several other subunits

Question 17

TFIID’s function in RNA pol II

Answer 17

Made up of TBP and TAFs

Main transcribing component

Question 18

TFIIA’s function in RNA pol II

Answer 18

Helps TFIID to bind

Question 19

TFIIB’s function in RNA pol II

Answer 19

Sets distance from TATA element to start site

Question 20

TBP’s function in RNA pol II

Answer 20

It has a sequence similar to the sigma part of prokaryotic RNA polymerase

An important part of TFIID

Question 21

The role of TFIIE/F/H/J/K in the RNA pol II complex

Answer 21

• Interaction with DAB complex and recruitment of pol II
• Blocks non-specific binding of pol II
• Promoter clearance
• Helicase
• Processitvity/elongation
• Transcription-coupled DNA repair

Question 22

RNA pol I: what is it made of and how does it work?

Answer 22

Upstream control element (UCE) and a core which acts as a promoter region

Upstream binding factor (UBF) binds to UCE and the core element and then selective factor 1 (SL1)

SL1 binds to the RNA and then transcription is initiated

Question 23

RNA Polymerase III (tRNA) genes: what are the main components and what happens with the promoter?

Answer 23

TFIIIB (TBP + 2 RNA Pol III specific TAFs) with TFIIIC downstream, as well as several other subunits

TFIIIC is the promoter but is downstream to RNA pol III and it then is released when TFIIIB is recruited and transcription has begun

Question 24

RNA III genes: unsual genes

Answer 24

May contain an extra transcription factor (TFIIIA) to help TFIIIC bind

Upstream promoters

Question 25

Operons

Answer 25

Clusters of genes that are transcribed by one promoter and one terminator that gives rise to polycistronic mRNA (mRNA that codes for multiple cistrons (sections of DNA))

Question 26

The lac operon: what is it, what occurs if lactose isn’t present, what occurs if lactose is present?

Answer 26

Allows for precise control on lactase production.

Lack of lactose leads to a repressor binding to the lac operon in the gene, preventing the mRNA for lactase production from finishing.

If lactose is present, allolactose binds to the repressor and causes it to dissociate from the lac operon, continuing mRNA transcription

Question 27

Cis-acting elements: what are they, how does they do it, and dominant or recessive?

Answer 27

Will only regulate DNA that is directly joined, ie the lac operon is affected by lactose directly neighboring the gene.

Will be directly touching the gene it is regulating

Mostly dominant

Question 28

Trans-acting factors: what are they, how does they do it, and dominant or recessive?

Answer 28

Will regulate genes more than just directly joined and is affected mostly by protein transport factors

Interfere with the gene itself or the cis-acting elements of the gene to regulate the genes

Mostly recessive

Question 29

Differences between cis-acting elements and trans-acting factors

Answer 29

CAE will lead to a permanent constitutional change while TAF will lead to a trans-recessive change

Question 30

Catabolite repression: what is it and what is an example?

Answer 30

The process of only metabolising sugars that are preferential despite being in the presence of other sugars

For example, several operons allowing metabolism of alternate carbon sources are repressed by glucose and only become active when all glucose is used up

Question 31

Catabolite repression with the lac operon: how does it work, how does it work with high amounts of glucose, how does it work with low amounts of glucose, and why does this even occur?

Answer 31

RNA polymerase requires the catabolite repressor protein (CRP)

Cyclic adenosine monophosphate (cAMP) binds to CRP, permitting DNA binding

When there are high amounts of glucose, there is low cAMP so the lac operon is off, even if lactose is available

When there are low amounts of glucose, there is high cAMP so lac operon is on if lactose present

These process occur as glucose is preferentially used as a carbon source

Question 32

Trp operon

Answer 32

Contains genes for the synthesis of tryptophan and, when there is sufficient tryptophan, the repressor binds to the operator and prevents transcription

Question 33

Trp operon and lac operon: how are they different, how do products affect operons, and how do substrates affect operons?

Answer 33

Trp operon is repressed by tryptophan (biosynthetic product) meanwhile the lac operon is induced by lactose (substrate)

Products of biosynthetic operons repress their operons and substrates for metabolism induce their operons