Gene organisation, transcription and regulation

Question 1

What are genes?

Answer 1

Units of inheritance

Code for proteins and fRNAs

Question 2

What is the purpose of gene expression?

Answer 2

Leads to cellular specialisation

Question 3

What do blood cells develop from?

Answer 3

Common progenitor cells

Differences result from differences in gene expression

Question 4

What is RNA?

Answer 4

Initial product of gene expression
Single stranded
ribose sugars
Uracil instead of thymine
Functional (tRNA, rRNA) or protein translation template (mRNA)

Question 5

What is transcription?

Answer 5

The process of DNA info being transcribed to RNA
DNA strands unwind
Ribonucleotide bases pair with bases on antisense (template) strand
Bases are joined by RNA polymerases to form phosophodiester bonds

Question 6

What are transcription factors?

Answer 6

Special gene regulatory proteins
Expression determined by cell lineage
Activators - activate gene expression (more copies)
Repressors - suppress gene expression

Question 7

What are the functions of the different types of RNA polymerase?

Answer 7

I - rRNA
II- mRNA
III- tRNA/5s RNA

Question 8

What is the initiation step and why is it needed?

Answer 8

Complex assembles at gene promotor
Level of transcription regulated by transcription factors
Required to build a transcription complex before RNA synthesis occurs

Question 9

What sequence specifies the initiation point for transcription?

Answer 9

TATA - gene promoter

After this, RNA Pol II will begin transcription

Question 10

What comprises the basal transcription complex?

Answer 10

TF IID (TATA binding protein) binds to minor groove, beginning to unwind DNA
TF IIA and IIB bind next
RNA Pol II binds to TF IIB with TF IIF attached
TF IIE H and J bind to Pol II

Question 11

How do transcription factors effect chromatin?

Answer 11

Recruit proteins with enzymatic activities to modify histones
Hyperactylation - genes expressed as DNA exposed
Hypoactylation - genes repressed as DNA hidden

Question 12

What are the key features of E.coli transcription?

Answer 12

Only one type of RNA polymerase, which has 4 subunits - 2 alpha and 2 beta
Gene promoter = TATAAA

Question 13

What are the key features of bacterial transcription?

Answer 13

Sigma factors bring RNA polymerase to different classes of genes
Occurs in the cytoplasm ∴ RNA made in same location as it is translated and can be used straight away
No introns ∴ bases contained in one continuous sequence

Question 14

What is pre-mRNA?

Answer 14

Primary transcript

contains introns and exons

Question 15

Why must pre-mRNA be spliced before being exported to the cytoplasm?

Answer 15

To remove introns

To add a nucleotide cap at 5’ end and add a poly-A tail to the 3’ end

Question 16

What are introns?

Answer 16

Non coding regions

begin with GU and end in AG

Question 17

What are exons?

Answer 17

Coding regions

end in AG

Question 18

Where is the splice donor site?

Answer 18

Located between the end 2 bases of the exon and GU of the intron

Question 19

Where is the splice acceptor site?

Answer 19

Comes after 15 pyramidine bases, any base, then CAG

Pyr15NCAG

Question 20

What are snRNPs and what is their function?

Answer 20

Small ribonuclear proteins produced from snRNA

Numbered and form the spliceosome

Question 21

Where do snRNPs bind and what do they form?

Answer 21

U1 binds to splice donor site
U5 binds to splice acceptor site
U2,4,6 bind in the middle
U1,2,4,5,6 form splicing complex used to cleave splice donor sequence

Question 22

How is the pre-mRNA spliced?

Answer 22

Cleaved at splice donor site
An A residue in the intron is used as the branch point to which UG binds
Phosphodiester bond between G and exon cleaved at splice acceptor site
Exons are joined by RNA ligase

Question 23

How is the ‘cap’ added to the 5’ end of mRNA?

Answer 23

Terminal phosphoanhydride bond is cleaved to form a diphosphate
GTP has two phosphates removed to form GMP
GMP attaches to the diphosphate = 5’-5’ linkage
7’ carbon in guanine is methylated to produce:
7-methylguanylate cap

Question 24

Why is a cap added to mRNA?

Answer 24

Prevent exonuclease degradation

Allow recognition by ribosomes

Question 25

What is polyadenylation?

Answer 25

The addition of the poly-A tail to pre-mRNA
Added one base at a time by poly-A-polymerase
Adds around 10-200 bases 11-30 bases after AAUAAA

Question 26

Why is a poly-A tail added to pre-mRNA?

Answer 26

Provides stability
Length allows monitoring of translation
Prevents translation of damaged mRNA

Question 27

What are micro RNAs (miRNAs)?

Answer 27

18-26 nucleotides in length

Involved in regulation of mRNAs

Question 28

How are genes regulated through RNA interference?

Answer 28

dsRNA produced then separated and divided into small ss-siRNA (small interfering RNA) by DICER
siRNA guides endonuclease activity to remove a ‘passenger’ strand
RNA induced silencing complexes are formed and they recognise and cleave target mRNA that is complimentary to the siRNA

Question 29

How do miRNAs act in gene regulation?

Answer 29

They degrade target mRNAs or inhibit their translation

Question 30

What are non-coding RNAs?

Answer 30

Any non translated RNA (not mRNA)

Question 31

What can long ncRNA affect?

Answer 31

epigenetic expression of genome

key for x inactivation in female cells

Question 32

What does antisense RNA do?

Answer 32

If complimentary, it will hybridise with mRNA more strongly than DNA binds
Prevents translation

Question 33

What is the purpose of the RNA induced silencing complex?

Answer 33

Acts in RNA interference
Incorporated siRNA or miRNA and uses it as a template for recognising a complementary mRNA target
complementary target binding triggeres RISC RNase which cleaves it