MBChB Yr1.

Regulation of gene expression

The ‘Central Dogma’ that describes the flow of genetic information in cells, and our current
understanding of the way that genes are regulated is the basis of modern molecular biology,
and the clinical insight and advances that this brings (Genetic diagnosis, new therapeutics,
gene therapies etc.).

This tutorial aims to guide you through the basic concepts of how the genetic code and gene
regulation works within the cell.

1. Gene regulatory regions & associated proteins

Annotate the regulatory DNA sequences and proteins on the hypothetical MedA locus. Pick
& choose from these potential terms: (i) RNA Polymerase II, (ii) Terminator sequence, (iii)
Nascent RNA transcript, (iv) DNA polymerase, (v) Klenow fragment, (vi) Transcription factor,
(vii) Topoisomerase II, (viii) promoter element, (ix) enhancer, (x) transcriptional start site
(TSS), (xi) Exons & introns.

(Make sure you know what they contribute to the transcription process)

A……………………… transcriptional start site ……………………………………..

B……………………enhancer ……………………..
C……………… transcriptional start site …………………………………..
D………… Exons & introns ……………………………………………………………………….
E…………… Terminator sequence ………………………………………………………………
F………… … Transcription factor ……………………………..
G………RNA POLYMERASE………………………………………..
H……… Nascent RNA transcript ……………………….
MBChB Yr1. Regulation of gene expression

2. Decoding the DNA sequence

2. What is the complementary strand of Sequence 1 (Written in a 5’ to 3’ format ) ?

Sequence 1: 5’ - ATG GAA GTC ATC CCC GAG CAG AGA - 3’

5’ - ATG GAA GTC ATC CCC GAG CAG AGA - 3’ (‘coding strand’)

TAC CTT CAG TAG GGG CTC GTC TCT

2. What protein is encoded by sequence 1? Show how you progress from the DNA
sequence to the protein sequence, using the table provided.

ATG GAA GTC ATC CCC GAG CAG AGA

AUG GAA GUC AUC CCC GAG CAG AGA

Met glu val ile pro glu gln arg

Table for decoding DNA sequence

MBChB Yr1. Regulation of gene expression

3. Assume sequence 1 has been mutated to sequence 2. What is the sequence of the new
protein?

Sequence 2: 5’ - ATG GAG GTC ATC CCC GAG CAG AGA - 3’

SEQ1 5’ - ATG GAA GTC ATC CCC GAG CAG AGA - 3

SEQ 2 5’ - ATG GAG GTC ATC CCC GAG CAG AGA - 3’

AUG GAG GUC AUC CCC GAG CAG AGA

Met glu val ile pro glu gln arg

4 . What is this type of mutation called?

……………silent mutation…………(causes a frameshift?)…………

5. Sequence 2 has mutated to sequence 3. What is the sequence of the new protein?

Sequence 3: 5’ – ATG GAG GT_ ATC CCC GAG CAG AGA GTA - 3’

SEQ 2 5’ - ATG GAG GTC ATC CCC GAG CAG AGA GTA - 3’

SEQ 3 5’ – ATG GAG GT- ATC CCC GAG CAG AGA GTA - 3’

Protein Met glu val ser pro ser arg glu TA

6. What is this type of mutation called?

………………………………deletion…………………………………………………

7. What can cause mutations to occur in DNA?

………radiation, age, errors in dna replication, smoking, chemical carcinogens……………..

8. How could mutations affect protein structure and function?

………………………can code for a different protein………………………

9. Why is mutation important in evolution?

……allows genetic variation, creating new alleles and if more favourable will survive to
adulthood and pass on effective mutation to next
generation…………………………………………..
MBChB Yr1. Regulation of gene expression

3. Chromatin & gene expression

DNA in eukaryotes is assembled into chromatin, a complex of proteins and enzymes that
helps package the 2m of DNA present in each cell. The fundamental unit of chromatin is the
nucleosome, an octamer of 8 histone proteins (H2A, H2B, H3 & H4), which assemble (on
average) every 200 bp of DNA.

10. Why would you think nuclesome assembly creates problems for gene regulation ?

……………Nucleosomes, which are the basic packaging units of chromatin, are stably
positioned in promoters upstream of most stress-inducible genes. These
promoter nucleosomes are generally thought to repress gene expression due to exclusion;
they prevent transcription factors from accessing their target sites on the DNA……..

9. Transcriptionally active genes often look like the lower pane, with nucleosomes
containing acetylated histones at gene regulatory regions. How do you think histone
acetylation could contribute to gene activity?
MBChB Yr1. Regulation of gene expression

……Acetylation of histones alters accessibility of chromatin and allows DNA binding

proteins to interact with exposed sites to activate gene transcription and downstream cellular
functions…….