IB Diploma Programme

Molecular Genetics
Chapter 8.3 Cell Signaling and Gene Regulation
Cell Signalling (Option B3)
★ Option B3: Microorganisms in biofilms cooperate through quorum sensing.
● Cell signalling is the communications between cells through molecules.
● This may occurs in both unicellular and multicellular orgnanisms.

Cell Signalling in bacteria

Quorum sensing
● Quorum sensing is a type of cell signaling which depends on cell density.
● Signalling molecules released by one cell binds to receptor molecules on anoth
er cell and activate genes that facilitate the development of the biofilm.
● When cell density is low, the concentration of the signalling molecule is low
and individual cells produces little signalling molecule.
● When cell density increases, the concentration of signalling molecule increase
s and stimulate individual cells to produce more signalling molecule by gene a
ctivation. (Positive feedback mechanism)
● The concentration of the signalling molecule increases with cell density, once
its concentration reaches a threshold (the quorum), biofilm starts to form and
behaviours of cells in the colony becomes coordinated and often shows emergent
property.
Teacher: Recall the meaning of emergent property, may mention example(s) of emergent
property of biofilm without explanation.
(For details of biofilm, please refer to 22.1 Microbiology.)
Gene Regulation (HL)
Introduction
● Gene regulation is a process which controls the expression of genes.
● The expression of genes can be altered by signalling molecules from other cell
s.

The significance of gene regulation

1. Organisms can produce a different gene product in response to environmental ch
ange
2. It helps the organisms to stop the production of a gene product to reduce ener
gy wastage when a gene product is not needed in a particular environment.
Teacher: Refer to the second diagram below. Using the example of E.coli below, It all
ows the cell to wisely use the resources in the surroundings and reduce energy wastag
e in producing useless proteins
3. It allows cell differentiation to occur
Teacher: Mention that it is by switching on some genes while switching off others.

○ Allow cells to respond to the changes in the environment

Gene regulation can be done by various means:
1. Nucleosome
● The formation of nucleosome prevent transcriptional enzymes from binding

2. DNA binding proteins

● Transcription factors bind to DNA and regulate transcription.

3. mRNA splicing
● The process enables a gene to produce more than one polypeptide
(For details of mRNA splicing, please refer to 8.2 Transcription and Translation)

★ HL 7.2: Gene expression is regulated by proteins that bind to specific ba

se sequences in DNA.
★ HL 7.2: The promoter as an example of non-coding DNA with a function.

● Gene expression can be regulated by proteins called transcription factors.

● Transcription factors bind to specific sequences in DNA and may either activat
e or inhibit transcription, known as activators and repressors respectively.
● They recruit or inhibit binding of DNA polymerase at the promoter sequence and
therefore regulate the transcription of genes.
● Examples where these transcription factors act: Operon in paokryotes, TATA box
in eukaryotes

★ HL 7.2: The environment of a cell and of an organism has an impact on gen

e expression.
More to know:
1. Lac operon
● Operon is a cluster of genes in prokaryotic DNA which is under the control o
f a single promoter
● The Lac operon in E. coli consists of a promoter, an operator and structural
genes (lactose-utilization genes)
Teacher: Explain promoter is where RNA polymerase binds, regulatory sequence is a s
equence which can produce TF while operator is where TF can binds. Structural genes
produce enzymes (proteins) for lactose metabolism.
● A regulatory sequence which always express, produces repressor (TF) molecul
e, which then binds to the operator gene and preventing the binding of RNA p
olymerase to the promoter sequence, hence inhibiting transcription.
● When lactose is present, lactose binds to the repressor molecule, preventing
it to bind with DNA. This allows transcription to occur as the promoter sequ
ence is now exposed to RNA polymerase.
 ● The mechanism allow E.coli to produce enzymes neccessary for lactose intake
and metabolism only when lactose is present.
Teacher: The enzymes are Beta-galactosidase (hydrolysis of lactose), lactose permea
se (for uptake of lactose) and thiogalactoside transacetylase (transfer acetyl grou
p C=OCH3 from acetyl CoA to Beta-galactoside). Only the former two appears to be ne
ccessary.

2. Trp operon in E.coli

● The regulatory sequence produces a repressor which usually cannot binds to t
he operator
● The structural gene is therefore normally transcribed and produces tryptopha
n (amino acid)
● When tryptophan is present in the environment, it binds to the repressor, al
lowing it to binds with the operator sequence, turning off the gene.
● The bacteria can therefore utilize tryptophan in the environment when it is
present, instead of synthesising by itself with the use of energy.
From the examples of operon above, one should understand that the environment of a
cell and of an organism has an impact on gene expression.

3. TATA box
● TATA box is a DNA sequence made of 5’TATAA3’ within the promoter region of
many eukaryotic genes.
● TATA box allows the binding of transcription factors
● The assembly of transcription factors and other proteins can facilitate the
binding of RNA polymerase and regulate transcription rate
Teacher: TATA box can either binds with histone or TF at any particular instant, th
e binding of one will inhibit the binding of the other, hence regulating gene expre
ssion.
★ HL 7.2: Nature of science: Looking for patterns, trends and discrepancies
--there is mounting evidence that the environment can trigger heritable c
hanges in epigenetic factors. (3.1)
★ HL 7.2: Nucleosomes help to regulate transcription in eukaryotes.
● Another group of proteins involved in gene regulation is histone.

● Acetylation of histones by histone acetyltransferase adds acetyl group t

o the lysine at the N-terminal of histones.
● The process remove positive charge on histones and reduces the attractio
n between the N-termini of histones and DNA, relaxing the condensed chro
matin.
● This allows the binding of transcription enzymes and enables transcripti
on.
● On the other hand, deacetylation of histones by histone deacetylase reve
rse the process and inhibit transcription.

★ HL 7.2: Analysis of changes in the DNA methylation patterns.

● DNA methylation is the addition of methyl group to cytosine in DNA nucleotides
 ● Methylation lead to gene silencing
Teacher: This may due to physical blockage to transcription proteins
● It is thought to be involved in many processes such as cell differentiation, a
nd the process is in general irreversible
Teacher: Recall how cell differentiate, the difference in methylation pattern in vari
ous cell types lead to a different proteome in them.
● Methylation pattern is maintained in daughter cells after cell division as DNA
methyltransferases helps to copy the methylation pattern in the newly synthesi

zed strand of DNA after its replication

 Teacher: DNA methyltransferase can only methylate CG bases which had paired up
with methylated CG.
● Methyl groups are erased shortly in zygote after fertilisation. New methyl gro
ups would then be added as embryo develops.
More to know -- Analysis of DNA methylation
● The percentage methylation level of a
isulfite Restriction Analysis (COBRA)
Method:
1. The DNA sample is treated with sodium
d cytosine to uracil while methylated
patterns
DNA can be determined using Combined B
bisulphite, which converts unmethylate
cytosine are not altered.

2. The DNA strand is replicated by Polymerase Chain Reaction (PCR)

3. The methylated allele and the unmethylated alleles are then digested by rest
riction enzymes
Teacher: Mention that the above steps eliminated the restriction sites of non-methy
lated DNA strand containing CG.
4. The fragments can be analysed with the use of electrophoresis

Teacher: The DNA samples may contains more than one CG which is methylated or non-m
ethylated. Thus the relative quantities of digested/undigested fragments in each co
lumn gives the percentage methylation.