BIOLOGY NOTES: (7.

2) FACTORS AFFECTING GENE EXPRESSION

Keywords:
 Cell differentiation- the process by which a cell becomes specialized for a particular
function.
 Transcription factors- proteins that bind to the DNA in the nucleus and affect the process
of transcribing the genetic material.
 Promoter sequences- are specific regions on the DNA to which transcription factors bind to
stimulate transcription.
 Enhancer sequences- specific regions of the DNA where transcription factors bind and
regulate activity in the DNA by:
o Changing structure of chromatin making it more or less available to RNA polymerase ~
stimulating or preventing gene expression.
 Pre-mRNA- the mRNA transcribed directly from DNA before it has been modified.
 Spliceosomes- enzyme complexes that act on pre-mRNA, joining exons together after the
removal of introns.
 DNA methylation- is the methylation (addition of methyl – CH3 group) of DNA to a
cytosine in the DNA molecule next to a guanine in a DNA chain and prevents the
transcription of a gene.
 DNA demethylation- is the removal of the methyl group from methylated DNA enabling
genes to become active so they can be transcribed.
 Chromatin- the DNA/protein complex that makes up the chromosomes.
 Heterochromatin- is the densely supercoiled and condensed chromatin where the genes are
not available to be copied to make proteins.
 Histone Acetylation- the addition of an acetyl (-COOH3) group to one of the lysines in the
histone structure. Which opens up the structure and activates the chromatin, allowing genes in
that area to be transcribed.
 Histone Methylation- the addition of a methyl group (-CH3) to a lysine in the histone.
Depending on the position of the lysine, methylation may cause inactivation or activation of
the region of DNA.
 Totipotent- describes an undifferentiated cell that can form any one of the different cell
types needed for an entire new organism.
 Embryonic Stem Cell- the undifferentiated cells of the early human embryo with the
potential to develop into many different types of specialize cells.
 Pluripotent- describes an undifferentiated cell that can form most of the cell types needed
for an entire new organism.
 Somatic/Adult stem cells- are undifferentiated cells found among normal differentiated
cells in tissue/organ that can differentiate when needed to produce any one major cell types
found in that particular tissue/organ.
 Multipotent- describes a cell that can form a very limited range of differentiated cells within
a mature organism.
How does gene expression take place?
 Gene expression is the condition where specified genes get switched on/off within a cell to
express certain characteristics within a cell through:
o Cell determination- position of blastomere within early embryo determines which
part of embryo will turn into the specific type of cell; the job of the cell is being
determined.
o Cell differentiation/specialization- is the process where the cell becomes specialized
for a particular function; the genes should be expressed differently.
How can gene expression be measured?
We should measure the degree of differentiation (gene expression) between cells by comparing
the proteins, they contain by using gel electrophoresis where we measure the level of
differentiation that has taken place & work out which genes have been expressed & suppressed.
We also use gene probes to allow a particular section of DNA and mRNA in a cell to be
identified. Very specific probes are used to find the unique sequence of nucleotides on DNA that
make up the gene using a stretch of RNA that has the complementary sequence, in a process aka
DNA-RNA hybridization.
How is gene expression Controlled?
Key stages for gene expression are Transcription (from DNA to mRNA) and Translation
(from mRNA to proteins). Diff. combinations are expressed in diff. cells, creating the variety
of structure and functions seen in diff. tissues. Exertion of control happens at any stage of the
process in which gene exp. is controlled. Diff proteins present in cell and their quantities
determines the type of cell and function in the body + proteins can be changed once synthesized
~ another level of control in gene exp.
Transcription Factors:
 Proteins that bind to DNA in nucleus and affect the process of transcribing genetic
material.
 Most common way of controlling gene exp. is by switching on & off transcription of
certain genes. (usually mRNA transcription is an effective point where we can control gene
exp.)
 TF have DNA-binding regions that enable them to bind to specific regions on DNA aka
promoter sequences. Others bind to regions aka enhancer sequences which regulates
activity of DNA by changing structure of chromatin (makes it more/less open to RNA
polymerase). TF can either stimulate (gene ON) or prevent (gene OFF) Transcription of gene,
~ gene exp. either expressed or suppressed.
 Open chromatin structure is linked to active gene exp. & Closed CS linked to gene
inactivity.
 Most common form of gene regulation.
RNA Splicing:
 RNA made in nucleus comes fm. The transcription of all the DNA making up the gene +
introns & exons (the non-coding DNA). RNA splicing is a form of epigenetic control.
 As soon as mRNA is transcribed, it’s not yet complete. Several processes take place to
modify it before it lines up on the ribosomes, ~ it is aka Pre-mRNA. Modifications involve
removal of introns (sometimes exons). Exons that should be transcribed are joined together
by enzyme complexes aka spliceosomes, that produce mature functional mRNA.
 Spliceosomes may join same exons in a variety of ways, this process is aka RNA splicing.
~ a single gene, may produce several versions of mRNA transcribed from same section of
DNA. Diff ver. of mRNA code for diff ver. arrangements of amino acids, which produce diff.
polypeptide chains, ~ produce diff. proteins. ~ single gene producing several diff.
phenotypes (in variety).
 Further modifications of proteins can take place after synthesis happens. A protein that is
coded for by a gene may remain intact, shortened, lengthened by enzymes to give protein
variety.
Epigenetics:
Is when certain chemicals attach to DNA or histone ~ gene exp. gets changed. It is Genetic
control by factors other than base sequences. The mechanisms are: DNA methylation, Histone
modification, Chromatin remodeling, Regulation by small and non-coding RNAs.
 DNA methylation-
ois the addition of methyl group.
oAlways occurs at the site where cytosine occurs next to guanine in the DNA chain w/
phosphate bond between them.
oMethyl grp is added by DNA methyltransferase enzyme.
oCan also modify structure of histones.
oAlways silences a gene or a sequence of genes. The methyl group changes the arrangement
of the DNA molecule ~ prevents transcription from happening.
oVery imp. In controlling gene expression and has a big role in processes including
embryonic development & X chromosome activation.
 DNA demethylation-
oInvolves the removal of the methyl group
oEnables genes to become active so they can be transcribed.
 Histone Modification-
oHistones are +ively charged proteins. DNA helicases wind around histones to form
chromatin which is the DNA/protein complex that makes up chromosome. Histones
determine structure of proteins.
oWhen chromatin is densely super coiled/condensed, genes are unable to be copied to make
chromatin this is aka heterochromatin.
 oActive chromatin is more loosely held w/uncoiled regions of DNA opening up more genes
for transcription so proteins are made.
 Histone acetylation-
oWhen acetyl group is added to lysine in histone structure.
o This usually opens up the structure, & activates chromatin, allowing genes in that area to
be transcribed.
 Histone methylation-
oWhen methyl group is added to lysine in histone structure.
oDepending on position of lysine, methylation may cause inactivation of the DNA or
activation of a region.
oMethylation is often linked to the silencing of a gene and even whole chromosome.
Non-Coding RNA:
 Non-coding RNA (ncRNA) seems to affect transcription of the DNA code or modifies the
product of transcription.
 Genes, even whole chromosomes are shown to be silenced by ncRNA’s.
 Calico cats-
oIn female mammals, one of the X chromosomes in every cell is inactivated at random.
oThis is largely due to the presence of an ncRNA called X-inactive specific transcript (Xist),
produced by the active Xist gene on the inactive chromosome.
oncRNA coats one of the X chromosomes in female cells and deactivates it. Chromosome
supercoils and condenses to form the stable, inactive Barr body.
 ncRNA in chromatin modification, acts on histones to make areas of DNA available or
unavailable for transcription.