Transcript Controlling the genes

Controlling the genes
Lecture 15
pp 267-280
Gene Expression
• Nearly all human cells have a nucleus
(not red
blood cells)
• Almost all these nucleated cells have all 23
pairs of chromosomes (actually 22 almost exact pairs
and one or more sex chromosomes)
• However, not all the genes in all these cells
are active all the time
• GENE EXPRESSION - the regulation of
which genes are expressed when - is the
process by which a gene's DNA sequence is
converted into the structures and functions of
a cell.
Across the board
• Bacterial cells exhibit control of gene
expression - not all the enzymes needed for
metabolism are expressed at all times - just
those for the nutrients present in the
environment at that time
• Multicellular organisms exhibit even more
elaborate gene expression - we have brain
cells, liver cells, kidney cells, etc. that
produce different sets of proteins from
different genes. We also have the same cell
type change which genes it expresses with
time - e.g. white blood cells when they start to
produce antibody
Common genes
• If one compares the genes that different
cell types express, one finds the
following:
– Housekeeping genes (histones,
polymerases, DNA repair, glycolysis, etc)
are commonly expressed by all cell types
– Specialized genes - these are produced
only by certain cell types and not others
(antibody genes)
Typical expression
• In humans we estimate that we have about
30,000 genes on the 23 chromosome pairs
• A differentiated human cell only expresses
between 10,000 and 20,000 of its genes
• Different genes can also be expressed at
different levels at different times
– These differences lead to different types, sizes,
function, and morphologies of cells
Expression switching
• Specialized cells may alter their expression
patterns if subjected to external signals
– Liver cells respond quickly to levels of different
enzymes in the blood.
Good example in your textbook at the top of page
270
Gene Expression Control
• We learnt recently that Proteins are made
from mRNA, which is itself made from DNA
• Any one of the steps along this pathway can
be controlled to dictate the presence or
absence of the protein
– We could perform alternative splicing as we saw in
the last lecture. We could control how much of the
mRNA was transported to the cytoplasm. We
could control how much protein was made by the
ribosomes. We could even regulate which proteins
were activated once they have been made.
• TRANSCRIPTIONAL CONTROL is the most
important
Gene Expression can be controlled at several different levels
08_03_control.steps.jpg
• LEARN THIS FIGURE inside out
Gene Regulatory Proteins
• Most genes have regions (normally upstream - 5’
direction) which bind regulatory proteins
• Proteins bind to the regulatory DNA sequences
(the promotor and, if present, the enhancer) to
activate the transcriptional machine
• These proteins recognize their target DNA based
on many factors, including DNA structure, base
sequences, and ionic interactions. These proteins
fit extremely well into the major groove of the DNA
helix - so much so that these are the tightest and
most specific molecular interaction known in
biology!
08_04_gene.reg.prot.jpg
Homo, finger and zipper
• Regulatory proteins which interact with DNA
can be placed into three important structural
motifs
– Homodomain motif - 3 linked alpha helices of the
protein make intimate contact with the DNA
– Zinc-finger motif - a molecule of zinc stabilizes a
alpha helix and a beta sheet structure of the
protein.
– Leucine zipper motif - two alpha helices, each
from different protein molecules come together to
make contact with the major grooves of the DNA
Repressors & Activators
• Genes can be regulated by both on switches
and off switches
• Gene repressors turn off or reduce gene
expression
• Gene activators turn on or enhance gene
expression
– Read page 273 for a good account
– Learn what an operon is here - a set of genes that
are transcribed into a single mRNA- questions on
the quiz on this for sure!
08_06_single.promot.jpg
08_07_repress.protein.jpg
The Lac Operon
• The best studied operon
• Classic example that every cell biology
student should memorize forever!!!
– Read all about it on page 275
Eukaryotic gene expression
• More complicated than that of bacteria
• 1) RNA Polymerase
– Bacteria have JUST one RNA polymerase
– Eukaryotes possess three RNA polymerases
(RNA Pol II transcribes the vast majority of genes)
• 2) General Transcription Factors (proteins)
must first assemble on the DNA before RNA
Pol can attach
Eukaryotic gene expression..
• 3) Eukaryotic regulators can act over
vast distances from the site of gene
transcription. Whilst such bacterial
elements act locally
• 4) Eukaryotic DNA folding and packing
has an impact on transcription too.
RNA Pol II initiation factors
• TFIID binds to the ‘TATA’ box - a short region
of DNA located about 25 bases upstream of
the gene start site
• TFIIA and TFIIB bind to TFIID causing local
unraveling of the DNA
• TFIIE, TFIIH, TFIIF, and RNA Pol II bind next
• Addition of phosphate groups to the RNA Pol
II allows transcription to commence, and
results in the release of the all the other
transcription initiation factors
08_10_transcr.factors.jpg
Mediator proteins
• Eukaryotic genes may be regulated by other
master switches which are vast distances
away from the local promoters. These are
known as ‘enhancer’ sequences.
• The cell can bring such regions together by
simply ‘looping out’ the DNA in between. The
enhancer and promoter are then held
together by mediator proteins, which stabilize
the transcription initiation complex
08_13_gene.activation.jpg
Chromatin Structure and
transcription
• Not too much is understood about the
interactions between gene expression and
chromatin structure
• We do know that heterochomatin regions of
DNA do not permit gene expression due to
the tight folding of the DNA around
nucleosomes
• Histone modifying proteins - those that add
acetyl groups to specific lysines in the tails of
histone proteins increase access, while those
that reduce acetylation result in repression of
transcription
08_14_chromatin.struc.jpg