Transcript Lecture 15 POWERPOINT here

Controlling the genes
Lecture 15
pp 267-280
Common Sense
 There are estimated to be 25,000 genes
within the human genome
 Between 30-60% are active in any one
cell type at any one time
 These include genes for living
 These include genes for tissue specificity
 What about the rest - turned off!
 How and what controls this?
To be or not to be active
 DNA regulated by DNA?
 DNA regulated by RNA?
 DNA regulated by proteins?
 DNA IS REGULATED BY PROTEINS
 HOW?
 Read on…….
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
25,000 genes on the 23 chromosome pairs
 A differentiated human cell only expresses
between 8,000 and 16,000 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 can 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 - (may be on the exam!)
Gene Expression Control
 We learnt recently that Proteins are made from
mRNA, which is itself made from DNA - central
DOGMA of biology
 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 and the most seen mechanism - sensible
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
 Learn the spelling too!
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 exam on this for sure!)
A bacterial gene unit - where several proteins are made
from one single mRNA molecule.
The important feature is that there is just one gene
regulatory sequence on the DNA controlling the
transcription of the DNA
08_06_single.promot.jpg
Can I get to that DNA please?
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 - please
Eukaryotic gene expression
 More complicated compared to bacteria
 4 steps: 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) Complex 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…
Learn this please
08_10_transcr.factors.jpg
Mediator proteins & bendy DNA
 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