Download IB104 - Lecture 15

I will be away next week at a conference in Europe. My colleague
Bettina Francis, with whom I alternate teaching this course bi-annually,
will give the lectures. Her PowerPoint style is more the classic bulletpoint style, so you might want to make a point of attending lecture.
On the next slide is a histogram of the raw scores out of 50 for the first
exam last Wednesday. Hopefully you will be able to find them online
soon, otherwise you will get your exams back in lab this week.
I indicate rough grade cutoffs. These are intended to give you an
indication of how you are doing. Half of you are doing okay (As and Bs),
but there a quite a few struggling (D and below). The latter need to reevaluate how they are approaching this class, for example, if your other
classes are going well, then make this your focus for three evenings each
week from now on for reading the relevant chapter and reviewing the
lecture file. Also consider joining a student study group, consult with
your TA during lab, and please feel free to come to me with unresolved
questions.
IB104 - Lecture 15 - Gene Regulation
Reading - Chapter 15 (not flower development)
1. All organisms need ways to regulate when genes are expressed and
how much protein is produced, and eukaryotes also need regulation of
where, that is, in which cells, genes are expressed. That is, temporal
and spatial regulation of gene expression is essential.
2. In bacteria the major form of control involves operons, complexes of
multiple genes that are co-regulated. The most famous is the Lac operon.
A
B
median
C
D
F
The Lac repressor gene is constitutively expressed at a low level so a
small amount of the Lac repressor protein is always present in the E. coli
cell. In the absence of lactose, this repressor binds the operator regions
that overlap the promoter of the Lac operon, preventing transcription.
repressor protein
lactose operon
regulatory
gene
transcription,
translation
repressor protein
promoter
gene 1
gene 2 gene 3
operator
operator in DNA
operator in DNA
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Lactose in the environment enters the cell and binds the Lac repressor,
changing its shape, and thereby freeing the operon to be transcribed.
No lactose present
allolactose
lactose
One context for this gene
regulation is when E. coli
bacteria find themselves in
the guts of young mammals.
Then they don’t need to
express their Lac operon.
mRNA
operator
promoter
operator
RNA
polymerase
gene 1
3. The Lac operon is an inducible operon, that is, in the presence of
lactose transcription is induced and the enzymes thus encoded
metabolize the lactose, upon which the operon is shutdown. This is also
another neat example of negative feedback regulation. The basics were
worked out by two Frenchmen, Jacques Monod and Francois Jacob
(Nobel prize in Physiology or Medicine 1965).
Bacterial cells have many of their genes organized in operons, and some
of them are instead repressible operons. These are ones where the genes
encode proteins involved in synthetic pathways, such as for amino acid
synthesis. When the amino acid is available in the environment, and the
bacteria no longer need to make their own, the bacteria can shut down
these operons. Here the repressor protein only binds the operator when
the end-product amino acid is present. For example, the His operon has
eleven genes encoding all the enzymes needed to make the amino acid
histidine from scratch, and is only transcribed if there is no available
histidine in the cell’s environment.
Lactose present
4. Multicelled eukaryotes: Several levels of control are used to build a
complicated organism like ourselves where only bone cells must make
bone, only blood cells must make hemoglobin, only cells in islets of
Langerhans must make insulin, only hair follicle cells make that
particular kind of keratin, only muscle cells make large amounts of
myosin and actin, etc. There can be controls at all the levels from DNA
to protein that we have examined in the past week. A. TRANSCRIPTIONAL - usually having to do with promoters and
interactions at the DNA level. This is perhaps the most important level of
gene regulation and the only one we will consider.
B. TRANSCRIPT PROCESSING - having to do with the splicing or
other modifications of pre-mRNAs.
C. TRANSLATIONAL - having to do with the behavior of ribosomes
on the transcript and the rapidity of degradation of the transcript.
D. POST-TRANSLATIONAL - modification of proteins by cutting or
phosphorylating or adding sugars, or complexing with other proteins, and
the rate of degradation of proteins.
5. Eukaryotic gene regulation at transcription - five levels.
A. Similar kinds of regulation to bacteria, but without the operon
structure, that is, one gene at a time, occur in eukaryotes to regulate
expression of various enzymes. For example, those involved in
detoxifying particular toxins are only produced when the relevant toxin
is encountered, which means they must also have receptors for relevant
toxins, and a mechanism for signalling need for the detoxification
enzyme. (Amazingly, nematodes like C. elegans independently evolved
operons, another remarkable case of convergent evolution.)
B. In multicelled organisms like animals, a lot of gene regulation
involves differential expression in various tissues. This means that there
is lots of specialization of tissues, meaning that while every cell still
contains all the DNA, only some genes are expressed. The complexity
of how this is accomplished is only starting to be un-ravelled, for
example, in Drosophila flies. Here the controls primarily involve
proteins called transcription factors that bind upstream of the
promoters and control the binding of RNA polymerase and transcription.
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Early development in Drosophila takes only 24 hours, and a series of
transcription factors progressively divides the embryo into segments.
Egg to
larva in
24 hours
Worker honey bees result from methylation of unknown genes.
Upon sequencing the bee genome, an Australian colleague and I searched
it for the genes known to perform DNA methylation in vertebrates (we
already knew that Drosophila flies do not have these genes - they must
have been lost by large deletions). We found them, and then my
colleague asked whether they and DNA methylation might be involved
in regulating whether females bees become sterile workers or fertile
queens. Normally queens result from female larvae fed especially rich
food, called Royal Jelly, but when he inactivated the DNA methylation
genes, most female bees developed as queens. Queens, or reproductive individuals,
are obviously the ancestral state, so
the derived worker developmental
pathway is apparently mediated by
epigenetic CpG methylation of some
genes in their genome. He is now
working to identify those genes, and
understand how they work.
C. DNA methylation and Epigenetics. This generally involves
methylation of cytosine when it occurs before a guanosine. That is, a
methyl group (-CH3), is attached to the single-ring base of the cytosine
when it occurs as a CpG (not a base pair, but a sequential pair of
nucleotides along a strand – p means phosphate). This “mark” is present
on the DNA of many different kinds of organisms, and has several
diverse roles, but the best studied is involvement in gene expression.
Because this mark is not inherited in the regular fashion of DNA
replication, but must be added anew after each DNA replication, it is
called “epigenetic”. We’re only beginning to understand the impacts of
epigenetic changes, but they are cause for concern. For example,
bisphenol-A (BPA) is an environmental toxin found in plastic bottles,
with effects via its similarity to steroid hormones like oestrogen, and because it modifies DNA methylation.
D. Changes can also occur in the organization of DNA. Histones are
the fundamental proteins involved in binding DNA into nucleosomes.
And several additional levels of packing are required to fit all the DNA
into a nucleus.
The level of
packing affects
whether genes
are expressed,
and is
mediated by
histone
modifications,
specifically,
addition of
acetyl groups
to the tails of
the histones.
Histone tail
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E. A truly major form of regulation at the chromosome level is the
inactivation of the X chromosome in female mammals. This occurs in a
mosaic pattern, seen clearly in calico cats, which are females with one
copy of a gene on the X chromosome for orange fur, and one for black
fur. They are a patchwork of orange and black splotches according to
which X chromosome is inactivated (white fur is differently controlled).
The condensed X
chromosome appears
cytologically as a dark
spot attached to the
nuclear membrane,
called a Barr body.
The best understood example is colon cancer, but today similar
progressions of gene mutations and losses are being shown for others.
6. Cancer is a somatic disease in which control of cell division is lost.
We now believe that cancer is largely a genetic disease in which genes
have been mutated in various ways. Regulation of cell division in normal
cells involves a balance of positive and negative controls, all involving
various proteins encoded by various genes.
One of the early breakthroughs was the discovery of oncogenes, that is,
genes that foster cancer development. They were discovered as genes in
cancer-causing viruses, and Harold Varmus and Michael Bishop got
the Nobel prize in medicine in 1989 for the discovery in 1975 that our
cells contain normal copies of these genes, called proto-oncogenes.
These are genes that normally promote cell division, so when overexpressed by an infecting virus, can convert cells to cancerous fates.
We now know that for a cell lineage to become a cancer it has to undergo
a series of mutations and genetic insults, even loss of chromosomes. This
process also removes at some point genes that impede cancer, for
example, by causing cell suicide, so-called suppressor genes.
There are seemingly endless varieties of cancer,
broadly classified by the major tissue or organs
they affect (breast, skin, lung, brain cancers), but
within each are many subtle subdivisions,
depending on precisely which kind of cell
started dividing out of control. The details are
crucial to improve both treatment and research.
Cancers seldom kill when restricted to one place,
however, after additional changes in a process
called metastasis, the cells lose adhesion to each
other and spread via the blood circulation,
eventually sticking in capillaries and forming
new tumors all over the body. This can happen
very rapidly for some cancers like melanomas
of the skin, which makes these particularly
dangerous and hence even youngsters like
yourselves should have annual checkups that
include a complete skin exam.
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