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AP Bio - Regulation of Gene Expression

Image Credits: Biology (Campbell) 9th edition, copyright Pearson 2011, & The Internet. Provided under the terms of a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. By David Knuffke. Modified by Eric Friberg
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Transcript of AP Bio - Regulation of Gene Expression

Regulation of Gene Expression
Prokaryotes
Eukaryotes
In prokaryotes, transcription and translation happen simultaneously (they are "coupled")

Prokaryotes regulate gene expression (and therefore their metabolism) almost entirely by regulating transcription.

The lack of a nucleus makes this very efficient.
Eukaryotes regulate gene expression (and therefore their metabolism) at every step of protein synthesis from pre-transcription to post-translation
Refer to organized clusters of genes that all contribute to a particular metabolic task.

Prokaryotes only!!!

2 Major Flavors:
Inducible
and
Repressible
Operons:
Inducible:
Repressible:
"Up Regulation":
Precursor
Enzyme 1
Enzyme 2
Enzyme 3
-
-
Gene 1
Gene 2
Gene 3
Gene 4
Gene 5
Product
Inhibition of
enzyme activity
Inhibition of
transcription
Francois Jacob & Jacques Monod
Nobel Prize: 1965
For metabolic pathways that are usually "off".

Ex: The
Lac Operon
(digests lactose)
For metabolic pathways that are usually "on".

Ex: The
Trp Operon
(synthesizes tryptophan)
When Lactose is absent:
The repressor protein (made by the
LacI
gene) is able to attach to the
operator
(a region of the promoter)
RNA polymerase cannot transcribe the
structural genes
(
LacZ
,
LacY
and
LacA
) that the cell needs to be able to digest lactose, since it can not attach to the promoter.
This is how things remain in the cell as long as there is no lactose present.
When Lactose is present:
The
inducer
molecule (
allolactose
, a form of lactose) binds to the repressor protein.
This changes the shape of the repressor protein so that it can not attach to the promoter.
RNA polymerase is then able to transcribe the structural genes that the cell needs to be able to digest lactose.
This is how things remain in the cell until lactose is digested
What kind of feedback?
When tryptophan is absent:
The repressor protein (made by the
TrpR
gene) is unable to attach to the operator
RNA polymerase can transcribe the structural genes (
TrpE
,
TrpD
,
TrpC
,
TrpB
, &
TrpA
) that the cell needs to be able to synthesize tryptophan.
This is how things remain in the cell as long as there is no tryptophan present.
When Tryptohan is present:
The
corepressor
molecule (
tryptophan
) binds to the repressor protein.
This changes the shape of the repressor protein so that it can attach to the promoter.
RNA polymerase can not transcribe the structural genes that the cell uses to synthesize tryptophan.
This is how things remain in the cell until tryptophan is no longer present.
What kind of feedback?
A way to increase the rate of transcription of an operon

Ex: The
CAP/cAMP
System
When Lactose is present and glucose is low:
Low glucose means the amount of
cyclic AMP
(
cAMP
) is high
cAMP binds to the
Catabolite Activator Protein
(
CAP
), activating it
The Activated
cAMP/CAP complex
increases the rate of transcription of the lac operon (and ~100 other catabolic operons), boosting the rate of transcription several fold.
When Glucose and Lactose are both present:
Normal glucose level means the amount of cyclic AMP (cAMP) is low
cAMP is not bound to CAP
CAP is inactive.
Very little lac structural gene transcription occurs.
What kind of feedback?
What kind of logic?
What kind of logic?
What kind of logic?
Levels of Control
1.DNA Access
2.Pre-Transcription
3.Post-Transcription
Recent research has uncovered many forms of "
non-coding" RNA
(
ncRNA
) molecules in cells.










We'll look at one example, active in regulation of gene expression post-transcription and pre-tranlstion
4.Pre-Translation
5.Post-Translation
The
decoupling of

Transcription
&
Translation

allows for
more control
points
Only keep necessary genes accessible.
In eukaryotes, DNA is "wound" around
histone
proteins.

The addition of
acetyl

groups
(
-CH2CH3
) to histones causes them to become less tightly packed, allowing for access to the DNA.



Heterochromatin
: more tightly packed DNA, unavailable for transcription.

Euchromatin
: less tightly packed DNA, available for transcription.
The opposite effects of acetylation.

The addition of
methyl groups
(
-CH3
)
to histones (replace acetyl groups and lead to more tight packaging).









Can also attach to DNA to block transcription machinery
All the actors need to be present for the play to begin.
Eukaryotic genes interact with many "upstream" regulatory elements. These are DNA sequences that precede a transcription unit that need to have specific proteins present for RNA polymerase to begin transcription.
The proteins that mediate RNA Polymerase are known as "
Transcription Factors
":
Control of transcription factor availability is one of the major ways that cells of a multicellular organism accomplish "
differential gene expression
", which in turn allows cells to "
differentiate
" to serve different functions in the organism.

This is crucial!!!
So many options lead to so many outcomes.
Following transcription,
5' capping
and
3' poly-adenylation
are necessary for eukaryotic mRNA to remain functional and be transported to the cytoplasm for translation.
"
Alternative splicing
" of exons allows for multiple functional (or non-functional) gene products to be made from a single primary transcript.

Anywhere from 75 - 100 percent of human genes with multiple exons probably undergo alternative splicing.

Shown here: the Troponin T gene produces 2 different mRNA sequences to produce 2 different gene products.

Not shown: A Drosophila gene that has enough exons to produce 19,000 different transcripts.
Lots still left to learn
RNA Interference (
RNAi
):
Mediated by a group of tiny RNA molecules ("
Micro RNA
" or
miRNA
).
Another version called
siRNA
is very similar.

The miRNAs are produced after the transcript for them is cleaved into multiple fragments by a "
dicer
" protein.

The miRNAs complex with proteins.

Any mRNA with a sequence complementary to an miRNA is "tagged" with the miRNA/protein complex.

Tagged miRNA molecules are not translated.

Nobel Prize: 2006
Don't let unnecessary proteins hang around.
Ubiquitin
(a protein so plentiful in all eukaryotic cells it is "ubiquitous"), will tag unnecessary proteins for transport to a proteasome. Inside the
proteasome
, the protein is broken down.
Nobel Prize: 2004
Proteasomes are abundant in eukaryotic cells (why?)
Big Question
Make sure you can:
Polyribosomes demonstrating the coupling of transcription and translation in prokaryotes:
Prokaryotic control of metabolism through control of transcription:
Wikipedias "list of RNAs"
(Oct. 2011):
Coding RNAs
How is gene expression controlled?
Explain the structure and function of all expression control systems described in this presentation.

Compare and contrast the expression control systems utilized in prokaryotic and eukaryotic cells.

Relate prokaryotic expression control systems to prokaryotic cellular organization and feedback mechanisms.

Relate eukaryotic expression control systems to eukaryotic cellular organization and the decoupling of transcription and translation.
RNAi
Methylation
X-Inactivation
One of the X's is repressed
with decreased acetylation
and increased methylation.

This results in one of the
chromosomes being more
condensed, and thus not
expressed.
Epigenetics
Heritable traits that are not determined by
DNA sequences.
-DNA Methylation
-Histone Modification
Parents experiences change the DNA expression of their offspring.
Developmental Genetics
Differentiation
Pattern Formation
Developmental Regulators
How do cells with the same genetic information acquire different structures and functions?
Cytoplasmic Determinants
Substances present in the cytoplasm of the egg cell that are unevenly distributed

Direct different gene expression in subsequent generations of cells.

Important in early development
Induction
Signals from surrounding cells that determine the course of a cell's genetic development.

Important in later development.
Determination
The regulatory events in a cell's genome that lead to differentiation of structure and function.

Once a cell commits to a particular fate, it can not uncommit.

Determination preceeds differentiation.
How is a body plan established in a developing organism?
Positional Information
The molecular signals that establish the body axes in a developing organism.

Much of the work on genetic development was done in Drosophila.
Lots of work, done over a long period of time.

We'll look at one specific example.
Homeotic Genes
Bicoid: An Example
Bicoid
is a protein that is present in a differential gradient in the unfertilized egg.

Cells that develop in a high concentration of bicoid become the anterior (head) of the organism.

Bicoid controls head development directly, so it is referred to as a "
morphogen
".
First discovered in Drosophila by Edward B. Lewis. Nobel Prize in 1995

Have since been discovered in all animal lineages.

Highly conserved sequences (what does that mean), including a characteristic "box" of bases called a "
homeobox
"
Clearly, something pretty important has to happen to get from (a) to (b)
Simplified diagram of determination leading to differentiation in a muscle cell
Morphological differences between normal (top) and bicoid mutant (bottom) fruit fly larvae
Distribution of bicoid in normal fruit fly egg and early-stage embryo
Antennapedia mutants have legs in the wrong places
eyeless mutants have vestigial eyes in odd places
It quickly becomes clear why these experiments are done in fruit flies
While vertebrates have more Homeotic genes than invertebrates, the sequences are very highly conserved.
Differences in homeobox expression patterns lead directly to differences in segmentation
Flouresscence image showing 7 different homeobox expression patterns in a fruit fly embryo.
Homeobox!
Polarity &
Cell Fate

"what goes where and how it's done"
One of the major developmental questions:
How do cells know where they are in the embryo, and what they should become?

Roughly: Cues from two main sources-
uneven distribution of protein molecules
signals from nearby cells ("
induction
")
unequal distribution of proteins in an early stage C. elegans embryo
Polarity of frog embryo's is determined by cues present prior to fertilization, and by direction of fertilization
Fate mapping
: done by staining cells in early stage embryos
Fate map of the C. elegans embryo (intestine map shown)
"things get freaky, easy"
Other
experiments
Funky Frog Fetuses:
By manipulating frog embryos at early stages of development, polarity is disturbed (with disturbing ease)
Removal of a specific region (the "
gray crescent
"), leads to an embryo lacking any dorsal structures
Transplantation of a specific region (the "
dorsal lip
") onto another embryo leads to a duplication of the embryo in opposite polarity.
transplantation of the organizer region (ZPA) leads to limb duplication.
Limb Development:
Chicken limb development is dependent upon specific "
organizer regions
"
We have a better understanding of plant development now than we ever did.

Here are some of the broad strokes
Genetics of Plant Development
Symmetry & Cell Division
Old thought:
Plane of division affected organ form.

New thought:
Plane isn't so important
even though these mutants are wacky, the leaves they make look fine
Symmetry is very important in determining cell fate

Symmetry is also important in determining polarity of a developing plant

Normal early divisions are asymmetrical. What happens when they are symmetrical?
However...
Pattern Formation
Overexpression of the KNOTTED-1 gene in tomato mutants leads to "super compound" leaves compared to the wild type
Animal cells differentiate due to lineage based mechanisms (who they are).

Plant cells differentiate due to position based mechanisms (where they are).
Pretty flowers?
Flowering is under genetic control.

Mutations in flower pattern formation genes lead to abnormalities
Any Questions?
Apoptosis
Programmed Cell Death
Cancer:
Uncontrolled Cell Division
Mutations Happen!
Every second of every day, your DNA is beset by entropic forces.
You have a whole series of genes that make sure mutated cells dont divide.
...but what happens when these genes get mutaed?
"Who watches the watchmen?"
- Juvenal
Proto-oncogenes
stimulate cell division
"The accelerator"
Oncogenes: mutated versions. Always "on".
Tumor Suppresor Genes
inhibit cell division
"The brake pedal"
mutated versions always "off".
Cancer requires ~6* mutations in different genes (it's a "multi-step" pathway)
The Stages of Cancer
* The "Knudson hypothesis" Suggested by Carl Nordling, based on the fact that cancer occurs on average as a sixth function of an indivdual's age. Who says math is useless?
A multistep model of colon cancer development
Metastasis is what kills people.


How do we treat cancer?
Gleevac: A novel cancer treatment
Dr. Saltzman!
projectstealth.org/
Full transcript