How do we regulate the expression of our genes Involved in gene expression DNA regulatory sequences Regulatory genes Small regulatory proteins RNAs Regulatory sequences Stretches of DNA that interact with regulatory proteins to control transcription ID: 776558
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Slide1
Gene Expression...What’s that?
Slide2How do we regulate the expression of our genes?
Slide3Involved in gene expression
DNA regulatory sequences
Regulatory genes
Small regulatory proteins (
RNAs
)
Slide4Regulatory sequences
Stretches of DNA that interact with regulatory proteins to control transcription.
Regulatory genes
A sequence of DNA encoding a regulatory protein or RNA.
Slide5Gene Regulation among bacteria
Bacteria cells are able to express the genes whose products are needed by the cell.EX: need for tryptophan.Have both positive & negative control mechanisms
Slide6-Expression of specific genes can be turned “on” by the presence of an inducer or can be inhibited by the presence of a repressor.
-
Inducers & repressors are small molecules that interact with regulatory proteins &/or regulatory sequences.
Slide7Regulatory proteins inhibit gene expression by binding to DNA and blocking transcription (negative control).
Regulatory proteins stimulate gene expression by binding DNA & stimulating transcription (positive control) or binding to repressors to inactivate repressor function.
Some
genes are continuously expressed; they are always turned “on” EX: ribosomal genes
Slide8Operons are one way in which genes are regulated.
Slide9The switch is the operator (segment of DNA) -it controls the access of RNA polymerase to the genes
- Regulatory proteins stimulate gene expression by binding to DNA & stimulating transcription (positive control) or binding to repressors to inactivate repressor function.
Operon= the operator, promoter, & genes they control –the entire stretch of DNA required for enzyme production for the tryptophan pathway.
Slide10Two types of Negative Gene Regulation
Repressible Operon
: transcription is usually on but can be inhibited (repressed) when a specific small molecule binds to a regulatory protein.
EX: tryptophan
Inducible
: usually off but can be stimulated (induced) when a specific small molecule interacts with a regulatory protein.
EX: lac operon (lactose)
http://biology-animations.blogspot.com/2007/11/lac-operon-animation.html
Slide11Repressible Operon (tryptphan)
Slide12Inducible lac operon
Slide13Which do you think is more common for inducible operons?- the gene in its non-repressed state? Or in its repressed state?What about repressible operons?
Inducible
operons are more commonly found in the repressed state.
Repressible
operons are more often actively transcribing, thus are not repressed
Slide14Which type of operon would be used for anabolic reactions (making new molecules)?
Repressible operons are only turned off when there is an excess of gene production
Slide15Which type of operon would be used for catabolic reactions (breaking down of molecules)?
Inducible operons are only turned on in the presence of
the
a
substance produced by
metabolism (metabolite) in order to break nutrients down.
Slide16Positive Gene Regulation vs Negative Gene Regulation
Positive:
When a regulatory protein interacts directly with the genome to switch transcription on.
Negative
: When the operons are switched off by the active form of the repressor protein
Slide17Positive Gene Regulation
When glucose is in short supply as an energy source, E. coli will use lactose. E. coli will then synthesize high quantities of the enzymes to breakdown the lactose.
How does the cell sense a shortage of glucose? cAMP accumulates when glucose is scarce. cAMP binds with CAP (the activator & regulatory protein) & stimulates the transcription of a gene
cAMP binds to CAP & CAP assumes its active shape. CAP attaches at the upstream end of the lac promoter which stimulates gene expression.
Slide18If the amount of glucose increases the
cAMP concentration falls & therefore CAP detaches from the operon.
The lac operon is under negative regulation by the lac repressor & positive regulation by CAP.
Slide19Can you hypothesize some other ways that might increase or completely shut down the transcription of a gene?
EX: activators that help the RNA polymerase have greater affinity with the promoter region.
Slide20What differences in gene regulation might we see in the eukaryotic genes?
Slide21When a Gene Turned Off Is a Matter of Life or Death: Epigenetic Influences on Gene Regulation
LET’S DO A CASE STUDY!!!
Slide22Identical twins share the same DNA but are they exactly identical?
WHY????
How might they be different?
Slide23Consider the cells that are in the tissue of your big toe.
Which genes are those cells going to need to use?
How much DNA will be present in a given cell that won’t be used at any point except when the cell replicates?
95-97% of the genome of any given cell goes
untranscribed
When a cell receives a signal to transcribe specific genes, what facilitates its search for the genes?
DNA is organized very precisely on a scaffolding of proteins that attach to nuclear lamina & cytoskeleton, thus every part of every strand is in a known location.
Slide24Slide25Each “bead” is a nucleosome.
-the basic unit of DNA packing
The looped domains coil & fold forming the characteristic metaphase chromosome
Slide26Transcriptional - These mechanisms prevent transcription.Posttranscriptional - These mechanisms control or regulate mRNA after it has been produced.Translational - These mechanisms prevent translation. They often involve protein factors needed for translation.Posttranslational - These mechanisms act after the protein has been produced.
Gene expression in eukaryotes is controlled by a variety of mechanisms
that range from those that prevent transcription to those that prevent expression after the protein has been produced.
5
kinds of general mechanisms that can be
used.
Slide27Gene expression can be regulated at any stage, but the key step is transcription
All organisms
Must regulate which genes are expressed at any given time
During development of a multicellular organism
Its cells undergo a process of specialization in form and function called cell differentiation
Slide28ON/OFF SWITCHES
VOLUME CONTROLS
Complete
loss of genes or chromosomes that occurs in amphibians after each phase of metamorphosis
Enhancers that bind ~1000 base pairs upstream of a promoter can help RNA
Polymerase find & bind to the promoter more often so that more transcriptions are made for say, insulin
Slide29Why is it an evolutionary advantage to be able to turn some genes off temporarily or permanently?
Having genes that are always turned on when the gene product is not needed would be wasteful & use up the resources within a cell.
Why are “volume controls” an advantage?
Some gene products are in very high demand & need to have a greater number of transcriptions made so that the cell can function efficiently.
Slide30Many key stages of gene expression can be regulated in eukaryotic cells
Signal
NUCLEUS
Chromatin
Chromatin modification:
DNA unpacking involving
histone acetylation andDNA demethlation
Gene
DNA
Gene availablefor transcription
RNA
Exon
Transcription
Primary transcript
RNA processing
Transport to cytoplasm
Intron
Cap
mRNA in nucleus
Tail
CYTOPLASM
mRNA in cytoplasm
Degradation
of mRNA
Translation
Polypetide
Cleavage
Chemical modification
Transport to cellular
destination
Active protein
Degradation of protein
Degraded protein
Slide31Regulation of Chromatin Structure
&Histone Modifications
Can affect the configuration of chromatin and thus gene expression
Slide32DNA Methylation
The addition of methyl groups to certain bases (usually cytosine) in DNA is associated with reduced transcription in some species.
Genes that are not being expressed have a tendency to be heavily methylated
Removal of the extra methyl groups can turn on certain genes.
Experiments have shown that deficient DNA methylation due to lack of a
methylating
enzyme leads to abnormal embryotic development. In these cases, DNA methylation is essential for the long-term inactivation of certain genes.
Slide33Epigenetic Inheritance
The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence is called: Epigenetic Inheritance
Chromatin modifications don’t necessarily involve a change in DNA and yet they may be passed on from parent to offspring
Let’s read an article
Slide34A certain laboratory strain of the fruit fly
Drosophila melanogaster
has white eyes.
If
the surrounding temperature of the embryos, which are normally nurtured at 25 degrees Celsius, is briefly raised to 37 degrees Celsius, the flies later hatch with red eyes.
If
these flies are again crossed, the following generations are partly red-eyed – without further temperature treatment – even though only white-eyed flies are expected according to the rules of genetics.
Slide35Combinatorial Control of Gene Activation
In Eukaryotes, the control of transcription depends largely on the binding of activators to DNA control elements.Will be able to activate transcription only when the appropriate activator proteins are present
Figure 19.7a, b
Enhancer
Promoter
Control
elements
Albumin
gene
Crystallin
gene
Liver cell
nucleus
Lens cell
nucleus
Available
activators
Available
activators
Albumin
geneexpressed
Albumingene notexpressed
Crystallin genenot expressed
Crystallin geneexpressed
(a)
(b)
Liver cell
Lens cell
Slide36upstream
The rate of gene expression can be increased or decreased by the binding of specific transcription factors, either activators or repressors to the control elements of the enhancers.
The combination of transcription factors binding to the regulatory regions at any one time determines how much, if any, of the gene product will be produced.
Slide37The combination of transcription factors binding to the regulatory regions at any one time determines how much, if any, of the gene product will be produced.
What determines how much of a gene product will be produced?
Slide38Gene regulation accounts for some of the phenotypic differences between organisms with similar genes.
Slide39Slide40Embryonic development
A zygote going through cell division over and over would just produce a ball of all the same type of cells with the same genes.
So…where does the differentiation come in?
A sequential program of gene regulation placed in the egg by the mom is carried out as cells divide.
Slide41How do they know this?
In the 1950’s F.C. Steward worked with carrots
Conclusion:
At least some differentiated (somatic) cells in plants are
totipotent
, able to reverse their differentiation and then give rise to all the cell types in a mature plant.
Slide42Using one or more somatic cells from a multicellular organism to make another genetically identical individual is called:
CLONING
Slide43Nuclear Transplantation in Animals
Not the same as plants regarding differentiated cells.Differentiated cells in animals do not develop into multiple cell types.
Conclusion:
The nucleus from a differentiated frog cell can direct development of a tadpole. However, its ability to do so decreases as the donor cell becomes more differentiated, presumably because of changes in the nucleus.
Slide44Reproductive Cloning of Mammals
Clone mammals using fully developed differentiated cell.Would need to “reprogram” to be totipotent
Slide45Problems Associated with Animal Cloning
Only a small % of cloned embryos develop normally.
Many exhibit defects
Prone to obesity, liver failure, premature death
The donor nuclei is seen to have more methyl groups on their DNA which will effect gene expression compared to non-cloned embryos.
Slide46Slide47Stem Cells
Cells that are undifferentiated & under the right conditions is able to differentiate.These cells are taken during the blastula stage (or blastocyst)
Slide48Embryonic Stem Cells
Cells that start to take different development paths to become specialized cells, such as blood stem cells, which means they can no longer produce any other type of cell.
Can
give rise to any and all tissues in the body
they can differentiate into some, but not all, cell types
.
Slide492 sources “tell” a cell which genes to express
Cytoplasm of egg
Environment around a particular cell
Slide50The
egg’s cytoplasm
contain
cytoplasmic
determinants (influence development)
Cytoplasm of the egg is distributed into other cells.
Depending on which portions of the zygotic cytoplasm a cell received determines the cells fate because of the variants of gene expression.
Slide51The environment around the particular cell.Interactions between embryonic cells help induce differentiation.
Slide52Once a cell has undergone determination it is irreversibly committed to being that type of cell.
Determination at the molecular level is when the cell is expressing tissue specific proteins.
Slide53Pattern Formation In Plants & Animals
Development of a spatial organization in which the tissues & organs of an organism are all in their characteristic places.
Slide54In Animals
Occurs in embryo stage.Cytoplasmic determinants & cell inductive signals provide positional informationCell lineagegenes affect formation
Slide55In Plants
Mechanisms for plant development
Cell lineage is less important
Depend more on positional information
Cell signaling & transcriptional regulation
Formation In Flowers
Environmental signals
Day length & temperature
Slide56LET’S GO GMO…OR NO
WHAT IS GMO?
THEN…
COME UP WITH A LIST OF
BENEFITS AND
CONCERNS
OF USING GMO’S
Slide57Plant Biotechnology
Innovations in the use of plants for human usage.
GMO’s (genetically modified organisms)
DNA/genotype of an organism is artificially changed
Use of GMO’s in agriculture and industry
GMO corn is engineered to produce its own insecticide
by transferring the
Bt
(
Bacillus
thuringiensis
)
crystal protein gene into the corn genome.
GMO soy is engineered to resist being sprayed with weed killers.
Slide58Why go GMO?
Let’s look at the GM corn:
More food is grown
Reduced the need to clear say rainforests to grow crops
Lowers cost of production
Less pesticides/ fertilizers/ chemicals in general
Slide59Concerns over GMO’s
Unknown risks to humans & the environment
When drugs are tested & results show concerns it can be stopped. Not so with crops.
Risk of soil contamination over long term
Possible human risks:
Transfer allergens
Effects on non-target organisms
Ex: caterpillar died consuming laboratory milkweed because of the pollen from the GM corn with
bt
gene
Transgene Escape
EX: GM crop for herbicide resistance & a wild relative have genetic transfer
Slide60Besides GMO’s there’s….
Slide61Artificial Selection
Slide62Types of Genes Associated with Cancer
Slide63Cancer results from genetic changes that affect cell cycle control
Slide64What types of things influence having cancer?
Mutations of genes associated with cell growth such as: random mutation, chemical carcinogens, X-rays, and some viruses.
Slide65Types of Genes Associated with Cancer
Oncogenes
Proto-
oncogenes
Tumor-Suppressor Genes
Slide66Cancer most often results from mutations in genes
Proto-oncogenes:
they often code for proteins that stimulate cell division, prevent cell differentiation or regulate programmed cell death (apoptosis).
Tumor suppressor genes-
produce proteins that signal cells when they are getting too crowded.
Slide67Oncogenes & Proto-Oncogenes
Converting Proto-Oncogenes into Oncogenes
Cancer causing genes
Genes that stimulate normal cell growth & division
Genetic changes that lead to an increase in product or a change in activity of protein
Slide68Tumor-Suppressor Genes
These genes encode proteins that prevent uncontrolled cell growth.
Repair damaged DNA
Control the adhesion of cells to each other or to the extracellular matrix
Components of cell signaling pathways that inhibit the cell cycle.
A mutation happens here and cells will divide uncontrollably = cancer.
Slide69Cell cycle – stimulating pathway
No growth factor even needed with this mutation
Slide70Cell cycle – inhibiting pathway
This signal is started because of damaged DNA.
May be the result of exposure to UV light
p53 gene halts cell cycle until DNA can be repaired or activate genes that are involved in DNA repair.
When DNA is irreparable the p53 gene activates the “suicide” genes that cause cell death (apoptosis).
Slide71Mutations that knock out the p53 gene or if the p53 gene is defective or missing…Can lead to excessive cell growth and cancer
Figure 19.12c
EFFECTS OF MUTATIONS
Protein
overexpressed
Cell cycleoverstimulated
Increased celldivision
Cell cycle notinhibited
Protein absent
Effects of mutations. Increased cell division, possibly leading to cancer, can result if the cell cycle is overstimulated, as in (a), or not inhibited when it normally would be, as in (b).
(c)
Slide72Multiple steps for the development of cancer.
More than one somatic mutation is needed to produce full-fledged cancer cells. (the older we get the more likely we are to develop cancer)
At least: 1 active oncogene and mutation or loss of several tumor-suppressor genes are recessive so both alleles must be “knocked out”
Slide73And finally…the telomerase gene is usually activated in many tumors
Enzyme prevents DNA from shortening and when activated removes a natural limit on the number of times a cell can divide
Slide74Genetic Predisposition & other Factors Contributing to Cancer
Slide75Risk Factors
Inheriting an
oncogene
puts you one step closer to accumulating the mutations for cancer.
Breast cancer: a person inheriting one mutant BRCA1 allele has a 60% probability of developing cancer before the age of 50 compared to someone homozygous for normal (2%).
DNA breakage
Minimize exposure to these agents:
UV radiation, chemicals from cigarette smoke, X-rays
Viruses
Viral integration; can contribute
oncogene
, alter tumor
supressor
genes, or convert proto-
oncogenes
to
oncogenes
.
Slide76Cancer TypeEstimated New CasesEstimated DeathsBladder76,96016,390Breast (Female – Male)246,660 – 2,60040,450 – 440Colon and Rectal (Combined)134,49049,190Endometrial60,05010,470Kidney (Renal Cell and Renal Pelvis) Cancer62,70014,240Leukemia (All Types)60,14024,400Lung (Including Bronchus)224,390158,080Melanoma76,38010,130Non-Hodgkin Lymphoma72,58020,150Pancreatic53,07041,780Prostate180,89026,120Thyroid64,3001,980
21%16% - 16%37%17%23%41%70%13%28%78%41%3%
How deadly?