Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and...
-
Upload
laurence-french -
Category
Documents
-
view
219 -
download
0
description
Transcript of Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and...
![Page 1: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/1.jpg)
Chromosomes and Gene Regulation
All cells can use their genes selectively – turning some on and keeping others off.
In multicellular organisms, gene expression is under complex controls. All cells have the same DNA sequences, they same chromosomes, and yet they each look and function very differently.
Cell differentiation is achieved by changes in gene expression. The differences between this neuron and the lymphocyte depend on the precise control of gene expression.
Same genome
Different genes expressed
Questions 2-4,6,7-9,11,12,15
![Page 2: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/2.jpg)
Eucaryotic DNA is packaged into Chromosomes. Human cells contain two of each chromosome, one maternal and one paternal – homologous chromosomes Sex chromosomes are non-homologous chromosomes, X from mom, Y from dad.
Bacteria typically have one circular DNA molecule. It is also associated with proteins that condense the DNA but less is know about the structure.
![Page 3: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/3.jpg)
Chromosomes are typically stained by dyes that distinguish between areas rich in A-T nucleotide
pairs and areas rich in C-G pairs. This results in a pattern of banding that is unique to each chromosome. Cytogeneticists use these to detect major chromosomal abnormalities.
centromere
large rRNA
![Page 4: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/4.jpg)
Cells can vary the structure of their chromosomes for DNA replication and for gene regulation. Chromatin = DNA plus proteins, the stuff chromosomes are made of.
The state of condensation of chromosomes varies according to the cell growth cycle. The mitotic chromosomes are highly condensed, in contrast to that of the interphase chromosome.
![Page 5: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/5.jpg)
The condensed state is important, allowing the duplicated chromosomes to be separated
Three types of specialized sequences found in all eucaryotic chromosomes ensure that chromosomes replicate efficiently.
many, to ensure speed
kinetochore = protein complex that binds the spindle and the centromere
![Page 6: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/6.jpg)
DNA polymerase requires a primer at the end of the chromatin. Without telemers, chromosomes would continually shorten.
Also protects ends from attack by the DNA-digesting enzymes – nucleases.
![Page 7: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/7.jpg)
A. chromatin spilling out of a lysed interphase nucleus
B. a mitotic chromosome, which is duplicated already
![Page 8: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/8.jpg)
A. chromatin isolated from an interphase nucleus = 30 nm
B. chromatin “unpacked” after isolation
![Page 9: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/9.jpg)
The nucleosome is the first and most fundamental packing level of chromatin.
Histones are small proteins with a high proportion of positively charged amino acids (lysine and arginine). These genes are the most highly conserved of all know eucaryotic proteins.
Form a histone octamer
![Page 10: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/10.jpg)
1/3 the lengthChromosomes have several levels of DNA packing. Histons H1 pulls the other histones together to form the typical 30-nm chromatin fiber
In the more compact state, RNA polymerase etc can not bind, and transcription stops.
cytoskeleton organizes the chromatin
![Page 11: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/11.jpg)
A typical mitotic chromosome
![Page 12: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/12.jpg)
• Interphase chromosomes contain both condensed and more extended forms of chromatin– highly condensed interphase chromatin, is called
heterochromatin and makes up about 10% of the chromatin and is transcriptionally inactive.
• normally active genes moved to this region are inactivated– euchromatin = all of the chromatin except
heterochromatin, varies– regions that are actively being transcribed into RNA or
easily available for transcription are more extended (10%) – active chromatin [30-nm fiber or 300nm]
• transcription (RNA polymerase) and replication (DNA polymerase are not obstructed by histones. It is thought that the DNA partially detaches from the histone core as a polymerase moves through, and reassembles immediately.
![Page 13: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/13.jpg)
Happens early in development
Female becomes a mosaic, half of the cells in each organ are maternal, half are paternal
![Page 14: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/14.jpg)
Position effects
A. ADE2 encodes an enzyme whose absence leads to the accumulation of a red pigment.
B. The white gene controls eye pigment production. When inactivated the flies have white eyes.
It is thought the heterochromatin areas can spread and control the expression of genes near them
![Page 15: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/15.jpg)
Interphase chromosomes are organized within the nucleus. The nuclear envelope is supported by two network of protein filaments, the nuclear lamina inside and intermediate filaments outside the membrane. Nuclear pores actively and specifically transport.
The interior is not a random jumble of DNA, RNA, etc. It is thought that DNA is organized by attachment of parts of the chromosomes to sites on the nuclear envelope or the nuclear lamina.
![Page 16: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/16.jpg)
![Page 17: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/17.jpg)
Gene regulation:
As an organism develops, cells differentiate into various types of cells.
Differentiation arises because cells make and accumulate different sets of RNA and protein molecules – they express different genes.
Most of the cells in an organism contain the entire genome. The difference between a muscle cell and a neuron depends on gene regulation.
![Page 18: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/18.jpg)
Gene (eucaryotic) control.
![Page 19: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/19.jpg)
Transcription is controlled by proteins binding to regulatory DNA sequences.
Promotor includes
RNA polymerase binding site
initiation site
Regulatory DNA sequences bound by gene regulatory protiens
some short – simple gene switches
some long and complex (eucaryotic)
molecular microprocessors which respond to a variety of signals, integrate them, and determine the rate of transcription.
Expression depends on
cell type
its environment
its age
extracellular signals
Edge of bases
![Page 20: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/20.jpg)
Gene regulatory proteins insert into the major groove, contacts and binds (noncovalently) to the edges of the bases (about 20 interaction), usually without disrupting the hydrogen bonds. This binding is very strong and very specific for the nucleotide sequence. Frequently DNA-binding proteins contain alpha-helices bind in pairs - dimerization - which doubles the contact area, increasing the strength and specificity of the interaction.
Homeodomain – a structural motif
Zinc finger motif
Leucine zipper motif
![Page 21: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/21.jpg)
An operon = a cluster of bacterial or viral genes transcribed from a single promoter.
A sequence of DNA within the promotor is recognized by regulatory proteins - the operator.
![Page 22: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/22.jpg)
Repressor protein switch genes on or off.
Is recognized well by RNA polymerase.
Bacteria in your gut after you eat a steak
Regulatory proteins like these are allosteric.
These regulators allow fast response to the environment because they are always present in the cell - constitutively expressed
![Page 23: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/23.jpg)
Activator proteins act on promoters that do not bind RNA polymerase on their own. These promoters are made fully functional by the addition of a bound activator protein which is also allosteric, activated by binding another molecule at a site different from the DNA binding site.
Example: CAP has to bind cyclic AMP (an intracellular signaling molecule) to bind DNA. Genes regulated by CAP are switched on in response to increases in cAMP, which is triggered by signals received by cell membrane receptors.
![Page 24: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/24.jpg)
Initiation of transcription in eucaryotic cells is more complex as compared to the simple, economical procaryotic genetic switches.
1. Three RNA polymerases (Table 1)
2. Eucaryotic RNA polymerases require general transcription factors to bind the promoter.
3. Gene regulatory proteins (repressors and activators) can influence initiation of transcription from regulatory sequences found thousands of nucleotide pairs away from the promoter - enhancers.
4. Transcription is impacted by the chromatin structure.
![Page 25: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/25.jpg)
![Page 26: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/26.jpg)
General transcription factors assemble on all promoters transcribed by RNA polymerase II
Start with binding of TFIID which binds a short DNA sequence with many A-Ts - TATA box - typically 25 nucleotides upstream from the transcription start site. This binding causes a dramatic distortion in the DNA. Figure 24.
Other factors assemble along with RNA polymerase = transcription initiation complex. TFIIH contains a protein kinase subunit which adds phosphates to RNA polymerase, releasing it from the complex to start transcription
![Page 27: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/27.jpg)
Start with binding of TFIID which binds a short DNA sequence with many A-Ts - TATA box
This binding causes a dramatic distortion in the DNA.
TBP is a subunit of TFIID which binds the TATA box.
Partially unwound areas
![Page 28: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/28.jpg)
A model for gene activation from an enhancer
General transcription factors usually can not efficiently initiate transcription alone.
Enhancers can be thousands of base pairs away, either upstream or downstream and can either increase or decrease transcription.
“Action at a distance”
![Page 29: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/29.jpg)
Chromatin structure effects gene transcription.
The presence of nucleosomes does not generally block elongation but they may inhibit initiation if they are positioned over a promoter
The effect of chromatin structure on transcription initiation is not well understood yet. More compact chromatin does block transcription.
The regulatory mechanisms involved in packaging interphase chromatin (heterochromatin, inactive X) are also still a mystery.
![Page 30: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/30.jpg)
Summary of gene activation and regulation in procaryotes and eucaryotes.
![Page 31: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/31.jpg)
Gene Regulatory sequences of a typical eucaryotic cell
Regulated by combinations of proteins over up to 50,000 nucleotide pairs
Combinatorial control can be positive or negative
![Page 32: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/32.jpg)
Model for the control of the human beta-globin gene
Some gene regulators like CP1 are present in many types of cells
Others like GATA-1 are only found in a few types of cells.
These are thought to contribute to the cell-type specificity of gene expression
![Page 33: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/33.jpg)
The expression of different genes can be coordinated by a single protein in eucaryotic cells. This can result in rapid switching on or
off of whole groups of genes.
Glucocorticoid steroid hormone is released in response to starvation or intensive physical activity. This hormone stimulates many different cells to do many different things, including liver cells to increase expression of many different genes, some to stimulate the production of glucose from amino acids. All of these genes responding to glucocorticoid steroid are regulated by the binding of the hormone-glucocorticoid receptor complex to a regulatory site.
Regulatory proteins specific for this gene
Regulatory proteins (combination control) specific for this gene
![Page 34: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/34.jpg)
Combinatorial control
many control one
Single protein control
one controls many
This system allows the dramatic differences between cell types to be controlled during differentiation and produced by differences in gene expression
Myoblasts (mucle precursor cells) fuse and produce actin and myosin, ion channel proteins, etc. One regulatory protein involved is MyoD.
Fiberblasts from the skin, transfected with MyoD behave like myoblasts. Other cells do not.
Stained green with an antibody that binds a muscle cell-specific protein.
![Page 35: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/35.jpg)
Combinatorial gene control generates different cell types.
A limited set of gene regulatory proteins can control the expression of a much larger number of genes.
Different combinations will produce different phenotypes
Notice that each daughter cell remembers the previous gene is activated.
![Page 36: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/36.jpg)
When differentiate cells divide, they produce the same type of cells. Muscle and Neurons do not divide, but others like fibroblasts, smooth muscle cells hepatocytes do. Two possible mechanisms include positive feedback loops and propagation of chromatin structure.
Positive feedback loops include proteins that regulate their own genes.
![Page 37: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/37.jpg)
Model for propagation of a condensed chromatin structure. As in X chromosome inactivation.
![Page 38: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/38.jpg)
The formation of an entire organ can be triggered by a single gene regulatory protein. Example, eye development in Drosophila, mice, and humans.
![Page 39: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/39.jpg)
![Page 40: Chromosomes and Gene Regulation All cells can use their genes selectively turning some on and keeping others off. In multicellular organisms, gene expression.](https://reader036.fdocuments.net/reader036/viewer/2022062413/5a4d1b837f8b9ab0599bbc7d/html5/thumbnails/40.jpg)