regulation of gene expression chapter 18. overview of gene expression the control of gene...

Regulation of

Gene Expression

Chapter 18

Overview of Gene Expression

The control of gene expression is vital to the proper and efficient functioning of an organism.

Cells control metabolism by either regulating enzyme activity –or- regulating the expression of genes coding for enzymes.

Regulation of Gene Expression

Figure 18.2

Control of Gene Expression in Bacteria

Bacteria often respond to environmental change by regulating transcription.

In bacteria, genes are often clustered into operons, with one promoter serving several adjacent genes.

An operator site on the DNA switches the operon on or off, resulting in coordinate regulation of the genes.

Prokaryotic Gene Regulation

Operons: The Basic Concept

An operon is essentially a set of genes and the switches that control the expression of those genes.

An operon consists of: operator promotor and genes that they control

All together, the operator, the promoter, and the genes they control – the entire stretch of DNA required for enzyme production for the pathway – is called an operon.


The Operon Model


Repressible & Inducible Operons

There are basically two types of operons found in prokaryotes: repressible operons and inducible operons.

Both the repressible and inducible operon are types of NEGATIVE gene regulation because both are turned OFF by the active form of the repressor protein.

In either type of operon, binding of a specific repressor protein to the operator shuts off transcription. Trp operon – repressible operon is always in the on

position until it is not needed and becomes repressed or switched off.

Lac operon – inducible operon is always off until it is induced to turn on.


Figure 18.3a – The trp Operon

http://bcs.whfreeman.com/thelifewire/content/chp13/1302002.html

Figure 18.3b – The trp Operon

http://highered.mcgraw-hill.com/olc/dl/120080/bio26.swf

Figure 18.4a – The lac Operon

http://www.sumanasinc.com/webcontent/animations/content/lacoperon.html

Figure 18.4b – The lac Operon

http://highered.mcgraw-hill.com/sites/dl/free/0072835125/126997/animation27.html

Positive Gene Regulation

When glucose and lactose are both present in its environment, E. coli prefer to use glucose.

Only when lactose is present AND glucose is in short supply does E. coli use lactose as an energy source, and only then does it synthesize appreciable quantities of the enzymes for lactose breakdown.

How does the E. coli cell sense the glucose concentration and relay this information to its genome?



Figure 18.5a – Positive Control

Figure 18.5b – Positive Control

Factors Affecting Ability of Repressor to Bind to Operator

• Co-Repressor : Activates a Repressoro Seen in the trp Operono Co-Repressor is tryptophano Turns normally “on” Operon “off”

• Inducer: Inactivates a Repressor, Induces the Gene to be Transcribedo Seen in the lac Operono Inducer is allolactoseo Turns normally “off” Operon “on”


Review: Structure/Function of Prokaryotic Chromosomes

1. shape (circular/nonlinear/loop)2. less complex than eukaryotes (no histones/less

elaborate structure/folding)3. size (smaller size/less genetic information/fewer

genes)4. replication method (single origin of replication/rolling

circle replication) 5. transcription/translation may be coupled6. generally few or no introns (noncoding segments)7. majority of genome expressed8. operons are used for gene regulation and control

□ NOTE: plasmids – more common but not unique to prokaryotes/not part of prokaryote chromosome


The Structure of the Chromosome

In Prokaryotes: The bacterial chromosome is a double-stranded,

circular DNA molecule associated with a small amount of protein

In a bacterium, the DNA is “supercoiled” and found in a region of the cell called the nucleoid

In Eukaryotes: Eukaryotic chromosomes have linear DNA

molecules associated with a large amount of protein

Chromatin is a complex of DNA and protein, and is found in the nucleus of eukaryotic cells

Histones are proteins that are responsible for the first level of DNA packing in chromatin

Chromosome Structure

Chromosome Structure of Eukaryotes

Eukaryotic chromosomes contain DNA wrapped around proteins called histones. The strands of nucleosomes are tightly coiled and

supercoiled to form chromosomes.

Eukaryotic Chromosomes

Eukaryotic Chromosomes

Control of Gene Expression in Eukaryotes

Eukaryotic gene expression can be regulated at any stage.

Because gene expression in eukaryotes involves more steps, there are more places where gene control can occur.

Opportunities for the control of gene expression in eukaryotes include:1. Chromatin Packing, modification2. Assembling of Transcription Factors3. RNA Processing4. Regulation of mRNA degradation and Control

of Translation5. Protein Processing and Degradation

Eukaryotic Gene Regulation

Overview Figure 18.6

THIS FIGURE IS HIGHLIGHTING KEY STAGES IN THE EXPRESSION OF A PROTEIN-CODING GENE.

The expression of a given gene will not necessarily involve every stage shown.

MAIN LESSON: each stage is a potential control point where gene expression can be turned on or off, sped up, or slowed down.

Expression of Genes in Eukaryotes

Eukaryotic cells face the same challenges as prokaryotic cells in expressing their genes, but with two main differences: The much greater size of the typical eukaryotic

genome; importance of cell specialization in multicellular

eukaryotes.

In both prokaryotes and eukaryotes, DNA associates with proteins to form chromatin, but in the eukaryotic cell, the chromatin is ordered into higher structural levels.


Eukaryotic Chromosome

StructureChromatin structure is based on successive levels of DNA packing.

Eukaryotic chromatin is composed mostly of DNA and histone proteins that bind to the DNA to form nucleosomes, the most basic units of DNA packing.

Additional folding leads ultimately to highly compacted heterochromatin, the form of chromatin in a metaphase chromosome.

In interphase cells, most chromatin is in a highly extended form, called euchromatin.


The Eukaryotic Genome

In prokaryotes, most of the DNA in a genome codes for protein, with a small amount of noncoding DNA that consists mainly of regulatory sequences such as promoters.

In eukaryotic genomes, most of the DNA (97% in humans) does NOT encode protein or RNA. This DNA includes introns and repetitive DNA:

Repetitive DNA are nucleotide sequences that are present in many copies in a genome, usually not within genes.


Chromatin Modifications Chromatin modifications affect the availability

of genes for transcription: The physical state of DNA in or near a gene is

important in helping control whether the gene is available for transcription.

Genes of heterochromatin (highly condensed) are usually not expressed because transcription proteins cannot reach the DNA.

DNA methylation seems to diminish transcription of that DNA.

Histone acetylation seems to loosen nucleosome structure and thereby enhance transcription.


DNA Methylation

DNA methylation is the attachment of methyl groups (-CH3) to DNA bases after DNA is synthesized. Methylation renders DNA inactive. Inactive DNA, such as that of inactivated mammalian X

chromosomes (Barr bodies), is generally highly methylated compared to DNA that is actively transcribed.

Comparison of the same genes in different types of tissues shows that the genes are usually more heavily methylated in cells where they are not expressed.

In addition, de-methylating certain inactive genes (removing their extra methyl groups) turns them on.

At least in some species, DNA methylation seems to be essential for the long-term inactivation of genes that occurs during cellular differentiation in the embryo.


Histone Acetylation

Histone acetylation is the attachment of acetyl groups (-COOH3) to certain amino acids of histone proteins; de-acetylation is the removal of acetyl groups. When the histones of nucleosome are

acetylated, they change shape so that they grip the DNA less tightly.

As a result, transcription proteins have easier access to genes in the acetylated region.


Transcription Initiation Transcription is controlled by the presence or

absence of particular transcription factors, which bind to the DNA and affect the rate of transcription.

Thus…transcription initiation is controlled by proteins that interact with DNA and with each other.

Once a gene is “unpacked”, the initiation of transcription is the most important and universally used control point in gene expression.


Eukaryotic Gene and its Transcript

Figure 18.8

Assembling of Transcription Factors1) Activator proteins bind to

enhancer sequences in the DNA and help position the initiation complex on the promoter.

2) DNA bending brings the bound activators closer to the promoter. Other transcription factors and RNA polymerase are nearby.

3) Protein-binding domains on the activators attach to certain transcription factors and help them form an active transcription initiation complex on the promoter.


Control elements are simply segments of noncoding DNA that help regulate transcription of a gene by binding proteins (transcription factors).

Post-Transcriptional Factors

Transcription alone DOES NOT constitute gene expression!

Post-transcriptional mechanisms play supporting roles in the control of gene expression: Alternative RNA splicing – where different mRNA

molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns.

Regulatory proteins specific to a cell type control intron-exon choices by binding to regulatory sequences within the primary transcript.



Alternative Splicing Offers New Combinations of Exons = New Proteins

The RNA transcripts of some genes can be spliced in more than one way, generating different mRNA molecules.

With alternative splicing, an organism can get more than one type of polypeptide from a single gene.


Further Control of Gene Expression

After RNA processing, other stages of gene expression that the cell may regulate are mRNA degradation, translation initiation, and protein processing and degradation. The life span of mRNA molecules in the cytoplasm

is an important factor in determining the pattern of protein synthesis in a cell.

Most translational control mechanisms block the initiation stage of polypeptide synthesis, when ribosomal subunits and the initiator tRNA attach to an mRNA.


Protein Processing and Degradation

The final opportunities for controlling gene expression occur after translation: Protein processing – cleavage and the addition

of chemical groups required for function. Transport of the polypeptide to targeted

destinations in the cell. Cells can also limit the lifetimes of normal proteins

by selective degradation – chopped up by proteasomes.


Overview Figure 18.6

THIS FIGURE IS HIGHLIGHTING KEY STAGES IN THE EXPRESSION OF A PROTEIN-CODING GENE.

The expression of a given gene will not necessarily involve every stage shown.

MAIN LESSON: each stage is a potential control point where gene expression can be turned on or off, sped up, or slowed down.

The Molecular Biology of Cancer

Certain genes normally regulate growth and division – the cell cycle – and mutations that alter those genes in somatic cells can lead to cancer. Proto-Oncogenes are normal genes that code

for proteins which stimulate normal cell growth and division.

Oncogenes – cancer causing genes; lead to abnormal stimulation of cell cycle. Oncogenes arise from genetic changes in proto-oncogenes:

1. Amplification of proto-oncogenes2. Point mutation in proto-oncogene3. Movement of DNA within genome

The Biology of Cancer

Genetic Changes Can Turn Proto-oncogenes into Oncogenes

http://www.learner.org/courses/biology/units/cancer/images.html


Tumor-Suppressor Genes

In addition to mutations affecting growth-stimulating proteins, changes in genes whose normal products INHIBIT cell division also contribute to cancer: Such genes are called tumor-suppressor

genes because the proteins they encode normally help prevent uncontrolled cell growth.


p53 Tumor Suppressor and ras Proto-Oncogeneshttp://www.learner.org/courses/biology/units/cancer/images.html

Mutations in the p53 tumor-suppressor gene and the ras proto-oncogene are very common in human cancers. Both are components of signal-transduction pathways

that convey external signal to the DNA in the cell’s nucleus.

Product of ras gene is G Protein (relays a growth signal and stimulates cell cycle). An oncogene protein that is a hyperactive version of

this protein in the pathway can increase cell division.

P53 protein – “guardian angel of the genome” DNA damage (UV, toxins) signals expression of p53

and p53 protein acts as transcription factor for gene p21 p21 halts cell cycle, allowing DNA repair P53 also can cause ‘cell suicide’ if damage is too great

Many cancer patients p53 gene product does not function properly!


Figure 18.21 Signaling pathways that regulate cell growth (Layer 2)

RAS and P53 contribute to uninhibited cell stimulation and growth- Tumor Formation

Figure 18.22 A multi-step model for the development of colorectal cancer


Review: Structure/Function of Eukaryotic Chromosomes

Chromatids 2/sister/pari/identical DNA/ genetic information distribution of one copy to each new cell

Centromere noncoding/uncoiled/narrow/constricted region joins/holds/attaches chromatids together

Nucelosome histones/DNA wrapped arround special proteins packaging compacting

Chromatin Form (heterochromatin/euchromatin) heterochromatin is condensed/supercoiled

proper distribution in cell division (not during replication) euchromatin is loosely coiled

gene expression during interphase/replication occurs when loosely packed Kinetochores

disc-shaped proteins spindle attachment/alignment

Genes or DNA brief DNA description codes for proteins or for RNA

Telomeres tips, ends, noncoding repetitive sequences protection against degradation/ aging, limits number of cell divisions




http://highered.mcgraw-hill.com/olc/dl/120082/bio34b.swf

http://www.learner.org/courses/biology/units/cancer/images.html

USEFUL ANIMATIONS

You should now be able to:

1. Explain the concept of an operon and the function of the operator, repressor, and corepressor

2. Explain the adaptive advantage of grouping bacterial genes into an operon

3. Explain how repressible and inducible operons differ and how those differences reflect differences in the pathways they control

NEED TO KNOW

4. Explain how DNA methylation and histone acetylation affect chromatin structure and the regulation of transcription

5. Define control elements and explain how they influence transcription

6. Explain the role of promoters, enhancers, activators, and repressors in transcription control

NEED TO KNOW

7. Explain how eukaryotic genes can be coordinately expressed

8. Describe the roles played by small RNAs on gene expression

9. Explain why determination precedes differentiation

10. Describe two sources of information that instruct a cell to express genes at the appropriate time

NEED TO KNOW

11. Explain how mutations in tumor-suppressor genes can contribute to cancer

12. Describe the effects of mutations to the p53 and ras genes

NEED TO KNOW

regulation of gene expression chapter 18. overview of gene expression the control of gene...

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lac operon inducible

trp operon repressible

type of operon

basic conceptan operon

set of genes

adjacent genes

expression of genes

trp operonhttp