14 Gene Regulation

Lecture Outline

I. Gene regulation in prokaryotes and eukaryotes: An overview

A. Bacteria grow quickly, have short lifespans, and have an independent existence

1. Economy characterizes regulatory mechanisms

2. Transcriptional level control is most efficient

B. Eukaryotes have gene regulation based on the specificity of the needs of the cell

II. Gene regulation in prokaryotes is economical

A. E. coli has 4288 genes that code for proteins, and over half have known functions

1. Constitutive genes are those that are constantly needed and therefore constantly transcribed

2. Regulation of metabolic activity may be accomplished by regulating the activity of enzymes or the quantity of enzymes produced

B. Operons in prokaryotes permit coordinated control of functionally related genes

C. Jacob and Monod isolated genetic mutants to study the lac operon experimentally in 1961

1. Mutant strains were separated into groups with a mutation that affects the entire mechanism or just one of the three mechanisms

a) E. coli growing on glucose have low amounts of 3 enzymes necessary for lactose metabolism

b) A mutant strain lacked all 3 enzymes for lactose metabolism

c) The genes for these enzymes were linked in the lactose operon

(1) An operon is a gene complex of functionally related, structural genes and the DNA sequences that regulate them

d) RNA polymerase binds to a single promoter upstream from the coding sequences

e) A single mRNA molecule is transcribed, carrying the genetic information for all 3 enzymes

(1) Termination sequences between the 3 coding sequences results in the synthesis of 3 separate enzymes but with 1 shared molecular switch

f) The operator overlaps the promoter and is upstream from the first structural gene

g) A repressor protein binds to the operator in the absence of lactose

h) The regulatory gene coding for the repressor protein is upstream of the operator and promoter

(1) This gene is constitutive (always A on@ )

(2) In the absence of lactose, the operator is always blocked by the repressor

i) If lactose is present, some molecules are converted to allolactose

j) Allolactose binds to the allosteric binding site on the repressor protein and blocks its binding to the operator

k) The operator is now A open,@ and transcription can proceed


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2. Constitutive genes produce even if lactose is absent, which is a waste of energy

a) Lactose absence led to no formation of repressor protein

b) Map position for this protein was found to be outside of the lac operon

3. Some had constitutive regulatory genes with map positions within the lac operon

a) These didn= t directly involve any of the 3 structural genes

b) They altered the repressor protein, preventing lactose from binding, keeping the operon turned A off@

4. An inducible gene is not transcribed unless a specific inducer inactivates its repressor

a) The lac operon is an inducible system

b) Inducible systems are typically kept in the A off@ state by a repressor

c) Inducible systems typically code for catabolic enzymes

d) Inducible systems allow the cell to save energy by only producing enzymes when the appropriate substrate is present

5. A repressible gene is transcribed unless a specific repressor/corepressor complex is bound to the DNA

a) Repressible systems are typically A on@ and code for molecules involved in anabolism

b) Repressible systems are turned A off@ when the end product is in high concentration

c) The tryptophan (try) operon is a repressible system

(1) Tryptophan is the corepressor and binds to an allosteric site on the repressor, allowing the repressor to bind to the operator and blocking transcription

6. Negative regulators repress transcription; positive regulators activate transcription

a) Both the lactose and tryptophan operons are examples of negative control systems

b) Some operons have positive controls involving activator proteins that bind to DNA and facilitate transcription

c) The lac operon has a catabolite activator protein (CAP), which increases the affinity of the promoter for RNA polymerase

7. A regulon is a group of functionally related operons controlled by a common regulator

a) CAP is an example of a regulon that controls transcription of a number of operons

8. Not all constitutive genes are transcribed at the same rate

D. Some posttranscriptional regulation occurs in prokaryotes

1. mRNA may be transcribed at varying speeds

2. mRNA molecules also vary in the speed in which they are translated

a) Some have A strong@ or efficient promoters, others have A weak@ or inefficient promoters, which cause mRNA transcription rates to vary

b) The lifespan of prokaryotic mRNA is relatively short

c) Some are translated up to 1000x faster than others

3. Posttranslational controls act as switches that activate or inactivate enzymes

a) Some regulation is seen in prokaryotes

b) Feedback inhibition acts by the end product binding to the first enzyme in the pathway, inactivating it


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III. Gene regulation in eukaryotes is multifaceted

A. Eukaryotic genes are typically not arranged in operon-like clusters

1. Most genes coding for enzymes needed in universal metabolic pathways are constitutive

2. Some genes are inducible and/or under temporal regulation

3. Other genes are under the control of tissue-specific regulation

B. Eukaryotic transcription is controlled at many sites and by many different regulatory molecules

1. Eukaryotic promoters vary in efficiency, depending on their upstream promoter elements

a) The TATA box is about 30 base pairs upstream from the initiation site

(1) DNA polymerase binds to the TATA box

b) The upstream promoter elements (UPEs) are 8B 12 bases that affect the efficiency of the promoter

2. Enhancers are DNA sequences that increase the rate of transcription

a) Enhancers increase the rate of mRNA synthesis

3. Transcription factors are regulatory proteins that have several functional domains and may work in various combinations

a) Transcription factors have been identified in eukaryotes; over 2000 so far in humans

b) These molecules have several structural units (domains) with different functions

c) Transcription typically requires multiple regulatory proteins that bind to the TATA box

d) Regulators may be activators (more common) or repressors

e) Some activators have A zinc fingers,@ which recognize certain DNA sequences

f) Some activators are functional only as dimers, and many are known as leucine zipper proteins

(1) Both homodimers and heterodimers are known

4. Transcription factors interact with the general transcription machinery

a) These proteins bind to the TATA region and stimulate transcription

5. Transcriptional units may overlap in eukaryotes

a) 1 gene may be transcribed in more than 1 way and produce different protein products by starting at different transcription initiation sites

b) This expression may be tissue-specific

6. The organization of the chromosome may affect the expression of some genes

a) Multiple copies of genes may be present

b) Arrangements of a chromosome may increase or decrease gene expression

c) Small RNA molecules can affect chromatin structure and decrease gene expression (RNA interference)

d) Gene amplification is the selective replication of essential genes, such as those coding for histones and both tRNA and rRNA

e) Gene inactivation occurs by changes in chromatin structure

(1) Heterochromatin is a highly condensed chromatin in which transcription cannot occur

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(2) Euchromatin is loosely arranged and can be actively transcribed

f) Gene inactivation occurs by DNA methylation

(1) Vertebrate genes may be inactivated by methyl groups added to DNA

C. The long-lived, highly processed mRNAs of eukaryotes provide many opportunities for posttranscriptional control

1. Some pre-mRNAs can be processed in more than one way

a) mRNA can be spliced in more than one way, depending on the tissue type; certain sequences can be introns or exons (differential mRNA processing)

2. The stability of mRNA molecules can vary

a) Hormones may affect the stability of mRNA

D. The activity of eukaryotic proteins may be altered by posttranslational chemical modifications

1. Some proteins are synthesized as inactive precursors in proteolytic processing (e.g., zymogens in the digestive tract)

2. Selective degradation regulates the protein product concentration

3. Chemical modification includes the addition or removal of functional groups of an enzyme

a) An example is removal (phosphatases) or addition of phosphate groups (kinases)



























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