Regulation of
Gene Expression

Regulation of
Gene Expression
 Important for cellular control and differentiation.

Understanding “expression” is a “hot” area in Biology.

General Mechanisms
1. Regulate Gene Expression
2. Regulate Protein Activity

Operon Model
 Jacob and Monod (1961) -
Prokaryotic model of gene control.
 Always on the National AP
Biology exam !

Operon Structure
1. Regulatory Gene
2. Operon Area a. Promoter b. Operator c. Structural Genes

Gene Structures

Regulatory Gene
 Makes Repressor Protein which may bind to the operator.
 Repressor protein blocks transcription.

Promoter
 Attachment sequence on the
DNA for RNA polymerase to start transcription.

Operator

The "Switch”, binding site for
Repressor Protein.
 If blocked, will not permit
RNA polymerase to pass, preventing transcription.

Structural Genes
 Make the enzymes for the metabolic pathway.

Lac Operon
 For digesting Lactose.
 Inducible Operon - only works (on) when the substrate (lactose) is present.

If no Lactose
 Repressor binds to operator.

Operon is "off”, no transcription, no enzymes made

If Lactose is absent

If Lactose is present
 Repressor binds to Lactose instead of operator.

Operon is "on”, transcription occurs, enzymes are made.

If Lactose is present

Enzymes
 Digest Lactose.
 When enough Lactose is digested, the Repressor can bind to the operator and switch the Operon "off”.

Net Result
 The cell only makes the
Lactose digestive enzymes when the substrate is present, saving time and energy.

Animation
 http://www.biostudio.com/d_
%20Lac%20Operon.htm

trp Operon
 Makes Tryptophan.
 Repressible Operon .

If no Tryptophan
 Repressor protein is inactive,
Operon "on”
Tryptophan made.

“Normal” state for the cell.

Tryptophan absent

If Tryptophan present
 Repressor protein is active,
Operon "off”, no transcription, no enzymes
 Result - no Tryptophan made

If Tryptophan present

Repressible Operons
 Are examples of Feedback
Inhibition.
 Result - keeps the substrate at a constant level.

Positive Gene
Regulation
 Positive increase of the level of transcription.
 Uses CAP -
C atabolite A ctivator P rotein
 Uses cAMP as a secondary cell signal.

CAP - Mechanism
 Binds to cAMP.
 Complex binds to the
Promoter, helping RNA polymerase with transcription.

Result
 If the amount of glucose is low (as shown by cAMP) and lactose is present, the lac operon can kick into high gear.

Eukaryotic Gene
Regulation
 Can occur at any stage between DNA and Protein.
 Be prepared to talk about several mechanisms in some detail.

Chromatin Structure
 Histone Modifications
 DNA Methylation
 Epigenetic Inheritance

Histone Acetylation
 Attachment of acetyl groups
(-COCH
3
) to AAs in histones.
 Result - DNA held less tightly to the nucleosomes, more accessible for transcription.

DNA Methylation
 Addition of methyl groups
(-CH
3
) to DNA bases.
 Result - long-term shut-down of DNA transcription.
 Ex: Barr bodies genomic imprinting

Epigenetics
 Another example of DNA methylation effecting the control of gene expression.
 Long term control from generation to generation.

Tends to turn genes “off”.

Do Identical Twins have Identical DNA?
 Yes – at the early stages of their lives.
 Later – methylation patterns change their DNA and they become less alike with age.

Transcriptional Control
 Enhancers and Repressors
 Specific Transcription
Factors
 Result – affect the transcription of DNA into mRNA

Enhancers
 Areas of DNA that increase transcription.
 May be widely separated from the gene
(usually upstream).

Posttranscriptional
Control
 Alternative RNA Processing
Ex - introns and exons
 Can have choices on which exons to keep and which to discard.
 Result – different mRNA and different proteins.

Another Example

Results
 Bcl-X
L
– inhibits apoptosis
 Bcl-X
S
– induces apoptosis
 Two different and opposite effects!!

DSCAM Gene
 Found in fruit flies
 Has 100 potential splicing sites.
 Could produce 38,000 different polypeptides
 Many of these polypeptides have been found

Commentary
 Alternative Splicing is going to be a BIG topic in Biology.
 About 60% of genes are estimated to have alternative splicing sites. (way to increase the number of our genes)

One “gene” does not equal one polypeptide (or RNA).

Other post transcriptional control points
 RNA Transport - moving the mRNA into the cytoplasm.
 RNA Degradation - breaking down old mRNA.

Translation Control
 Regulated by the availability of initiation factors.
 Availability of tRNAs, AAs and other protein synthesis factors. (review Chapter 17).

Protein Processing and Degradation
 Changes to the protein structure after translation.
 Ex: Cleavage
 Modifications
 Activation
 Transport
 Degradation

Protein Degradation
 By Proteosomes using
Ubiquitin to mark the protein.

Noncoding RNA
 Small RNA molecules that are not translated into protein.
 Whole new area in gene regulation.
 Ex - RNAi

Types of RNA
 MicroRNAs or miRNAs.
 RNA Interference or RNAi using small interfering RNAs or siRNAs.
 Both made from RNA molecule that is diced into double stranded (ds) segments.

RNAi
 siRNAs or miRNAs can interact with mRNA and destroy the mRNA or block transcription.
 A high percentage of our
DNA produces regulatory
RNA.

Morphogensis
 The generation of body form is a prime example of gene expression control.
 How do cells differentiate from a single celled zygote into a multi-cellular organism?

Clues?
 Some of the clues are already in the egg.
 Cytoplasmic determinants – chemicals in the egg that signal embryo development.
 Made by Maternal genes, not the embryo’s.

Induction
 Cell to cell signaling of neighboring cells gives position and clues to development of the embryo.

Fruit Fly Studies
 Have contributed a great deal of information on how an egg develops into an embryo and the embryo into the adult.

Homeotic (Hox) Genes

Any of the “master” regulatory genes that control placement of the body parts.

Usually contain “homeobox” sequences of DNA (180 bases) that are highly conserved between organisms.

Comment
 Evolution is strongly tied to gene regulation. Why?
 What happens if you mutate the homeotic genes?
 Stay tuned for more
“evo-devo” links in the future.

When things go wrong

Example case
 Bicoid (two tailed) – gene that controls the development of a head area in fruit flies.
 Gene produces a protein gradient across the embryo.

Result
 Head area develops where
Bicoid protein levels are highest.
 If no bicoid gradient – get two tails.

Other Genes
 Control the development of segments and the other axis of the body.

Gene Expression and Cancer
 Cancer - loss of the genetic control of cell division.
 Balance between growthstimulating pathway
(accelerator) and growthinhibiting pathway (brakes).

Proto-oncogenes
 Normal genes for cell growth and cell division factors.
 Genetic changes may turn them into oncogenes (cancer genes).
 Ex: Gene Amplification,
Translocations, Transpositions,
Point Mutations

Proto-oncogenes

Tumor-Suppressor
Genes
 Genes that inhibit cell division.
 Ex - p53, p21

Cancer Examples
 RAS - a G protein.
 When mutated, causes an increase in cell division by over-stimulating protein kinases.
 Several mutations known.

Cancer Examples
 p53 - involved with several
DNA repair genes and
“checking” genes.
 When damaged (e.g. cigarette smoke), can’t inhibit cell division or cause damaged cells to apoptose.

Carcinogens
 Agents that cause cancer.
 Ex: radiation, chemicals
 Most work by altering the
DNA, or interfering with control or repair mechanisms.

Multistep Hypothesis
 Cancer is the result of several control mechanisms breaking down (usually).
 Ex: Colorectal Cancer requires 4 to 5 mutations before cancer starts.

Colorectal Cancer

News Flash
 Severe damage to a chromosome that causes it to
“shatter” can lead to immediate cancer.

Doesn’t always take a long time and multiple steps.

Can Cancer be Inherited?
 Cancer is caused by genetic changes but is not inherited.
 However, oncogenes can be inherited.
 Multistep model suggests that this puts a person “closer” to developing cancer.

Example – BRAC1
 BRAC1 is a tumor suppressor gene linked with breast cancer.
 Normal BRAC1 – 2% risk.
 Abnormal BRAC1 – 60% risk.
 Runs in families. Some will have breasts removed to avoid cancer risk.

Homework
 Read Chapter 20
 Lab – Gel Electrophoresis.
Lab report – 2/9
 New Discussion Forum – articles found under “labs”.
 Chapter 18 – Fri. 2/10
 No broadcast Mon. 2/6

Summary
 Know Operons
 Be able to discuss several control mechanisms of gene expression.
 Be familiar with gene expression and development of organisms.

Summary
 How control of DNA can lead to cancer.