Chapter 18: Regulation of Gene Expression

How gene can be regularted?

Through Feedback inhibition or Gene regualtion

Operon Model

-Present only in bacteria (prokaryotes)

-Gene expression Regulator

What is an Operator?

Regulatory switch in a segment of DNA

Positioned near the Promotor

What is Operon?

-Entire stretch of DNA

-Includes Operator, Promotor and Genes

What is Repressor?

Protein that Switch OFF operon

How does the repressor turn off the transcription?

The repressor protein binds to the operator and it BLOCKS RNA Polymerase

What is a Corepressor?

Molecule that cooperates with a repressor protein ro

What type of feedback would the repressor and corepressor will be?

Negative feedback

By default the trp operon is on or off?

On for tryptophan synthesis (transcription)

What happens when there are high level of tryptophan ?

It binds to the repressor protein and turn off the operon

What is Repressive Operon?

An operon that is usually ON until binding of a repressor to the operator shuts off the transcription

What is an example of Repressive Operon?

trp Operon

What is Inducible Operon?

-Operon that is usually OFF

-Inducer Inactivates the repressor and turns on the transcription

What is an example of Inducible Operon?

Lac Operon

Lac operon inducer is

Lactose

Inducible enzymes usually functions as

Catabolic Pathway, the synthesis is induced by a chemical signal

Repressive enzymes usually function as

Anabolic Pathway, The synthesis is repressed by high level of the end product.

Where does a repressor bind an operon?

Operator

Is trp and lac operon Negative of Positive Gene Regulation?

Negative

Positive Gene Regulation means

Positive Control through Stimulatory Protein

What is Catabolite Activator Protein (CAP)?

Transcription activator

How does CAP work? E.coli with low glucose

-CAP is activate by binding with cAMP

-Activated CAP attaches to the promotor of the lac operon

CAP attached to the promotor will

Increase the affinity of RNA polymerase and accelerates the transcription

What happens when glucose level increase with E. coli

CAP detaches from lac operon

When CAP detaches, does the transcription stops?

NO, It returns to a normal rate

Does CAP have other function?

Yes, It helps other operons that encode enzymes that is used catabolic pathways

What happens when gene expression has an abnormality

Disease or cancer

Differential Gene Expression

The expression of different gene by cells with the same genome

True/False: Gene expression is regulated at single stage

False, It is regulated at many stages

What is Heterochromatin?

Tightly packed, dense form of chromatin that usually does not get expressed

What do you need in order the gene to be expressed?

chemical modification of histone and DNA of chromatin

What is a Histone?

Small, positively charged protein that DNA wraps around

Histone Modification: Histone Acethylation

-Acetyl group attaches to the lysine residues on the histone tail on the N terminal of H3 and 4

What is the effect of acethylation?

-Since the histone is + and DNA -, Acetyl group neutralizes the positive charge of the lysine

-Reduces the Attraction between the histone and DNA

-Chromatin become less compact and makin DNA more accessible for transcription

What is Euchromatin?

Looser chromatin

Histone Modification: Methylation

Addition of methyl group to the histone

Effect: Heterochromatin

Histone Modification: Phosphorylation

Addition of phosphate group to a methylated AA

Effect: Euchromatin

DNA Modification: DNA Methylation

Addition of methyl group to certain bases of DNA

Effect: Reduced transcription in some species

DNA Methylation: Genomic Imprinting

-Only one allele of a gene is expressed (either mother or father)

-How: One allele is silenced by the DNA methylation

Imprinted Gene

Silenced allele

Epigenetic Inheritance

-Transmission of gene expression patterns from one generation to the next without changing the DNA sequence.

-It involves heritable chemical modification that regulate how genes are turned on and off

What are some of the chemical modification of Epigenetic Inheritance?

-DNA Methylation

-Histone modification

-Non coding RNA

A researcher found a method she could use to manipulate and quantify phosphorylation and methylation in embryonic cells in culture. In one set of experiments she succeeded in decreasing methylation of histone tails. Which of the following results would she most likely see?

decreased chromatin condensation

Pre- Transcription Regulation: Control Element

-Segment of Non coding DNA that serve as binding site for transcription factor

-Helps regulate Transcription

Transcription Factor

An assistance proteins required to initiate transcription for Eukaryotic RNA polymerase

Proximal Control Element

-Located close to the promotor

-Helps to initiate transcription

Example of Proximal Control element

TATA Box

Distal Control Element

-Either Enhancer(activator) of Silencer

-Located Far away from gene even located in an intron

What is an Activator?

-Regulatory protein that increases the rate of transcription

Activator has two domain (area)

1.Binds to DNA

2.Activated the Transcription

True/ False: Some transcriptional factors are repressor

True

Combinational Control Gene Activation

Particular combination of control element activate transcription with appropriate activator protein are present

Chromatin Loop

-3D folding of DNA that brings distant element together

-Function: Regulates gene expression, enhancer-promoter contact

Post Transcription Regulation: Alternate RNA Splicing

Removal of Intron = multiple mature mRNA and encodes different protein

This binds to a site in the DNA far from the promoter to stimulate transcription:

activator

The life span of mRNA in the cytoplasm determines

the protein synthesis

The life span on mRNA of eukaryotes reside

On the nucleoside sequence of the untranslated region of 3’ end of the molecule

Initiation of Translation regulation

It can be regulated by binding proteins to a sequence of mRNA

Proteasomes

Giant protein complexes that break down damaged, misfolded and un-needed protein

Termination of Translation regulation: Folding of protein

Fold the protein to specific shape to function properly

Termination of Translation regulation: Cleavage (cutting)

Some parts of the protein are cut to function properly

Termination of Translation regulation: Chemical Modification

Phosphorylation

Methylation

Acethylation

The small fraction of DNA that consist of NON protein coding gene for

RNA→ rRNA and tRNA

True/ False: The whole DNA codes for protein

False, a small portion codes for protein, small fraction of non protein coding for RNA molecules, regulatory sequence, introns, repetitive sequences and other unclear regulatory functions

the two points of Non coding RNA that regulation gene expression are

-mRNA translation

-chromatin configuration

mRNA Trnaslation Regulation: MicrRNAs (miRNAs)

-Small single stranded RNA molecules that can bind to mRNA

-Function: Degrade mRNA and block its translation

What is RNA interference (RNAi)?

A phenomenon of inhibition of gene expression by RNA molecules

The RNA interference is caused by

Small interfering RNAs (siRNAs)

siRNA function

Are known to block large amount of genes in some fungi

Chromatin Configuration: In some yeast siRNA causes

heterochromatin formation and block large region of chromosomes

Chromatin Configuration: piwi associated RNA (piRNAs) induce

heterochromatin which it cause blocking large region of chromosome

Transposons

blocked the expression of parasitic DNA element in the genome

Increase number of miRNA in species may cause

morphological complexity to increase over evolutionary time

Gene Expression orchetrates

the developmental programs of animals

Gene program for Embryonic Development: Cell differentiation

Cell become specialized in structure and functionCe

Cell differentiation gives

morphogenesis

Morphogenesis is

physical process that give an organism its shape

Cytoplasmic Determinants

Materials in the egg that influence early development

In unfertilized egg cytoplasm it contains

RNA, protein and other substances that are distributed unevenly

When zygote divides by miosis

The cell contains different cytoplasmic determinants which lead to different gene expression

Induction is

Is a signal to the molecules from embryonic cell that causes transcriptional changes in nearby target cells

Sequential Cell Differentiation: Determination

Final committing state of the cell, after it precede to differentiation

Example: Myo D

MyoD is

A regulatory protein that commits cell to become skeletal muscle

Pattern Formation

Development of a spatial organization of tissue and organs

Ex: Animals: begins with an establishment of major axes

Positional Information:

-Molecular cue that control the pattern formation

-Tells a cell its location relative to the body axes and to the neighboring cell

Pattern formation was extensively studies through

Drosophila melanogaster (fruit fly)

In Drosophila the cytoplasmic determinant in unfertilized egg determines

the axis before fertilization

Homeotic Gene

-Lewis (scientist who decoded the pattern formation of Drosophila) discovered that it controls the pattern formation in late embryo, larva and adult stages

-Master regulatory gene that control development of organism and body plan segment pf body structure

Nüsslein-Volhard and Wieschaus studied

Segment Formation: how organism form repeating body units (segments ) during early developmemt

Nüsslein-Volhard and Wieschaus study consist of

Creating a mutant to look for corresponding genes

What does it mean by Embryonic Lethals

Cause death during embryogenesis

The cytoplasmic determinants that initially establish the axes of the body of Drosiphila is encoded by

Maternal effect gene

Maternal Effect gene is also known as

Egg polarity gene: It controls the orientation of the egg and the fly

Bicoid gene

Maternal Effect Gene that affects the front half of the body

What happens when the embryo mother has no functional Bicoid?

The front half of its body is missing and has duplicated posterior structure in both ends

Morphogenesis

Determines the embryo’s axes and other feature

The product of the bicoid gene in Drosophila could be considered a(n):

cytoplasmic determinant

Cancer is caused by

-genetic change that effects the cell cycle control

-mutation to genes that regulate cell growth and division

-tumor virus

Oncogne

Cancer causing gene

Proto Oncogene

Normal cellular gene with normal cell growth and division