Introns and Exons

• DNA is interrupted by short sequences that are not in the final mRNA– Called introns– Exons = RNA kept in the final sequence

Gene Regulation

• Ability of an organisms to control which genes are present in response to the environment

Prokaryotic cells turn genes on and off by controlling transcription.

• A promotor is a DNA segment that allows a gene to be transcribed.

• An operator is a part of DNA that turns a gene “on” or ”off.”

• An operon includes a promoter, an operator, and one or more structural genes that code for all the proteins needed to do a job.– Operons are most common in prokaryotes.– The lac operon was one of the first examples of gene regulation

to be discovered.– The lac operon has three genes that code for enzymes that

break down lactose.

• The lac operon acts like a switch.

– The lac operon is “off” when lactose is not present.– The lac operon is “on” when lactose is present.

Trp operon

lac operon

Points of control• The control of gene expression

can occur at any step in the pathway from gene to functional protein1. packing/unpacking DNA2. transcription3. mRNA processing4. mRNA transport5. translation6. protein processing

7. protein degradation

1. DNA packing as gene control• Degree of packing of DNA regulates transcription

– tightly wrapped around histones • no transcription• genes turned off heterochromatin

darker DNA (H) = tightly packed euchromatin

lighter DNA (E) = loosely packed

H E

DNA methylation• Methylation of DNA blocks transcription factors

– no transcription genes turned off– attachment of methyl groups (–CH3) to cytosine

• C = cytosine– nearly permanent inactivation of genes

• ex. inactivated mammalian X chromosome = Barr body• Methylation results in a human disease called fragile X syndrome; FMR-1 gene is

silenced by methylation.

Histone acetylation Acetylation of histones unwinds DNA

loosely wrapped around histones enables transcription genes turned on

attachment of acetyl groups (–COCH3) to histones

conformational change in histone proteins transcription factors have easier access to genes

Fig. 18.13

Methylation of H19 inactivates transcription

(involved in expression of insulin like growth factor)

Fig. 18.10a

Chromatin remodelingAcetylation of histones enhances access to promoter region and facilitates transcription.

Epigenetic Inheritance

• Although the chromatin modifications just discussed do not alter DNA sequence, they may be passed to future generations of cells

• The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence is called epigenetic inheritance

• http://learn.genetics.utah.edu/content/epigenetics/intro/

2. Transcription initiation

• Control regions on DNA– promoter

• nearby control sequence on DNA (TATA box )• binding of RNA polymerase & transcription factors• “base” rate of transcription

– enhancer• distant control

sequences on DNA• binding of activator

proteins• “enhanced” rate (high level)

of transcription

Model for Enhancer action

• Enhancer DNA sequences – distant control sequences

• Activator proteins – bind to enhancer sequence &

stimulates transcription• Silencer proteins

– bind to enhancer sequence & block gene transcription

Turning on Gene movie

Transcription complex

Enhancer

ActivatorActivator

Activator

Coactivator

RNA polymerase II

A

B F E

HTFIID

Core promoterand initiation complex

Activator Proteins• regulatory proteins bind to DNA at distant

enhancer sites• increase the rate of transcription

Coding region

T A T A

Enhancer Sitesregulatory sites on DNA distant from gene

Initiation Complex at Promoter Site binding site of RNA polymerase

Fig. 18-9-3

Enhancer TATAbox

PromoterActivators

DNAGene

Distal controlelement

Group ofmediator proteins

DNA-bendingprotein

Generaltranscriptionfactors

RNApolymerase II

RNApolymerase II

Transcriptioninitiation complex RNA synthesis

3. Post-transcriptional control• Alternative RNA splicing

– variable processing of exons creates a family of proteins

• RNA processing is also an important part of gene regulation in eukaryotes.

• mRNA processing includes three major steps.– Introns are removed and exons are spliced together.– A cap is added.– A tail is added.

Regulation by alternative splicing

Calcitonin gene-related peptide

4. Regulation of mRNA degradation• Life span of mRNA determines amount of

protein synthesis– mRNA can last from hours to weeks

RNA processing movie

5. Control of translation• Block initiation of translation stage

– regulatory proteins attach to 5' end of mRNA • prevent attachment of ribosomal subunits & initiator

tRNA• block translation of mRNA to protein

Control of translation movie

6-7. Protein processing & degradation

• Protein processing– folding, cleaving, adding sugar groups,

targeting for transport• Protein degradation

– ubiquitin tagging– proteasome degradation

Protein processing movie

Concept 18.3: Noncoding RNAs play multiple roles in controlling gene expression

• Only a small fraction of DNA codes for proteins, rRNA, and tRNA

• A significant amount of the genome may be transcribed into noncoding RNAs

• Noncoding RNAs regulate gene expression at two points: mRNA translation and chromatin configuration

RNA interference• Small interfering RNAs (siRNA)

– short segments of RNA (21-28 bases)• bind to mRNA• create sections of double-stranded mRNA• “death” tag for mRNA

– triggers degradation of mRNA

– cause gene “silencing”• post-transcriptional control• turns off gene = no protein produced

NEW!

siRNA

Action of siRNA

siRNA

double-stranded miRNA + siRNA

mRNA degradedfunctionally turns gene off

Hot…Hotnew topicin biology

mRNA for translation

breakdownenzyme(RISC)

dicerenzyme

initiation of transcription

1

mRNA splicing

2

mRNA protection3

initiation of translation

6

mRNAprocessing

5

1 & 2. transcription - DNA packing - transcription factors

3 & 4. post-transcription - mRNA processing

- splicing- 5’ cap & poly-A tail- breakdown by siRNA

5. translation - block start of translation

6 & 7. post-translation - protein processing - protein degradation

7 protein processing & degradation

4

4

Gene Regulation

Cancers result from a series of genetic changes in a cell lineage

– The incidence of cancer increases with age because multiple somatic mutations are required to produce a cancerous cell

– As in many cancers, the development of colon cancer is gradual

Eukaryotic Gene Regulation

• Hox genes – controls differentiation of genes– Responsible for general body

pattern of most animals– Order of genes is order of

body parts

Review questionsWhat does DNA polymerase do?What does Helicase do?What does ligase do?Match the bases below.

5’ – A T C G T A – 3’List 3 differences between RNA/DNA.What are the 3 types of RNA?Where does RNA go after it is made?Transcribe the DNA below.

A T C G T A

What does RNA attach to when it leaves the nucleus?

Amino Acids are the building block of ________.What type of RNA brings an amino acid?When does translation stop?Where is the codon located? Anticodon?What is a codon?Translate the mRNA strand below.

A G C G A GTranslate the DNA strand belowATG CTA TGCA