©1999 timothy g. standish job 38:36 36who hath put wisdom in the inward parts? or who hath given...

©1999 Timothy G. Standish

Job 38:36

36 Who hath put wisdom in the inward parts? or who hath given understanding to the heart?


The Eukaryotic The Eukaryotic GenomeGenome

Timothy G. Standish, Ph. D.


Eukaryotes Have Large Eukaryotes Have Large Complex GenomesComplex Genomes

The human genome is about 3 x 109 base pairs or ≈ 1 m of DNA

That’s a lot more than a typical bacterial genome

E. coli has 4.3 x 106 bases in its genome Because humans are diploid, each nucleus

contains 6 x 109 base pairs or ≈ 2 m of DNA That is a lot to pack into a little nucleus!


Only a Subset of Genes is Only a Subset of Genes is Expressed at any Given TimeExpressed at any Given Time

It takes lots of energy to express genes Thus it would be wasteful to express all genes all the time By differential expression of genes, cells can respond to

changes in the environment Differential expression, allows cells to specialize in

multicelled organisms. Differential expression also allows organisms to develop

over time.


Eukaryotic DNA Must be Eukaryotic DNA Must be PackagedPackaged

Eukaryotic DNA exhibits many levels of packaging

The fundamental unit is the nucleosome, DNA wound around histone proteins

Nucleosomes arrange themselves together to form higher and higher levels of packaging.


A TT AG CC G

G C

TA

T

AG

C

C G

G C

T A

A T

Packaging DNAPackaging DNA

Histone proteins

Histoneoctomer

B DNA Helix 2 nm


A TT AG CC G

G C

TA

T

AG

C

C G

G C

T A

A T


Histone proteins

B DNA Helix

Histoneoctomer

2 nm


A TT AG CC G

G C

TA

T

AG

C

C G

G C

T A

A T


Histone proteins

Histoneoctomer

Nucleosome

11 nm

B DNA Helix 2 nm



A TT AC G

C G

G C

T A

A T



A TT AC G

C G

G C

T A

A T

Protein scaffold

11 nm“Beads on a string”

30 nm

Tight helical fiber

Looped Domains200 nm



G

C

A

T

Protein scaffold

Metaphase Chromosome

700 nm

11 nm

30 nm200 nm

2 nm

Looped Domains

Nucleosomes

B DNA Helix

Tight helical fiber


Highly Packaged DNA Cannot Highly Packaged DNA Cannot be Expressedbe Expressed

The most highly packaged form of DNA is “heterochromatin”

Heterochromatin cannot be transcribed, therefore expression of genes is prevented

Chromosome puffs on some insect chromosomes illustrate where active gene expression is going on


DNA

Cytoplasm

NucleusG AAAAAA

Export

Degradation etc.G AAAAAA

Control of Gene ExpressionControl of Gene Expression

G AAAAAA

RNAProcessing

mRNA

RNA

Transcription

Nuclear pores

Ribosome

Translation

Packaging

ModificationTransportation

Degradation


Logical Expression Control PointsLogical Expression Control Points DNA packaging Transcription RNA processing mRNA export mRNA masking/unmasking and/or

modification mRNA degradation Translation Protein modification Protein transport Protein degradation

Increasing cost

The logical place to control

expression is before the

gene is transcribed


A “Simple” Eukaryotic GeneA “Simple” Eukaryotic Gene

Terminator Sequence

Promoter/Control Region

Transcription Start Site

3’5’

RNA Transcript

Introns

Exon 2 Exon 3Int. 2Exon 1 Int. 1

3’ Untranslated Region5’ Untranslated Region

Exons


5’DNA

3’

EnhancersEnhancers

Enhancer Transcribed Region

3’5’ TF TFTF

3’5’ TF TFTF

5’ RNA

RNAPol.

RNAPol.

Many bases

Promoter


Eukaryotic mRNAEukaryotic mRNA

Protein Coding Region

3’ Untranslated Region5’ Untranslated Region

Exon 2 Exon 3Exon 1 AAAAAG 3’5’

3’ Poly A Tail5’ Cap

RNA processing achieves three things: Removal of introns Addition of a 5’ cap Addition of a 3’ tail

This signals the mRNA is ready to move out of the nucleus and may control its lifespan in the cytoplasm


““Junk” DNAJunk” DNA It is common for only a small portion of a eukaryotic cell’s DNA

to code for proteins In humans, only about 3 % of DNA actually codes for the about

100,000 proteins; 50,000 in older estimates, 150,000 in more recent estimates

Non-coding DNA was once called “junk” DNA as it was thought to be the molecular debris left over from the process of evolution

We now know that much non-coding DNA plays important roles like regulating expression and maintaining the integrity of chromosomes


The Globin Gene FamilyThe Globin Gene Family Globin genes code for the

protein portion of hemoglobin In adults, hemoglobin is made

up of an iron-containing heme molecule surrounded by 4 globin proteins: 2 globins and 2 globins

During development, different globin genes are expressed which alter the oxygen affinity of embryonic and fetal hemoglobin

Fe


Model For Evolution Of The Model For Evolution Of The Globin Gene FamilyGlobin Gene Family

Ancestral

Globin geneDuplication

Duplication and Mutation

Chromosome 16 Chromosome 11

Transposition

Mutation

Duplication and Mutation

AdultEmbryo FetusEmbryo Fetus andAdult

Pseudogenes () resemble genes, but may lack introns and, along with other differences, typically have stop codons coming soon after the start codons.


Antibody Diversity Results Antibody Diversity Results From Differential SplicingFrom Differential Splicing

Humans produce antibodies to many millions of different antigens

The human genome codes for less than 200,000 genes

Antibodies are proteins, so how are many millions of different antibodies produced by so few genes?

The answer lies in differential splicing of DNA


SSSS

Light Chain

Light ChainSS

SS

Antibody StructureAntibody Structure

Constant Constant

Constant Constant

VV

VV

Antigen binding site

Antigen binding

site

Heavy Chains


Antigen Antigen BindingBinding

Variable

Light

Variable

Heavy

Antigen 1Antigen 3

Antigen 2


An Antibody “Gene”An Antibody “Gene” DNA coding for antibodies are made up of

many exons referred to as genes Different exons are spliced together to make

the many different antibodiesV2 V4V1 V3 IntronJ2 J3J1 Constant

V2 J2V1 V3 Intron Constant

Random splicing of DNA as cell differentiates

J2V3 ConstantTranslation produces a light chain with a variable region at one end

J2V3 Intron ConstantTranscriptionJ2V3 ConstantRNA Processing


Classes of ImmunoglogulinsClasses of ImmunoglogulinsIgG - A monomer - Most abundant antibody in blood. IgG easily leaves the circulatory system to fight infection and crosses the placenta conferring passive immunity to a fetus.IgD - A monomer - Found on the surface of B cells probably allowing recognition of antigens thus triggering differentiation into plasma and memory B cellsIgE - A monomer - The least common antibody. The tails attach to mast cells and basophils. When antigens bind, they signal release of histamine.

IgA - A dimer - Produced by cells in the mucus membranes to prevent attachment of pathogens. IgA is also found in many body secretions including milk.IgM - A pentamer - First antibody to appear following exposure to an antigen. Because it declines rapidly in the blood, high IgM levels indicate a current infection.


CancerCancer Regulation of cell division is vital in multi-celled

organisms Cancer can be defined as uncontrolled division of

cells As regulation of cells is achieved through genes

expressed in those cells, mutation of those genes can result in the loss of regulation and consequently cancer

©1999 timothy g. standish job 38:36 36who hath put wisdom in the inward parts? or who hath given...

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