Transcript Foundations of Biology - Geoscience Research Institute

Job 38:36
36 Who hath put wisdom in
the inward parts? or who
hath given understanding
to the heart?
©1999 Timothy G. Standish
The Eukaryotic
Genome
Timothy G. Standish, Ph. D.
©1999 Timothy G. Standish
Eukaryotes Have Large
Complex 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!

©1999 Timothy G. Standish
 It
Only a Subset of Genes is
Expressed at any Given Time
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.
©1999 Timothy G. Standish
Eukaryotic DNA Must be
Packaged
 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.
©1999 Timothy G. Standish
Packaging DNA
Histone
octomer
Histone proteins
B DNA Helix
2 nm
©1999 Timothy G. Standish
Packaging DNA
Histone
octomer
Histone proteins
B DNA Helix
2 nm
©1999 Timothy G. Standish
Packaging DNA
11 nm
Histone
octomer
Histone proteins
Nucleosome
B DNA Helix
2 nm
©1999 Timothy G. Standish
Packaging DNA
©1999 Timothy G. Standish
Packaging DNA
©1999 Timothy G. Standish
Packaging DNA
“Beads on
a string”
11 nm
30 nm
Tight helical
fiber
Looped
200 nm Domains
Protein scaffold
©1999 Timothy G. Standish
Packaging DNA
Nucleosomes
11 nm
30 nm
Tight helical fiber
Metaphase
Chromosome
700 nm
200 nm Looped Domains
2 nm
B DNA Helix
Protein scaffold
©1999 Timothy G. Standish
Highly Packaged DNA Cannot
be 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
©1999 Timothy G. Standish
Control of Gene Expression
Cytoplasm
Packaging
Degradation
DNA
Transcription
Transportation
Modification
RNA
RNA
Processing
mRNA G
G
AAAAAA
Nucleus
Export
Degradation etc.
AAAAAA
Translation
©1999 Timothy G. Standish
Logical Expression Control Points
Increasing cost
DNA packaging
 Transcription
 RNA processing
 mRNA export
 mRNA masking/unmasking
and/or modification
 mRNA degradation
 Translation
 Protein modification
 Protein transport
 Protein degradation

The logical
place to
control
expression is
before the
gene is
transcribed
©1999 Timothy G. Standish
A “Simple” Eukaryotic Gene
Transcription
Start Site
5’
5’ Untranslated Region
Introns
Exon 1 Int. 1
Promoter/
Control Region
3’ Untranslated Region
Exon 2
3’
Int. 2 Exon 3
Exons
Terminator
Sequence
RNA Transcript
©1999 Timothy G. Standish
Enhancers
DNA
Many bases
5’
3’
Enhancer
5’
Promoter
TF
Transcribed Region
3’
TF
5’
TF TF RNA
RNA
Pol.
Pol.
5’
3’
RNA
©1999 Timothy G. Standish
Eukaryotic mRNA
5’ Untranslated Region
5’ G
Exon 1 Exon 2
3’ Untranslated Region
Exon 3
AAAAA
3’
Protein Coding Region
5’ Cap

RNA processing achieves three things:




3’ Poly A Tail
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
©1999 Timothy G. Standish
“Junk” 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

©1999 Timothy G. Standish
The Globin Gene Family
Globin genes code for the
a
b
protein portion of hemoglobin
 In adults, hemoglobin is made
Fe
up of an iron-containing heme
molecule surrounded by 4
globin proteins: 2 a globins
b
a
and 2 b globins
 During development, different globin genes are
expressed which alter the oxygen affinity of
embryonic and fetal hemoglobin

©1999 Timothy G. Standish
Model For Evolution Of The
Globin Gene Family
Ancestral
Globin gene
Duplication
Mutation
a
b
Transposition
Chromosome 16
a
z
z
b
Duplication and Mutation
e
g
Duplication and Mutation
Gg
a2 a1 yq
e
Ag
a
yz ya2 ya1
Chromosome 11
b
yb
d
b
Embryo
Fetus and
Embryo Fetus
Adult
Adult
Pseudogenes (y) resemble genes, but may lack introns and, along with other
differences, typically have stop codons coming soon after the start codons.
©1999 Timothy G. Standish
Antibody Diversity Results
From 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
©1999 Timothy G. Standish
Antibody Structure
Antigen
binding
site
V
V
V
Light
Chain
Antigen
binding
site
V
SS
SS
Light
Chain
Heavy Chains
©1999 Timothy G. Standish
Antigen
Binding
Antigen 1
Antigen 3
©1999 Timothy G. Standish
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 antibodies
V1
V2
V3
V4
J1 J2 J3 Intron Constant
Random splicing of
DNA as cell differentiates
V1
V2
V3 J2 Intron Constant
Transcription V3 J2 Intron
RNA Processing V3 J2
Translation produces a light chain
V3 J2
with a variable region at one end
Constant
Constant
Constant
©1999 Timothy G. Standish
Classes of Immunoglogulins
IgG - 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 cells
IgE - 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.
©1999 Timothy G. Standish
Cancer
 Regulation
of cell division is vital in multicelled 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
©1999 Timothy G. Standish