Download The Organization and Control of Eukaryotic Genomes

The Organization and Control
of Eukaryotic Genomes
Chapter 19
REMEMBER: Prokaryotic Genomes
http://highered.mcgraw-hill.com/olc/dl/120077/bio25.swf
1.
2.
3.
4.
5.
6.
7.
8.
shape (circular/nonlinear/loop)
less complex than eukaryotes (no histones/less
elaborate structure/folding)
size (smaller size/less genetic information/fewer
genes)
replication method (single origin of replication/rolling
circle replication)
transcription/translation may be coupled
generally few or no introns (noncoding segments)
majority of genome expressed
operons are used for gene regulation and control
□
NOTE: plasmids – more common but not unique to
prokaryotes/not part of prokaryote chromosome
Overview Figure 19.7
•
Opportunities for the control of gene
expression in eukaryotes:
1.
2.
3.
4.
5.
Chromatin Packing, modification
Assembling of Transcription Factors
RNA Processing
Regulation of mRNA degradation and Control of
Translation
Protein Processing and Degradation
•
THIS FIGURE IS HIGHLIGHTING KEY
STAGES IN THE EXPRESSION OF A
PROTEIN-CODING GENE.
•
The expression of a given gene will not
necessarily involve every stage shown.
•
MAIN LESSON: each stage is a potential
control point where gene expression can be
turned on or off, sped up, or slowed down.
Expression of Genes
 Eukaryotic cells face the same challenges as
prokaryotic cells in expressing their genes, but
with two main differences:


The much greater size of the typical eukaryotic
genome;
importance of cell specialization in multicellular
eukaryotes.
 In both prokaryotes and eukaryotes, DNA
associates with proteins to form chromatin, but
in the eukaryotic cell, the chromatin is ordered
into higher structural levels.
Eukaryotic Chromosome Structure
Chromatin structure is based on
successive levels of DNA packing.
Eukaryotic chromatin is composed
mostly of DNA and histone proteins
that bind to the DNA to form
nucleosomes, the most basic units of
DNA packing.
Additional folding leads ultimately to
highly compacted heterochromatin,
the form of chromatin in a metaphase
chromosome.
In interphase cells, most chromatin is in
a highly extended form, called
euchromatin.
The Eukaryotic Genome
 In prokaryotes, most of the DNA in a genome
codes for protein, with a small amount of
noncoding DNA that consists mainly of
regulatory sequences such as promoters.
 In eukaryotic genomes, most of the DNA (97%
in humans) does NOT encode protein or RNA.

This DNA includes introns and repetitive DNA:

Repetitive DNA are nucleotide sequences that are
present in many copies in a genome, usually not
within genes.
Gene Amplification, Loss, or Rearrangement
 Gene amplification, loss, or rearrangement
can alter a cell’s genome during an
organisms lifetime:

Sometimes the number of copies of a gene or
gene family temporarily increases in the cells
of some tissues during a particular stage of
development:


Known as gene amplification – a potent way of
increasing expression of the genes enabling a
developing egg to make enormous numbers of
ribosomes.
Genes can also be selectively lost in certain
tissues (seen in early insect development).
Rearrangement in the Genome
 All organisms seem to have transposons:

These can increase or decrease the
production of one or more proteins depending
on where the sequence inserts (jumps).
Cellular Differentiation
 Gene expression must be controlled on a long-term
basis for cellular differentiation during an organism’s
development.
 In all organisms, the expression of specific genes is
most commonly regulated at the level of transcription
by DNA-binding proteins.

For this reason, the term gene expression is often
equated with gene activity – transcription – for both
prokaryotes and eukaryotes.
 However, the greater complexity of eukaryotic cell
structure and function provides opportunities for
controlling gene expression at additional stages.
Overview Figure 19.7

Opportunities for the control of gene expression in
eukaryotes:
1.
2.
3.
4.
5.
Chromatin Packing, modification
Assembling of Transcription Factors
RNA Processing
Regulation of mRNA degradation and Control of
Translation
Protein Processing and Degradation

THIS FIGURE IS HIGHLIGHTING KEY STAGES IN
THE EXPRESSION OF A PROTEIN-CODING
GENE.

The expression of a given gene will not necessarily
involve every stage shown.

MAIN LESSON: each stage is a potential control
point where gene expression can be turned on or off,
sped up, or slowed down.
Chromatin Modifications
 Chromatin modifications affect the availability of genes
for transcription:


The physical state of DNA in or near a gene is important
in helping control whether the gene is available for
transcription.
Genes of heterochromatin (highly condensed) are
usually not expressed because transcription proteins
cannot reach the DNA.
 DNA methylation seems to diminish transcription of
that DNA.
 Histone acetylation seems to loosen nucleosome
structure and thereby enhance transcription.
DNA Methylation
 DNA methylation is the attachment of methyl groups
(-CH3) to DNA bases after DNA is synthesized.



Inactive DNA, such as that of inactivated mammalian X
chromosomes, is generally highly methylated
compared to DNA that is actively transcribed.
Comparison of the same genes in different types of
tissues shows that the genes are usually more heavily
methylated in cells where they are not expressed.
In addition, demethylating certain inactive genes
(removing their extra methyl groups) turns them on.
 At least in some species, DNA methylation seems to
be essential for the long-term inactivation of genes
that occurs during cellular differentiation in the
embryo.
Histone Acetylation
 Histone acetylation is the attachment of acetyl
groups (-COCH3) to certain amino acids of
histone proteins; deacetylation is the removal
of acetyl groups.


When the histones of nucleosome are
acetylated, they change shape so that they
grip the DNA less tightly.
As a result, transcription proteins have easier
access to genes in the acetylated region.
Transcription Initiation
 Transcription initiation is controlled by
proteins that interact with DNA and with each
other.
 Once a gene is “unpacked”, the initiation of
transcription is the most important and
universally used control point in gene
expression.
Eukaryotic Gene and its Transcript –
Figure 19.8
Assembling of Transcription Factors
1) Activator proteins bind to
enhancer sequences in the
DNA and help position the
initiation complex on the
promoter.
2) DNA bending brings the
bound activators closer to
the promoter. Other
transcription factors and
RNA polymerase are nearby.
3) Protein-binding domains
on the activators attach to
certain transcription factors
and help them form an active
transcription initiation
complex on the promoter.
http://highered.mcgrawhill.com/olc/dl/120080/bio28.
swf
Control elements are simply segments of noncoding DNA
that help regulate transcription of a gene by binding
proteins (transcription factors).
Post-Transcriptional Factors
 Transcription alone DOES NOT constitute gene
expression!
 Post-transcriptional mechanisms play supporting
roles in the control of gene expression:



Alternative RNA splicing – where different mRNA
molecules are produced from the same primary
transcript, depending on which RNA segments are
treated as exons and which as introns.
Regulatory proteins specific to a cell type control
intron-exon choices by binding to regulatory sequences
within the primary transcript.
http://highered.mcgrawhill.com/olc/dl/120080/bio31.swf
Alternative Splicing Offers New
Combinations of Exons = New Proteins
The RNA transcripts of some
genes can be spliced in more
than one way, generating
different mRNA molecules.
With alternative splicing, an
organism can get more than
one type of polypeptide from a
single gene.
Further Control of Gene Expression
 After RNA processing, other stages of gene
expression that the cell may regulate are
mRNA degradation, translation initiation, and
protein processing and degradation.


The life span of mRNA molecules in the
cytoplasm is an important factor in determining
the pattern of protein synthesis in a cell.
Most translational control mechanisms block
the initiation stage of polypeptide synthesis,
when ribosomal subunits and the initiator
tRNA attach to an mRNA.
Protein Processing and Degradation
 The final opportunities for controlling gene
expression occur after translation:



Protein processing – cleavage and the
addition of chemical groups required for
function.
Transport of the polypeptide to targeted
destinations in the cell.
Cells can also limit the lifetimes of normal
proteins by selective degradation – chopped
up by proteasomes.
The Molecular Biology of Cancer
 Certain genes normally regulate growth and division
– the cell cycle – and mutations that alter those
genes in somatic cells can lead to cancer.


Proto-Oncogenes are normal genes that code for
proteins which stimulate normal cell growth and
division.
Oncogenes – cancer causing genes; lead to abnormal
stimulation of cell cycle.
 Oncogenes arise from a genetic changes in protooncogene
1. Amplification of proto-oncogenes
2. Point mutation in proto-oncogene
3. Movement of DNA within genome
Genetic Changes Can Turn Proto-oncogenes into
Oncogenes
http://www.learner.org/courses/biology/units/cancer/images.html
Tumor-Suppressor Genes
 In addition to mutations affecting growth-
stimulating proteins, changes in genes whose
normal products INHIBIT cell division also
contribute to cancer:

Such genes are called tumor-suppressor
genes because the proteins they encode
normally help prevent uncontrolled cell growth.
p53 Tumor Suppressor and ras Proto-Oncogenes
http://www.learner.org/courses/biology/units/cancer/images.html
 Mutations in the p53 tumor-suppressor gene and the ras proto-
oncogene are very common in human cancers.
 Both are components of signal-transduction pathways that
convey external signal to the DNA in the cell’s nucleus.
 Product of ras gene is G Protein (relays a growth signal and
stimulates cell cycle).
 An oncogene protein that is a hyperactive version of this protein
in the pathway can increase cell division.
 P53 protein – “guardian angel of the genome”
 DNA damage (UV, toxins) signals expression of p53 and p53
protein acts as transcription factor for gene p21



p21 halts cell cycle, allowing DNA repair
P53 also can cause ‘cell suicide’ if damage is too great
Many cancer patients p53 gene product does not function
properly!
Figure 19.14 Signaling pathways that regulate cell growth (Layer 2)
RAS and P53 contribute to uninhibited cell stimulation and growth- Tumor Formation
Figure 19.15 A multi-step model for the development of colorectal cancer
Review: Structure/Function of Eukaryotic Chromosomes
•
Chromatids
–
–
•
2/sister/pari/identical DNA/ genetic information
distribution of one copy to each new cell
Centromere
–
–
•
noncoding/uncoiled/narrow/constricted region
joins/holds/attaches chromatids together
Nucelosome
–
–
•
histones/DNA wrapped arround special proteins
packaging compacting
Chromatin Form (heterochromatin/euchromatin)
–
heterochromatin is condensed/supercoiled
•
–
euchromatin is loosely coiled
•
•
proper distribution in cell division (not during replication)
gene expression during interphase/replication occurs when loosely packed
Kinetochores
–
–
•
disc-shaped proteins
spindle attachment/alignment
Genes or DNA
–
–
•
brief DNA description
codes for proteins or for RNA
Telomeres
–
–
tips, ends, noncoding repetitive sequences
protection against degradation/ aging, limits number of cell divisions
Useful Animation Websites
 http://highered.mcgraw-
hill.com/olc/dl/120080/bio31.swf
 http://highered.mcgrawhill.com/olc/dl/120077/bio25.swf
 http://highered.mcgrawhill.com/olc/dl/120080/bio28.swf
 http://highered.mcgrawhill.com/olc/dl/120082/bio34b.swf
 http://www.learner.org/courses/biology/units/c
ancer/images.html