 Gene Control in Eukaryotes
In eukaryotic cells, the ability to express biologically active
proteins comes under regulation at several points:
1. Chromatin Structure: The physical structure of the DNA,
as it exists compacted into chromatin, can affect the ability
of transcriptional regulatory proteins (termed
transcription factors) and RNA polymerases to find access
to specific genes and to activate transcription from them.
The presence modifications of the histones and of CpG
methylation most affect accessibility of the chromatin to
RNA polymerases and transcription factors.
2. Epigenetic Control: Epigenesis refers to changes in the
pattern of gene expression that are not due to changes in
the nucleotide composition of the genome. Literally "epi"
means "on" thus, epigenetics means "on" the gene as
opposed to "by" the gene.
3. Transcriptional Initiation: This is the most
important mode for control of eukaryotic gene
expression. Specific factors that exert control include
the strength of promoter elements within the
DNA sequences of a given gene, the presence or
absence of enhancer sequences (which enhance the
activity of RNA polymerase at a given promoter by
binding specific transcription factors), and the
interaction between multiple activator proteins and
inhibitor proteins.
4. Transcript Processing and
Modification: Eukaryotic mRNAs must be capped
and polyadenylated, and the introns must be
accurately removed (see RNA Synthesis Page). Several
genes have been identified that undergo tissue-specific
patterns of alternative splicing, which generate
biologically different proteins from the same gene.
5. RNA Transport: A fully processed mRNA must leave the
nucleus in order to be translated into protein.
6. Transcript Stability: Unlike prokaryotic mRNAs, whose
half-lives are all in the range of 1 to 5 minutes, eukaryotic
mRNAs can vary greatly in their stability. Certain unstable
transcripts have sequences (predominately, but not
exclusively, in the 3'-non-translated regions) that are
signals for rapid degradation.
7. Translational Initiation: Since many mRNAs have multiple
methionine codons, the ability of ribosomes to recognize
and initiate synthesis from the correct AUG codon can
affect the expression of a gene product. Several examples
have emerged demonstrating that some eukaryotic
proteins initiate at non-AUG codons. This phenomenon
has been known to occur in E. coli for quite some time, but
only recently has it been observed in eukaryotic mRNAs.
8. Small RNAs and Control of Transcript Levels: Within the
past several years a new model of gene regulation has
emerged that involves control exerted by small non-coding
RNAs. This small RNA-mediated control can be exerted
either at the level of the translatability of the mRNA, the
stability of the mRNA or via changes in chromatin
structure.
9. Post-Translational Modification: Common modifications
include glycosylation, acetylation, fatty acylation, disulfide
bond formations, etc.
10. Protein Transport: In order for proteins to be
biologically active following translation and processing,
they must be transported to their site of action.
11. Control of Protein Stability: Many proteins are rapidly
degraded, whereas others are highly stable. Specific amino
acid sequences in some proteins have been shown to bring
about rapid degradation.
Gene Control in Prokaryotes
 genes are clustered into operons: gene clusters that
encode the proteins necessary to perform coordinated
function
 prokaryotic genes that encode the proteins necessary
to perform coordinated function are clustered into
operons.
 The lac operon consists of one regulatory gene
(the i gene) and three structural genes (z, y, and a).
The i gene codes for the repressor of the lac operon.
The z gene codes for β-galactosidase (β-gal), for the
hydrolysis of the disaccharide, lactose into its monomeric
units, galactose and glucose. y gene codes for permease,
increases permeability of the cell to β-galactosides.
The a gene encodes a transacetylase.
 During normal growth on a glucose-based medium,
the lac repressor is bound to the operator region of
the lac operon, preventing transcription. However, in
the presence of an inducer of the lac operon, the
repressor protein binds the inducer and is rendered
incapable of interacting with the operator region of the
operon. RNA polymerase is thus able to bind at the
promoter region, and transcription of the operon ensues.
 The lac operon is repressed, even in the presence of
lactose, if glucose is also present. This repression is
maintained until the glucose supply is exhausted. The
repression of the lac operon under these conditions is
termed catabolite repression and is a result of the
low levels of cAMP that result from an adequate
glucose supply.
Transcription
 DNA is transcribed to make RNA (mRNA, tRNA, and
rRNA)
 Transcription begins when RNA polymerase binds to
the promoter sequence
 Transcription proceeds in the 5'  3' direction
 Transcription stops when it reaches the
terminator sequence
The Process of Transcription
Figure 8.7
The Process of Transcription
Figure 8.7
RNA Processing in Eukaryotes
Figure 8.11
Translation
 mRNA is translated in
codons (three
nucleotides)
 Translation of mRNA
begins at the start
codon: AUG
 Translation ends at
nonsense codons: UAA,
UAG, UGA
Figure 8.2
The Genetic Code
 64 sense codons on mRNA
encode the 20 amino acids
 The genetic code is
degenerate
 tRNA carries the
complementary anticodon
Figure 8.2
The Process of Translation
 Components needed to
begin translations come
together.
Figure 8.9
The Process of Translation
 On the assembled
ribosome, at tRNA
carrying the first amino
acid in paired with the
start codon on the
mRNA.the place where
this firsts tRNA sits is
called the p site.A tRNA
carrying the second
amino acid approaches.
Figure 8.9
The Process of Translation
 The second codon of the
mRNA pairs with a tRNA
carrying the second
amino acids joins to the
seconds by a peptide
bond. This attaches the
polypeptide to the tRNA
in the p site.
Figure 8.9
The Process of Translation
The ribosome moves along
the mRNA until the
second tRNA is in the p
site. The next codon to
be translated is brought
into the a site. The firsts
tRNA now occupies the
e site.
Figure 8.9
The Process of Translation
 The second amino acid is
paired with the start
codon on the mRNA. Is
release from the e site.
Figure 8.9
The Process of Translation
 The ribosome continues
to move along the mRNA
and new amino acids are
added to the polypeptide
Figure 8.9
The Process of Translation
 When the ribosome
reaches a stop codon,
the polypeptide is
released.
Figure 8.9
The Process of Translation
 Finally, the last tRNA is
released ,and the
ribosome comes apart.
The released polypeptide
forms a new protein.
Figure 8.9
Regulation
 Constitutive genes are expressed at a fixed rate
 Other genes are expressed only as needed
 Repressible genes
 Inducible genes
 Catabolite repression
Operon
Figure 8.12
Inducible operon (lac operon)
Figure 8.12
Inducible operon (lac operon)
Figure 8.12
Repressible operon (trp operon)
Figure 8.13
Repressible operon (trp operon)
Figure 8.13
 The trp operon encodes the genes for the synthesis of
tryptophan. This cluster of genes regulated by a
repressor that binds to the operator sequences. The
activity of the trp repressor for binding the operator
region is enhanced when it binds tryptophan known as
a corepressor. Since the activity of the trp repressor is
enhanced in the presence of tryptophan, the rate of
expression of the trp operon is graded in response to
the level of tryptophan in the cell.
 Expression of the trp operon is also regulated
by attenuation.
Attenuation
 The attenuator plays an important regulatory role
in prokaryotic cells because of the absence of
the nucleus in prokaryotic organisms. The attenuator
refers to a specific regulatory sequence that, when
transcribed into RNA, forms hairpin structures to stop
transcription when certain conditions are not met
CATABOLITE REPRESSION
 Many inducible operons are not only controlled by
their respective inducers and regulatory genes, but
they are also controlled by the level of glucose in the
environment. The ability of glucose to control the
expression of a number of different inducible operons
is called CATABOLITE REPRESSION.
Catabolite Repression
(a) Growth on glucose or lactose alone
(b) Growth on glucose and lactose
combined
Figure 8.14
 Lactose present, no
glucose
 Lactose + glucose
present
Figure 8.15