
Gene Expression and Regulation

The link between DNA and protein
DNA contains the “molecular blueprint” of every
cell
 Proteins are the construction workers of the cell
 Proteins control cell shape, function, reproduction,
and synthesis of biomolecules
 Therefore, there must be a flow of information from
DNA to protein


DNA provides instructions for protein
synthesis via RNA intermediaries



DNA in eukaryotes is kept in the nucleus
Protein synthesis occurs at ribosomes in the
cytoplasm
RNA differs structurally from DNA in three ways
 RNA has the sugar ribose
 RNA is usually single-stranded
 RNA contains the nitrogenous base uracil (U)
instead of thymine (T)

DNA provides instructions for protein
synthesis via RNA intermediaries

There are three types of RNA involved in protein
synthesis
 Messenger RNA (mRNA) carries a copy of DNA
gene information to the ribosome in the cytoplasm
 Ribosomal RNA (rRNA) plus proteins make up
the structure of ribosomes
 Transfer RNA (tRNA) brings amino acids to the
ribosome

DNA provides instructions for protein
synthesis via RNA intermediaries

RNA occurs in many other roles besides protein
synthesis
 RNA is used as the genetic material in some
viruses, such as HIV
 Ribozymes – enzymatic RNA
 “Regulatory” RNA
 MicroRNA

Overview : Genetic information is transcribed
into RNA and then translated into protein
mRNA carries the code for protein synthesis from
DNA to the ribosomes
 Ribosomal rRNA and proteins form ribosomes
 Transfer tRNA carries amino acids to the ribosomes
for addition to the growing protein


Overview: Genetic information is transcribed
into RNA and then translated into protein

DNA directs protein synthesis in a two-step process
1. Transcription - Information in a DNA gene is
copied into RNA (like a court transcription – same
language just a copy of information)
2. Translation - the genetic information contained in
the mRNA is converted to another language by
Messenger RNA, tRNA, amino acids, and a
ribosome, to synthesize a protein
gene
DNA
(nucleus)
(cytoplasm)
Transcription of the
gene produces an
(a) Transcription
mRNA with a
nucleotide sequence
complementary to one
messenger RNA of the DNA strands
Translation of the mRNA
produces a protein molecule
with an amino acid sequence
determined by the nucleotide
sequence in the mRNA
(b) Translation
ribosome
protein
Fig. 12-2

The genetic code uses three bases to specify an
amino acid


The genetic code provides the rules
Given that there are 20 amino acids but only four
bases, statistically, the smallest number of bases that
could combine to yield a different sequence for each
of the 20 amino acids is three
 A two-base code could produce only 16
combinations
 The three-base code has the potential to create 64
combinations

The genetic code uses three bases to specify an
amino acid

Marshall Nirenberg and Heinrich Matthaei cracked
the genetic code by creating artificial mRNAs of
known sequence and observing what proteins they
produced
 For example, an mRNA strand composed entirely
of uracil (UUUUUUUU…) produced a protein
consisting entirely of the amino acid phenylalanine
 Therefore, they concluded that the triplet UUU is
the codon for phenylalanine

The genetic code uses three bases to specify an
amino acid




Base triplets in DNA (sequence of 3 nucleotides)
Codons in mRNA specifies a unique amino acid in
the genetic code
Each mRNA also has a start codon (AUG) and one of
three stop codons (UAG, UAA, and UGA)
Some amino acids are specified by as many as six
different codons

The genetic code uses three bases to specify an
amino acid

Decoding the codons of mRNA is the job of tRNA
and ribosomes
 Each unique tRNA has three exposed bases, called
an anticodon, which are complementary to codon
bases in mRNA

Overview of transcription

Transcription of a DNA gene into RNA has three
stages
1. Initiation - A promoter region at the beginning of
the gene marks where transcription is to be
initiated
2. Elongation - The “body” of the gene corresponds
with where elongation of the RNA strand occurs
3. Termination - A termination signal at the end of
the gene marks where RNA synthesis is to
terminate
DNA
gene 1
gene 2
gene 3
RNA
polymerase
DNA
direction of
transcription
promoter
beginning of
gene (3´ end)
1 Initiation: RNA polymerase binds to the promoter region of DNA near the beginning of a gene,
separating the double helix near the promoter.
Fig. 12-3 (1 of 4)
RNA
DNA template strand
2 Elongation: RNA polymerase travels along the DNA template strand (blue),
unwinding the DNA double helix and synthesizing RNA by catalyzing the addition of ribose
nucleotides into an RNA molecule (red). The nucleotides in the RNA are complementary to
the template strand of the DNA.
DNA 
C
G
T
A
-
RNA
G
C
A
U
Fig. 12-3 (2 of 4)
Fig. 12-3 (3 & 4 of 4)
termination signal
3 Termination: At the end of the gene, RNA polymerase encounters a DNA sequence
called a termination signal. RNA polymerase detaches from the DNA and releases the
RNA molecule.
DNA
RNA
4
Conclusion of transcription: After termination, the DNA completely rewinds into a
double helix. The RNA molecule is free to move from the nucleus to the cytoplasm for
translation, and RNA polymerase may move to another gene and begin transcription once
again.
gene
growing
end of
RNA
gene
molecules
DNA
beginning
of gene
Fig. 12-4

Messenger RNA synthesis differs between
prokaryotes and eukaryotes

Messenger RNA synthesis in prokaryotes
 Genes for related functions are adjacent and are
transcribed together
 Because prokaryotes have no nuclear membrane,
translation and transcription are not separated in
space or time
 As the mRNA molecule separates from the DNA,
ribosomes immediately begin translating it to
protein
Fig. 12-5
gene regulating
DNA sequencesgene 1
gene 2
gene 3
genes coding enzymes in a
single metabolic pathway
(a) Gene organization on a prokaryotic chromosome
DNA
mRNA
ribosome
direction of transcription
RNA
polymerase
DNA
mRNA
protein
ribosome
(b) Simultaneous transcription and translation in prokaryotes

Messenger RNA synthesis in eukaryotes



In eukaryotes, the DNA is in the nucleus and the
ribosomes are in the cytoplasm
The genes that encode the proteins for a metabolic
pathway are not clustered together on the same
chromosome
Each gene consists of two or more segments of DNA
that encode for protein, called exons, that are
interrupted by other segments that are not
translated, called introns
Fig. 12-6
exons
DNA
promoter
introns
(a) Eukaryotic gene structure
DNA
1 Transcription
pre-mRNA
2 An RNA cap and tail are added
cap
tail
3 RNA splicing
finished mRNA
4 Finished mRNA is moved
to the cytoplasm for translation
(b) RNA synthesis and processing in eukaryotes
introns
are cut
out and
broken
down

Possible functions of intron-exon gene
structure
1.
2.
Through alternative splicing of the exons in a gene,
a cell can make multiple proteins from a single
gene
Fragmented genes may provide a quick and
efficient way for eukaryotes to evolve new proteins
with new functions
 If breaks in chromosomes occur in introns, exons
may remain intact and be spliced to other
chromosomes in ways that produce new, useful
proteins

During translation, mRNA, tRNA, and
ribosomes cooperate to synthesize proteins

Like transcription, translation has three steps
1. Initiation
2. Elongation
3. Termination
Initiation:
amino acid
met
met
tRNA
preinitiation
complex
catalytic site
anticodon
methionine
tRNA
UAC
small
ribosomal
subunit
second tRNA binding site
UAC
mRNA
GC A U G G U U C A
first
tRNA
binding
site
large
ribosomal
subunit
U AC
GC A U G G U U C A
start codon
1 A tRNA with an attached
methionine amino acid binds
to a small ribosomal subunit,
forming a preinitiation complex.
2 The preinitiation complex binds
to an mRNA molecule. The
methionine (met) tRNA anticodon
(UAC) base-pairs with the start
codon (AUG) of the mRNA.
3 The large ribosomal subunit binds
to the small subunit. The methionine
tRNA binds to the first tRNA site on
the large subunit.
Fig. 12-7 (1-3 of 9)
Elongation:
catalytic
site
peptide
bond
U A C C A A
U A C C A A
G C A U GG U U C A
G C A U G G U U C A
initiator tRNA
detaches
C
A A
G C A U G G U U C A U A G
ribosome moves one codon to the right
4 The second codon of mRNA
(GUU) base-pairs with the
anticodon (CAA) of a second
tRNA carrying the amino acid
valine (val). This tRNA binds to
the second tRNA site on the large
subunit.
5 The catalytic site on the large
subunit catalyzes the formation
of a peptide bond linking the
amino acids methionine and
valine. The two amino acids are
now attached to the tRNA in
the second binding site.
6 The "empty" tRNA is released and the
ribosome moves down the mRNA, one
codon to the right. The tRNA that is
attached to the two amino acids is now in
the first tRNA binding site and the second
tRNA binding site is empty.
Fig. 12-7 (4-6 of 9)
Termination:
C A A GU A
C A A G U A
completed
peptide
stop codon
G C A U G G U U C AU A G
C A U G G U U C AU A G
C GA A U C UAGUAA
7 The third codon of mRNA
(CAU) base-pairs with the
anticodon (GUA) of a tRNA
carrying the amino acid
histidine (his). This tRNA enters
the second tRNA binding site
on the large subunit.
8 The catalytic site forms a
peptide bond between the amino
acids, leaving them attached to the
tRNA in the second binding site.
The tRNA in the first site leaves,
and the ribosome moves one codon
over on the mRNA.
9 This process repeats until a
stop codon is reached; the
mRNA and the completed
peptide are released from the
ribosome, and the subunits
separate.
Fig. 12-7 (7-9 of 9)
gene
(a) DNA
A T G G G A G T T
complementary
DNA strand
template DNA
strand
T A C C C
T C A A
etc.
etc.
codons
A U G G G A G U U
etc.
(b) mRNA
anticodons
(c) tRNA
U A C
C C U
C A A etc.
amino acids
(d) protein
methionine glycine
Fig. 12-8
valine
etc.
1.
2.
How is genetic material encoded in DNA and
RNA?
Distinguish between transcription and
translation. (define and locate)


Mutations are changes in the base sequence of
DNA caused by mistakes during replication or by
various environmental factors
Mutations take many forms and can affect protein
function in many ways

Mutations fall into five categories
 Inversions
 Translocations
 Deletions
 Insertions
 Substitutions

Inversions and translocations


These mutations may be relatively benign if entire
genes, including their promoter, are merely moved
from one place to another
However, if a gene is split in two, it will no longer
code for a complete, functional protein
 Severe hemophilia is often caused by an inversion
in the gene that encodes a protein required for
blood clotting


Deletions and insertions
Depending on how many nucleotides are involved,
deletions and insertions can cause a misreading of a
gene’s codons during transcription or replication
 The codons in THEDOGSAWTHECAT is
changed by deletion of the letter “E” to THD OGS
AWT HEC AT
 Such mutations are called frameshift mutations

Deletions and insertions
Proteins that result from deletions and insertions
have a very different amino acid sequence and
almost always are nonfunctional
 Deletions and insertions of three nucleotides (or a
multiple of three) do not cause a shift of the reading
frame and, so, may simply subtract or add a
harmless amino acid to the protein


Point mutation (nucleotide substitution)

A point mutation sometimes does not change the
amino acid sequence of the protein
 Because many amino acids are encoded by more
than one codon, the mutation may cause the same
amino acid to be added
 A known point mutation in the beta-globin gene
for hemoglobin causes CTC to change to CTT, but
since both codons code for glutamic acid, the
protein is unchanged

Point mutation (nucleotide substitution)

A mutated protein may function normally
 In beta-globin, a point mutation of the CTC codon to GTC
causes glutamic acid (hydrophilic) to be replaced with
glutamine (also hydrophilic), but the resulting protein
functions well

Point mutation (nucleotide substitution)

Some substitutions cause an altered amino acid
sequence that change protein function dramatically,
usually for the worse
 The substitution of an adenine for a thymine in the
CTC  CAC mutation in a hemoglobin gene
causes valine (hydrophobic) to replace glutamic
acid (hydrophilic)
 Placing this hydrophobic amino acid on the
outside of the hemoglobin molecule leads to the
clumping of hemoglobin and distortion of the red
blood cell seen in sickle cell anemia

Point mutation (nucleotide substitution)


The point mutation may introduce a premature stop
codon, leading to an mRNA that produces an
incomplete protein
Such a mutation in the beta-globin gene prevents
production of functional beta-globin protein
 This leads to beta-thalassemia
 People with this mutation have only alpha-globin
subunits and require frequent blood transfusions
to survive because it doesn’t bind O2 as well.



The human genome contains 20,000 to 30,000
genes
A given cell “expresses” (transcribes) only a
small number of genes
Some genes are expressed in all cells, such as
genes coding for RNAs, since all cells require
proteins

Other genes are expressed only in certain types
of cells, at certain times in an organism’s life, or
under specific environmental conditions
 For example, even though every cell in your body
contains the gene for casein, the major protein in
milk, this gene is expressed only in certain cells in
the breast, only in mature women, and only when
a woman is breast-feeding

Regulation of gene expression may occur at three
different levels
1.
2.
3.

Rate of transcription, regulation determines which genes
in a cell are expressed
Rate of translation, regulation determines how much
protein is made from a particular type of mRNA
At the level of protein activity, regulation determines
how long the protein lasts in a cell and how rapidly
protein enzymes catalyze specific reactions
Although these general principles apply to both
prokaryotic and eukaryotic organisms, there are some
differences as well

In eukaryotic cells, transcriptional regulation
occurs on at least three levels
The individual gene – promoters have several
binding sites
 Regions of chromosomes – too tightly wound
 Entire chromosomes
 In female mammals, one entire X chromosome is
condensed (Barr bodies)


In female mammals, one entire
X chromosome is condensed

This effect can be observed in the
fur patterns of calico cats
 The X chromosome of a cat
contains a gene for fur
pigmentation
 Different patches of skin cells in
a cat inactivate different X
chromosomes