DNA Structure & Gene

Expression
Ms. Martel
 3.1 – DNA STRUCTURE
DNA is a chain of nucleotides.
Each nucleotide is made up of
three subunits.
Phosphoric acid (phosphate
group)
Pentose sugar (deoxyribose)
Nitrogen containing base
There are 4 possible bases.
Two are purines with a double ring:
Adenine (A) and Guanine (G)
Two are pyrimidines with a single
ring: Thymine (C) and Cytosine (C)
A DNA strand has a backbone made up of
alternating phosphate and sugar molecules.
The bases are attached to the sugar but project
to one side.
DNA’s two strands twist about one another in the
form of a double helix.
The strands are held together by hydrogen
bonding between the bases: A&T forming two
hydrogen bonds, and G&C forming three
hydrogen bonds.
Purine is always paired with a
pyrimidine.
This is called complementary
base pairing.
When the DNA helix unwinds,
it resembles a ladder.
The sides of the ladder are the
sugar-phosphate backbones,
and the rungs of the ladder are
the complementary paired
bases.
The two DNA strands are
antiparallel, meaning they
are oriented in the opposite
direction.
3.2 – DNA REPLICATION

 Each new cell requires an exact copy of the DNA

contained in the chromosomes.
 DNA replication is the process of copying one DNA
double helix into two identical double helices.
The process is carried out by an enzyme called
DNA polymerase.
DNA polymerase uses each original strand as a
template for the formation of a complementary
new strand.
Because of this DNA replication is termed
semiconservative.
1. The enzyme DNA helicase
unwinds and “unzips” DNA
by breaking the hydrogen
bonds between the bases.
2. New complementary DNA
nucleotides fit into place by
the process of the
complementary base
pairing. Once positioned
they are joined by DNA
polymerase.
3. DNA strands are oriented in
an antiparallel configuration,
therefore, DNA polymerase
may add new nucleotides to
only one end of the chain.
DNA synthesis occurs in the
opposite direction.
The leading strand follows
the helicase enzyme, while
the lagging strand forms
short segments of DNA
called Okazaki fragments.
4. The enzyme DNA ligase
connects the Okazaki
fragments and seals any
breaks in the sugar
phosphate backbone.

5. The two double helix

molecules are identical to
each other.
Molecular mechanisms of DNA
replication – fig 4.5
 3.3 – GENE
EXPRESSION

Gene expression is the

process of using a gene
sequence to synthesize
(make) a protein.
It relies on the participation
of several different forms of
RNA molecules including:
Messenger RNA – mRNA
Transfer RNA – tRNA
Ribosomal RNA - rRNA
Gene expression requires
two processes called
transcription & translation.
Transcription takes place in
the nucleus and translation
takes place in the
cytoplasm.
During transcription, a
portion of DNA serves as a
template for mRNA
formation.
During translation, the
sequence of mRNA bases
determines the sequence of
amino acids in a
polypeptide.
Genetic information lies
in the sequence of
bases in DNA.
mRNA determines the
sequence of amino acids
in a protein.
Transfer RNA assists mRNA
during protein synthesis
by bringing amino acids
to the ribosomes.
Proteins determine the
structure and function of
cells and the physical
characteristics of the
organism.
Transcription

During transcription, the gene serves as a

template for the production of an RNA molecule.
Genes contain instructions for protein formation,
and the formation of mRNA, tRNA, and rRNA.
We will focus on the formation of mRNA, the first
step in protein synthesis.
Messenger RNA
The purpose of mRNA is to
carry genetic information
from the DNA to the
ribosomes for protein
synthesis.
mRNA is formed through
transcription which occurs in
the nucleus.
It begins when RNA
polymerase binds tightly to a
promoter.
This opens up the DNA helix so
that complementary base
pairing can occur in the same
way as DNA replication.
RNA polymerase inserts
the RNA nucleotides, and
an mRNA molecule
results.
mRNA has a sequence of
bases complementary to
that of the DNA.
The nucleotide thymine is
replaced with uracil in
RNA strands.
Processing of mRNA

 After the mRNA is transcribed, it must be processed

before entering the cytoplasm.
 Most genes in humans are interrupted by segments
of DNA that are not part of the gene.
 These portions are called introns.
 The other portions are called exons because they
are expressed.
 Only exons result in a protein product.
 Ordinarily, processing brings together all the exons
of a gene.
Translation

This is the second process by which gene

expression leads to protein synthesis.
Translation requires several enzymes, and several
different types of RNA molecules, including
mRNA, tRNA, and rRNA.
The Genetic Code

The sequence of bases in DNA is transcribed into

mRNA, which codes for a sequence of amino
acids to form a polypeptide.
Each triplet of nucleotides is called a codon.
Most amino acids are coded for by more than
one codon.
There are 64 codons, 61 code for amino acids,
the remaining are stop codons.
 Transfer RNA

Transfer RNA molecules bring amino

acids to the ribosomes, the site of
protein synthesis.
On one end of the tRNA molecule is the
amino acid, and on the other end is an
anticodon.
An anticodon is a triplet of 3 bases
complementary to the codon of mRNA.
When a tRNA-amino acid complex
comes to the ribosome, its anticodon
pairs with an mRNA codon.
During transcription, the base sequence in DNA
is copied into a sequence of bases in mRNA.
During translation, tRNA’s bring amino acids to
the ribosomes in the order dictated by the base
sequence of mRNA.
The sequence of amino acids form a
polypeptide chain, aka a complete protein.
 Ribosomes and Ribosomal RNA

Ribosomes are found in the cytoplasm

and on the ER where translation also
occurs.
Ribosomes are composed of many
proteins and several ribosomal RNA’s.
rRNA is produced in the nucleolus within in
nucleus.
The rRNA joins with proteins manufactured
in the cytoplasm to form two ribosomal
subunits.
A ribosome has a binding site
for mRNA as well as for 3 tRNA
molecules.
These binding sites facilitate
complementary base pairing
between tRNA anticodons
and mRNA codons.
As ribosomes moves down
the mRNA molecule, new
tRNAs arrive, and a
polypeptide forms and grows
longer.
Translation terminates once
the polypeptide is fully
formed and an mRNA stop
codon is reaches.
Translation Requires Three Steps

During translation, the codons of an mRNA base

pair with the anticodons of tRNA molecules, who
are carrying a specific amino acid.
The order of the codons, determines the
sequence of amino acids in a polypeptide.
Protein synthesis involves three steps: initiation,
elongation, and termination.
Initiation
Initiation is the step that brings all the translation
components together.
Initiation factor proteins assemble the ribosome
subunits, as well as the mRNA, and initiator tRNA.
The small ribosomal subunit attaches to the mRNA
start codon (AUG).
The initiator anticodon UAC pairs with the start
codon, and the large ribosomal subunit joins the
small.
A ribosome has three binding sites for tRNA.
P site – peptide site
A site – amino acid site
E site – exit site.
The initiator tRNA binds to the P site.
The A site is for tRNA carrying the next amino
acid.
Elongation

This is the step in which a polypeptide increases in length one

amino acid at a time.
Elongation requires elongation factors, which facilitate the
binding of tRNA anticodons to mRNA codons at a ribosome.
Elongation is a series of 4 steps.
• 1. A tRNA with an
attached peptide is
already at the P
site.
• The tRNA carrying
the next amino
acid in the chain is
arriving at the A
site.
2. Once the next
tRNA is in place at
the A site, the
peptide chain will
be transferred to
this tRNA.
3. energy is needed
to make this
transfer.
The energy forms a
peptide bond,
which makes the
peptide one amino
acid longer by
adding the peptide
from the A site.
4. finally, translocation
occurs.
The mRNA moves forward
one codon length.
The peptide bearing tRNA
is at the P site.
The “spent” tRNA now
exits.
The new codon is at the
site and is ready to receive
the next complementary
tRNA.
Termination
This is the final step in protein
synthesis.
Here the polypeptide and the
assembled components are
separated from one another.
Termination requires the stop
codon and a protein called a
release factor which cleaves the
polypeptide from the last tRNA.
Then the polypeptide begins to
take on its 3-D shape.
Review of Gene Expression

 A gene is expressed when its protein product has

been synthesized.
 Protein synthesis requires the process of transcription
and translation.
 During transcription, a segment of a DNA strand
serves as a template for the formation of mRNA.
 During translation, tRNAs bring attached amino
acids to the ribosomes.
tRNA anticodons pair with codons, the amino acids
become sequences in the order originally specified
by DNA.
3.4 – GENE MUTATIONS & CANCER

A gene mutation is a permanent change in the

sequence of bases in DNA.
The effect of this change can range from no
effect to complete inactivity.
Germ-line mutations occur in the sex cells and
can be passed to subsequent generations.
Somatic mutations occur in the body’s cells are
not passed on to future generations.
 Causes of
Mutations

Gene
mutations may
be caused by:
Errors in
replication
Mutagens
The activity of
transposons
Errors in Replication

These are a rare source of mutations.

DNA polymerase, the enzyme that carries out
replication, and proofreads the new strand
against the old.
Typically mismatched pairs are then replaced
with the correct nucleotide.
There is typically only one mistake for every 1
billion pairs replicated.
Mutagens
These are environmental
influences that cause
mutations in humans.
This includes radiation and
certain organic chemicals.
The rate of mutations
resulting from mutagens is
generally low because
DNA repair enzymes
constantly monitor and
repair any irregularities.
Transposons
These are specific DNA sequences that have the
ability to move within and between chromosomes.
This sometimes alters neighboring genes by increasing or
decreasing their expression.
 Effect of
Mutations on
Protein Activity
Point mutations
involve a
change in a
single DNA
nucleotide.
Therefore a
possible change
in an amino
acid.
Frameshift mutations occur most often because
one or more nucleotides are either inserted, or
deleted from DNA.
The result can be a completely new sequence of
codons and nonfunctional proteins.
Here is how this occurs – codons are read from a
starting point as in the sentence:
THE CAT ATE THE RAT
If the letter C is deleted, the reading frame is
shifted:
THE ATA TET HER AT-
Nonfunctional Proteins

A nonfunctioning protein can have a dramatic

effect on phenotype.
Cell reactions that build up or break down
biological molecules operate in a sequential
series.
This is called a metabolic pathway.
Each step is regulated by the activity of a
particular enzyme.
If a faulty code for enzyme Ea is inherited,
a person is not able to convert molecule A
to B.
Molecule A (phenylalanine) builds up in the
system, and can cause mental impairment and
other symptoms of PKU.
Or, if a person inherits a faulty code for enzyme
Eb, this individual will develop albinism.
Mutations Can Cause Cancer
The development of cancer involves a series of
accumulating mutations that an be different for
each type of cancer.
Tumor suppressor genes ordinarily stop cell
division
Proto-oncogenes stimulate cell division, but are
usually turned off in fully differentiated non-
dividing cells.
When proto-oncogenes mutate, they become
oncogenes that are active all the time.
 Carcinogenesis begins with the
loss of tumor-suppressor gene
activity.
When tumor suppressor
genes are inactive and
oncogenes active, cell
division occurs
uncontrollably.
 Cancers usually follow a
common multistep progression.
Most begin as abnormal cell
growth that is benign, or
noncancerous.
Additional mutations may
cause the abnormal cells to
fail to respond inhibiting
signals.
The growth is now malignant
meaning is it cancerous and
has the ability to spread.
Characteristics of Cancer Cells

Cancer cells are genetically unstable.

Cancer cells appears to be linked to
mutagenesis.
This allows the cell to continually divide until a
tumor forms.
Tumor cells undergoes multiple mutations and
also tend to have chromosomal aberrations and
rearrangements.
Cancer cells do not correctly regulate the cell
cycle.
The normal controls of the cell cycle do not
operate to stop the cycle, and allow them to
differentiate.
Therefore cancer cells are nonspecialized
Both the rate of cell division and the number of
cells increase.
Cancer cells escape the signals for cell death.
A cell that has genetic damage or problems with
the cell cycle will initiate apoptosis.
Cancer cells do not respond to internal signals to
die, and continue to divide even with genetic
damage.
Normal cells have a built-in limit to the number of
times they can divide before they die.
Cancer cells turn on a gene that allows them to
divide incessantly, exhibiting characteristics of
“immortality.”
Cancer cells can survive and proliferate
elsewhere in the body.
Cancer cells travel through the blood and
lymphatic vessels and invade new tissue and form
new tumors.
This process is known as metastasis.
As the tumor grows it must increase the blood
supply through angiogenesis.
This robs normal tissues of nutrients and oxygen.
 3.6 – BIOTECHNOLOGY
PRODUCTS AND GENE
THERAPY

Transgenic bacteria,
plants, and animals
are often called
genetically modified
organisms (GMO’s)
The products they
produce are called
biotechnology.
Transgenic Bacteria

Transgenic bacteria are grown in huge vats

called bioreactors.
The bacteria express the cloned gene, and the
gene product is usually collected from the
medium the bacteria are grown in.
The products found in the medium can include
items such as insulin, human growth hormone,
and hepatitis B vaccine.
Transgenic bacteria
have many uses
including but not limited
to:
GM bacteria can be
used to help strawberries
be resistant to frost.
GM bacteria have been
developed to eat oil that
can help clean up oil
spills.
Transgenic Plants
With the help of
biotechnology, scientists
have developed a plant
known as the pomato.
Which produces potatoes
below ground and tomatoes
above ground.
They have also developed
soybeans that are resistant to
common herbicide that is
sprayed to kill weeds that
compete with soybeans.
Transgenic Animals

Techniques have been developed to insert

genes into the eggs of animals.
One application of this is gene farming.
This is the use of transgenic farm animals to
produce pharmaceuticals.
The desired proteins appear in the animals milk
where humans are able to harvest proteins or
hormones such as human growth hormone.
Gene Therapy

If a genetic disorder is detected, gene therapy

can sometimes be a course of treatment.
Gene therapy is the insertion of genetic material
into human cells for the treatment of genetic
disorder or other illnesses.
Viruses that are modified to be safe, can be used
to transport a normal gene into the body.
Another way is to inject the gene directly into a
particular region of the body.
Ex Vivo Gene Therapy

One method of ex vivo gene therapy involves bone

marrow stem cells being removed from the patient,
and infecting them with a virus that carries a normal
gene, so it can be inserted into their DNA.
The cells are then returned to the patient, where they will
ideally produce more cells with the normal gene.
In Vivo Gene Therapy

Gene therapy is increasingly relied upon as a

part of cancer treatment.
Genes are being used to make healthy cells
more tolerant of chemotherapy, while making
tumor cells more sensitive.
This could significantly increase the effectiveness
of the chemotherapy, without as many adverse
side effects.