Genetic devices

Lecture 2
By
Alaa Hussein Younus
The Normal Human Chromosomes
• Normal human cells contain 23 pairs of homologous chromosomes:
i. 22 pairs of autosomes.
ii. 1 pair of sex chromosomes.

• Autosomes are the same in males and females

• Sex chromosomes are:
i. XX in females
ii. XY in males.
• Both X are homologous. Y is much smaller than X and has only a few genes.
 Chromosomes
• One member of each chromosome pair is
derived from each parent.
• Somatic cells have diploid complement of
chromosomes i.e. 46.
• Germ cells (Gametes: sperm and ova) have
haploid complement i.e 23.
• Individual chromsomes are recognized by
i. arm lengths ( p- short, q -long).
ii. centromere position (metacentric,
sub-metacentric, acrocentric,
telocentric).
Composition of Chromosome
Figure shows the
bacterial cell, the
genetic material is in
the region called
nucleoid, there is no
nuclear membrane.
 Types of histone modifications
Chromatin Modifications Functions Regulated

Acetylation Transcription, Repair, Replication, Condensation

Methylation (lysines) Transcription, Repair

Methylation (arginines) Transcription
Phosphorylation Transcription, Repair, Condensation
Ubiquitylation Transcription, Repair
Sumoylation Transcription
ADP ribosylation Transcription
Deimination Transcription
Proline Isomerization Transcription

Post-translational modifications on histone proteins alter chromatin structure

and, consequently, chromatin function
Summary of Chromosome Folding
Level of folding Consists of Base pair/turn

DNA double helix Nucleotides 10

Nucleosomes 200 bp each 100

30 Nanometer fiber 6 Nucleosomes /turn 1,200

Loops 50 Solenoids/loop 60,000

Miniband 18 loops 1,080,000

Chromatid 1,000,000 minibands

Central Dogma
• The central dogma of molecular
biology describes the two-step
process, transcription and
translation, by which the
information in genes flows into
proteins:
DNA → RNA → protein
DNA replication
DNA Replication
DNA replication is the process of making new strands of DNA using
another DNA as a template.
- DNA replication is catalyzed by the enzyme, DNA polymerase whose
structure is quite different in both prokaryotic and Eukaryotic cells.
- However, the process is semi-conservative in both prokaryotic and
eukaryotic organisms, This means after the replication, each double
stranded DNA is made up of one original strand (template) and a
newly synthesized strand.
• DNA replication consists of 3 major steps:
Initiation, Elongation and Termination
The DNA
replication is
semi-
conservative
 DNA replication occurs in 5’-3’ direction
 This means the hydroxyl (OH) on the 3’ on the starting
nucleotide attacks the alpha phosphate on the incoming
nucleotide thus establishing a phosphodiester bond
 DNA replication does not start de novo but require short
strings of RNA oligos called primers
 Primers are synthesized by the enzyme primase
DNA replication
 Steps of DNA Replication

1)The first major step for the DNA Replication to

take place is the breaking of hydrogen bonds
between bases of the two antiparallel strands. The
unwounding of the two strands is the starting point.
The splitting happens in places of the chains which
are rich in A-T.
That is because there are only two bonds between
Adenine and Thymine (there are three hydrogen
bonds between Cytosine and Guanine). Helicase is
the enzyme that splits the two strands. The
initiation point where the splitting starts is called
"origin of replication".The structure that is created
is known as "Replication Fork".
• 2) One of the most important steps of
DNA Replication is the binding of RNA
Primase in the initiation point of the 3'-5'
parent chain.
RNA Primase can attract RNA nucleotides
which bind to the DNA nucleotides of the 3'-
5' strand due to the hydrogen bonds
between the bases. RNA nucleotides are the
primers (starters) for the binding of DNA
nucleotides.
Similar processes also happen during the steps of DNA
Replication of prokaryotes though there are some
differences.
• 3) The elongation process is different
for the 5'-3' and 3'-5' template.

• a)5'-3' Template: The 3'-5' proceeding

daughter strand -that uses a 5'-3'
template- is called leading
strand because DNA Polymerase ä can
"read" the template and continuously
adds nucleotides (complementary to
the nucleotides of the template, for
example Adenine opposite to Thymine
etc).
• b)3'-5'Template: The 3'-5' template cannot
be "read" by DNA Polymerase ä. The
replication of this template is complicated
and the new strand is called lagging strand.
In the lagging strand the RNA Primase adds
more RNA Primers. DNA polymerase ĺ reads
the template and lengthens the bursts. The
gap between two RNA primers is called
"Okazaki Fragments".

The RNA Primers are necessary for DNA

Polymerase ĺ to bind Nucleotides to the 3'
end of them. The daughter strand is
elongated with the binding of more DNA
nucleotides.
• 4) In the lagging strand the DNA Pol I -
exonuclease- reads the fragments and
removes the RNA Primers. The gaps are
closed with the action of DNA Polymerase
(adds complementary nucleotides to the
gaps) and DNA Ligase (adds phosphate in
the remaining gaps of the phosphate -
sugar backbone).
• Each new double helix is consisted of one
old and one new chain. This is what we
call semiconservative replication.
• 5) The last step of DNA Replication is the Termination. This
process happens when the DNA Polymerase reaches to an end
of the strands. We can easily understand that in the last
section of the lagging strand, when the RNA primer is
removed, it is not possible for the DNA Polymerase to seal the
gap (because there is no primer). So, the end of the parental
strand where the last primer binds isn't replicated. These ends
of linear (chromosomal) DNA consists of noncoding DNA that
contains repeat sequences and are called telomeres. As a
result, a part of the telomere is removed in every cycle of DNA
Replication.

• 6) The DNA Replication is not completed before a mechanism

of repair fixes possible errors caused during the replication.
Enzymes like nucleases remove the wrong nucleotides and the
DNA Polymerase fills the gaps.

• Termination is achieved with the bi-directional synthesis

converging at a single point called TER
Enzymes of DNA Replication
Helicase: Unwounds a portion of the DNA Double Helix.
• Topoisomerases relieve tensional force generated due to winding
RNA Primase: Attaches RNA primers to the replicating strands.
DNA Polymerase delta (ä): Binds to the 5' - 3' strand in order to bring nucleotides and
create the daughter leading strand.
DNA Polymerase epsilon (å): Binds to the 3' - 5' strand in order to create discontinuous
segments starting from different RNA primers.
Exonuclease (DNA Polymerase I): Finds and removes the RNA Primers
DNA Ligase: Adds phosphate in the remaining gaps of the phosphate - sugar backbone
Nucleases: Remove wrong nucleotides from the daughter strand.
• SSB holds single strands together preventing them to fold and form helical structures