DNA structure and

Function
DR.HAMDAN ZAKI HAMDAN
 Genetic Foundation
❑ Perhaps the most remarkable features of living
cells and organisms is their ability to reproduce
themselves for countless generations.
❑ DNA is the secret of life.
❑ People
changed from nation to others
according to their DNA.
❑ Specific
Race acquires new characteristic
according to the new DNA that engage to.
Johannes Friedrich Miescher
1868
❑ Johannes Friedrich Miescher a Swiss
physician and biologist.
❑ He carried out the first systematic
chemical studies of cell nuclei
❑ He was the first researcher to isolate and
identify nucleic acid.
❑ He isolate a phosphorus-containing
substance, which he called “nuclein,”
from the nuclei of pus cells (leukocytes)
obtained from discarded surgical
bandages. Also from sperm of Salmon.
 Phoebus Levene
❑ Thefirst who discovered
the deoxyribo
nucleotides and named it
Adenine, Guanine,
Thymine and Cytosine.
❑ Thenhe changed the
Miescher’s named
nuclein to a Nueclotides.
 Fredrick Griffith’s Experiment (1928)

❑ Griffith shows that non-virulent

Streptococcus pneumonia
became virulent even after
killing the virulent bacteria by
heating.
❑ He did this by using a lab mice.
 Avery Experiment (1944)
❑ Avery and his colleagues
confirmed the Griffith
observation.
❑ They isolate the DNA among
other bacteria components
from heat-killed bacteria.
❑ And add only the DNA of the
killed bacteria to the non-
virulent bacteria.
❑ Non-surprisingly, the non-
virulent bacteria became
virulent.
Cont.

❑ So they deduced that DNA is responsible

for transforming the Non-virulent bacteria
to virulent.
❑ And this mean DNA is responsible for the
storing and carrying the genetic materials.
❑ Such conclusions open to debate as
protein impurities perhaps the cause of this
transformation.
Cont.

❑ Latertreating DNA with proteolytic enzymes

didn’t harboring the DNA from transforming the
virulence characteristics.
❑ While
treating the DNA with deoxyribonucleases
(DNA-hydrolyzing enzymes) did.
 Alfred D. Hershey and Martha
Chase (1952)
❑ They try to confirm that it is
the DNA not the protein
responsible of the carrying
genetic materials.
❑ They use 2 phage (virus
infecting bacteria).
❑ The first its DNA labelled
with P32 and the second its
protein coat labeled with
S35.
Cont.

❑ Theirresult shows that the DNA not the

protein that lead to cell division and
generate more viruses.
❑ This
finding consolidate the concept of
DNA as a genetic material furthermore.
 Erwin Chargaff 1940

❑ He tries to
quantify the
nucleotides
content in
different
organisms.
 Chargaff’s Experiment

Organism Adenine % Thymine % Cytosine% Guanine %

Octopus 33.2 33.2 17.6 17.6

Sea Urchin 32.8 32.1 17.3 17.7
Rat 28.6 28.4 20.5 21.4
Grasshopper 29.3 29.3 20.7 20.5
Human 30 30 20 20
Chargaff’s conclusion
❑ Thebase composition of DNA generally varies
from one species to another.
❑ DNA specimens isolated from different tissues of
the same species have the same base
composition.
❑ The base composition of DNA in a given species
does not change with an organism’s age,
nutritional state, or changing environment.
Cont.

❑ Nowit is very obvious that the cellular

content of:
A=T.
G=C.
Purine = Pyrimidine
Summation of all = 100%.
Rosalind Franklin and Maurice
Wilkins (1950)
❑ Theyuse X-ray diffraction
pattern.
❑ Their
work shows that
DNA fiber is double
strand helical structure.
James Watson and Francis Crick
1953
❑ They saw the pictures that
made by Franklin and think
about DNA structure.
❑ They get used all the
available information
regarding the DNA.
❑ In 1953 they postulated 3D
model that explain the
Franklin finding and Chargaff
finding and their model
widely accepted.
In 1962 Watson, Crick and Wilkins
Awarded Nobel Prize.
Cont.

❑ RosalindFranklin passed away in1958 suffering from

ovarian cancer.
❑ Unfortunately Nobel prize didn’t awarded to a died
person.
❑ Therefore
her significant contribution to this discovery
passed unnoticed and without acknowledgment.
Human Genome Project
❑ In2003 the first draft for Human Genome
sequences is established.
❑ Thisproject considered starting point for new era
of science and medicine.
❑ HamMap project started to identify genes
associated with human disease and differential
response to pharmaceuticals.
Central Dogma of
Molecular Biology
DNA Structure
DNA Double helix
❑ The two strands run antiparallel and
twisted around an axis.
❑ The
backbone represented by the
deoxyribose-phosphate, while the inward
face represented by the nitrogenous
bases (Stacked together).
Cont.
❑ The twisted movement of the DNA around this
virtual axis make generation of two grooves
structures.
❑ Major and Minor grooves.
❑ Thesegrooves make DNA accessible for the
regulatory proteins, and enzymes responsible
for DNA and RNA synthesis.
❑ Actinomycin,act as anticancer and work by
preventing DNA and RNA synthesis.
Base pairing rule
❑ Always:
❑ Adeninepaired with
Thymine (two hydrogen
bonds).
❑ Guanine paired with
Cytosine (Three hydrogen
bonds).
There are many forms for DNA, at
least 6 forms (A-E and Z).
❑ Watson and Crick in their 1953 model
prescribe the B form, (Physiological DNA).
❑ The B form is said to be right handed.
❑ It has 10 residues per turn.
❑A form is a dehydrated B form.
Structure of DNA
❑ Inhuman cells DNA is present in two organelles
Nucleus and Mitochondria.
❑ Mitochondria contain 1% of the total cellular DNA.
It is circular chromosomes not like nuclear one.
❑ It encodes mainly the respiratory chain enzymes.
❑ Mitochondria is inherited form maternal side.
❑ Sotherefore used as a determinant for the
maternal inherited disease or ethnicity.
Structure of DNA cont.
❑ Single Human cell contain 46 chromosomes.
❑ Remember every chromosomes composed of
DNA.
❑ Collectively all chromosomes in one cell its DNA
length is about 1 Meter.
❑ So, there is a need to compact this DNA.
❑ Therefore,DNA wrapped around a positive
charged protein named Histones to compact
the DNA structure further.
Histones and Nucleosome

❑ Histones
are basic proteins that
form a positive charge protein.
❑ Four
histones protein(H2A, H2B,
H3 and H4) assembled together
and form a core protein called
Nucleosome.
❑ H1 histone protein act as a linker
histones.
Nucleosome
Different function of the histones

❑ It
participate in activation and deactivation of
gene expression.
❑ Assistin chromosome assembly during DNA
replications.
❑ Chromosomal condensation.
❑ Nucleosomes associate with
each other to form a more
compact structure termed
the 30 nm fiber.
❑ Histone H1 plays a role in this
compaction.
❑ The 30 nm fiber shortens the
total length of DNA another
seven-fold.
 Compaction level
in euchromatin

During interphase
most chromosomal Compaction level
regions are in heterochromatin
euchromatic
Chromosome
Cont.
❑ Each nucleated cell have a 44 chromosomes in
addition to 2 sex chromosomes (X or Y).
❑ normal male person karyotyping is 44+ XY. And
normal female karyotyping is 44+XX.
❑ Every chromosome composed of sister
chromatids linked together by a centromere. It is
rich in AT sequences and complexed with
proteins.
❑ The chromosomal ends named as telomere. It is
composed of TG repeat region.
Elizabeth Blackburn
52
53
High resolution karyotype
 Heterochromatin vs Euchromatin
❑The compaction level of interphase chromosomes
is not completely uniform
❑Euchromatin:
❑Lesscondensed regions of chromosomes.
❑Transcriptionally active.
❑Heterochromatin:
❑Tightly compacted regions of chromosomes
❑Transcriptionally inactive (in general).
❑Constitutive Heterochromatin ?
❑Facultative Heterochromatin. ? Cell differentiation.
 What make the pancreatic cell 58
secrete insulin not a hydrochloric
acid?
❑ Although both
cells (pancreatic
and gastric cells)
share the same
genetic
information!!
 Cont. 60

❑ This is the direct result of

regulation of gene
expression since intra
uterine life which lead
to cellular
differentiation.
 Cont. 61

❑ Collectivelyit lead to
development of a
complex human body
with multiple and
diverse specialized
cells.
Coding DNA

❑ This
is part of DNA that will give rise to
mRNA and then protein upon expression
and translation.
❑ There
is about 30 000- 40 000 genes in the
human genome.
❑ Onlyhalf of these genes functions are
known.
❑ Each gene is composed of introns and (9
in average)exons. E.g of the longest gene
found is titin which have 178 exons !
❑ There
is some non-coding region in the
mRNA known as 5-UTR and 3-UTR.
Discontinuous gene

❑ Thisis usually located at different regions in

the DNA and could be separated by
thousand of base pairs.
❑ Perhapsanother gene found inside nothe
gene sequence.
Pseudogenes
❑ This
is a non-functional copy of a gene which
occurs as a result of change in the gene
sequence.
❑ Structurally it is similar to the functional gene.
❑ There are two types:
❑ Conventional pseudogenes: It though it have
some evolutionary basis and the gene lost its
activit by mutations.
 Cont.
❑ Processed
pseudogenes:
This is the insertion of
the mRNA of that
gene in the DNA. By
doing so the gene
have no promoter
region which is
necessary to the
expression process.
DNA repeats
❑ represents about 44% of the whole
genome.
❑ Generally two types:
❑ Genome wide-repeats:
This are four types and shared its originated
from a transposable elements. These are
LINEs, SINEs, LTR and DNA transposons. Some
mediated by RNA and other not.
❑ Tandem repeats:
Microsatellite is an example and
dinucleotide is the commonest one.
NON coding DNA
❑ About 1.1% of the total human genome is coding
for the human proteins.
❑ That means almost all the chromosomal DNA is
not coding.
❑ So what are the functions of these non coding
DNA regions?
1. Act as a regulator for gene expression in different
stages (differentiaon, adaptation to stress
conditions, ..).
2. Protective functions for the coding DNA.
❑ Noncoding DNA is composed of repetitive DNA
which is composed of 30%.
❑ These repeats such as microsatellites sequences
which is found as dinucleotide repeats as (AC) or
trinucleotide repeats as (CGG).
❑ These trinucleotide repeat if increased in numbers
is associated with some diseases like Fragile X
syndrome and Huntington chorea.
Physical characteristic of DNA
❑ It is widely accepted that DNA have a
negative charge.
❑ DNA could be denaturated if exposed to:
1. High temperature more than 95C (please
notice that this high temperature will just
separate the two strands which are fixed
by hydrogen bonds not the
phosphodiester bond), additionally area
rich in GC region need higher
temperature than AT rich region !! Why?.
Cont.
❑ Basic pH will also cause disruption of the
hydrogen bonding which end with separation
of two strands.
❑ Surprisingly, DNA strands have an ability to re-
connect together after removing the
denaturating agents (cooling of temperature
and readjust the pH).
❑ this character make scientist to think
differently about DNA specially in
recombinant technology.
RNA structure and
Function
Importance of RNA

❑ Since 1950 scientist pay more attention to

RNA.
❑ As DNA is just confined to nucleus and to
carry the gene messages they should be
another molecule that carry this message
from nucleus to cytosol.
❑ RNA levels increase during protein synthesis.
Cytosolic and nuclear RNA, therefore it was
though it is the primary candidate for
carrying this messages.
François Jacob and Jacques
Monod RNA 1961

❑ Theyproposed the
name “messenger
RNA.
Cont.

❑ ThemRNA in eukaryote usually carry one

gene transcript which code for one
protein. While in prokaryote it carries more
than one gene transcript that code for
more than one protein.
❑ Accordingly, named monocistoronic or
polycistronic.
RNA structure

❑ They
are polymers of ribonucleotides (Purine
and Pyrimidine).
❑ They
are connected to each others by 3-5
phosphodiester bond similar to that in DNA.
Differences between RNA and DNA
❑ RNA nucleotides have a ribose sugar not deoxy
ribose sugar as in DNA.
❑ Nucleotides include (A,G,C and U) instead of
Thymidine.
❑ RNA usually found in single strand. Exception is
forming hairpin structure.
❑ There
are no base pairing role as in DNA, so the
content of A not equal U nor G equal C.
Cont.

❑ RNA easily hydrolyzed by alkali while DNA

is not.
❑ RNAis distributed in cytosol, nucleus, and
mitochondria.
❑ DNA and RNA differed in their functions.
❑ What is the function of DNA?
Functions of RNA
❑ AlthoughRNA have several types, their functions
in general contributed to protein synthesis.
❑ Some viruses have RNA instead of DNA to carry
their genetic materials.
❑ However, some viruses (HIV) posses an enzyme
named reverse transcriptase which convert the
viral genome RNA to DNA.
Messenger RNA (mRNA)
❑ This class of RNA its major function is
conveying the gene messages from the DNA
to ribosomes in the cytosol to be translated as
a protein.
❑ Its
stability and size are highly variable.
However in general it is stable.
 Eukaryotic mRNA have special
structure:
1. Cap structure (7-methylguanosine triphosphate).
This cap attached to the first mRNA nucleotide which
is also methylated.
What is the function of the cap?
Protecting from sun light!!? Sure not
Help in RNA recognition to ribosome.
Protect the mRNA against the attack of hydrolytic
enzymes (5′-exonucleases enzyme).
Poly A tail

❑ The 3 end of mRNA recive polymers of

Adenine that about 20-250. hence named
poly A tail.
❑ Its
function also to protect the mRNA from
hydrolytic enzymes (3 exonuclease).
TRANSFER RNA (tRNA)

❑ Itis considered as adaptor molecule for

protein synthesis.
❑ Its size is relatively same 74-95 nucleotides.
❑ Itis also transcribed from the DNA and
then reach the cytosol.
❑ There are at least 20 species of tRNA (one
tRNA for every amino acid).
Cont.
❑ tRNA folded and formed cloverleaf
shape structure.
❑ All tRNA have four major arms:
❑ acceptor arm (CpCpAOH), in this arm the amino
acids will be attached to tRNA through the
hydroxyl group of the adenine.
❑D arm.
❑ TѪC arm.
❑ Extra arm.
Cont.

❑ tRNA considered unstable in eukaryotes.

Ribosomal RNA (rRNA)

❑ Itis considered as machinery for protein

synthesis.
❑ Its
location in the cytosol attached with
endoplasmic reticulum.
❑ Itis receiving the mRNA and then tRNA
identify the amino acids then protein
synthesis start sequentially.
Cont.

❑ Structurally, rRNA composed of 2 major subunits:

❑ Larger subunits which weight 60 S (Svedberg
units).
This subunit further have other smaller subunits (5S,
5.8 S, and 28S rRNA in addition to protein).
❑ Smaller units which weight 40 S. this also have
further single smaller subunit (18S in addition to
proteins).
Cont.

❑ It is quite stable compared to other RNA.

❑ rRNA component performs the peptidyl
transferase activity and thus is an enzyme
(a ribozyme). Remember the structure of
enzymes.
 DNA

mRNA

rRNA

Growing Peptide
Amino acids
Small nuclear RNA (snRNA)

❑ TheseRNA molecules in general used to

process the RNA molecule and also used
for gene regulation.
Interference RNA (iRNA)

❑ Sometimes named as short interfering RNA

or silencing RNA.
❑ It has two or single strand RNA.
❑ Itis RNA that acts like a defense
mechanisms against abnormal RNA
whether it is originated from infectious
organisms or cancer cells.
Thank You