Lecture 7

Introductory
Genetics
GEN201
Prof. Ranya Amer Dr. Zahra
Hussein
Table of contents
DNA
structure Types of DNA
01 02
DNA Translating
Replication the genetic
03 04 code
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1
DNA Structure
 DNA: The Basis of Life

• DNA is also referred to as “the genetic material”

or “the molecule of heredity”.

• Every living thing on earth, from the smallest

bacteria to the largest whale, uses DNA to store
genetic information and transmit that info from
one generation to the next.

• The structure of DNA provides a simple way for

the molecule to copy itself and protects genetic
messages from getting garbled.
 Deconstructing DNA
• The DNA length in one cell would be a little over six feet long
(2M)!
• We have around 100,000,000,000,000 cells in our body.
• Each of us has enough DNA to reach from here to the sun and
back, more than 300 times.
How is all of that DNA packaged so tightly into
chromosomes and squeezed into a tiny nucleus of 10
micrometers?
• DNA is tightly packed in a process called DNA Packaging

“Folding the whole DNA of organism into a compact

 Chemical composition of the DNA
• Each DNA molecule contains four specific nitrogen-rich bases:
Adenine (A), Guanine (G), Thymine (T), Cytosine ©
❑ Purines: The two purine bases are adenine and guanine. The
word purine means a compound composed of two rings.
❑ Pyrimidines: The two pyrimidine bases are thymine and
cytosine. The term pyrimidine refers to chemicals that have a
single-ring structure.
Purine is a heterocyclic aromatic organic compound composed of a
pyrimidine ring fused with an imidazole ring.
• DNA is a linear, double helical structure.
• Nucleotides are arranged in two long strands that form a spiral
called a double helix.
• The structure of the double helix is somewhat like a ladder, with
the base pairs forming the ladder’s steps and the sugar and
phosphate molecules forming the vertical sides.
• Each DNA strand is a long polymer of simple units called
nucleotides, with a backbone made of sugars and
phosphate groups joined by phosphor diester bonds.
• Guanine is paired with cytosine by three H-bonds
• Adenine is paired with thymine by two H-bonds
Nucleotide is a monomer: composed of three
function groups
• Nucleotides are the true building blocks of DNA. They are composed
of deoxyribose sugar (pentose sugar), one phosphate, and one
of the four bases either purine (two-ring structure, A and G) or
pyrimidines (single-ring structure, C and T)
 Doubling up: Adding the second strand
• The second strand is oriented in opposite directions, which is
called Antiparallel
• Adenine complements thymine, and guanine complements
cytosine.
• Therefore, in every DNA molecule, the amount of one base is
equal to the amount of its complementary base. This
condition is known as Chargaff’s rules.
• Why are DNA strands antiparallel? due to the high level of
stability achieved in an antiparallel configuration. The
importance of an antiparallel DNA double helix structure is
because of its hydrogen bonding between the
 Why is DNA a stable storage form for genetic
• DNA is more resistant to hydrolysis because it contains deoxyribose
information?
sugar, which is characterized by the presence of an H atom instead
of OH in position 2 that doesn’t promote hydrolysis of the
phosphodiester bond.
• Thymine in the place of uracil “a very friendly base” confers
additional stability because thymine has greater resistance to
photochemical mutation, making the genetic material more stable.
• DNA is double-stranded which provides a template for the
correction of errors and the removal of DNA damage.
• Presence of a large number of hydrogen bonds between
complementary base pairs in a DNA double helix.
Why are the strands of a DNA
molecule said to be complementary?
● Due to this base pairing principle the bases from one strand
consistently paired on its match bases on the opposite strand (ex.
A=T).
● Each DNA strand has the necessary information to make a copy
of the other DNA strand.
● The two strands are not identical but are complementary.
Note
• A DNA strand is measured by the number of base pairs it has.
• The sequence of bases in DNA isn’t random.
• The genes are encoded in the base sequences.
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2
Types of DNA
 Nuclear DNA
• DNA found in cell nucleolus
• It’s responsible for the majority of functions that cells carry
out.
• Large size (over a million bases). The nuclear genome of
humans comprises approximately 3.2 billion base pairs.
• Nuclear DNA is packaged into many chromosomes and
passed from parent to offspring (bi-parental inheritance).
• Low mutation rate.

When it says “sequencing of the human genome”, they mean

 Mitochondrial DNA (mtDNA)
• For a long time, biologists thought our DNA resides only in the
nucleus.
• In 1963, a couple at Stockholm University discovered DNA outside
the nucleus in structures called mitochondria.
• Mitochondria are cellular organelles located in the cytoplasm and
represent the site of the cell’s energy production (ATP
production).
• Mitochondrial DNA is the circular chromosome found inside
mitochondria.
Characteristics:
• Single Circular double-stranded DNA molecule
• Is inherited only from the mother
• Is very short (16 kb in length)
• Codes for only 37 genes which responsible for making
enzymes involved in oxidative phosphorylation (ATP
production)
• Has no reparation system (high mutation rate)
 Although sperms contain many mitochondria, Why is mitochondrial
DNA inherited only from mothers and not fathers?
● Sperm contain relatively many mitochondria, but these are degraded
after fertilization (paternal mitochondria might have an internal self-
destruct mechanism).
● The egg has thousands of mitochondria which are passed to the
developing embryo. Although the reasons are not fully understood but
might be for the following reasons:
1.Sperm needs lots of energy to fertilize an egg because it has to swim as fast
as it can for several hours. During that time, its mitochondria generate
maximum energy, metabolizing sugar and generating lots of reactive
oxygen which may damage the mitochondrial genome.
2. It might be also due to the sperm providing almost no cytoplasm
 Chloroplast DNA (cpDNA)
• cpDNA is the DNA located in chloroplasts, which are
photosynthetic organelles located only within the cells of plants
and photosynthetic algae.
• Similarities between the DNA of mitochondria and
chloroplasts and the DNA of bacteria are an important line of
evidence supporting the endosymbiotic theory, which suggests
some of the organelles in eukaryotic cells originated as free-living
prokaryotic cells.
Characteristics:
• Circular DNA double-stranded molecules.
• Inheritance of cpDNA can be either maternal or paternal.
• Size range 120-200 kb (majority of plants fall into 120-160
kb)
• Contains about 120-130 genes, primarily participating in
photosynthesis and protein synthesis.
• Low mutation rate.
 Mitochondrial DNA Chloroplast DNA
Found inside the mitochondria, ATP Located in chloroplasts, a photosynthetic
producing organelles located in cytoplasm organelles located in the cytoplasm of plants
in eukaryotes. and photosynthetic algae
Single Circular double stranded DNA Single Circular double stranded DNA molecule
molecule
Inherited only from mother (maternal) Inheritance can be either maternal or paternal

Very short (16 kb in length) Size range 120-200 kb

Contains only 37 genes, responsible for Contains about 120-130 genes, primarily for
enzymes involved in the oxidative photosynthesis and protein synthesis
phosphorylation (ATP production)
Has no reparation system (high mutation Low mutation rate
rate)
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3
DNA Replication
 DNA Replication
• DNA replication is the process by which the
genome's DNA is copied in cells. Before a
cell divides, it must first copy (or replicate) its
entire genome so that each resulting daughter
cell ends up with its complete genome.

• Replication is part of reproduction (producing

eggs and sperm), development (making all
the cells needed by a growing embryo), and
maintaining normal life (replacing skin, blood,
and muscle cells).
DNA Replication
● The process of replication follows a very specific
order:
1. The helix is opened up to expose single strands of
DNA.
2. Nucleotides are strung together to make new
partner strands for the two original strands.

● For successful replication, several players must be

present:
- Template DNA is a double-stranded molecule that
provides a pattern to copy
- Nucleotides are the building blocks necessary to make
new DNA
- Enzymes and various proteins that do the unzipping
and assembly work of replication (DNA synthesis).
 DNA Replication
1. Replication Initiator Protein, DNaA.
- Replication always starts at specific
locations on the DNA, which are called
origins of replication. The origin
sequence is recognized by the replication
initiator protein, DnaA.
- The origin sequence has mostly A/T
base pairs making the DNA strands
easier to separate.

- Prokaryotes, for example E. coli, have a

single origin of replication on its
chromosome.
- Eukaryotes usually have multiple linear
chromosomes, each chromosome with
 DNA Replication
2. DNA Helicases
- Attaches to replication origins, catalyzes the disruption of the hydrogen bonds
that hold the two strands of double-stranded DNA together.
3. Single Strand Binding Proteins (SSBs)
- Stabilize the separated strands of DNA near the replication fork and prevent
their re-annealing, keeping them from coming back together into a double
helix., preventing the recoil.
4. Topoisomerase enzyme
- Changing the topology of DNA via untwisting of the
double helix (alters the supercoiling of double-
stranded DNA) by cutting the phosphate backbone
into either one strand or double strands.
 DNA Replication
5. Primase (a type of RNA Polymerase)
- It catalyzes the synthesis of short RNA primer (5-10 bases) required
to start replication.
- RNA primer is complementary to the DNA template, which provides a
3' end for DNA polymerase to work on.
- DNA polymerase adds nucleotides only on the free 3’OH (The 5′-
phosphate group of the new deoxyribonucleotide binds to the 3′-OH group
of the last deoxyribonucleotide of the growing strand), meaning that DNA
synthesis on the new strands always proceeds in the 5‘3‘ direction.
 DNA Replication
6. DNA polymerase III
Once the RNA primer is in place, DNA polymerase III "extends" it. It adds
DNA nucleotides (dNTPs) to the primer(s), synthesizing the DNA of both
the leading and the lagging strands.
● One new strand, which runs 5' to 3' towards the replication fork, is the
easy one. This strand is made continuously because the DNA polymerase
is moving in the same direction as the replication fork. This continuously
synthesized strand is called the leading strand.
● The other new strand, which runs 5' to 3' away from the fork, is trickier.
This strand is made in fragments discontinuously and is called
the lagging strand.
● On the lagging strand DNA synthesis happens in short fragments
called Okazaki Fragments.
● Each Okazaki Fragment requires a new primer which is an RNA
primer.
 DNA Replication
7. DNA polymerase I
Because of its 5′ to 3′ exonuclease activity, DNA polymerase I removes
RNA primers and fills the gaps between Okazaki fragments with DNA.
8. DNA ligase (sticker)
Join “seal” the DNA fragments together by creating a phosphodiester
bond using ATP.

Only after all RNA primers are removed and replaced by DNA and
nicks are sealed, we can say DNA synthesis is complete.
 DNA Replication

Termination of replication is the process by

which the progress of the DNA replication stops
or blocks at a specific locus, via interaction
between a termination site sequence in the
DNA and a terminus site-binding protein that
binds to this sequence to physically stop DNA
replication.
 Proofreading characteristic of DNA
polymerase

DNA Polymerase Proofreading: an

error correction mechanism in the form

of a 3' to 5' exonuclease activity that

enables DNA polymerase to check every

nucleotide and remove incorrect

“mismatched” nucleotides from the

primers terminus before further primer

extension.
 RNA: Like DNA but
Features
Different
DNA RNA

DNA is a double-stranded molecule It is a single-stranded helix

Structure consisting of a long chain of consisting of a short chain of
nucleotides. nucleotides.

Transmits genetic information to make It transfers the genetic code

Function other cells and new organisms. Long- from the nucleus to the
term storage of genetic information ribosomes to make proteins.

Deoxyribose sugar Ribose sugar

phosphate backbone phosphate backbone
Composition
adenine, guanine, cytosine, adenine, guanine,
thymine bases. cytosine, uracil bases.

Located in the nucleus of a cell and in Located in the cytoplasm,

Location
the mitochondria. nucleus, and ribosome.

Due to its deoxyribose sugar, which

RNA, containing a ribose sugar, is
contains one less oxygen-containing
Reactivity more reactive and less stable than
hydroxyl group, DNA is a more stable
DNA
molecule than RNA,
RNA: Like DNA but
Different
● DNA is such an important molecule that it must be
protected from decomposition.
● The absence of one oxygen atom is part of the key to
extending DNA’s longevity. When the 2’ oxygen is missing,
as in deoxyribose, the sugar molecule is less likely to
get involved in chemical reactions (because oxygen is
chemically aggressive).
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4
Translating
the genetic code
 Central dogma
The central dogma of life is a theory that is an explanation of the flow of
genetic information within a biological system. It is often stated that
"DNA makes RNA, and RNA makes protein. Once "information" has
passed into protein it cannot get out again.
Translating the genetic code
● Genetic code: The sequence of nucleotides
“instructions” contained in genetic material
that determines the specific amino acid
sequence in the synthesis of proteins.

● Codon: A sequence of three consecutive

nucleotides in a DNA or RNA molecule that
codes for a specific amino acid.

● Translation: The process of translation can be

seen as the decoding of instructions for
making proteins, involving mRNA in
transcription as well as tRNA.
The genes in DNA encode protein molecules,
which are the "workhorses" of the cell, carrying
The genetic code features
(properties)

1. The genetic code is a triplet code, each

“word” within the mRNA contains three
ribonucleotide letters

2. The code is non-overlapping meaning

that each nucleotide is part of only one codon-
a single nucleotide cannot be part of two
adjacent codons

3. The code is unambiguous ”clear” Each

codon is always specific for only a particular
amino acid

4. The code is degenerate, meaning the

occurrence of more than one codon for a
 5. The code is predominant “nearly
universal” ( i.e. code is pretty similar
in most of the organisms).
It means that codon, which codes
methionine in humans, does the same
in prokaryotes. This point is not
exactly true as recently, scientists
have discovered many exceptions to
this rule. The genetic code is not
universal, but it is still predominant.

6. The code is comma-less, meaning

that no nucleotide or comma (or
punctuation) is present in between
two codons.

7. Genetic code has polarity i.e., 5’ to

3’ direction.
To conclude, If it reads
the code: triplet,innon-overlapping,
the opposite
direction it yields
unambiguous, a different protein.
degenerate, predominant,
comma-less, and has polarity
Translating the Genetic Code
Discovering the Good in a Degenerate

• With three nucleotides per codon, there are 4 x 4 x 4 = 64 possible

codons, which is more than enough to specify 20 different amino
acids.

• Only 61 of the 64 codons are used to specify the 20 amino acids

found in proteins.

• The three codons (UAG, UGA, UAA) that don’t code for any amino
acid simply spell “stop,” telling the ribosome to cease the translation
process.

• In contrast, the one codon that tells the ribosome that an mRNA is
ripe for translating — the “start” codon (AUG) — codes for an amino
acid, methionine.
 Translating the Genetic Code

The 64 codons of the genetic code, as written by mRNA

 Wobble theory

• In 1966, Francis Crick proposed the Wobble Hypothesis to

explain the partial degeneracy of the genetic code in that

some t-RNA molecules can recognize more than one

codon

• A wobble base pair is a pairing between two nucleotides in

RNA molecules that does not follow Watson-Crick base pair

rules.
Thanks
!
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