SAT II Biology E/M Dr Haitham AbdAllah

0100 36 777 19

DNA

- consists of 2 complementary strands running in

opposite directions ( 3' end to 5' end , 5' to 3') .
- It is polymer made of repeating units called
nucleotides…. Each nucleotide consists of → (5-
carbon sugar (deoxyribose), phosphate group
, nitrogenous base ‫هام‬

N.B : Between G and C → 3 hydrogen bonds

( stronger; more stable ) than between A and T ( 2 H.
bonds only ) ( see test 8 q: 56-60 )

DNA Replication ( synthesis ) ( during S-phase

of interphase )

DNA can replicate itself, it can make exact replica ( copy) of itself when
cells want to divide

Steps:

1. double helix unwinds by breaking the

hydrogen bonds, this is accomplished by
the enzyme helicase then the 2 strands
separate

2. Next to each separated strand, enzyme

called DNA polymerase lines up
nucleotides acc. To base pair rulesto form
new second strands (complementary
strands )

3. If a strand of DNA to be copied has a

nucleotide sequence : AAATCGGAC, Then
new strand has the seq. TTTAGCCTG

4. Hydrogen bonds form between base pairs to form ‘’ rungs’’ ‫ ساللم‬of the ladder, bonds
form between the sugar-phosphate components ‫ األجناب‬of the newly formed
nucleotides
5. New double stranded molecules twist up into double helices

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Cellular and molecular biology
SAT II Biology E/M Dr Haitham AbdAllah
0100 36 777 19

6. The 2 new molecules of DNA that are produced, each consists of 1 old strand, 1 new
strand. This is called Semi-conservative way ‫هام جدا‬

* Each separated DNA strand acts as Template ‫ قالب او موديل‬to form new
complementary strand ( new partner )

* It means that its bases directs construction of complementary strand alongside it

* DNA Polymerase : catalyzes replication and proofreads each new DNA strand,
Fixing errors and minimizing
occurance of mutations

* N.B: Each time DNA replicates,

some nucleotides from ends of
chromosomes are lost. To protect
against possible loss of genes at
ends of chromosomes, some
eukaryotic cells have special non-
sense nucleotide sequences at end
of chromosomes that repeat
thousands of times called
telomeres which protect
chromosome from
deterioration or fusion with
neighboring chromosome

Chromosomes ( the same set in each cell ):

 The 46 chromomsomes in any of your somatic cells are identical to the 46

chromosomes in any other cell

 Different individuals DO NOT have the same set of chromosomes except

identical twins ‫ توأم متطابق‬Each identical twin has exactly same chromosomes
as the other

Homologous chromosomes: ( similar but not identical )

Chromosomes come in pairs…. Each human somatic cell has 23 pairs of

chromosomes…. Or 2 sets every set consists of 23 chromosomes…. One set from dad,
other from mom.

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Cellular and molecular biology
SAT II Biology E/M Dr Haitham AbdAllah
0100 36 777 19

Cells that have 2 sets of chromosomes are called diploid ( each chromosome has a
homologous partner )

RNA :

Single stranded , consists of 5-carbons sugar (ribose), phosphate , nitrogenous

bases ( Adenine , Uracil , Guanine, cytosine )

3 types of RNA :

1. mRNA : Messenger RNA → carries messages

directly from DNA in nucleus to cytoplasm
during making of protein

The triplet ( 3 )nucleotides of mRNA

such as AAC or UUU are called codons

2. tRNA : Transfer RNA →carries amino acids

to the mRNA at the ribosome in order to
form poly peptide. The triplet nucleotides of
tRNA are complementary to codons of mRNA
and r called Anticodons.

tRNA is shaped like cloverleaf

3. rRNA : Ribosomal RNA → makes up

ribosomes along with proteins (structural)

Protein synthesis : (occurs in ribosomes) → 3

steps : transcription, RNA processing and
translation

transcription translation
DNA RNA Protein

1 – Transcription
The process by which DNA makes RNA, it is
facilitated by RNA polymerase enzyme and occurs
in nucleus

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Cellular and molecular biology
SAT II Biology E/M Dr Haitham AbdAllah
0100 36 777 19

 The triplet codes in DNA are transcribed into a codon sequence in mRNA

If sequence in DNA triplets is

AAA TAA CCG GAG

Then the complementary sequence of codons in mRNA is UUU AUU GGC CUG

Codon = 3 nucleotides sequence on mRNA

2- RNA processing
After transcription and before the newly formed strand of RNA is shipped out
‫يخرج‬of the nucleus to the cytoplasm, this initial transcript is processed or
edited by series of enzymes ‫النسخة تتعدل‬

 The enzymes remove pieces of RNA

that do NOT code for any protein.
These non coding regions that are
removed are called Introns (intervening sequences) ‫اعتراضية‬

remaining portions are called Exons

(expressed sequences or coding
regions), are pieced back together to form
the final transcript

 As a result, mRNA that leaves the nucleus

becomes shorter ‫اتشالت منه الحتت اللى مالهاش الزمة‬

3-Translation: occurs in ribosome

 mRNA sequence converted into
protein
 Proteins act as critical structural components of cells, as well as controlling
such processes as catalysis, movement, and communication between cells.

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Cellular and molecular biology
SAT II Biology E/M Dr Haitham AbdAllah
0100 36 777 19

 Amino acids in cytoplasm are carried by tRNA to codons of mRNA strand

present at ribosome

mRNA → codon

tRNA → Anti-codon

- Anti-codon (contained
in anti-codon loop) → special
region on tRNA that can base
pair with codons on mRNA … the anticodon must be complementary ‫مكمل له أو متوافق‬
‫ معاه‬to codon to base pair with it

Ex : if a codon has sequence of nucleotides AUG then anticodon is UAC

AUG codes for methionine….. so methionine would attach to this tRNA

Genetic code:

- List of 64 possible codons and amino

acids that are translated from those codes

- Some amino acids are coded by more than

1 codon ex : codons UCU, UCC, UGA , UCG
all code for amino acid Serine ‫هام‬

- So some tRNA molecules can bind to 2 or

more different codons‫هام‬

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Cellular and molecular biology
SAT II Biology E/M Dr Haitham AbdAllah
0100 36 777 19

Ribosome:

- The organelle that synthesizes protein…. mRNA binds to ribosome and tRNA carries
amino acids from cytoplasm to ribosomes

- There r 2 binding sites on ribosome( P-

site), (A-site) ….. mRNA binds to ribosome
so that 1st codon in P-site and 2ndinA-site

- Once mRNA is bound, tRNAs carrying the

appropriate amino acids comes and base pairs with codon on mRNA, then ribosome
forms a peptide bond between 2 amino acids.

 Once peptide bond is formed. The 1st and now empty tRNA is released from
ribosome and return to cytoplasm to bind with another amino acid
 Ribosome slides down 1 codon so that codon in A-site shifts to P-site and
next codon in sequence moves to A-site ‫اللى عليه الدور‬

process is repeated Until every codon on

mRNA base pairs with anticodon on tRNA
and peptide bonds are formed between
amino acidsand stop codon appears in A-site Start
codon

Stop codons ‫هام جدا‬

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Cellular and molecular biology
SAT II Biology E/M Dr Haitham AbdAllah
0100 36 777 19

[UAA , UGA , UAG ] 3 of possible 64 codons don’t specify any amino acid ….

They specify ‘’STOP’’ → stop translating, protein synthesis is finished

When Stop codon appears in A-site ‫ خالص كده مفيش أمينو أسيد جديد‬, final tRNA is
released from ribosome and completed protein is released

* P-site stands for Peptide where the growing peptide is attached to ribosome

*A-site stands for Amino acid where next amino acid is attached to growing protein

AUG is start codon, because it’s the 1st

codon on all mRNAs and methionine is the
1st amino acid in all proteins

N.B : RNA polymerase

DNA RNA ( transcription )

Reverse transcriptase
RNA DNA

 30,000 expressed genes = 30,000 different proteins ( gene expression = protein

synthesis )

For questions see test 8 q: 49-42 , test 14 q : 11-14

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Cellular and molecular biology
SAT II Biology E/M Dr Haitham AbdAllah
0100 36 777 19

Gene regulation

o Every cell does not constantly synthesize every polypeptide it has the ability to
make. For example, cells in pancreas are not always producing tons of insulin
because it is not always needed
o That means that every gene in a cell is not turned on all the time. How does a cell
know when to turn on a gene or when to turn it off? This is actually a very complex
process in humans and one that is not understood well. However, a simple model
for gene regulation can be found in bacteria in a region of DNA called the operon
o operon is actually a cluster of functional genes + switches ‫ مفاتيح التشغيل‬that turn
them on and off
o two types of operons. One is the Lac or inducible operon → is normally turned
off unless it is actively induced or triggered to turn on by something in
environment
o The other is repressible operon, which is always turned on unless it is actively
turned off because it is temporarily not needed
o Some of the parts of operon. The two most relevant ones are the promoter and
the operator
1. promoter is the binding site of RNA polymerase. RNA polymerase must
always bind to DNA before transcription can take place.
2. So promoter is like an “on” switch
3. The other region is operator → This is binding site for repressor, which
turns off the Lac operon
4. Another part of operon, with a funny name, is the TATA box (named for its
sequences of alternating adenine and thymine), which helps RNA
polymerase bind to promoter

Human Genome

o human genome (an organism’s genetic material) → consists of 3 billion base

pairs of DNA and about 20,000 genes
o 97 % of our DNA does NOT code for protein product
o Some of this DNA consists of regulatory sequences that control gene expression (
protein synthesis )
o Some are introns that interrupt genes
o Much of the DNA consists of repetitive sequences that may repeat ten million
times and never get transcribed
o Some of DNA are pseudogenes ‫ → جينات كاذبة‬former genes that have accumulated
mutations over a long time. Scientists are only beginning to understand the make-
up of DNA

Genetic engineering and recombinant DNA

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Cellular and molecular biology
SAT II Biology E/M Dr Haitham AbdAllah
0100 36 777 19

o Recombinant DNA means → taking DNA from two sources and combining them in
one cell ( this technique is used in lab production of insulin )
o genetic engineering or biotechnology → branch of science that uses
recombinant DNA techniques for practical purposes
o gene replacement therapy and environmental cleanup → 2 important areas of
study in genetic engineering

o Scientists are trying to learn how to → insert functioning genes into cells to replace
nonfunctioning ones in humans

 If they are successful → it would mean an end to genetic diseases like cystic
fibrosis and sickle cell anemia

o Microbes are being engineered to degrade oil at oil spills or to decontaminate

harmful chemicals at toxic mining sites or in water treatment

o there is growing concern about safety of genetically modified organisms (GMO)

 Ex 1 : Farmed salmon have been genetically modified by addition of an

extra growth hormone gene so they grow more quickly,

 Ex 2 : corn has been engineered to include foreign genes for resistance to

herbicides and insect pests

 One concern is that these genetically modified organisms ( GMO ) will be

released into the wild, thus spreading their engineered genes to wild species

 Another is that these foreign genes might adversely affect people who eat
the genetically engineered organisms

o Restriction Enzymes important tool for scientists working with DNA

o They cut DNA at specific recognition sequences or sites, such as GAATTC

‫ اما تالقي السيكونس ده تقطع عنده‬and are sometimes referred to as molecular
scissors ‫االنزيمات دى زى المقصات‬
o They were first discovered in bacteria → Bacteria use the enzymes to cut
(and thereby destroy) foreign DNA such as viral DNA →This would restrict
growth of virus

o restriction fragments pieces of DNA that result from cuts made by

restriction enzymes

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Cellular and molecular biology
 SAT II Biology E/M Dr Haitham AbdAllah
0100 36 777 19

o Restriction enzymes give us the ability to “cut and paste” (recombine)

DNA into custom combinations ‫زى ما احنا عاوزين‬
o Plasmid → small circular piece of DNA frequently found in bacteria and
sometimes in yeast. plasmid is not considered to be part of bacterial or yeast
genome and can reproduce independently of the microorganism. And because
plasmid is DNA, its sequence contains restriction sites ‫سيكونس ممكن يتقطع عنده‬
‫ (زى ما قلنا فوق‬see prokaryotic cell)

Gel Electrophoresis

o Gel electrophoresis separates large molecules of DNA on the basis of their rate of
movement through an agarose gel in an electric field
o The smaller the molecule, the faster it runs through gel
o If necessary, concentration of the agarose gel can be changed to provide better
separation of tiny DNA fragments
o In order to run DNA through a gel, it must first be cut up by restriction enzymes
into pieces small enough to migrate through gel
o Once separated on gel → DNA can be analyzed in many ways
o Figure 10.9 shows an electrophoresis gel with 4 samples of DNA. The DNA in lanes 1,
2, and 4 were previously cut with restriction enzymes;
o the DNA in lane 3 was left uncut. Each sample is running in its own lane. The shorter
pieces of DNA run farther and faster through the gel

Lane 1 contains four bands of DNA, three larger

pieces and one short piece

Lane 2 contains two pieces of DNA, one large and

one tiny. Lane 3 contains one very large and uncut
piece of DNA

Lane 4 contains two pieces of DNA

‫الخالصة القطع الصغيرة هتعدى بسرعة كأنه فلتر و القطع الكبيرة هتعدى‬
‫ببطء‬

Polymerase Chain Reaction

 Devised in 1985, polymerase chain reaction

(PCR) is a cell-free automated technique by which a piece of DNA → can be rapidly
copied or amplified
 Billions of copies of fragment of DNA can be produced in few hours

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Cellular and molecular biology
SAT II Biology E/M Dr Haitham AbdAllah
0100 36 777 19

 Once DNA is amplified, these copies can be studied or used in a comparison with
other DNA samples

Questions 1-4

(A) Transcription
(B) Translation
(C) Replication
(D) Transpiration
(E) Splicing
1. Results in the production of RNA
2. Includes the removal of the introns
3. Is said to be semi-conservative
4. The "reading" of mRNA codons in groups of three nucleotides
Ans : 1- A 2- E 3- C 4- B

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Cellular and molecular biology