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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 ماه

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 )

A and T ( 2 H. bonds only ) ( see test 8 q: 56-60 )
DNA can replicate itself, it can make exact replica ( copy) of itself when cells
DNA can replicate itself, it can make exact replica ( copy) of itself when
cells want to divide
new strand has the seq.
TTTAGCCTG

DNA Replication ( synthesis ) ( during S-phase of interphase )

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

DNA to be copied has a nucleotide sequence : AAATCGGAC, Then 4. Hydrogen bonds form between

4. Hydrogen bonds form between base pairs to form ‘’ rungs’’ مللاس of the ladder, bonds form between the sugar-phosphate components بانجلأا of the newly formed nucleotides

5. New double stranded molecules twist up into double helices

64

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

consists of 1 old strand , 1 new strand . This is called Semi-conservative way ادج

Semi-conservative way ادج ماه

* Each separated DNA strand acts as Template ليدوم وا بلاق to 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

 The 46 chromomsomes in any of your somatic cells are identical to the 46
 The 46 chromomsomes in any of your somatic cells are identical to the 46
chromosomes in any other cell
cells are identical to the 46 chromosomes in any other cell * N.B : Each time

* 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 ):



Different individuals DO NOT have the same set of chromosomes except identical twins قباطتم مأوت Each 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.

65

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 )

, nitrogenous bases ( Adenine , Uracil , Guanine, cytosine ) Cellular and molecular biology 3
Cellular and molecular biology
Cellular and molecular biology

3 types of RNA :

The triplet ( 3 )nucleotides of mRNA such as AAC or UUU are called codons
The triplet ( 3 )nucleotides of mRNA
such as AAC or UUU are called codons
tRNA is shaped like cloverleaf
translation Protein
translation
Protein

1. mRNA : Messenger RNA carries messages directly from DNA in nucleus to cytoplasm during making of protein

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.

3.

rRNA : Ribosomal RNA makes up ribosomes along with proteins (structural)

Protein synthesis : (occurs in ribosomes) 3 steps : transcription, RNA processing and translation

→ 3 steps : transcription, RNA processing and translation transcription DNA RNA 1 – Transcription The

transcription

DNA RNA 1 – Transcription
DNA
RNA
1 – Transcription

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

66

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
2- RNA processing
After transcription and before the newly formed strand of RNA is shipped out
جرخيof the nucleus to the cytoplasm, this initial transcript is processed or
edited by series of enzymes لدعتت ةخسنلا
 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) ةيضارتعا
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 ةمزلا شاهلام ىللا تتحلا هنم تلاشتا
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.

67

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

m RNA → codon t RNA → An t i-codon -
m RNA → codon
t RNA
An t i-codon
-
Ex : if a codon has sequence of nucleotides AUG then anticodon is UAC AUG
Ex : if a codon has sequence of nucleotides AUG then anticodon is UAC
AUG codes for methionine…
so methionine would attach to this tRNA
List of 64 possible codons and amino
acids that are translated from those codes

Anti-codon (contained in anti-codon loop) special region on tRNA that can base pair with codons on mRNA … the anticodon must be complementary قفاوتم وأ هل لمكم هاعم to codon to base pair with it

وأ هل لمكم هاعم to codon to base pair with it Genetic code : - -

Genetic code:

-

هاعم to codon to base pair with it Genetic code : - - Some amino acids

- Some amino acids are coded by more than 1 codon ex : codons UCU, UCC, UGA , UCG all code for amino acid Serine ماه

- So some tRNA molecules can bind to 2 or more different codonsماه

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Serine ماه - So some tRNA molecules can bind to 2 or more different codons ماه

Cellular and molecular biology

SAT II Biology E/M

Ribosome:

Dr Haitham AbdAllah 0100 36 777 19

- 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)

so that 1 st codon in P-site and 2 nd inA-site

mRNA binds to ribosome

in P-site and 2 n d inA-site mRNA binds to ribosome process is repeated Until every
in P-site and 2 n d inA-site mRNA binds to ribosome process is repeated Until every

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

- 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 1 st 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 رودلا هيلع ىللا

in sequence moves to A-site رودلا هيلع ىللا Start codon Stop codons ادج ماه 69 Cellular
in sequence moves to A-site رودلا هيلع ىللا Start codon Stop codons ادج ماه 69 Cellular
Start codon
Start
codon

Stop codons ادج ماه

69

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 ديدج ديسأ ونيمأ شيفم هدك صلاخ , final tRNA is released from ribosome and completed protein is released

AUG is start codon, because it’s the 1 st codon on all mRNAs and methionine
AUG is start codon, because it’s the 1 st
codon on all mRNAs and methionine is the
1 st amino acid in all proteins
RNA polymerase

RNA ( transcription )

* 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

N.B :

where next amino acid is attached to growing protein N.B : DNA Reverse transcriptase RNA DNA

DNA

Reverse transcriptase

RNA

RNA DNA

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

70

Cellular and molecular biology

SAT II Biology E/M

Gene regulation

Dr Haitham AbdAllah 0100 36 777 19

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 ليغشتلا حيتافم that turn
o
operon is actually a cluster of functional genes + switches ليغشتلا حيتافم that 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.
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 are introns that interrupt genes

Some of this DNA consists of regulatory sequences that control gene expression ( protein synthesis )

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 o
o
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 ةبذاك تانيج former 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

71

Cellular and molecular biology

SAT II Biology E/M

Dr Haitham AbdAllah 0100 36 777 19

o

o

o

Recombinant DNA means taking DNA from two sources and combining them in

one cell ( this technique is used in lab production of insulin )

genetic engineering or biotechnology branch of science that uses

recombinant DNA techniques for practical purposes

gene replacement therapy and environmental cleanup

study in genetic engineering

2 important areas of

o Scientists are trying to learn how to → insert functioning genes into cells to
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
هدنع عطقت هد سنوكيسلا يقلات اما and are sometimes referred to as molecular
scissors تاصقملا ىز ىد تاميزنلاا

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 restriction enzymes

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

pieces of DNA that result from cuts made by

72

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 نيزواع انحا ام ىز

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 هدنع عطقتي نكمم سنوكيس قوف انلق ام ىز( see prokaryotic cell)

Gel electrophoresis separates large molecules of DNA on the basis of their rate of movement
Gel electrophoresis separates large molecules of DNA on the basis of their rate of
movement through an agarose gel in an electric field
The smaller the molecule, the faster it runs through gel
If necessary, concentration of the agarose gel can be changed to provide better
separation of tiny DNA fragments
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
Once separated on gel → DNA can be analyzed in many ways
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;

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

pieces of DNA run farther and faster through the gel Gel Electrophoresis o o o o

Gel Electrophoresis

o

o

o

o

o

o

o

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

and uncut piece of DNA Lane 4 contains two pieces of DNA ىدعته ةريبكلا عطقلا و

ىدعته ةريبكلا عطقلا و رتلف هنأك ةعرسب ىدعته ةريغصلا عطقلا ةصلاخلا ءطبب

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

73

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
(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