DNA structure and protein synthesis

1. Nucleic Acidsand Protein Synthesis
Almost all cells contain two types of nucleic acids:
1. DNA (Deoxyribonucleic acid).
2. RNA (Ribonucleic acid).
The structure of nucleic acids:
Both DNA and RNA are nucleic acids, polymers/macromolecules made up of many smaller
molecules/monomers called nucleotides, so therefore the DNA & RNA are Polynucleotides.
The Nucleotide is made up of three smaller molecules:
• A phosphate Group.
• Pentose Sugar {either ribose or deoxyribose).
• A nitrogen base.
There are 5 types of nitrogen bases, which belong to one of two groups
Purine (double ringed) Pyrimidine (single ringed)
Adenine
A
Guanine
G
Uracil Cytosine
U C
Thyamine
T
Each Nucleic acid contains 4 types of bases only in its structure
The DNA molecule contains, the bases A,C,T,G while the RNA contains A,C,U,G
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2. 1
/ Sugar-phosphate backbone
s• end/ (on blue background)
Nucleoslde
r--"--.
Nitrogenous bases
Pyrimidines
,,t,_,.CH3
HN
O'~ 'W' H
H
Nitrogenous
base Cytosine (C) Thymine (T, In ONA) Uracil (U, In RNA)
-o-Lo-~~-
b
- ,.
Phosphate
group 3· 2·
Sugar
(pentose)
' ,i..._________
OH
3' end
(al Polynucleotlde, or nuclelc acid
(bl Nudeotlde
Formation of a polynucleotide:
NH2
hN..._c)<:::-N
Hl II I
N,..<:'.,N#CH
H
Adenine (A)
s·
HOC~H
2 OH
•· H ,.
H 1•
1
. H
OH H
·Sugars
Oeoxyrib(lse Un DNA}
Guanlne(G)
s·
H
t.J,~
~
w-
OH OH
Rlbose (In RNA)
During the interphase (period between 2 succes$!Ve divisions), many nucleotides are linked
together (by a condensation reaction) to form a.120.lY!]ucleotide.
They are linked by a phosphodiester bond between.!: of one nucleotide and~ of the other.
The polynucleotide chains are made of alternating sugars and phosphates linked together, with
the nitrogen bases projecting sideways.
The strand is said to have 3'and S'end.
The Structure of DNA molecule (by Watson &Crick)
It's made of two polynucleotide strands lying side by side, the two strands are held together by
H bond between the nitrogen bases according to the rule of base pairing c=G& A=T
The two strands twist around each other to form a double helix, they run in opposite
directions/antiparallel to allow the bases to fit exactly with each other.
In each base pair, one base belongs to the double ringed purines while other belongs to the
single ringed pyrimidines. The A & T pair has 2 H bonds, while C & G pair has 3H bonds.
The base pairing helps to:
• Stabilize the molecule.
• Allows the DNA to replicate.
• Gives the DNA the 3 dimensional configuration.
The width of the DNA molecule is about 2nm, each twist contains 10 pairs of nucleotides and
measures 3.4nm in length.
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3. 3.4 nm
]~.34 nm
The structure of DNA
Differences between DNA and RNA:
P.O.C.
ar
structure
Location
Re lication
Stabili
Existence
Molecular mass
Ratio between
bases
Amount
DNA Replication:
DNA
oeo ribose
Doubl
Nucleus/s
More stable
Permanent
Up to 150 X 10'>7
A/T, G/ C = 1
Constant forall cells
(except gametes)
H
"'- " · ••••0
~ ., " "
••·•
•
H
-,~
o sugar
Adenine (A) Thymine (T)
H
I
o
~~--
-~~
Q
I
N- H• •· ··O Sugar
H
Guanine (G) Cytosine (C)
Base pairing in DNA.
RNA
Ribose
A,G,U,C
/ nucleus
can't
Less stable
Tem porary
Up to 2 X 10
A/U , G/C varies
varies from cell to cell
accordingto metabolic
activities
Before a cell divides, its DNA is replicated (in the interphase) so that each new cell receives a
complete copy of the original genetic information.
Mechanism of DNA Replication
1. The Two strands unwind/unzip, due to the breakdown ofH bonds between the bases by
Helicase enzyme.
2. Each one ofthe two strands acts as a template to which a complementary set of nucleotides
(always present in the nucleus) would attach according to the rule of base pairing by H bonds
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4. I I I I
3. The sugar of one nucleotide Is joined to the phosphate of the next nucleotide to form a new
polynucleotlde chain which Is catalyzed by an enzyme called DNA polymerase and the extra
phosphates are broken off.
The replication process is called semi-conservative because each new double helix has an old
strand (parental) and one new strand. or we can say one of the parental strands is conserved
/present in each daughter double helix.
Requirements if replication:
• Free nucleotides.
• Enzymes (Helicase & polymerase).
• Energy source (ATP) to activate the nucleotides.
In the nucleus, there are nucleotides to which 2 extra phosphates have been added to activate the
nucleotides, enabling them to take part in the reaction.
The two extra phosphates are broken off and released into the nucleus after the new DNA is
formed.
Orlglnal DNA Orlglnal ONA strands
prledapan
Experimental Evidence for semi-conservative Di!J :-er,,(j7Y:.
'•.'.•.
- m
Two Identical
ONA molecules:
half new. half
from orlgln•I
• Meselson and Stahl grow bacteria for many generations in a medium containing heavy isotope
NlS, until they were certain that heavy N had incorporated into the entire DNA.
• Then the bacteria with heavy DNA were grown in a medium containing normal nitrogen.
• Samples of bacteria were then taken at intervals & relative amounts of the 2 types of N were
estimated by a technique which depends on the fact that compounds contain NlS are slightly
heavier than those containing N14.
• The heavy & light DNA was separated by high speed centrifuge.
- Nl S
- Nl4
N14
between N14 & N15
N 15
C:::0,,,- c::::::>-
1et 1'9llc:aUon Znd 19pllc:allon
40

5. Protein Synthesis:
Watson and crick suggested that the genetic information which passed from one generation to
another might reside in the sequence of bases of single DNA strand so therefore the DNA
nucleotide base sequence determines the amino acid sequence of protein molecules.
The single DNA molecule contains shorter sections called genes.
Gene: is a se uence o nucleotides art o a DNA molecule which codes or a of e tide.
~structions are coded on/ in one o the two strands o the DNA molecule Anti- sense codin
strand.
A row of three bases, called a codon specifies one amino acid so the genetic code is said to be
triplet.
Why is the code triplet?
• If one base determines the position of a single amino acid in a protein then the protein could
only contain 4 amino acids.
• If 2 bases code for 1 amino acid, then 16 amino acids could be specified into the protein
molecule.
• Only a code composed of 3 bases could incorporate 20 amino acids into the structure of
protein molecule, such a code would produce 64 combinations of bases.
Properties of the genetic code
1. Universal: the same triplet code for the same amino acid in all living organisms
2. Degenerate: a given amino acid may be coded by more than one codon
3. Not overlapped: no base of a given triplet contributes to part of the code of the adjacent triplet
There are 3 types of RNA, all are synthesized from DNA and involved in protein synthesis:
1. Messenger RNA (MRNA): carries the instructions for protein synthesis from nucleus to
ribosomes.
2. Transfer RNA (tRNA):transfers amino acids from amine.' acid pool in cytoplasm to
ribosomes. Each amino acid has its own RNA.
3. Ribosomal RNA (rRNA): involved in translation of mRNA into a sequence of amino acids in
polypeptide chain in ribosomes.
Transcription: It's the mechanism by which the base sequence of a DNA strand is converted to the
complementary base sequence of mRNA.
1. A specific length (cistron) of the DNA molecule which
codes for a polypeptide unwinds by the breakage of
H bonds between the bases of the complementary strands.
2. One of the DNA strands (Anti-sense) acts as a template for
the formation of a complementary strand of mRNA, this
molecule is formed by the linking of the free
ribonucleotides under the influence of
RNA polymerase enzyme and according to the rule
ofbase pairing except U instead of T.
3. The mRNA leaves the nucleus through nuclear
pores to reach ribosomes in the cytoplasm.
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6. Difference between Transcription and Replication:
Replication Transcription
The whole DNA molecule Part of ONA (gene) only
unwinds unwinds
The 2 DNA strands act as a Only one strand(antl-sense) acts
template for synthesis of new as a template
strands
DNA polymerase Is Involved RNA i:>_olymerase Is Involved
A pairs with T A pairs with U
Occurs before cell division Occurs during protein
svnthesls
Semi-conservative DNA Rewinds
Translation: It's the mechanism by which the triplet base sequence of mRNA is converted to a
specific sequence of amino acids in a polypeptide chain and it occurs in the ribosomes
1. The mRNA is attached to a ribosome at a site called ribosome binding site.
2. The Ribosome accommodates 2 tRNA molecules where it contains 2 tRNA sites where a codon
from mRNA can attach by base pairing to a molecule of tRNA. each tRNA has a special triplet of
nucleotides called anticodon at one end.
3. At the opposite end the tRNA is linked to a specific amino acid (amino acid binding site) the
linkage of tRNA molecules to their corresponding amino acids is called amino acid activation. it
requires the use of ATP molecules and catalyzed by a specific enzyme & whole structure is called
tRNA-amino acid complex.
4. The first codon to be translated from a mRNA moiccule is always the sequence AUG which
corresponds to the amino acid methionine & called initiation codon.
5. When the 2 amino acids are brought together they're linked to each other by peptide bond (by
condensation reaction which is catalyzed by Peptidyle transferase enzyme) at the same time the
1st tRNA is disconnected from its amino acids & leaves the ribosome which moves along the
mRNA to bring the next codon into position.
6. As this process continues, the ribosome travels along the mRNA strand adding more amino acids
to the growing polypeptide chain.
7. The sequence of the Ribosome reading & translating the mRNA codes continues until it comes
to a codon signaling stop (UAA/UAG/UGA) (stop codon).
Several Ribosomes become attached to a molecule of mRNA, the whole structure is called Polysome
and this allows several identical protein molecules can be made from one set of instructions/mRNA
3 '
Amino acid
attachmont slto
42
structure of tRNA

7. 0
5'
0
5'
0 l
5'
s ·
5'
e
II 3'
5'
-Movement of ribosome
, 3' S'
Steps during translation
Polysome
Stop
c odcnl
Antlaodon
3'
_ Movement of ribosome
3'
;ii 3'
features of DNA molecule that allow it to act as a genetic material It can:
Replicate: being copied perfectly so it can pass unchanged into the new cells that are
produced when an old cell divides.
Store Information: For making proteins that determine characteristics of the organism and
since it's a stable molecule the information remain intact from one generation to the next.
DNA controls all metabolic reactions:
All metabolic reactions are controlled by enzymes.
Enzymes are protein in nature and so their synthesis is controlled by the DNA and so the DNA
controls metabolic reactions.
Any change in the DNA that codes for one enzyme leads to a stop of a chemical reaction which
in turn leads to metabolic disorder.
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