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DNA SYNTHESIS

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(REPLICATION)
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https://www.youtube.com/watch?v=gG7uCskUOrA
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https://www.youtube.com/watch?v=TNKWgcFPHqw
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central dogma of biology

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DNA AND RNA MOLECULE
DNA Replication Is Semiconservative Each
DNA strand serves as a template for
the synthesis of a new strand,
producing two new DNA molecules,
each with one new strand and one old
strand

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The Meselson-Stahl experiment.
(a) Cells were grown for many generations

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in a medium containing only heavy

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nitrogen, 15N, so that all the nitrogen in

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their DNA was 15N, as shown by a single
band (blue) when centrifuged in a CsCl

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density gradient. (b) Once the cells had
been transferred to a medium containing
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only light nitrogen, 14N, cellular DNA
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isolated after one generation equilibrated
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at a higher position in the density gradient

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(purple band).
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(c) Continuation of replication for a second

generation yielded two hybrid DNAs and
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two light DNAs (red), confirming

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semiconservative replication
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Defining DNA strands at the replication fork.

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A new DNA strand (red) is always synthesized in the 5’ 3’ direction. The

template is read in the opposite direction, 3’ 5’. The leading strand is
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continuously synthesized in the direction taken by the replication fork. The

other strand, the lagging strand, is synthesized discontinuously in short pieces
(Okazaki fragments) in a direction opposite to that in which the replication fork
moves. The Okazaki fragments are spliced together by DNA ligase
Synthesis of Okazaki fragments.
a) At intervals, primase

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synthesizes an RNA primer for a
new Okazaki fragment. Note that

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if we consider the two template
strands as lying side by side,

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lagging strand synthesis formally

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proceeds in the opposite
direction from fork movement.

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(b) Each primer is extended by
DNA polymerase III.

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(c) DNA synthesis continues until
the fragment extends as far as
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the primer of the previously NA
added Okazaki fragment. A new
primer is synthesized near the
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replication fork to begin the

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process again.
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Elongation of a DNA chain.
(a) DNA polymerase I activity requires a single
unpaired strand to act as template and a primer
strand to provide a free hydroxyl group at the 3
end, to which a new nucleotide unit is added.
Each incoming nucleotide is selected in part by

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base pairing to the appropriate nucleotide in the
template strand. The reaction product has a new

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free 3 hydroxyl, allowing the addition of another
nucleotide.

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(b) The catalytic mechanism likely involves two Mg2
ions, coordinated to the phosphate groups of the

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incoming nucleotide triphosphate and to three

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Asp residues, two of which are highly conserved
in all DNA polymerases. The top Mg2 ion in the

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figure facilitates attack of the 3-hydroxyl group of
the primer on the phosphate of the nucleotide
triphosphate; the lower Mg2 ion facilitates

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displacement of the pyrophosphate. Both ions NA
stabilize the structure of the pentacovalent
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transition state. RNA polymerases use a similar
mechanism
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DNA synthesis on the leading
and lagging strands.
Events at the replication fork are
coordinated by a single DNA

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polymerase III dimer, in an integrated
complex with Dna B

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helicase. This figure shows the

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replication process The lagging strand is
looped so that DNA synthesis proceeds

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steadily on both the leading and lagging
strand templates at the same time.

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Red arrows indicate the 3 end of the
two new strands and the direction of

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DNA synthesis.
Black arrows show the direction of

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movement of the parent DNA through NA
the complex. An Okazaki fragment is
being synthesized on the lagging strand.
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 RY
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RNA SYNTHESIS
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(TRANSCRIPTION)
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https://www.youtube.com/watc
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h?v=NDIJexTT9j0
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TRANSKRIPSI

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Transcription by RNA
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polymerase in E. coli
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GENETIC CODE
 FRANCIS CRICK

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How The Genetic Information

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◼

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Encoded In The Four Letter

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Language Of Nucleic Acids Could
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Be Translated Into The 20 Letter
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Language Of Protein?
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AT LEAST THREE NUCLEOTIDE
RESIDUES OF DNA ARE REQUIRED

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TO ENCODE EACH AMINO ACID

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THE FOUR CODE LETTERL
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OF DNA A, T, G AND C
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 RY
PROTEIN SYNTHESIS

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(TRANSLATION)

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• General cloverleaf secondary structure
of tRNAs.
• The large dots on the backbone
represent nucleotide residues; the blue
lines represent base pairs.
• Characteristic and/or invariant residues

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common to all tRNAs are shaded in pink.

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• Transfer RNAs vary in length from 73 to
93 nucleotides. Extra nucleotides occur

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in the extra arm or in the D arm. At the

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end of the anticodon arm is the
anticodon loop, which always contains

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seven unpaired nucleotides. The D arm
contains two or three D (5,6-

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dihydrouridine) residues, depending on
the tRNA. In some tRNAs, the D arm has
only three hydrogen-bonded base pairs.

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In addition to the symbols explained in NA
Figure 27–11: Pu, purine nucleotide; Py,
pyrimidine nucleotide; G*, guanylate or
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2-O-methylguanylate.
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Amino acyl t RNA RY
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Pairing relationship of codon and

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anticodon

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a) Alignment of the two RNAs is

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antiparallel.
The tRNA is shown in the

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traditional cloverleaf

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configuration. NA
(b) Three different codon pairing
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relationships are possible when

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the tRNA anticodon contains

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inosinate
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Initiation complex

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Formation of the initiation complex

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in bacteria.

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The complex forms in three steps at

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the expense of the hydrolysis of GTP

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to GDP and Pi.
IF-1, IF-2, and IF-3 are initiation
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factors.
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P designates the peptidyl site, A the

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aminoacyl site, and E the exit site.

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Here the anticodon of the tRNA is

oriented 3 to 5, left to right
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elongation
First elongation step in bacteria:
binding of the second aminoacyl-tRNA.

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The second aminoacyl-tRNA enters the

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A site of the ribosome bound to EF-Tu

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(shown here asTu), which also contains

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GTP.
Binding of the second aminoacyl-tRNA

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to the A site is accompanied by

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hydrolysis of the GTP to GDP and P and
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release of the EF-Tu–GDP complex from

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the ribosome. NA
The bound GDP is released when the
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EF-Tu–GDP complex binds to EF-Ts, and

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EF-Ts is subsequently released when

another molecule of GTP binds to EF-Tu.
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This recycles EF-Tu and makes it

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available to repeat the cycle.

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elongation

Second elongation step in bacteria:

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formation of the first peptide bond.
The peptidyl transferase catalyzing this reaction

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is the 23S rRNA ribozyme.

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The N-formylmethionyl group is transferred to

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the amino group of the second aminoacyl-tRNA

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in the A site, forming a dipeptidyl-tRNA. At this
stage, both tRNAs bound to the ribosome shift

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position in the 50S subunit to take up a hybrid
binding state.
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The uncharged tRNA shifts so that its 3 and 5
ends are in the E site.
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Similarly, the 3 and 5 ends of the peptidyl tRNA

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shift to the P site.

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The anticodons remain in the A and P sites.

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elongation

Elongation Step 3: Translocation

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In the final step of the elongation cycle,
translocation, the ribosome moves one

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codon toward the 3 end of the mRNA

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This movement shifts the anticodon of the
dipeptidyl tRNA, which is still attached to

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the second codon of the mRNA, from the A

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site to the P site, and shifts the deacylated
tRNA from the P site to the E site, from

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where the tRNA is released into the cytosol.

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The third codon of the mRNA now lies in
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the A site and the second codon in the P
site.
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Movement of the ribosome along the

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mRNA requires EF-G (also known as

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translocase) and the energy provided by

hydrolysis of another molecule of GTP
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 Termination
Termination of protein synthesis in
bacteria.
Termination occurs in response to a

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termination codon in the A site.

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First, a release factor, RF (RF-1 or RF-2,

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depending on which termination codon is

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present), binds to the A site. This leads to
hydrolysis of the ester linkage between the

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nascent polypeptide and the tRNA in the P

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site and release of the completed
polypeptide.

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Finally, the mRNA, deacylated tRNA, and NA
release factor leave the ribosome, and the
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ribosome dissociates into its 30S and 50S

subunits.
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 Transcription and translation
Coupling of transcription
and translation in bacteria.

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The mRNA is translated by

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ribosomes while it is still being

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transcribed from DNA by RNA

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polymerase. This is possible

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because the mRNA in bacteria
does not have to be transported

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from a nucleus to the cytoplasm

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before encountering ribosomes. NA
In this schematic diagram the
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ribosomes are depicted as

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smaller than the RNA

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polymerase.
In reality the ribosomes (Mr 2.7
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106) are an order of magnitude

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larger than the RNA polymerase

(Mr 3.9 105).
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Directing eukaryotic proteins with the appropriate signals to the endoplasmic reticulum. This process
involves the SRP cycle and translocation and cleavage of the nascent polypeptide. The steps are
described in the text. SRP is a rod-shaped complex containing
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a 300 nucleotide RNA (7SL-RNA) and six different proteins (combined M 325,000). One protein subunit
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of SRP binds directly to the signal sequence, inhibiting elongation by sterically blocking the entry of
aminoacyl-tRNAs and inhibiting peptidyl transferase. Another protein subunit binds and hydrolyzes GTP.
The SRP receptor is a heterodimer of (M 69,000) and (M 30,000) subunits, both of which bind and
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hydrolyze multiple GTP molecules during this process.

PROTEIN SYNTHESIS IS INHIBITED BY
ANTIBIOTIC AND TOXIN

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• PUROMYCIN

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• TETRACYCLINES

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• CHLORAMPHENICOL

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• STREPTOMYCIN
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• CYCLOHEXIMIDE
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• DIPHTERIA TOXIC
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• RICIN
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Alur genetik

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Amino Acis Synthesis

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• Glutamine

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Synthetase Is a

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Primary
Regulatory Point

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in Nitrogen

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Metabolism

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 RY
• More than a dozen

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known biosynthetic
reactions use

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glutamine as the major

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physiological source of

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amino groups

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• the enzymes catalyzing

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these reactions are NA
called glutamine
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amidotransferases
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Overview of amino acid biosynthesis.

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The carbon skeleton precursors derive from
three sources: glycolysis (pink), the citric acid

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cycle (blue), and the pentose phosphate

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pathway (purple)

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Amino Acid Biosynthetic Families,
Grouped by Metabolic Precursor

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Biosynthesis of
proline and arginine

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from glutamate in

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bacteria

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Biosynthesis of serine from 3-

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phosphoglycerate and of glycine

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from serine in all organisms

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Three Nonessential and Six Essential Amino Acids Are Synthesized from
Oxaloacetate and Pyruvate

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Biosynthesis of
cysteine from

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homocysteine and

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serine in mammals

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 RY
Biosynthesis of six essential amino acids
from oxaloacetateand pyruvate in bacteria:

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methionine, threonine, lysine, isoleucine,
valine, and leucine.

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Here, and in other multistep pathways, the

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enzymes are listed in the key. Note that L,L-
,-diaminopimelate, the product of step 14 , is

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symmetric.

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The carbons derived from pyruvate (and the
amino group derived from glutamate) are
not traced beyond this point, because

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subsequent reactions may place them at NA
either end of the lysine molecule
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