Central Dogma of Molecular

Biology
- describes the three-step process: replication, transcription and
translation, by which the information in genes flow into proteins: DNA
synthesis (replication), RNA synthesis (transcription), and Protein
synthesis (translation)
The chemical structure of DNA:
- is made up of nucleotide unit that forms a chain (polynucleotide)
- its unit of nucleotide is made up of phosphate and nucleoside
connected by covalent bond called phospho-diester linkages
- its nucleoside is made up of sugar and nitrogen base which is
connected by N-glycosidic bond, a covalent bond
- its sugar is called 2’ deoxy-D-ribose while in RNA is D-ribose
(2’ deoxy indicates that oxygen is missing from the 2’ position of
ribose)
- its base pairs represent the steps or the ladder
Nucleotide structure
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- its area that contains the specific base sequence is called the promoter site
exon- is the section in DNA where genes are found
intron- is the non-sense portion of DNA without the presence of gene
genome- is the sum of all genes in the cell
per twist or helix or turn of the DNA contains 10 base pairs which has a length of 3.4
nm (34 A = angstrom) and has a width of 2.0 nm., at an angle of 36 degree/step.
nucleotide is joined to a nucleotide by phosphate esters between 5’ phosphate
group of one nucleotide and 3’ hydroxyl group of the other nucleotide

5’ end is called C5’

3’ end is called C3’
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nitrogen base pair is connected by hydrogen bond (2 for A and T, 3 for
G and C)

Nitrogen bases has 2 groups as pair:

1) purine (has double ring) – adenine and guanine (A-G)
2) pyrimidine (has single ring)- cytosine and thymine (C-T)
adenine in one side of the strand should be paired with thymine at the
other side of the strand (A - T), while cytosine should be paired with
guanine (C – G)
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However, in RNA, thymine should be replaced with uracil (there is no
thymine in RNA).
DNA is an antiparallel strand, when replicated, each single strand serves as
template to the newly forming antiparallel strand, the leading ( with 5’ to 3’
direction) and lagging (with 3’ to 5’ direction) Thus, forming 2 identical DNA
which is semi-conservative.
Its base sequence is responsible for dictating the amino acid sequence

Though prokaryotes have DNA, they could not reproduce because their DNA
is naked (not associated with protein because they don’t have ribosomes)
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genetic information is stored as a sequence of nucleotide in DNA
For information to be transferred to generation, DNA must be copied
For information to be used, it must be decoded and implemented to
release protein.
Organization of the genetic material:
Chromosome is found only in eukaryotes
- is a highly condensed chromatin which is visible during cell division
Chromatin is made up of DNA wound around histone, a protein
- is like a rosary or beads on a string. Each bead represents histone
protein, called histone octamer because of 8 histone proteins,
namely: H2A (2), H2B (2), H3 (2), and H4 (2)
- its string represents DNA
octamer + DNA = nucleosome (repeating unit of chromatin)
each octamer is coiled by DNA at 1 and ¾ times covering 140 base pairs.
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Nucleosome could be brought closer to form more compact fiber done
by linker DNA with another histone protein called H1.
solenoid- a much more compact fiber of nucleosomes formed by coiling
about itself.
When solenoids wound around each other, it forms a chromosome.
DNA replication:
DNA as the genetic material stores all information for all the traits of an
individual in the nucleotide sequence.

Traits are expressed through the action of proteins directly (when the
protein is classified as structural) or indirectly (when the protein
is classified as an enzyme).

RNA is a copy of DNA base sequence which will be interpreted or

decoded into an amino acid sequence of protein in the process of
translation. The resulting protein could express the trait.
• The DNA structure
Picture of a replicating DNA
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DNA replication is exact because the 2 strands separate to function as
templates, by virtue of specific base pairing (Chargaff’s rule)
- is the blue-print of life
- it has sugar-phosphate as the backbone which is
extremely stable under all conditions due to base stacking
(the tendency of the hydrophobic N-bases to pile one on
top of the other) and H-bonds
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In eukaryotes, replication and transcription occurs in the nucleus, while
in prokaryotes, all processes occurs in the cytoplasm.

RNA polymerase (RNA transcriptase), is an enzyme specialized for

transcription in prokaryotes.

Termination of transcription happens only when enzyme has reached

the termination point.
Further transcription is prevented when protein factor called rho binds
to RNA polymerase/transcriptase and dissociate it from DNA.
Replication process:
o Process by which copies of DNA are made so that information are passed on to
offspring
o DNA replication – is an enzyme catalyzed process that begins with 1) unwinding
of double helix to produce single stranded template using helicase enzyme (HUP)
o Each strand (the two new strands) is a complementary to its old template strand,
resulting to 2 identical double helix DNA described by Cricks that the fitting
together of 2 DNA strands is just like a hand in a glove. The hand & glove when
separate, a new hand is formed inside the glove and a new glove is formed
around a hand, the process is described as semi-conservative replication because
of the presence of old & new strand.
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- the process uses an ATP
Another protein, helix destabilizing protein (HDP), is used to destabilize the
helix. This protein binds to the single stranded DNA at the separation point,
called the Y-fork.
Another protein, DNA gyrase (relaxing protein), is used to relax the twisting
tension created by the unwinding process.
2) Priming of the templates formed
- uses enzyme RNA polymerase from RNA primers to add into the leading
strand. It only needs 1 primer. The lagging strand needs several primers
using RNA primase because its complementary strand opens in a 3’ to 5’
direction. Its short segment of primers called Okazaki fragments.
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3) elongation of the complementary strand using DNA polymerase III in
coordination with other proteins, adding DNA nucleotides
complementary to the bases of the template in a 5’ to 3’ direction
starting from 3’OH end of each primer.
4) excision of the primers and its replacement with DNA
5) sealing or joining of gaps in the portion where there are unjoined
Okazaki fragments of the complementary strands using DNA ligase
enzyme.
Summary:
o The process in the joint nucleotides of new nucleotides to create new
DNA strands involve many steps &many different enzymes.
o Addition of new nucleotides unit in a group chain takes place in the 5’
to 3’ direction using DNA polymerase enzyme
o The original 5’ – 3’ strand is synthesized continuously in a single piece
while the compliment of the original 3’-5’ is synthesized not
continuous in the small pieces linked by DNA ligase
The structure of genetic material
• This chapter distinguishes the features between DNA & RNA as genetic material
• Explain the structural organization of the chromosome
• Discuss how DNA is replicated in prokaryotes and eukaryotes

• Have you wondered why you look different from your neighbors? Or why identical
twins are almost indistinguishable from each other?

• These distinct differences are partly influenced by the environment wherein they
were raised.

• But large proportion of them can be explained by a chemical bases – the biomolecule
(DNA) which is preserved in the nucleus which can be replicated & transmitted from
generation to generation
Transcription and Translation:
DNA - contains all the necessary information to build a whole organism
from a single cell
- does not do the work but employ others, the proteins

Proteins- are produced under the direction of the DNA

-the actual builders of the organism's body
3 types of RNA:
mRNA- has codon, codes for sequence of amino acids
tRNA- has anticodon, brings the coded amino acids
rRNA- translate and connects amino acids (proteins)
AUG(Methionine)

- is an initiation codon which is found in the

initiation site of translation.

In an mRNA, its 5’ end is provided with a cap,

which is a recognition signal of the ribosome
for binding. Its 3’ end is provided with a Poly
tail, that plays role in mRNA’s stability.
•For bacteria, its initiation codon is GUG.
•There are 3 termination codons:
1.UAA*
2.UAG*
3.UGA*
*do not code for any amino acid
Wobble Hypothesis (Francis Crick)

•These are synonymous codon which differ

only in the third base because the third base
is either not specifically recognized or
recognized only as purine or pyrimidine, due
to shaky interaction with the 3rd base, with
the anticodon of the t-RNA leading to the
reduced specificity.
rRNA
• complex with protein to form ribosomes
• site of protein synthesis
• is consist of small and large subunits with density
of 30s and 50s respectively. Their subunits join at
protein synthesis to form 70s which has 2
important sites:
• A Site (amino-acyl site)
• P Site (peptidyl site)
The Translation
- has 6 significant stages
1. activation of amino acid

•are attached to their respective t-RNA

•requires ATP
•mediated by amino-acyl synthetase
(enzyme) which is specific for different tRNA.
2. initiation of polypeptide chain

•this is initiated by AUG as initiation codon

•there is an attachment of 30s subunit to the
AUG codon with the help of 2 proteins called
initiation factors 1 and 3 (IF1 and IF3)
• IF1 – is believed to increase the rate of dissociation
of the 70s complexes to 50s and 30s
• IF3 – stabilizes the 30s subunit to prevent it from
binding to mRNA, followed by the attachment of the
tRNA complex with anticodon UAG corresponding to
AUG, a initiation codon.
• formylated methionine – the first amino acid
3. The binding of another tRNA complex
GTP- as the next codon.
4. Formation of the peptide bond between the
carboxylic end of the first amino acid and the amino
end of the next.
5. Elongation of the polypeptide chain
- is done by elongation factor, the Tu protein
(EF-Tu)
6. Termination of the polypeptide chain

•Occurs when the ribosomes encounters any

one of the termination codons (UAA, UAG,
UGA)