● By which RNA is used to produce proteins is called

DNA REPLICATION, TRANSCRIPTION, AND translation

TRANSLATION
STRUCTURE OF DNA
OUTLINE ● DNA is composed of 4 nucleotides each containing:
I Overview Adenine (A), Cytosine (C), Thymine (T), or Guanine (G)
II Central Dogma of Molecular Biology
A Structure of DNA ● Follows the Chargaff’s Rule
B Organization of DNA ○ the amounts of A=T , G=C
i The Basic Principle
○ Purines = Pyrimidines
III DNA Replication
A Models of Replication
○ the rule states that, DNA from any species of any
B DNA Replication is Semi Conservative organism should have a 1:1 stoichiometric ratio of
C Origins of Replication purines and pyrimidines
D Mechanism of Replication ● A double-stranded helix with antiparallel strands
IV Transcription ○ These strands run on opposite directions
A. Synthesis of RNA Transcription ● Nucleotides in each strand are linked by 5’-3’ (5-prime to
B. Post Termination RNA Processing 3-prime) phosphodiester bonds
C. RNA Processing
● Bases on the opposite strands are linked by hydrogen
V Translation/Building a Polypeptide
A Initiation of Translation
bonding:
B Elongation of Polypeptide ○ A with T
C Termination ○ G with C
VI Summary of Transcription and Translation
A Post-Translation

OVERVIEW:
● The genetic material is stored in the form of DNA in
most organisms
● In humans, the nucleus of each cell contains 3 × 10⁹
base pairs of DNA distributed over 23 pairs of
chromosomes, and each cell has 2 copies of the
genetic material, known collectively as the human
genome
● The human genome contains around 30,000 genes,
each of which codes for 1 protein
● It (genes) is normally a stretch of DNA that codes for a
type of protein/ for an RNA chain that has a function in
the organism
● Genes hold the information to build and maintain an
organism’s cells and pass genetic traits to offspring.
● Genes is also as the unit of heredity
ORGANIZATION OF DNA
CENTRAL DOGMA OF MOLECULAR BIOLOGY CHROMOSOME -> CHROMATIN -> NUCLEOSOME ->
HISTONES -> DNA

● 1st in the order is your

chromosome
● If you magnify your
chromosome, you will be able
to observe the chromatin
● Magnify further and you will
be able to observe the
nucleosome
○ Which are made up of
8 histone proteins
● These histone proteins are the site on which the DNA
wraps around

BASIC PRINCIPLE: BASE PAIRING TO A TEMPLATE

● States that DNA makes RNA, then RNA makes proteins STRAND
● The process by which DNA is copied to RNA is called ● This is the basic principle of DNA replication
transcription
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● The relationship between the structure and function is CONSERVATIVE

manifested in the double helix ● The parental strands stay together and the daughter
● Since the 2 strands of DNA are complementary, each strands are also together
strand acts as a template for building a new strand in ● The term ‘conservative’ comes from the fact that the two
replication parental strands of the DNA molecule are conserved

DNA REPLICATION SEMI-CONSERVATIVE

● The parent molecule unwinds, and two new daughter
● A method of replication that suggests that the two parental
strands are built based on base-pairing molecules
DNA strands serve as a template for new DNA
● The copying of DNA is remarkable in its speed and
● After replication, each double-stranded DNA contains one
accuracy
strand from the parental DNA (old) and one new daughter
● Involves unwinding the double helix and synthesizing into
strand
two new strands
● It is called semi-conservative because only one parental
● More than a dozen enzymes and other proteins participate
strand is conserved in the two DNA molecules
in DNA replication
● The replication of a DNA molecule begins at special sites
called origins of replication, where the two strands are DISPERSIVE
separated ● After replication, the two daughter DNAs have alternating
segments of both parental and newly synthesized DNA
interspersed in both strands
● The two old parental strands alternates with the two new
DNA molecules– old, new, old, new
● Parent strands are not conserved; it was dispersed

DNA REPLICATION IS SEMI-CONSERVATIVE

(a) The parent molecule has 2 complementary strands of

DNA. Each base is paired by hydrogen bonding with its
specific partner: A with T , G with C

(b) The first step in replication is separation of the 2 DNA

strands or the unwinding of the parental strand

(c) Each parental strand now serves as a template that

determines the order of nucleotides along a new,
complementary strand

(d) The nucelotides are connected to form the

sugar-phosphate backbones of the new strands. Each
“daughter” DNA molecule consists of:
● 1 parental strand & 1 new strand
● Discovered by Meselson and Stahl using E.coli DNA, they
determined that DNA replicated via the semi-conservative
MODELS OF REPLICATION method of replication
● Each 2-stranded daughter molecule is only half new
○ Because it contains one old strand and one new
strand
● One original strand was used as a template to make the
new strand

ORIGINS OF REPLICATION
● A eukaryotic chromosome may have hundreds or even
thousands of replication origins
● In eukaryotes, DNA replication begins at many sites along
the giant molecule of each chromosome

1. Replication begins at specific sites where the two

parental strands separate and form replication
bubbles

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You have your single-stranded parental DNA, here you have

your primer (red), and then the primase which synthesizes the
primer. The primase joins RNA nucleotides into the primer.
Then, your DNA polymerase adds the DNA nucleotides to the
primer, forming your newly made DNA.
● The direction is always going from the 5’ (5 prime) end to
the 3’ (3 prime) end.
● DNA synthesis on the leading strand is continuous
● Lagging strand grows in the same general direction as the
● The replication fork is a structure that forms within the leading strand
long helical DNA during replication. ○ Same direction as the replication fork
○ It is created by the ○ However, DNA is made in the 5’ to 3’
helicases that break direction
down the hydrogen ○ Therefore, DNA synthesis on the lagging end
bonds holding the two is discontinuous
DNA strands together. ● DNA is added as short fragments (Okazaki Fragments)
Maong mu form siya that are subsequently ligated together
og fork.
○ The resulting
structure: two
branching prongs of
the parental strand
● In this micrograph, three
replication bubbles are
visible along the DNA of a
cultures Chinese hamster
cell (TEM) ● Since the direction of the lagging strand is in the opposite,
it starts in 3’ towards 5’
2. The bubbles expand laterally, as DNA replication ○ Thus, DNA cannot be synthesized
proceeds in both directions continuously
○ This is why we get our Okazaki Fragments
○ What happens is that RNA primase adds the
primer (green) and then DNA polymerase
synthesizes DNA by fragments
○ RNA primase (first red fragment), then adds
3. Eventually, the replication bubbles fuse, and primer (green)
synthesis of the daughter cells is complete. ● Always follows or goes towards the direction of the
replication fork

DIFFERENT ENZYMES IN DNA REPLICATION

MECHANISM OF DNA REPLICATION

DNA POLYMERASE
● Catalyzes DNA replication
● Needs an RNA primer
● Adds DNA nucleotides to the 3’ end of the growing strand

RNA PRIMASE
● Synthesizes primer on the DNA strand

DNA HELICASE
● Unwinds the double helix

BINDING PROTEINS
● Stabilizes the separate strands/template strands

PRIMASE
● Catalyzes the synthesis of short RNA primers to template
strand to which nucleotides are added

DNA POLYMERASE III

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● Binds nucleotides to form new strands, extending the ● DNA Polymerase (bean-shaped) enzyme adds DNA
strand in the 5’ to 3’ direction nucleotides to the RNA primer (green) following the 5’ to 3’
direction and the direction of the replication fork
DNA POLYMERASE I (EXONUCLEASE)
● Removes RNA primer and replaces it with DNA/inserts the
correct bases

LIGASE
● Joins DNA fragments (Okazaki fragments) into a
continuous daughter strand and seals other nicks in the
phosphate backbone

● DNA Polymerase adds DNA nucleotides to the RNA

primer.
● DNA polymerase proofreads bases added and replaces
incorrect nucleotides

REPLICATION

● Leading strand synthesis continues in a 5’ to 3’ direction.

● Discontinuous synthesis produces 5’ to 3’ DNA segments
called Okazaki Fragments.
You have your RNA primer (green). Then, this is your Okazaki
fragments (gaps in between). Again, synthesis in the lagging
strand is discontinuous and nucleotides are added in
fragments (Okazaki fragments).
● First step: unwinding or unzipping
● Helicase proteins (big pink oval) binds to DNA sequences
called origins and unwinds DNA strands
● Binding proteins (lavender circles) prevent single strands
from rewinding. Mao ni sya ang magpugong sa strands
● RNA primase protein (red oblong) makes a short segment
of RNA complementary to the DNA, a primer/RNA primer.

● Next, the exonuclease activity of DNA polymerase 1

(yellow) removes the RNA primers (green).

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● DNA polymerase proofreads and repairs accidental

mismatched pairs
● Chances of a mutation occurring at any one gene is over 1
in 100,000
● Because the human genome is so large, even at this rate,
mutations add up. Each of us probably inherited 3-4
mutations!

PROOFREADING AND REPAIRING DNA

● DNA polymerases proofread newly made DNA, replacing
● Polymerase activity of DNA polymerase 1 fills the gaps.
any incorrect nucleotides.
● Ligase (light green) forms bonds between
● In mismatch repair of DNA, repair enzymes correct errors
sugar-phosphate backbone.
in base pairing
The RNA primer on the leading strand and the primer on the
● In nucleotide, excision DNA repair, nucleases cut out and
lagging strand has already been removed and the DNA
replace damaged stretches of DNA
polymerase (purple) is the one that fills the gaps left by the
removed RNA primer.
So here on the lagging strand, the primers (2 green bars on the
pic) have not been removed. Once these are removed, it will
leave a gap. Polymerase is the one that will fill in those gaps.
Meanwhile, the Ligase (light green rectangles) will form the
bonds between the sugar phosphate backbones. It will seal or
join the fragments into a continuous strand.

REPLICATION FORK OVERVIEW

● Enzymes unwind the parental double helix. So, the

enzymes or helicase unwinds the double parental helix.
● Proteins stabilize unwound parental DNA. ● A thymine dimer distorts the DNA molecule.
● The leading strand is synthesized continuously by DNA ○ Dimers are molecular lesions formed from thymine
polymerase. or cytosine bases in DNA via photochemical
● The lagging strand is synthesized discontinuously. RNA reactions. In this case, it is a dimer formed from
polymerase synthesizes a short RNA primer which is then thymine since it is a thymine dimer. These dimers
extended by DNA polymerase. can potentially lead to mutation and even possibly
● DNA polymerase digests RNA primer and replaces it with cancer.
DNA. ● A nuclease enzyme cuts the damaged DNA strand at two
● DNA ligase joins the discontinuous fragments of the points and the damaged section is removed.
lagging strand. ● Repair synthesis by a DNA polymerase fills in the missing
nucleotides.
PROOFREADING ● DNA ligase seals the free end of the new DNA to the old
● DNA must be faithfully replicated, however mistakes DNA, making the strand complete.
occur.
○ DNA polymerase inserts the wrong nucleotide ACCURACY OF DNA REPLICATION
base in 1/10,000 bases. ● The chromosome of E.coli bacteria contains about 5
○ DNA polymerase has a proofreading ability and million base pairs.
can correct errors ○ This chromosome is capable of copying this DNA
● Mismatch repair: ‘wrong’ inserted base can be removed in less than an hour
● Excision repair: DNA may be damaged by chemicals, ● The 46 chromosomes of a human cell contain about 6
radiation, etc. Mechanism to cut out and replace with billion pairs of DNA.
correct bases. ○ Takes the human cell a few hours to copy this
DNA
MUTATIONS ○ With amazing accuracy- an average of 1 per billion
● A mismatching of base pairs can occur at a rate of 1 per nucleotides
10,000 bases
PROTEIN SYNTHESIS

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● The information content of DNA is in the form of specific

sequences of nucleotides along the DNA strands.
● The DNA inherited by an organism leads to specific traits
by dictating the synthesis of proteins.
● The process by which DNA directs protein synthesis, gene
expression, includes two stages called transcription and
translation

TRANSCRIPTION & TRANSLATION

● Cells are governed by a cellular chain of command
● DNA > RNA > Protein

TRANSCRIPTION DIAGRAM:
● Is the synthesis of RNA under the direction of DNA ● This is the DNA molecule. The RNA polymerase pries the
● Produces messenger RNA (mRNA) DNA strands apart and hooks together the RNA
nucleotides
TRANSLATION ● (Green line in the middle) - RNA strand; (Attached to RNA
● Is the actual synthesis of a polypeptide which occurs strand) - RNA nucleotides
under the direction of mRNA ● Thymine is replaced by uracil
● Occurs on ribosomes
● In a eukaryotic cell, the nuclear envelope separates RNA
transcription from translation ● RNA is single stranded unlike DNA which is double
● Extensive RNA processing occurs in the nucleus stranded.
● RNA is short, only 1 gene long, whereas DNA is very long
and contains main genes.
● RNA uses the sugar ribose instead of deoxyribose which
is used in DNA.
● RNA uses the bases uracil (U) instead of thymine (T)
which is used in DNA.

TYPE OF RNA FUNCTIONS

Messenger RNA (mRNA) Carries information

specifying amino acid
sequences of protein from
DNA to ribosomes
● The nucleus provides a separate compartment for
Transfer RNA (tRNA) Serves as adapter molecule
transcription. The original RNA transcript, called
in protein synthesis;
pre-mRNA, is processed in various ways before leaving
translates mRNA codons
the nucleus as mRNA.
into amino acids
TRANSCRIPTION
Ribosomal RNA (rRNA) Plays catalytic (ribozyme)
● Transcription is the DNA directed synthesis of RNA
roles and structural roles in
● RNA Synthesis:
ribosomes
○ Is catalyzed by RNA polymerase which pries the
DNA strands apart and hooks together the RNA
nucleotides Primary transcript Serves as a precursor to
○ Follows the same base-pairing rules as DNA except mRNA, rRNA, or tRNA,
that in RNA, uracil substitutes for thymine before being processed by
○ Uracil is a base exclusive to only RNA, while splicing or cleavage. Some
Thymine is a base exclusive to only DNA. Cytosine, intron RNA acts as
Adenine, and Guanine are used by both RNA and ribozyme, catalyzing its own
DNA splicing

Small nuclear RNA Plays structural and catalytic

(snRNA) roles in spliceosomes, the
complexes of protein and
RNA that splice pre-mRNA

SYNTHESIS OF RNA
● The stages of transcription are:
○ Initiation
○ Elongation
○ Termination

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TERMINATION
● Specific sequences in the DNA signal termination of
transcription.
● When one of these is encountered by the polymerase, the
RNA transcript is released from the DNA and the double
helix can zip up again
1. INITIATION - After RNA polymerase binds to the promoter,
the DNA strands unwind, and the polymerase initiates TRANSCRIPTION OVERVIEW
RNA synthesis at the start point on the template strand.
2. ELONGATION - The polymerase moves downstream,
unwinding the DNA and elongating the RNA transcript
5->3’ In the wake of transcription, the DNA strands re-form
a double helix.
3. TERMINATION - Eventually, the RNA transcript is
released, and the polymerase detaches from the DNA.

INITIATION
● Promoters signal the initiation of RNA synthesis
● Transcription factors help eukaryotic RNA polymerase
recognize promoter sequences

STAGE 1
● Promoters signal initiation of RNA synthesis

STAGE 2
● RNA polymerase unwinds the DNA double helix and
synthesizes a single RNA strand against the DNA
template strand

STAGE 3
● RNA polymerase encounters specific DNA sequences that
signal the termination of RNA transcription, and the RNA
transcript is finally released

In the picture:
ELONGATION
● RNA polymerase synthesizes a single strand of RNA 1 is the initiation stage.
against the DNA template strand (anti-sense strand), 2 and 3 are the elongation stage
adding nucleotides to the 3’ end of the RNA chain. 4 is termination stage
● As RNA polymerase moves along the DNA, it continues to 5 is the release of RNA transcript
untwist the double helix, exposing about 10 to 20 DNA
bases at a time for pairing with RNA nucleotides POST TERMINATION RNA PROCESSING
● Most mRNAs aren't ready to be translated into protein
directly after being transcribed from DNA. This would
mean that mRNA requires processing.
● Transcription of RNA processing occurs in the nucleus.
After this the messenger RNA moves to the cytoplasm for
translation.

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● The cell adds a protective cap to one end, and a tail of A’s ● Together with their respective exons are seen in the
(adenines) to the other end. These both function to protect picture
the RNA from enzymes that degrade it

INTRONS
● Non-coding regions that most of the genome consists
● Allow for alternative RNA splicing
● Non-coding regions may have specific chromosomal
functions or regulatory purposes
● An RNA copy of a gene is converted into messenger RNA
by doing 2 things:
a. Add protective bases to the ends
b. Cut out the Introns
Domain 1: Coded by exon 1 in green.
ALTERATION OF MRNA ENDS Domain 3: Coded by exon 3 in purple
● Each end of a pre-mRNA molecule is modified in a
particular way TRANSLATION
● 5’ end receives a modified nucleotide (5’ cap) ● RNA-directed synthesis of a polypeptide
● 3’ end gets a poly A-tail or a poly-adenine tail ● Involves:
● 5’ cap and 3’ cap in yellow are added to the pre- mRNA (in a. mRNA
red) b. Ribosome
● 5’ cap and the poly-adenine tail make it more stable and - Ribosomal RNA
protect it from degradation. c. Transfer RNA
d. Genetic Coding
- Specifically codons

RNA PROCESSING
PRE-MRNA
● Original transcript from the DNA
● Contains transcripts of both introns and exons

SPLICING
● Process to remove introns to produce
messenger RNA (mRNA)

GENETIC CODE
● Genetic information is encoded as a sequence of base
triplets, or codons

DOMAINS
● Modular architecture consisting of discrete structural and
functional regions that proteins often have Base triplets/Codons (shown in picture orange): UGG, UUG,
● In many cases, different exons code for the different GGC, UCA
domains in a protein

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CODONS
● Always a triplet of RNA bases
● sequence of base triplets/codons determine which amino
acid will be produced
● three base codes for the production of a specific amino
acid, sequence of three of the four different nucleotides
● could be a mix of A,C,T,G ANTICODON
● since there are 4 bases and 3 positions in each codon, ● The “anticodon” is the 3 RNA bases that match the 3
there are 4x4x4 = 64 possible codons bases of the codon on the mRNA molecule.
● 64 codons but only 20 amino acids. Therefore, most ● Not only are the base pair region and 3 loops are
amino acids have more than 1 codon characteristics of all tRNAs but so is the base sequence of
● 3 of the 64 codons are used as stop signals. They are the amino acid attachment side of 3’ end (ACC) and the
found at the end of every gene and mark the end of the anticodon triplets (AAG) is unique to each TRNA type
protein ● Since the bases of our anticodon (AGG), the bases of
● one codon is used as a START signal and this is found at mRNA molecule would be UUC
the start of every protein ○ A pair with U
● Universal = occurs in all living organisms ○ G pair with C
● Codon in messenger RNA is either translated into an
amino acid or serves as a translational start/stop signal ASTERISK MARK BASES
● The asterisk mark bases have been chemically modified, a
characteristic of tRNA

THREE-DIMENSIONAL RNA
● Three-dimensional tRNA molecules is roughly “L” shaped

Start codon: AUG

Stop codons: UAA,UAG,UGA
● First letter of every codon represents the first mRNA base
which is located on the 5’ end.
● The second letter represents the 2nd mRNA base RIBOSOMES
● The 3rd or the last letter represents the last/3rd mRNA base ● Facilitate specific coupling or tRNA anticodons with mRNA
which is located on the 3’ end codons during protein synthesis

TRANSFER RNA RIBOSOMAL RNA

● Consists of a single strand of RNA that is only about 80 ● The 2 ribosomal subunits are constructed of proteins and
nucleotides long RNA molecules named ribosomal RNA (rRNA)
● Each carries a specific amino acid on one end and has an
anticodon on the other end
● A special group of enzymes pairs up the proper tRNA
molecules with their corresponding amino acids
● tRNA brings the amino acids to the ribosomes which are
the sites of protein synthesis

● Computer model of functioning ribosome

● This is a model of a bacterial ribosome, showing its overall
shape
● The eukaryotic ribosome is roughly similar
● A ribosomal subunit is an aggregate of ribosomal RNA
molecules and proteins
● In the model, you can see the large and small subunit
which are the 2 ribosomal subunits
● You can also see the mRNA, tRNA molecule, and the
growing polypeptide which is coming out of the exit tunnel

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● Arrival of a large ribosomal subunit completes the initiation

BUILDING A POLYPEPTIDE complex
● This will eventually will become protein ○ Proteins called initiation factors (not shown) are
required to bring all the translation components
together.
○ GTP (Guanosine-5'-triphosphate) provides the
energy for the assembly. Initiator tRNA is in the P
site; A site is available to the tRNA bearing the
next amino acid

ELONGATION OF THE POLYPEPTIDE CHAIN

● Amino acids are added one by one to the proceeding
amino acid

● Schematic model with mRNA and tRNA

● A tRNA fits into a binding site when its anticodon
base-pairs with an mRNA codon
● The P site holds the tRNA attached to the growing
polypeptide
● The A site holds the tRNA carrying the next amino acid to
be added to the polypeptide chain
● Discharged tRNA leaves via the E site
● The P-site or peptidyl is the second binding site for tRNA
in the ribosome
● The other two sites are the A-site or aminoacyl, which is
the first binding site in the ribosome, and the E-site or exit,
the third
● We can divide translation into 3 stages 1. CODON RECOGNITION
○ Initiation ● Anticodon of an incoming aminoacyl tRNA base pairs with
○ Elongation the complementary mRNA codon in the A site
○ Termination ● Hydrolysis of GTP increases the accuracy and efficiency
of this step
AUG START CODON
● The AUG start codon is recognized by methionyl-tRNA 2. PEPTIDE BOND FORMATION
(Met) ● An rRNA molecule of the large subunit catalyzes the
● Once the start codon has been identified the ribosome formation of a peptide bond between the new amino acid
incorporates amino acids into a polypeptide chain in the A site and the carboxyl end of the growing
● RNA is decoded by tRNA (transfer TNA) molecules, which polypeptide in the P site attaches the polypeptide to the
each transport specific amino acids to the growing chain tRNA in the A site
● Translation ends when a stop codon (UAA, UAG, UGA) is
reached 3. TRANSLOCATION
● Ribosome translocate the tRNA in the A site to the P site
INITIATION OF TRANSLATION ● Empty tRNA in the P site is moved to the E site,where it is
● The initiation stage of translation brings together mRNA, released
tRNA bearing the first amino acid of the polypeptide, and ● mRNA moves along with its bound tRNAs, binging the
two subunits of a ribosome. next codon to be translated into the A site

TERMINATION OF TRANSLATION

● A small ribosomal subunit binds to a molecule of mRNA .

○ In a prokaryotic cell, the mRNA binding site on
this subunit recognizes a specific nucleotide
sequence on the mRNA just upstream of the start
codon. ● Final stage
○ An initiator tRNA, with the anticodon UAC, ● When a ribosome reaches a stop codon on mRNA, the A
base-pairs with the start codon, AUG.This tRNA site of the ribosome accepts a protein called a release
carries the amino acid methionine(Met). factor instead of tRNA. There is no corresponding tRNA.

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● Release factor hydrolyzes the bond between the tRNA in ● Polypeptides fold spontaneously into their active
the P site and the last amino acid of the polypeptide chain; configuration, and they spontaneously join with other
thus, the polypeptide is this freed from the ribosome polypeptides to form the final proteins
● Two ribosomal subunits and the other components of the ● Sometimes other molecules are also attached to the
assembly dissociate polypeptides; sugars, lipids, phosphates, etc.
○ All of these have special purposes for protein
RELEASE FACTOR function
● Small protein attached to the stop codon.
● Causes the whole complex to fall apart:
○ Messenger RNA– which can be translated many
times to produce many protein copies
○ Two Ribosome Units
○ New Polypeptide

SUMMARY OF TRANSCRIPTION AND TRANSLATION

1. RNA IS TRANSCRIBED FROM A DNA TEMPLATE

RESULTING TO TRNA TRANSCRIPT

2. THE RNA TRANSCRIPT/PRE-MRNA IS SPLICED

AND MODIFIED TO PRODUCE MRNA WHICH MOVES
FROM THE NUCLEUS TO THE CYTOPLASM

3. MRNA ATTACHES TO RIBOSOME

4. AMINO ACID ACTIVATION

● Each amino acid attaches to its proper tRNA with the help
of a specific enzyme and ATP

5. TRANSLATION
● Succession of tRNAs add their amino acids to the
polypeptide chain as the mRNA is moved through the
ribosome one codon at a time
● When completed, the polypeptide is released from the
ribosome

POST-TRANSLATION
● New polypeptide is now floating loose in the cytoplasm, if
translated by a free ribosome
● Might also be inserted into a membrane, if translated by a
ribosome bound to the endoplasmic reticulum

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