Introduction

Welcome! Due to time constraints, I have

prepared a module on the Central Dogma and
Metabolism. The module will be a learner
centered learning tool which will give you an
opportunity to study at your own pace and at
your own discretion. Just make sure that you will
be able to go through all of this as well as go
through the other PowerPoint Presentations
accompanying the module. Remember that you
need to answer and submit the exercises
incorporated hereon and you will need a
reference book to answer some of the questions.
You may also make use of the internet at your
own convenience.
 The Central Dogma of Life.
replication
 Central Dogma
One of the main objectives of biochemistry is
to understand the nature of the DNA.
Biochemistry deals with the processes
occurring when characteristics are passed on
from parent to offspring and the eventual
expression of these inherited traits. These
processes do not happen simultaneously and
the cell goes through a mechanism that
involves several pathways that happen during
the cell cycle.
 Cell Cycle
• The cell undergoes a life cycle that starts from
the occurrence of cell division. Somatic or
body cells undergo mitotic division while sex
cells or the gametes undergo meiosis. The
mitotic division leads to the inheriting 46
chromosomes while meiosis is responsible for
the halving the number of chromosomes to
23.
 Exercise 1
• Why should there only be 23 chromosomes
for the egg cell and the sperm cell? How many
chromosomes does a bone cell have? Why
should it have this kind of number?
The newly formed daughter cells will now undergo different
phases until it also undergoes cell division. There are different
phases that a living cell can go through - the interphase,
mitosis/meiosis, and cytokinesis.
The interphase is composed of the following:
• G0 – this phase is after cell division. Only some cells pass
through this step wherein the cell is somewhat inactive after
cytokinesis.
• G1 – the cell produces materials necessary for cell growth.
• S – the cell synthesizes materials such as enzymes, proteins,
and other molecules. This is also the time for DNA replication.
• G2 – the cell prepares for the next cell division by correcting
errors in replication and producing proteins needed for the
next phase
The cell may enter mitosis/meiosis after a while and undergo
prophase, metaphase, anaphase, and telophase. Cytokinesis
will be involving the cleaving of the cell membrane to produce
daughter cells.
 Prophase Metaphase

Anaphase Telophase
 Exercise 2
Do all cells go through the different phases of
the cell cycle at the same time? Why?
 REPLICATION
• The replication of the DNA happens during the S phase
of the cell cycle. It has been portrayed as the first step
in the Central Dogma. However, since there are
proteins and other molecules produced by the cell
during G1, it means that there have been transcription
and translation that happened already. Thus, DNA
replication as the first step of the Central Dogma is a
general representation.
• This process happens at the nucleus and makes use of
RNA primers to start the production of the
complimentary strand. The primers will be changed
into DNA at the end. Replication is generally viewed to
have the following steps:
 a. Unwinding of the double helix
• The replication process starts at the origin
(ori). The DNA strand has these special sites
that act as replication forks or places along
the strand where replication happens.
Unwinding of the double helix occurs at these
sites made possible by the enzyme helicase.
Several enzymes come together to produce
new DNA strands.
 b. Elongation of the complimentary
strand
• The double helix has two strands that are
connected via complimentary base pairing. The
hydrogen bonds between the complimentary
bases are broken and the two strands are
separated within the replication forks. One
strand is at the 5’-3’ direction while the other is
at the 3’-5’ direction. Both strands will be
combined with newly produced DNA strands.
Thus, replication is said to be semi conservative
since the resulting two double stranded DNA
after replication will both have an old strand and
a new strand.
• The new strands of DNA will be produced by the
enzyme DNA polymerase. This enzyme produces
DNA strands at a 5’-3’ direction. Thus, the 3’-5’
strand of the original double helix (called as
leading strand) will have its complimentary strand
produced continuously. While the 5’-3’ strand of
the original double helix (called as the lagging
strand) will not experience continuous production
of its complimentary strand. The lagging strand
will have its complimentary strand produced by
parts known as okazaki fragments. These
fragments will be later joined together by a DNA
ligase.
 c. Proofreading
• The newly formed two DNA double strands
will be checked for errors by another type of
DNA polymerase. If an error occurred, the
enzyme will also perform the needed
correction. Later on, the double stranded DNA
will be reforming its helix structure with the
help of the enzyme topoisomerase.
 Exercise 3
• What will happen if the DNA polymerase that
makes the proofreading cannot function
properly?
 TRANSCRIPTION
• When the time comes that a certain trait needs to be
expressed, the information from the DNA will be
transcribed to produce a messenger RNA (mRNA) that will
be the basis for the production of a protein. This protein
will eventually lead to the expression of the characteristic.
Thus, transcription does not happen immediately. It only
happens when it is triggered by hormones or other signals
when needed by the organism.
• The transcription process also happens at the nucleus and
makes use of an enzyme complex involving RNA
polymerase. There is only one strand of the DNA that will
undergo transcription. This is the 3’-5’ strand since the
mRNA produced will be in the 5’-3’ direction.
• Transcription generally has the following steps:
 a. Initiation
• The DNA is unwound by the enzyme complex
and is prepared for transcription. RNA primers
are available for the production of the mRNA.
 b. Elongation
• The enzyme RNA polymerase is responsible
for the production of the complimentary RNA
strand. Only the 3’-5’ strand of the DNA will
be used as a template and the production of
the mRNA will be at 5’-3’ direction. An
important thing to remember is that the RNA
strand will be using uracil (U) rather than
thymine (T). Thus, a DNA sequence 3’-
GATTACAACATTAG-5’ will be 5’-
CUAAUGUUGUAAUC-3’ in the mRNA.
 c. Termination
• The resulting mRNA strand will be released by
the enzyme complex. The DNA helix will be
reformed.
 d. Splicing
• The sequences in the DNA are classified into
coding (if it is used to express a certain trait) and
non coding (if it is not used to express a certain
trait). The coding sequences are known as exons
while the non coding portions are known as
introns. Upon the release of the mRNA after
transcription, it will undergo splicing in the
complex known as a spliceosome. The introns are
taken out and the mature mRNA is left with only
the exons.
 RNA transcript (pre-mRNA)
5
Exon 1 Intron Exon 2

Protein
1
snRNA Other proteins

snRNPs

Spliceosome

2 5

Spliceosome
components
Cut-out
intron
mRNA
3
5
Exon 1 Exon 2
 Exercise 4
• What will be the resulting mRNA for this
double stranded DNA?
5’-GGATTACCAGATATATAGAGACGCGCGCTA-3’
3’-CCTAATGGTCTATATATCTCTGCGCGCGAT-5’
 TRANSLATION
• The final part of the Central Dogma is the synthesis of
proteins by using the code given by the mRNA that
came from the DNA. This process is done in the
ribosome and is facilitated by an enzyme complex.
• The ribosome is composed of a small and large
ribosomal RNA (rRNA) coming together. This unit may
be imagined as having 3 distinct sites during
translation: E – exit site, P – peptidyl site and A – acyl
site. These sites are locations at the ribosome where
the tRNA can move to. The tRNA’s are the carriers of
amino acids that will be used to produce the peptide.
• The translation process generally has the following
steps:
 a. Initiation
• The two subunits of the ribosome come
together. The mRNA is attached to the
ribosome and the tRNA’s are made available.
 TRANSCRIPTION DNA

mRNA
Ribosome
TRANSLATION

Polypeptide
Exit tunnel
Growing
polypeptide

tRNA
molecules
Large
subunit
E
P
A

Small
subunit

5
mRNA 3

(a)
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.
 P site (Peptidyl-tRNA
binding site)
A site (Aminoacyl-
tRNA binding site)
E site
(Exit site)

Large
subunit
E P A

mRNA
binding site
Small
subunit

(b) Schematic model showing binding sites. A ribosome has an mRNA

binding site and three tRNA binding sites, known as the A, P, and E sites.
This schematic ribosome will appear in later diagrams.
 b. Elongation
• The mRNA is read 3 bases at a time (called as
codon). A codon has a resulting anti codon that
is present in a specific tRNA. This particular
tRNA carries a specific amino acid that is
distinctive to this particular codon.
Example:
• The codon GCU has an anti codon CGA present
in the tRNA that carries the amino acid alanine.
 3
A
Amino acid C
attachment site C
A 5
C G
G C
C G
U G
U A
A U
U C A U
* C A C A G U A G
A C U C *
G * *
C G U G U * C G A G G
* * U C *
A G G
* G AG C
(a) G C Hydrogen
Two-dimensional structure. The four base-paired regions and three U A bonds
loops are characteristic of all tRNAs, as is the base sequence of the
amino acid attachment site at the 3 end. The anticodon triplet is * G
A
unique to each tRNA type. (The asterisks mark bases that have been A* C
chemically modified, a characteristic of tRNA.)
* U
A
A G

Anticodon
• The codons and their corresponding amino
acids are presented in the genetic code. For
GCU, look for G at the left side, then C at the
top labels and then U at the right side. It
shows that GCU is a codon for alanine.  
 Second mRNA base
U C A G
UUU UCU UAU UGU U
Phe Tyr Cys
UUC UCC UAC UGC C
U Ser
UUA UCA UAA Stop UGA Stop A
Leu
UUG UCG UAG Stop UGG Trp G

Third mRNA base (3 end)

CUU CCU CAU CGU U
First mRNA base (5 end)

His
CUC CCC CAC CGC C
C Leu Pro Arg
CUA CCA CAA CGA A
Gln
CUG CCG CAG CGG G

AUU ACU AAU AGU U

Asn Ser
AUC lle ACC AAC AGC C
A Thr
AUA ACA AAA AGA A
Met or Lys Arg
AUG start ACG AAG AGG G

GUU GCU GAU GGU U

Asp
GUC GCC GAC GGC C
G Val Ala Gly
GUA GCA GAA GGA A
Glu
GUG GCG GAG GGG G
• The mRNA contains a long sequence and the
ribosome searches for the start codon, AUG. It
codes for formyl-methionine at the start and
methionine for the succeeding AUG’s in the
mRNA sequence. It means that a new peptide
will have f-met as its first residue. This will be
modified after the peptide is released by the
ribosome. There are also stop codons (UAA,
UGA and UAG) that signal the end of
elongation and the release of the peptide.
DNA Gene 2
molecule
Gene 1

Gene 3

DNA strand 3 5
(template) A C C A A A C C G A G T

TRANSCRIPTION

U G G U U U G G C U C A
mRNA 5 3
Codon
TRANSLATION

Protein Trp Phe Gly Ser

Amino acid
 Large
ribosomal
P site subunit
A C 5
3 U
t t
Me 5 A U G 3 Me

Initiator tRNA
GTP GDP
E A
mRNA

5 3 5 3
Start codon

mRNA binding site Small Translation initiation complex

ribosomal
subunit

1 2
A small ribosomal subunit binds to a molecule of The arrival of a large ribosomal subunit completes
mRNA. In a prokaryotic cell, the mRNA binding site the initiation complex. Proteins called initiation
on this subunit recognizes a specific nucleotide factors (not shown) are required to bring all the
sequence on the mRNA just upstream of the start translation components together. GTP provides
codon. An initiator tRNA, with the anticodon UAC, the energy for the assembly. The initiator tRNA is
base-pairs with the start codon, AUG. This tRNA in the P site; the A site is available to the tRNA
carries the amino acid methionine (Met). bearing the next amino acid.
• The ribosome looks for the start codon AUG and the tRNA with the
corresponding anti codon binds to the ribosome at the P site. The A site then
accepts the tRNA with the anti codon for the next codon after AUG. The f-
met from the P site will connect to the amino acid from the A site producing
a dipeptide. The tRNA from the P site moves to the E site for exit and the
tRNA with the dipeptide moves to the P site. The A site is now free to accept
the tRNA with the anti codon for the third codon of the mRNA. This goes on
until the ribosome encounters a stop codon that will signal the end of
elongation.
• Example:
The mRNA sequence is 5’-GAGAUCAUGGCUUCGCGUAAAUAAAGCAUC-3’
The translation will start at AUG and stop at UAA. Thus the portion that will be
translated will only be 5’-AUGGCUUCGCGUAAAUAA-3’. Its going to be
broken into three’s:
• AUG – f-met
• GCU – ala
• UCG – ser
• CGU – arg
• AAA – lys
• UAA – stop
• The other bases will not be used for coding. The resulting pentapeptide will
be: f-met-ala-ser-arg-lys.
 1
Codon recognition. The anticodon
TRANSCRIPTION DNA
Amino end of an incoming aminoacyl tRNA
mRNA
of polypeptide base-pairs with the complementary
Ribosome
TRANSLATION mRNA codon in the A site. Hydrolysis
Polypeptide
of GTP increases the accuracy and
E efficiency of this step.
mRNA 3
Ribosome ready for P A
next aminoacyl tRNA site site
5
2 GTP

2 GDP

E E

P A P A

2
GDP Peptide bond formation. An
3 GTP rRNA molecule of the large
Translocation. The ribosome subunit catalyzes the formation
translocates the tRNA in the A of a peptide bond between the
site to the P site. The empty tRNA new amino acid in the A site and
in the P site is moved to the E site, E
the carboxyl end of the growing
where it is released. The mRNA polypeptide in the P site. This step
moves along with its bound tRNAs, attaches the polypeptide to the
bringing the next codon to be P A
tRNA in the A site.
translated into the A site.
 c. Termination
• The stop codon signals the end of translation.
The resulting peptide is released and the
ribosomal units break apart into rRNA and
proteins.
 Release
factor
Free
polypeptide

5
3 3
3
5 5
Stop codon
(UAG, UAA, or UGA)
1 When a ribosome reaches a stop 2 3
The release factor hydrolyzes The two ribosomal subunits
codon on mRNA, the A site of the the bond between the tRNA in and the other components of
ribosome accepts a protein called the P site and the last amino the assembly dissociate.
a release factor instead of tRNA. acid of the polypeptide chain.
The polypeptide is thus freed
from the ribosome.
 d. Post Translational Modification
• The peptide may proceed to the endoplasmic
reticulum for modification like adding a sugar
unit (glycosylation) and others. If the peptide
is to be used readily inside the cell, it does not
have to go to the endoplasmic reticulum.
Those that go to the endoplasmic reticulum
are secreted out of the cell.
 Ribosomes

mRNA

Signal
peptide
ER
membrane
Signal-
recognition Signal
particle peptide
Protein
(SRP) SRP removed
receptor
protein

CYTOSOL

ER LUMEN Translocation
complex
 Exercise 5
• What will be the resulting mRNA and peptide
for the following double stranded DNA?

• 5’-ATTATATATACCATGCTGGGGTTTAGCTAGGTCAATGGCT-3’
• 3’-TAATATATATGGTACGACCCCAAATCGATCCAGTTACCGA-5’
 Mutation
• There could be possible errors that can
happen from replication to translation.
Mutation can be caused by several mutagens.
• There are also several types of mutations.
 Exercise 6
• Search for the possible mutagens that can
cause DNA or RNA mutations.
 a. Point mutation
This is replacement of a single base in the sequence. It can be
any of the following:
• -missense mutation creates a change in a base that results to
a codon that expresses a different amino acid.
• GCU to CCU – from alanine to proline
• -nonsense mutation creates a change in a base that results to
a stop codon.
• UAC to UAA – from tyrosine to stop codon
• -silent mutation creates a change in a base that results to a
different codon that still expresses the same amino acid.
• GCU to GCG – still alanine
A change from a nucleotide with the same type of base (purine
to purine like G to A and A to G; pyrimidine to pyrimidine like
C to T or T to C) is called a transition point mutation. A change
from a nucleotide with a different type of base (pyrimidine to
purine like G to T or C to A) is called transversion.
 Wild type

A U G A A G U U U G G C U A A
mRNA
5 3
Protein Met Lys Phe Gly
Stop
Amino end
Carboxyl end
Base-pair substitution

No effect on amino acid sequence

U instead of C

A U G A A G U U U G G U U A A

Met Lys Phe Gly

Stop

Missense A instead of G

A U G A A G U U U A G U U A A

Met Lys Phe Ser Stop

Nonsense
U instead of A

A U G U A G U U U G G C U A A

Met
Stop
 b. Frame shift mutation
This can be insertion of a single base or a
sequence. It can also be a deletion of a base
or a sequence.
• Insertion:
• GCUGCG to GCUAGCG – from ala-ala to ala-ser
• Deletion:
• GCUAGCG to GUAGCG – from ala-ser to val-ala
 Wild type

A U G A A G U U U G G C U A A
mRNA 5 3
Met Lys Phe Gly
Protein Stop

Amino end Carboxyl end

Base-pair insertion or deletion
Frameshift causing immediate nonsense
Extra U

A U G U A A G U U U G G C U A

Met
Stop
Frameshift causing
extensive missense U Missing

A U G A A G U U G G C U A A

Met Lys Leu Ala

Insertion or deletion of 3 nucleotides:

no frameshift but extra or missing amino acid

A A G Missing

A U G U U U G G C U A A

Met Phe Gly

Stop
 c. Spontaneous mutation
• These are errors caused by polymerases.
 Exercise 7
• What will be the resulting peptide for the DNA
double strand in #5 if:
– The 17th residue was replaced with C at the 5’-3’
strand?
– The 18th residue of the resulting mRNA was
deleted?
– The 20th residue of the 3’-5’ strand was replaced
with T?
– All the pyrimidines of the mRNA was replaced
with A?