Central Dogma of

Molecular Biology
MTY1109 – Biochemistry for Nursing (Laboratory)

Department ofDepartment
Medical Technology,
of MedicalBiochemistry
Technology, Biochemistry
Cluster – 2021-2022
Cluster – 2021-2022
The Central Dogma of Molecular Biology

Department of Medical Technology, Biochemistry Cluster – 2021-2022

 Refers to the process of making copies of genetic
information, converting information in DNA into RNA,
and then RNA into proteins.
Replication - making copies of genetic information

The Central Dogma

of Molecular Biology Transcription – conversion of DNA to RNA.

Reverse Transcription – conversion of RNA to DNA;

viruses only

Translation – conversion of mRNA into a protein;

protein synthesis

Department of Medical Technology, Biochemistry Cluster – 2021-2022

 Genes, Introns, and Exons

• Nucleotide sequences that carry

GENES specific instructions for the cell,
usually for protein synthesis

• Smallest hereditary unit; smallest

form of genetic information passed
from parent to offspring

• A single strand of DNA can carry

multiple genes.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

Genes:
Prokaryotes vs
Eukaryotes
• In prokaryotes, the
entire gene codes for a
protein/molecule.

• In eukaryotes, the gene

consists of coding Prokaryotic and eukaryotic gene organization.
(exons) and non-coding
(introns) regions.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

Gene Expression
in Prokaryotes
and Eukaryotes

Department of Medical Technology, Biochemistry Cluster – 2021-2022

Introns and Exons
• Introns are the non-coding regions of eukaryotic genes.
• Exons are the coding regions of eukaryotic genes.

• Introns are removed and exons are joined together at the end of
transcription to form the final mRNA product via a process called RNA
splicing.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

Introns and Exons
• Only 3% of human DNA actually codes for proteins, but non-coding
regions still play a role.

• Satellites are highly repetitive, non-coding DNA sequences; longer

satellites provide structural stability to chromosomes.

• Mini-satellites and microsatellites are shorter repeats, and are used to

monitor mutations implicated in diseases, such as cancer.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

Introns and Exons

Schematic diagrams of gene organization between different organisms. Note how

many genes, exons and introns are present in each, relative to the number of bases.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

DNA Replication

Department of Medical Technology, Biochemistry Cluster – 2021-2022

 DNA Replication

• Process by which DNA makes copies of itself.

• Occurs in a semi-conservative manner – DNA strands of the parent DNA

becomes the template for the daughter strands.

• Replication occurs on both strands of the DNA. The strand running from 3’
to 5’ towards the fork is called the leading strand. The strand running from
5’ to 3’ towards the fork is called the lagging strand.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

 DNA Replication

• Begins at the origin of replication; a chromosome can have multiple origins.

• The replication fork is where replication actively occurs.

• The assembly of proteins that facilitate DNA replication is called the

replisome.

• The opening in the DNA where replication takes place is generally called the
‘replication bubble.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

DNA Replication

The replisome at the replication fork; the ‘replication

bubble.’ Department of Medical Technology, Biochemistry Cluster – 2021-2022
 The Replisome
• DNA Gyrase/Topoisomerase – prevents DNA from supercoiling by introducing breaks to the
DNA to relieve stress
• Helicase – ‘unzips’ the double stranded DNA; breaks the hydrogen bonds between base pairs
• Primase – synthesizes primers
• Primers are short RNA sequences that bind to the parent DNA strand; serves as the
jumping off paint for DNA polymerase
• Clamp Protein – keeps DNA polymerase in place
• DNA Polymerase – synthesizes the new DNA strand; DNA polymerase can only add
nucleotides to an existing nucleotide chain and cannot initiate replication, hence the need for
primers
• DNA Ligase - joins the Okazaki fragments in the lagging strand
• Single-stranded Binding Proteins (SSB) – stabilizes/protects the single stranded region of
the DNA during replication

Department of Medical Technology, Biochemistry Cluster – 2021-2022

 Leading Strand vs Lagging Strand

• DNA polymerase synthesizes the new strand by adding nucleotides at the free
3’-hydroxyl group, and therefore the new strand grows from 5’ to 3’.

• In the leading strand, which runs from 3’ to 5’, replication is continuous.

• In the lagging strand, which runs from 5’ to 3’, replication is discontinuous.

• Instead of one long strand of new DNA, the polymerase makes use of
several primers to make fragments of the new DNA, called Okazaki
fragments. These Okazaki fragments are then joined together at the end of
replication.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

Replication in Summary
1. Opening of DNA Superstructure. Acetylation of histone lysine
residues weakens binding to DNA, making DNA available for
interaction with enzymes.
2. DNA Relaxation. DNA tends to supercoil as replication proceeds
(think of splitting yarn, where the more it is split, the tighter the
unsplit portion becomes); DNA gyrase prevents this.
3. DNA Unwinding. Via helicase.
4. Primer Synthesis. Via primase.
5. DNA Elongation. Via DNA polymerase.
6. DNA Ligation. Primers are removed, Okazaki fragments and any
breaks in the DNA are joined together via DNA ligase.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

DNA replication - 3D - YouTube
Replication in Summary

Department of Medical Technology, Biochemistry Cluster – 2021-2022

 DNA Repair: Base Excision Repair

• Base Excision Repair (BER) involves the replacement of an incorrect of

damaged base with the correct nucleotide.
• This requires the hydrolysis of the faulty base from the sugar-phosphate
backbone to form an AP site (apurininc/apyrimidinic), followed by the
removal of the sugar-phosphate unit of the incorrect nucleotide. DNA
polymerase then introduces the correct, and DNA ligase mends the break
to complete the repair.

• Only one base is removed, but depending on the DNA polymerase used, it
may result to a ‘short patch’ (only one nucleotide is replaced) or a ‘long patch’
(more than one nucleotide is replaced).

Department of Medical Technology, Biochemistry Cluster – 2021-2022

 DNA Repair: Nucleotide Excision Repair

• Nucleotide Excision Repair (NER) involves the replacement of a stretch of

bases with the correct nucleotides.

• Similar in principle to BER, but NER removes a section of the DNA strand
instead of a single base and makes use of a different DNA polymerase from
BER.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

BER vs NER

Comparison of DNA repair via (a) BER and (b) NER.

Department of Medical Technology, Biochemistry Cluster – 2021-2022
Gene Expression: Transcription

Department of Medical Technology, Biochemistry Cluster – 2021-2022

Transcription

• First step in gene expression, occurs in the nucleus (eukaryotes).

• Before transcription, DNA must first be unwound by binding proteins.

• Helicase attaches to the unwound DNA to break the H-bonds between

base pairs.

• The transcription bubble is the opening in the double helix where

transcription takes place.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

 Transcription
• Template strand – DNA strand that is transcribed; also called (-) strand or antisense
strand
• Coding strand - DNA strand that is NOT transcribed; also called (+) strand or sense
strand

• RNA polymerase (RNA pol) – enzyme responsible for RNA synthesis; there are three (3)
types depending on the RNA to be produced.
• RNA Pol II for mRNA

Department of Medical Technology, Biochemistry Cluster – 2021-2022

 Transcription

Recall that genes are DNA sequences that code for a specific protein, or carry
specific instructions for the body.

Genes have coding (exons) and non-coding (introns) regions, and these make
up the structural gene.
Genes also have the promoter and terminator regions, which make up the
regulatory regions of the gene.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

 Transcription: The Promoter Region

• The promoter region is where the RNA polymerase initially binds, and is found
several nucleotides upstream.
• ‘upstream’ means before the beginning of the transcription site
• ‘downstream’ means after the beginning of the transcription site

• RNA pols cannot recognize the promoter region on their own, and require the help of
transcription factors.

• The promoter also identifies which strand is the template. The coding strand has no
promoter region.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

 Transcription: The Promoter Region
• Within the promoter region is the consensus sequence and the initiation
signal.

• The consensus sequence identifies the precise nucleotide at which

transcription should begin, e.g. the TATA box.
• The initiation signal give RNA pol the signal when to start.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

Transcription: The Terminator Region
• The terminator region is a string of nucleotides at the end of a gene that
signals RNA pol to transcription.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

Transcription: Elongation

• Elongation is the process of adding the appropriate complementary

nucleotide as RNA pol moves downstream along the gene.

• RNA pol reads the DNA template from 3’ to 5’, and therefore synthesizes
RNA from 5’ to 3’.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

Transcription

• Transcript is the general term used to refer to the product of

transcription.

• For mRNA, the initial transcript still contains all the introns and
unstranscribed regions, and is referred to as the pre-mRNA.

• Pre-mRNA undergoes additional reactions before it can be considered a

fully functional mRNA, called the mature mRNA.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

Transcription

• Organization and processing of a gene transcript.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

 Post-Transcription Modifications

• Pre-mRNA undergoes three processes before it becomes a mature mRNA:

• 5’ capping – addition of a methylated guanine group to the 5’ end of the

transcript.
• 3’ polyadenylation – addition of several adenosine residues to the 3’ end of
the transcript, forming a poly(A) tail.
• RNA splicing – removal of the introns from the transcript and joining of the
exons.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

 Post-Transcription Modifications

• 5’ capping – protects the mRNA from exonucleases; aids in mRNA transport

to the cytosol; allows for the initiation of translation

• 3’ polyadenylation – protects the mRNA from exonucleases

• RNA splicing – leaves behind the exons that contains the code for the amino
acids in a protein

Department of Medical Technology, Biochemistry Cluster – 2021-2022

Transcription in Summary
1. DNA Unwinding. Binding proteins and helicase unwind and opens up DNA.
2. Initiation. RNA pol and transcription factors recognize the promoter
sequence and bind to DNA.
3. Elongation. RNA pol reads the template and synthesizes the pre-mRNA.
4. Termination. RNA pol recognizes the terminator region, stops transcription
and releases itself from the template.
5. 5’ Capping.
6. 3’ Polyadenylation.
7. RNA Splicing.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

 Transcription in Summary
Transcription (DNA to mRNA) - YouTube

Department of Medical Technology, Biochemistry Cluster – 2021-2022

Gene Expression: Translation

Department of Medical Technology, Biochemistry Cluster – 2021-2022

 Translation

Synthesis of proteins from

mature (spliced) mRNA

RNA-protein complexes called

ribosomes are used

Department of Medical Technology, Biochemistry Cluster – 2021-2022

Translation
Ribosomes
Has four rRNA (ribosomal RNA) molecules
distributed in two subunits
Each subunit: 65% rRNA and 35% protein

The active site is in the ribosomal subunit

rRNA is the active site

The predominance of rRNA at the active site

gives it the impression of a ribozyme
The mRNA binds to the small subunit of the
ribosome
Note: S means “sedimentation coefficient”. The in-
depth discussion for what this means is beyond the
scope of this course.
Department of Medical Technology, Biochemistry Cluster – 2021-2022
Ribosomes

Three sites in the ribosome:

A site – “attachment site”
for tRNAs
P site – polypeptide
formation site
E site – “exit site” for
tRNAs

Department of Medical Technology, Biochemistry Cluster – 2021-2022

 The Genetic Code

The base sequence in mRNA determines the amino acid sequence in

protein synthesis
The base sequence of an mRNA molecule involves 4 different bases - A, C,
G, and U
Codon: A three-nucleotide sequence in an mRNA molecule that codes for a
specific amino acid
64 codons in total
Genetic code: The assignment of the 64 mRNA codons to specific
amino acids
 3 of the 64 codons are termination codons (STOP codons)

Department of Medical Technology, Biochemistry Cluster – 2021-2022

The Genetic Code
The start codon (AUG)
also codes for
Methionine

Stop codons are UAA,

UGA, and UAG

The genetic code is

highly degenerate. This
means there are
multiple codons for
most amino acids.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

 The Genetic Code

 The degeneracy of the genetic code

makes it less prone to mutations.
 Degeneracy – multiple codons per
amino acid
 The genetic code is universal
 Codons for humans are the same for
other organisms as well (with some
exceptions)
 Codons are matched with anticodons in
corresponding transfer RNAs (tRNAs)

Note: This is just another visual representation of

the genetic code.
Department of Medical Technology, Biochemistry Cluster – 2021-2022
Transfer RNAs (tRNAs)

Anticodons
Complementary
pairs of codons

Each codon has a

corresponding
anticodon, therefore a
corresponding tRNA as
well.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

 Translation in Summary
tRNA Activation
1. tRNA activation
 tRNAs are “loaded” with their
corresponding amino acids.
2. Initiation
 Ribosome detects start
codon, Met tRNA attaches to
P site.

Department of Medical Technology, Biochemistry Cluster – 2021-2022

Translation in Summary
*E site not shown here
3. Elongation
-Bond between 1st and
2nd amino acid forms
-First tRNA goes to E
site and exits ribosome
-At the same time, a
new charged tRNA goes
to the A site
-Cycle repeats until stop
codon is encountered

Department of Medical Technology, Biochemistry Cluster – 2021-2022

Translation in Summary

4. Termination

- Ribosome detects stop

codon. The Release
Factor binds to the A site,
opening the ribosome
and releasing the newly
synthesized polypeptide

Department of Medical Technology, Biochemistry Cluster – 2021-2022

Life Science - Protein synthesis (Translation) - YouTube
Translation in Summary

Department of Medical Technology, Biochemistry Cluster – 2021-2022

THANK YOU!!

Department of Medical Technology, Biochemistry Cluster – 2021-2022