Central Dogma and
Gene Expression
M.K. BIOLOGI SEL DAN MOLEKULER
Program Studi Agroteknologi
Fakultas Pertanian - Universitas Padjadjaran
Semester Genap 2023/2024
@FD
What are Central Dogma
and Gene Expression?
Central Dogma :
The concept of a DNA-based gene encoding an
RNA-based message that is then translated
into a protein (Iwasa & Marshall, 2016)
Gene Expression :
A process by which genes produce RNAs and
proteins and exert their effect on the
phenotype of an organism (Snustad &
Simmons, 2012)
Source : Alberts et al. (2014) Essential Cell Biology. pp. 3
Topics will be discussed :
• DNA
• RNA
• Replication
• Transcription
• Translation
• Gene expression regulators
DNA and RNA
The overview
Source : Clark et al. (2019) Molecular Biology. pp. 73 Source : Clark et al. (2019) Molecular Biology. pp. 70
Major Classes of Non-Translated RNA
Source : Clark et al. (2019) Molecular Biology. pp. 85
Gene Structure
and Its Expression
in Eukaryotes
Source : Zerbini et al. (2014) Transgenic plants in Biotechnology and Plant Breeding. pp. 181
Terminology
Intron : non-coding region of a eukaryotic gene that is transcribed into an RNA molecule
but is then excised by RNA splicing when mRNA is produced.
Exon : part of a eukaryotic gene that consists of DNA coding for a sequence of nucleotide in
mRNA; thus, an exon can encode the sequence of amino acids in a polypeptide or protein.
Gene : a sequence of functional DNA which could be transcribed and/or translated into a
protein, regulate gene expression, and renowned as a unit of heredity.
RNA splicing : the process that covalently joins exon sequences of RNA and eliminates the
intervening intron sequences.
Transcriptional regulatory elements : nucleotide sequences of a gene that are involved
in regulation of genetic transcription.
Central Dogma
How the genetic information flows
Replication
• Replication is the process by which
the DNA of the ancestral cell is
duplicated, prior to cell division
(Clark et al., 2019).
• DNA replication (DNA synthesis)
underlies the mechanism of
heredity.
• Resulting two identical copies of the
original DNA.
• Two steps : (1) separation of DNA
strands and (2) building the new
strands using the ‘template strand’
Synthesis of Leading and Lagging
Strands of DNA
• Strand is synthesized
continuously in the
direction of replication fork
movement.
• The lagging strand is
synthesized in small pieces
(Okazaki fragments)
backward from the overall
direction of replication.
• The Okazaki fragments are
then joined by the action
Source : Cooper (2019) The Cell : A molecular approach. pp. 218 of DNA ligase.
A gene
Transcription
5’ 3’
• Transcription is the conversion of 3’ 5’
information from DNA into its RNA
equivalent (Clark et al., 2019).
• The enzyme RNA polymerase opens
the DNA strands and synthesizes an
RNA complementary to only one of
5’ 3’
the DNA strands.
• The decision to transcribe a gene is 5’
3’ 5’
the most important step in the
control of gene expression.
• Transcription starts and stops at
distinct sites at the ends of a gene.
3’
5’
Structure of Eukaryotic Genes
Source : Cooper (2019) The Cell : A molecular approach. pp. 189
Genes are made of parts represented in the mRNA (exons) and parts that are transcribed but
not present in the mRNA (introns).
Introns are removed from the primary transcript and exons are spliced together to make mRNA.
In some genes more than 90% of the pre-mRNA is destroyed, never to appear in the mRNA.
Translation
• Translation is the synthesis of proteins
using genetic information carried by
mRNA (Clark et al., 2019).
• The sequence of amino acids
determines the structure, and
therefore the function, of a protein.
• Translation involves transfer of
information from nucleic acids to an
entirely different type of
macromolecule.
• This decoding process is carried out by
ribosomes.
Source : Clark et al. (2019) Molecular Biology. pp. 85
4 Steps in Translation
A charged tRNA The carboxyl end of A shift of the large The small subunit moves
carrying the next the polypeptide chain subunit relative to the exactly three nucleotides
amino acid to be (amino acid 3 in step small subunit moves the along the mRNA molecule,
added to the 1) is uncoupled from two tRNAs into the E and bringing it back to its
STEP 1
polypeptide chain the tRNA at the P site P sites of the large original position relative
binds to the vacant a and joined by a subunit to the large subunit
site on the ribosome peptide bond to the
by forming base pairs free amino group of
with the mRNA codon the amino acid linked
that is exposed in to the tRNA at the A
mRNA site
Source : Alberts et al. (2014) Essential Cell Biology. pp. 246
THE GENETIC CODE
Source : Clark et al. (2019) Molecular Biology. pp. 83 - 84
General Protein Functions
Source : Alberts et al. (2014) Essential Cell Biology. pp. 122
Gene Expression Regulation
How gene expression is regulated in the cell level
• Transcription of the gene to give the primary
transcript.
• Processing of the primary transcript to give
Gene expression mRNA.
may be regulated at • Stability of mRNA to degradation.
several different • Translation of mRNA to give polypeptide
stages: chains.
• Processing and assembly of polypeptide chains
Source : Clark et al. (2019) Molecular and any necessary co-factors to give a
Biology. pp. 523 functional protein.
• Control of activity of an enzyme or other
protein.
• Degradation of protein.
How gene expression are controlled in eukaryotic cells
Source : Alberts et al. (2014) Essential Cell Biology. pp. 265
Overview of the Central Dogma of
Molecular Biology and Processes Involved
in Relaying the Flow of Genetic
Information
• In Central Dogma, genetic information is relayed
from DNA to RNA to protein.
• DNA packaging is a crucial determinant in
regulating genome integrity and stability.
• Chemical modifications at the DNA levels are
crucial factors in the development of epigenetic
memory.
• Eukaryotic mRNA processing governs mRNA
stability and determines its translational fate.
• Posttranslational protein modifications add one
more layer in the dynamic modulation of
complex biological processes.
• RNAP : RNA polymerase.
Source : Pramanik et al. (2021) https://doi.org/10.1016/j.molp.2020.11.002
Regulation of Transcription in Eukaryotes
Control of Methylation of DNA in Eukaryotes
• Transcription in eukaryotic cells is controlled by
proteins (transcription regulators) that bind to
specific regulatory sequences and modulate the
activity of RNA polymerase (Alberts et al., 2014).
• Promoter and regulatory DNA sequences are
used to switch the gene on or off (Alberts et al., Reversible
2014.
• Methylation in eukaryotes generally silences
gene expression.
• Alternative splicing is a post-transcriptional
control of gene expression and an important
regulatory step in determining which functional
proteins are produced from gene expression. Source : Clark et al. (2019) Molecular Biology. pp. 576
Alternative splicing allows multiple proteins to be encoded by a single gene
Source : Cooper (2019) The Cell : A molecular approach. pp. 194
Regulation of Protein Synthesis - Translation
• Regulation at the level of mRNA.
• Regulation by cleavage of mRNA.
• Regulation by mRNA-Binding Protein.
• Regulation by antisense RNA.
• Regulation by mRNA upstream and downstream regions.
• Premature termination causes attenuation of transcription.
• Riboswitches – RNA acting directly as a control mechanism.
• Regulation of mRNA by methylation.
Source : Clark et al. (2019) Molecular Biology. Chapter 18.
Modified version of the central
dogma of molecular biology
The classical “DNA-RNA-protein”
pathway is extended by
functional role of non-coding
RNAs (ncRNAs).
Small ncRNAs : miRNAs, siRNAs,
snoRNAs, and piRNAs.
MRE : miRNA Recognition
Elements
Source : Cajal et al. (2019) https://doi.org/10.3389/fgene.2019.00281
Reversible chemical modifications that
regulate the flow of genetic information
• In the central dogma, genetic information
is passed from DNA to RNA and then to
protein.
• Epigenetic DNA modifications are known
to have important roles in regulating cell
differentiation and development.
• Reversible RNA modifications add an
additional layer of dynamic regulation of
biological processes.
Source : Fu et al. (2014) https://doi.org/10.1038/nrg3724
Gene Expression in Plants
• The expression of gene regulators of plant development is controlled by several
internal and external factors (Baranov et al., 2019).
• The internal factors are hormones, sucrose, and some mineral elements.
• The external factors are temperature and light.
• In the regulation of differentiation and development, an important role is played
by genes that contain promoters sensitive and specific to phytohormones and to
such environmental factors as light and temperature (Baranov et al., 2019).
Gene Expression in Flower Development - a study case in Arabidopsis
(Source: Ryan et al. (2015) https://doi.org/10.1186/s12864-015-1699-6)
Expression Profiles of Known Floral Regulators
• Flower development was induced in ~four-week-old plants using
dexamethasone solution.
• Floral buds were harvested at different time-points after the
treatment and the genes expression were analyzed.
Note :
AP3 (APETALA3) & AG (AGAMOUS): floral homeotic genes.
AMS (ABORTED MICROSPORE): pollen wall formation.
EMS1/EXS (EXTRA MICROSPOROCYTES1/ EXTRA SPOROGENOUS CELLS) & DYT1
(DYSFUNCTIONAL TAPETUM1): early anther development.
Abiotic Stress
Source :
http://caps.ncbs.res.in/stifdb/help.html
Any question is
welcome J
