MODULE: Biology: Cellular and Molecular Biology

CHAPTER TWO: Genetics and Epigenetics

Friday October 28th, 2022 Zineb Rchiad Ph.D.

 Outline
1. Definition of a cell nucleus

2. Structure of the cell nucleus

1. Nuclear membrane
2. Nuclear pores
3. Nuclear Transport
4. Nuclear lamina and its functions
5. Nucleolus
6. Nucleaoplasm & nuclear bodies

3. Function of the cell nucleus

4. Differences between Prokaryotes and Eukarytes Nuclear Lamina

10/27/22 2
 What Is the Nucleus?
q The cell nucleus is the most noticeable organelle within
the eukaryotic cell, and perhaps the most important and 1 nucleus per cell
defining feature of eukaryotic cells.

q Most of the cell’s DNA is contained in the nucleus, while a

small amount of it is found in mitochondria.

q The majority of human cells have a single nucleus, although Multinucleate: Osteoclasts
there are several cell types that have multiple nuclei (e.g.
osteoclasts) or don't have a nucleus at all (erythrocytes).

Anucleate: Red Cells

10/26/22 3
 Nucleus vs. Nucleoid
q The nucleus is absent in prokaryotes and the lack of this organelle is used as a basis to distinguish whether a cell is a
prokaryote or a eukaryote.

q However, prokaryotes have a region in their cell where the genetic material is located. This region is called a
nucleoid (which means nucleus-like, ). It is nucleus-like and not bound by a nuclear envelope that separates the
genetic material from the cytoplasm.

10/26/22 4
 Nuclear Membrane
q The nucleus surrounds the DNA with a protective membrane
called the nuclear envelope, similar in structure to the cell
membrane that protects the entire cell.

q The nuclear envelop is a double membrane. Each membrane

is a phospholipid bilayer associated with proteins, and the
two membranes are divided by 20 to 40 nm of space.

q The outer membrane is continuous with the cell’s endoplasmic reticulum, and therefore the space between the inner and
outer nuclear membranes links to the lumen of the endoplasmic reticulum.
q Like the endoplasmic reticulum, the outer nuclear membrane has ribosomes attached to it. Contrastingly, the inner
membrane of the nuclear envelope is attached to proteins that are specific to the nucleus, and therefore found nowhere else.

10/26/22 5
 Nuclear Membrane

Schematic outline of the NPC, showing

the relative position of Nup proteins
and surrounding structures.
ONM: outer nuclear membrane,
INM: inner nuclear membrane.
Central cross sections of simultaneous imaging of DNA, nuclear lamina, and NPC: nuclear pore complex
nuclear pore complex (NPC) epitopes by 3D-SIM. Immunostaining with Nup: nucleoporins

antibodies against lamin B (green) and antibodies that recognize different

NPC epitopes (red). DNA is counterstained with DAPI (blue). Scale bar indicates 1 µm. 6
10/27/22 Schermelleh et al., Science, 2008
 Nuclear Pores
q The nuclear envelope is perforated with tiny pores with
diameters of around 100 nm called nuclear pores. These
pores regulate the passage of molecules between the
nucleus and cytoplasm, permitting some to pass through the
membrane, but not others.

q These pore complexes regulate the movements of

macromolecules, RNAs and proteins into and out of the
nucleus. This movement of molecules is known as nuclear
transport.

q Each pore is lined with a structure of 50 to 100 different

proteins known as the nuclear pore complex.
Electron micrographs revealing (c) eight filaments attached to
the cytoplasmic ring and (D) the nuclear basket attached to the
nuclear ring. Scale bars, 100 nm.
7
10/26/22 Cohen et. Al., Molecular Biology, 2012
 Nuclear Transport
q Nuclear transport refers to the mechanisms by which
molecules move across the nuclear membrane of a cell.
q Nuclear pore complexes (NPCs) tightly control the
movement of molecules across the nuclear envelope
and establish a permeability barrier.
q This barrier blocks the passive diffusion of molecules
>40 kilodaltons (kDa) in size.
q To enter or exit the nucleus, large cargo molecules (e.g. RNA, some proteins) require association with nuclear transport
proteins called importins to enter the nucleus and exportins to exit (monodirectional).
q The traffic of RNAs and proteins through the nuclear pore complex is particularly important, as they play a role in gene
expression.

10/27/22 8
 Nuclear Lamina
q The inner nuclear membrane is internally lined by protein
filaments meshwork organised in a net-like fashion, called
nuclear lamina. The proteins that make up the nuclear
lamina are known as lamins, which are intermediate filament
proteins. These support the nuclear envelope, ensuring that
the overall shape and structure of the nucleus is maintained.

q The nuclear lamina, along with protein fibers called

the nuclear matrix, is also thought to aid in the organisation
of genetic material, allowing it to function more efficiently.

9
10/26/22 Deviri et al., Nature Physics, 2019
 Functions Of The Lamina
q In addition to lamins there is another set of membrane proteins
called lamina-associated proteins, which help to mediate the
interaction between the lamina and inner nuclear membrane.

q The nuclear lamina, along with protein fibers called the nuclear
matrix, is also thought to aid in the organisation of genetic material,
allowing it to function more efficiently. The interface at the nuclear lamina A schematic
representing the complex protein-DNA interface at the
q Lamins interact with and help anchor many INM proteins. Lamins
nuclear lamina where lamins mediate interactions
also interact with cytoskeletal proteins.
between nuclear envelope proteins and chromatin.
q Lamins are necessary to constrain heterochromatic LADs to the Here lamins A and B are represented in red and lamin C is
nuclear lamina. LADs are enriched in epigenetic machinery involved
shown in cyan. Lamins have different dispositions across
in maintaining a repressive state, including the enzymes involved in
the nuclear periphery, with lamin C displaying a higher
H3K27 methylation, H3K9 methylation and DNA methylation.
concentration near NPCs than other lamin variants.

10/27/22 10
Nucleolus
q The nucleolus is a membrane-less organelle within the nucleus that manufactures
ribosomes, the cell's protein-producing structures.

q Through the microscope, the nucleolus looks like a large dark spot within the
nucleus.

q After a cell divides, a nucleolus is formed when chromosomes are brought together
into nucleolar organizing regions. During cell division, the nucleolus disappears.

q The nucleolus is the site of ribosomal RNA production. Inside the nucleolus, rRNA
molecules are combined with proteins to form ribosomes. The nucleolus is involved
in rRNA transcription, pre-rRNA processing and ribosome subunit assembly.

10/26/22 11
 Structure of the nucleus:
Nucleoplasm & Nuclear Bodies
q Like the cytoplasm of a cell, the nucleoplasm is semi-liquid, and fills the
empty space in the nucleus. It is a protoplasm and surrounds the
chromosomes and nucleoli inside the nucleus. It also has various
proteins and enzymes dissolved within it.

q Nuclear bodies can be found in the nucleoplasm, and these include

structures such as Cajal bodies, Gemini bodies, and Polycomb bodies.

q The nuclear bodies do not all perform the same function

q One of the nuclear body proteins appears to be involved in

transcriptional active regions, chromatin regulation (ND10)
transcriptional activation (SP140), protein degradation (clastosome).

q Nuclear bodies are found to be increased in embryonic cells, cancer cells,

as well as in cells which have a high metabolic rate, such as neurons, and
in autoimmune diseases.

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 Functions
q The nucleus has very important roles to play inside the cell. As it contains genetic material, it
coordinates cell activities like protein synthesis and cell division.

q The nucleus functions include:

ü Govern the genetic information of the cell and thus the heredity characteristics of an organism,

ü Control of the protein and enzyme synthesis

ü Control of cell division and cell growth

ü Storage of DNA and RNA

ü Regulation of the transcription of the mRNA to protein

ü Production of ribosomes

10/26/22 13
Prokaryotic vs Eukaryotic Cells
q Prokaryotes are primitive organisms lacking a
nucleus and membrane-bound organelles.

q The term ‘prokaryote’ is derived from the Greek

words ‘pro’ = before and ‘karyon’, ‘kernel’. Together
it means ‘before nuclei’.

q In contrast, eukaryotes are advanced organisms

with a well-defined nucleus and membrane-bound
organelles.

q The term ‘eukaryotes’ is derived from the Greek words ‘eu’ =goo’ and ‘karyon’ = kernel, meaning ‘true nuclei’.

10/26/22 14
10/27/22 15
Take Home Message: Key facts about the cell nucleus
q Definition: A membranous organelle of the eukaryotic cell that contains the cellular genetic material

q Different from nucleolus and nucleolid

q Structure: Nuclear membrane, nuclear lamina, nucleolus, chromosomes, nuclear bodies and nucleoplasm

q Functions:
ü Govern the genetic information of the cell and thus the heredity characteristics of an organism,
ü Control of the protein and enzyme synthesis
ü Control of cell division and cell growth
ü Storage of DNA and RNA
ü Regulation of the transcription of the mRNA to protein
ü Production of ribosomes

10/27/22 16
 MODULE: Biology: Cellular and Molecular Biology

CHAPTER TWO: Genetics and Epigenetics

Session2: DNA and RNA Structure

Thursday November 3rd, 2022 Zineb Rchiad Ph.D.

1
Table of Contents
1. Basics
2. History of DNA Discoveries
3. DNA
1. Nucleotides
2. DNA Structure
3. Directionality
4. Locus Locations
5. DNA Packaging
4. Differences between DNA and RNA
5. RNA (Session 3: The central Dogma of Molecular Biology)

2
 Basics
q DNA (DeoxyriboNucleic Acid) is the genomic material in cells that contains the genetic information used in (i) the
development and functioning of all known living organisms and (ii) carrying and transmitting the hereditary material or the
genetic instructions from parents to offsprings.

q Most of the DNA is located in the nucleus, although a small amount can be found in mitochondria (mitochondrial DNA).

Gene Chromosome Genome Metagenome

A structure of DNA &
A gene is the basic
proteins within the nucleus
physical and functional
carrying genetic information
unit of heredity.
in the form of genes.
All the genetic material present in
A genome is an organism’s
an environmental sample,
complete set of DNA,
consisting of the genomes of the
including all of its genes. individual organisms in the sample.

3
History of DNA Discoveries

4
Griffith’s Experiment:
First Step Towards the Discovery of DNA
o Genetic information: Unknown in its biochemical nature.
o In 1928, bacteriologist Frederick Griffith was trying to develop a
vaccine against pneumonia using two related strains of bacteria,
known as R and S.
o S strain: formed smooth colonies. Mice injected with live S bacteria
developed pneumonia and died.
o R strain: formed colonies with a rough appearance and were non-
virulent.
o Griffith injected mice with heat-killed S bacteria: no disease in mice.
o Observations:
o Harmless R + Harmless S= virulence!
o Blood sample from the dead mouse contained living S
bacteria!
o Conclusion:
o R-strain bacteria + "transforming principle” =
"transformation" into virulent S bacteria.
o R-strain bacteria must have taken up a "transforming principle"
from the heat-killed S bacteria, which allowed them to "transform"
into S bacteria and become virulent. 5
In 1945, Avery, McCarty and McCloud demonstrated that this "transforming principle" was DNA
 Chargaff’s Rules
Watson and Crick
q The structural organization of the DNA molecule was correctly
proposed in 1953 by James Watson and Francis Crick.

q Their efforts were guided by an understanding of molecular distances

and bond angles developed by Linus Pauling, and were based upon
some key experimental discoveries:

§ DNA is composed of nucleotides made up of a sugar, phosphate

and base – Phoebus Levene, 1919

§ DNA is composed of an equal number of purines (A + G) and

pyrimidines (C + T) – Erwin Chargaff, 1950
§ DNA is organised into a helical structure – Rosalind Franklin, 1953 (data shared without permission)
§ Their work was published in Nature in 1953.

6
 Photograph 51
q Photograph 51 tells the dramatic tale of the race to the double helix in
the years between 1951 and 1953, when Rosalind Franklin was using X-
ray diffraction to take images of DNA.
q X-ray diffraction photo obtained in May, l952 at King's College, London by
the gifted crystallographer Rosalind Franklin, later on passed to Wilkins in
an act of considerable generosity,
q In January 1953, Watson visited King´s College London. While visiting,
Wilkins showed Watson one of Franklin´s X-ray diffraction images of DNA,
Photo 51, without Franklin´s knowledge. From the image, Watson
concluded that DNA was helical.
q Later, Watson and Crick received an internal King´s College London
research report written by Franklin about her DNA diffraction images.
From that report, Crick determined that DNA contains two strands, with
each strand running in opposite directions.
q Franklin died in 1958 at 37 because of ovarian cancer, before the award of
the 1962 Nobel Prize in physiology or medicine was awarded to Watson,
Crick and Wilkins.
Nobel Prize in 1962
7
 Nucleotides
q DNA and RNA are polymers (in the case of DNA, often very long polymers), and
are made up of monomers known as nucleotides. When these monomers
combine, the resulting chain is called a polynucleotide.
q Nucleotides are the building blocks of DNA and RNA, which are composed of a
sugar group, a phosphate group, and a nitrogen base. The sugar and phosphate
groups link the nucleotides together to form each strand of DNA. Adenine (A),
Thymine (T), Guanine (G) and Cytosine (C) are four types of nitrogen bases.
q Each nucleotide is made up of three parts:
1. A phosphate group.
2. a nitrogen-containing ring structure called a nitrogenous base,
3. a five-carbon sugar group,
q Polynucleotide: Poly= multiple, multiple nucleotides linked by chemical bonds.

8
 Nucleotides
q Nitrogenous bases: The nitrogenous bases of nucleotides are
organic (carbon-based) molecules made up of nitrogen-containing
ring structures. Each nucleotide in DNA contains one of four
possible nitrogenous bases: adenine (A), guanine (G) cytosine (C),
and thymine (T). Adenine and guanine are purines, meaning that
their structures contain two fused carbon-nitrogen rings. Cytosine
and thymine, in contrast, are pyrimidines and have a single carbon-
nitrogen ring.

q Sugars: In addition to having slightly different sets of bases, DNA

and RNA nucleotides also have slightly different sugars. The five-
carbon sugar in DNA is called deoxyribose, while in RNA, the sugar
is ribose. These two are very similar in structure, with just one
difference: the second carbon of ribose bears a hydroxyl group,
while the equivalent carbon of deoxyribose has a hydrogen instead.
The carbon atoms of a nucleotide’s sugar molecule are numbered as
1ʹ, 2ʹ, 3ʹ, 4ʹ, and 5ʹ (1ʹ is read as “one prime”).

9
 Phosphodiester Bonds
q The phosphodiester bonds that join one DNA nucleotide to another

always link the 3’ carbon of the first nucleotide to the 5’ carbon of the

second nucleotide.

q This forms a covalent bond between the oxygen sticking off the 3’

carbon of the first nucleotide, and the phosphorous atom in the

phosphate group that sticks off the 5’ carbon of the second nucleotide.

These bonds are called 3’-5’ phosphodiester bonds.

q Each time nucleotides are bound together, a water molecule is

removed (or “lost”) through a process called dehydration synthesis.

10
Base Pairing in DNA
q Can any two bases decide to get together
and form a pair in the double helix?

q Base pairing is highly specific: This means

that the two strands of a DNA double
helix have a very predictable relationship
to each other.

q Two hydrogen bonds connect T to A;

three hydrogen bonds connect G to C.

11
 Double Helix
q The DNA structure can be thought of as a twisted ladder. This structure

is described as a double-helix.

q Among the three components of DNA structure, sugar (or deoxyribose)

is the one which forms the backbone of the DNA molecule. The

nitrogenous bases of the opposite strands form hydrogen bonds,

making the ladder-like structure.

q The order of the nitrogenous bases determines the genetic code or the

DNA’s instructions: DNA directionality.

12
 Directionality in DNA
q the order of DNA bases spells out the instructions in our genes. But this information
only makes sense if we know where to begin reading and which direction to read in.

q These sugar rings each contain five carbon atoms which are numbered in a clockwise
direction, from 1’ (pronounced one prime) to 5’ (pronounced five prime). Each ring is
joined to its neighbouring phosphate groups by bonds on 3’ and 5’.

q When we look at a sequence of DNA, we read it in the 5ʹ-3ʹ direction.

qThe strands of DNA in the double-helix run in opposite directions and genes can be encoded on either strand:
Transcription can take place along the chromosome in both directions.
qThe two strands of the helix are:
qAntiparallel and
qComplementary

13
 Locus Location
q Chromosomes are ordered numerically by their length – the longest pair in a
human cell is chr. 1, the second longest is chr. 2, etc., down to the smallest, chr.
22.
q The sex chromosomes, X and Y, are excluded from this nomenclature.
q Centromeres divide the chr. into 2 arms: The longer arm is q and the shorter is p,
q The position of a gene in a chr. is the locus. This is helpful when referencing
specific variations in the chr. For example, a patient with a ‘7q deletion’ has a
piece of DNA missing on the long arm of one copy of chr. 7.
q Staining chromosomes with particular dyes (e.g. Giemsa stain) will additionally
generate unique banding patterns.
q The region in which a locus is positioned can be identified via three points of
reference:
q Denoting the chr.: e.g. 7q31 refers to chromosome 7,
q Denoting the arm: e.g. 7q31 is on the q arm,
q The G band location: e.g. 7q31 is at the longitudinal position 31.

14
 DNA Packaging
q The haploid human genome contains approximately 3
billion base pairs of DNA packaged into 23
chromosomes.

q most cells in the body are diploid, that makes a total

of 6 billion base pairs of DNA per cell.

q each base pair is ~ 0.34 nm -> (0.34 × 10-9) × (6 × 109)=

each diploid cell contains about 2 meters of DNA .

q it is estimated that the human body contains about 50

trillion cells—which works out to 100 trillion meters of
DNA per human. This means that each of us has
enough DNA to go from here to the Sun and back
more than 300 times!

15
Beads on a String

q Histones are a family of small, positively

charged proteins termed H1, H2A, H2B, H3,
and H4.
q DNA is negatively charged, due to the
phosphate groups in its phosphate-sugar
backbone, so histones bind with DNA very
tightly.

In this micrograph, nucleosomes are A 30nm fiber of

indicated by arrows. chromatin.
Scale bar = 50nm.
16
Olins et al., Nature, 2003
 Structural Differences Between DNA and RNA
q Ribonucleic acid (RNA) is a nucleic acid which is directly involved in
protein synthesis. Ribonucleic acid is an important nucleotide with
long chains of nucleic acid present in all living cells. Its main role is to
act as a messenger conveying instructions from DNA for controlling
protein synthesis.

q RNA contains the sugar ribose, phosphates, and the nitrogenous

bases adenine (A), guanine (G), cytosine (C), and uracil (U). DNA
and RNA share the nitrogenous bases A, G, and C. Thymine is usually
only present in DNA and uracil is usually only present in RNA.

17
Take-Home Messages
q The DNA molecules contain instructions a living entity requires to grow, develop and reproduce. These instructions are present inside each cell
and are inherited from the parents to their offspring.

q DNA is made up of nucleotides which contain a nitrogenous group, a phosphate group, and a sugar group. The order of the nitrogenous bases –
thymine(T), guanine(G), cytosine(C), and adenine(A), determins the genetic code.

q Genes are formed by the order of the nitrogenous bases present in the DNA which is crucial for protein synthesis. RNA is another nucleic acid
that translates genetic information into proteins from DNA.

q The nucleotides are linked together for the formation of two long strands which spiral to produce a structure known as the double-helix which
resembles that of a ladder wherein the sugar and phosphate molecules form the sides while the rings are formed by the bases.

q The bases located on one strand pair up with the bases on the other strand, as in – guanine pairs with cytosine and adenine pairs with thymine.

q The DNA molecules are extremely long and hence without the right packaging, they cannot fit into cells. Thus, DNA is tightly coiled to produce
formations referred to as chromosomes. Every chromosome has a single DNA molecule.

18
 MODULE: Biology: Cellular and Molecular Biology

CHAPTER TWO: Genetics and Epigenetics

Session3: The Central Dogma of Molecular Biology

Thursday November 3rd, 2022 Zineb Rchiad Ph.D.

11/2/22 1
Table of Contents
1. Types of RNA
1. Coding RNA
2. Non-coding RNAs
1. Housekeeping ncRNAs
2. Regulatory ncRNAs
2. RNA Structure
3. The Central Dogma of Molecular Biology
4. From nucleotide to Phenotype
1. Genetic Code
2. Code Crackers: George Gamow and the Triplet Theory
3. Codons
4. Anticodons
5. Reading Frame
5. Protein Synthesis and Organization

11/2/22 2
 RNA Structure
q A ribonucleotide in the RNA chain contains ribose, one of the
four nitrogenous bases (A, U, G, and C), and a phosphate group.

q The ribonucleic acid has all the components same to that of the
DNA with only 2 main differences within it. RNA has the same
nitrogen bases called the adenine, Guanine, Cytosine as that of
the DNA except for the Thymine which is replaced by the uracil.

q Genetic material is encoded in RNA or DNA as genetic

material. For instance, some viruses may have RNA as their
genetic material, while others have DNA as the genetic material.
The Human Immunodeficiency Virus (HIV) contains RNA, which is
then converted into DNA after attaching itself to the host cell.

11/2/22 3
Types Of RNA: mRNA and HouseKeeping ncRNAs
tRNA– The transfer RNA or the tRNA carries amino acids to ribosomes while translation
mRNA – The messenger RNA or the mRNA encodes amino acid sequences of a polypeptide
rRNA – The ribosomal RNA or the rRNA produces ribosomes with the ribosomal proteins that are organelles
responsible for the translation of the mRNA.

11/2/22 4
Types Of RNA: Regulatory ncRNAs

11/2/22 5
Messanger RNA Structure
q The subtle structural difference between the sugars, and the double-stranded nature, give DNA added stability, making DNA more
suitable for storage of genetic information, whereas the relative instability of RNA makes it more suitable for its more short-term
functions.
q mRNA is relatively unstable and short-lived in the cell, especially in prokaryotic cells, ensuring that proteins are only made when
needed.
q RNA can fold upon itself, with the folds stabilized by short areas of complementary base pairing, forming a 3D structure.
q Based on protein expression, the mRNA is categorized into the following types:

1. Monocistronic mRNA: mRNA common in eukaryotes, which

carries the exon sequences coding for a single protein.
2. Polycistronic mRNA: mRNA common in bacteria and
bacteriophages, which carries the exon sequences that code
for multiple proteins.

11/2/22 6
Ribosomal RNA Structure
q The eukaryotic ribosome is made of a 60S and a 40S subunit.
There are two short rRNA molecules less than two hundred
nucleotides in length (5S and 5.8S), and two RNA molecules
that are much longer – one that has over five kilobases
(28S), and another nearly two kilobases (18S).

q In all, the eukaryotic ribosome has a Svedberg coefficient of

80S. In addition, eukaryotic cells also have rRNA in
mitochondria and chloroplasts. Ribosomes can be associated
with the endoplasmic reticulum or be present as free-
floating complexes in the cytoplasm.

7
11/2/22
 Transfer RNA
q Transfer RNA (tRNA) is a small RNA molecule that
plays a key role in protein synthesis.

q tRNA serves as a link (or adaptor) between the

messenger RNA (mRNA) molecule and the growing
chain of amino acids that make up a protein.

q Each time an amino acid is added to the chain, a

specific tRNA pairs with its complementary
sequence on the mRNA molecule, ensuring that the
Transfer RNA (A) Tertiary structure of the phenylalanine tRNA from
appropriate amino acid is inserted into the protein yeast showing the anticodon (grey), the acceptor stem (violet) with
being synthesized. the nucleotides CAA at the 3′ OH end (yellow). Image modified from
‘TRNA-Phe yeast’ Yikrazuul (licensed under CC BY-SA 3.0). (B)
Clover leaf representation of the secondary structure of tRNA.

11/2/22 8
The Central Dogma Information

of Molecular Biology
Transcript

Function

Phenotype

11/2/22 9
From nucleotide
To Phenotype
Why was this a tricky problem?
In one of the simplest potential codes, each nucleotide
in an DNA or RNA molecule might correspond to one
amino acid in a polypeptide. However, this code cannot
actually work, because there are 20 amino acids
?
commonly found in proteins and just 4 nucleotide bases
in DNA or RNA. Thus, researchers knew that the code
must involve something more complex than a one-to-
one matching of nucleotides and amino acids.

11/2/22 10
 Code Crackers & The Triplet Theory
q In the mid-1950s, the physicist George Gamow extended this line of thinking to deduce that the genetic code was
likely composed of triplets of nucleotides.
George Gamow
q He proposed that a group of 3 successive nucleotides in a gene might code for one amino acid in a polypeptide.
Gamow's reasoning was that even a doublet code (2 nucleotides per amino acid) would not work, as it would
allow for only 16 ordered groups of nucleotides (42), too few to account for the 20 standard amino acids used to
build proteins. Nirenberg
q A code based on nucleotide triplets, however, seemed promising: it would provide 64 unique sequences of
nucleotides (43), more than enough to cover the 20 amino acids.
q Gamow’s triplet hypothesis seemed logical and was widely accepted. However, it had not been experimentally
proven, and researchers still did not know which triplets of nucleotides corresponded to which amino acids.
q The cracking of the genetic code began in 1961, with work from the American biochemist Marshall Nirenberg. For
the first time, Nirenberg and his colleagues were able to identify specific nucleotide triplets that corresponded to
particular amino acids. Their success relied on two experimental innovations: Khorana
ü A way to make artificial mRNA molecules with specific, known sequences.
ü A system to translate mRNAs into polypeptides outside of a cell (a "cell-free" system). Nirenberg's system
consisted of cytoplasm from burst E. coli cells, which contains all of the materials needed for translation.
q For their contributions, Nirenberg and Khorana (along with another genetic code researcher, Robert Holley)
received the Nobel Prize in 1968.

11/2/22 11
 Genetic Code
The genetic code is endowed with many characteristic
properties:
1. Triplet nature: 3 nucleic acids code for each of the known
20 amino acids. Each triplet is called ‘codon’
2. Degeneracy: The code is degenerate which means that
the same amino acid is coded by more than one base
triplet. Degeneracy does not imply lack of specificity in
protein synthesis.
3. Non-overlapping: adjacent codons do not overlap.
4. Commaless: There is no signal to indicate the end of one
codon and the beginning of the next.
5. ~ Universal: the same sequences of 3 bases encode the same amino acids in all life forms from simple microorganisms
to complex, multicellular organisms such as human beings.
6. Non-ambiguity: A particular codon will always code for the same amino acid.
7. Polarity: The genetic code has polarity, that is, the code is always read in a fixed direction, i.e., in the 5ʹ → 3ʹ direction.

11/2/22 12
 Codons
q A codon is a DNA or RNA sequence of
three nucleotides (a trinucleotide) that
forms a unit of genomic information
encoding a particular amino acid or
signaling the termination of protein
synthesis (stop signals).

q There are 64 different codons: 61

specify amino acids and 3 are used as
stop signals.

11/2/22 13
 Special Codons START CODON

U U U
Go Are Are
Away Away Gone
11/2/22 14
 AntiCodon
q An anticodon is a trinucleotide sequence
located at one end of a transfer RNA (tRNA)
molecule, which is complementary to a
corresponding codon in a messenger RNA
(mRNA) sequence.

q Each time an amino acid is added to a growing

polypeptide during protein synthesis, a tRNA
anticodon pairs with its complementary codon on
the mRNA molecule, ensuring that the appropriate
amino acid is inserted into the polypeptide.

11/2/22 15
 Reading Frame
qA reading frame is a way of dividing the sequence
of nucleotides in a nucleic acid (DNA or RNA)
molecule into a set of consecutive, non-
overlapping triplets.

qThese triplets equate to amino acids or stop

signals during translation, they are called codons.

qAn open reading frame (ORF) is a reading frame

that has the potential to be transcribed into RNA
and translated into protein.

11/2/22 16
 Protein Synthesis
q In biological systems, Protein synthesis is carried out inside the

cell. In prokaryotes, it occurs in the cytoplasm. In eukaryotes, it

initially occurs in the nucleus to the mRNA transcript of the

coding region of the DNA. The transcript leaves

the nucleus and reaches the ribosomes for translation into

a protein molecule with a specific sequence of amino acids.

q Protein synthesis generally includes transcription, translation,

and post-translational events, such as protein folding,

modifications, and proteolysis.

11/2/22 17
Levels of Protein Organization
q Proteins are large, complex molecules that play many important roles in the body.
q They are critical to most cell functions and are required for the structure, function and regulation of the
body’s tissues and organs. A protein is made up of one or more long, folded chains of amino acids (each called
a polypeptide), whose sequences are determined by the DNA sequence of the protein-encoding gene.

18
 Chef Analogy Meal

Kitchen Boy

Ingredient

Chef

Recipe

11/2/22 19
 Exceptions to the central dogma
q The biggest revolution in the central dogma was the discovery of retroviruses, which transcribe RNA into DNA through the use of a
special enzyme called reverse transcriptase: RNA → DNA → RNA → protein.

q Also, some virus species are so primitive that they use only RNA → proteins, having not developed DNA.

q With the discovery of prions, a new exception to the central dogma has been discovered, Protein → Protein. That is, proteins directly
replicating themselves by making conformational changes in other proteins. List of identified human prion diseases (Center for
disease Control & prevention CDC).
q Creutzfeldt-Jakob Disease (CJD)
q Variant Creutzfeldt-Jakob Disease (vCJD)
q Gerstmann-Straussler-Scheinker Syndrome
q Fatal Familial Insomnia
q Kuru

q Although retroviruses, certain primitive viruses, and prions may violate the central dogma, they are technically not considered
"alive", and thus the rule that "all cellular life follows the central dogma" still holds true.

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 Take Home Message
q RNA is single-stranded and contains a ribose, one of the four nitrogenous bases (A, U, G, and C), and a

phosphate group.

q RNAs can be coding or non-coding (Housekeeping ncRNAs, Regulatory ncRNAs).

q The central dogma of molecular biology states that genetic information flows only in one direction, from

DNA, to RNA, to protein, or RNA directly to protein, with rare exceptions.

q The genetic code ensures the translation of information from DNA to protein.

q The genetic code is organised as triplets, degenerate, non-overlapping, commaless, universal, non-

ambiguous and polar.

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 MODULE: Biology: Cellular and Molecular Biology

CHAPTER TWO: Genetics and Epigenetics

Sessions 4 & 5: Epigenetics

Friday November 4th, 2022 Zineb Rchiad Ph.D.

11/4/22 1
Overview
Session 1 • Introduction to epigenetic programming
• Euchromatin and Heterochromatin
• Chromatin remodeling
• Epigenetic Modifications:
• Histone modifications
• DNA methylation
• Noncoding RNAs

• Epigenetic writers, erasers and readers

Session 2 • Epigenome Mapping Toolkit
• ChIP-seq
• BS-seq
• MeDIP
• Epigenetic Phenomena
• Epistasis and Epigenetics

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Epigenetic Regulation
and Definition
Observations:
• Each of the more than 200 different cell types in the human body
contains an identical copy of the genome but expresses a distinct set
of genes. How does a genome guide a limited set of genes to be
expressed at different levels in distinct cell types?
• Smoking and over-eating can make the genes for obesity over-
express themselves and the genes for longevity under-express
themselves.
Definition
Mechanisms of gene regulation that can be inherited through mitosis
and meiosis, but can be established and released without changing the
DNA sequence

As the second dimension to the genome, the

epigenome contains key information specific to
every type of cells.

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11/4/22 4
 Epigenetic mechanisms:
üDNA methylation,
üHistone methylation,
üHistone Deacetylation.

Involved in the regulation of:

üCellular growth,
üDifferentiation,
üApoptosis,
üTransformation,
Levels Of Epigenetic üTumor progression.

Modifications
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 DNA Methylation
o DNA methylation: transfer of a methyl group from S-adenosylmethionine
(SAM) to the 5-carbon position of the pyrimidine ring of cytosine, resulting in
a 5 methylcytosine (5mC).

o SAM is a versatile molecule used in many biological reactions. It is a

commonly used methyl donor in biologically important methylation reactions,
including DNA methylation, RNA methylation, & protein methylation.

o 4–6% of all cytosines and 60%–80% of CpG dinucleotides are methylated,

making methylation the most abundant epigenetic mark.

o DNA methylation:

o Gene silencing,

o Heterochromatin formation,

o Recruitment of histone-modifying enzymes.

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 DNA Methylation
o The CpG sites or CG sites are regions of DNA where
a cytosine nucleotide is followed by a guanine nucleotide in the
linear sequence of bases along its 5' → 3' direction. CpG sites
occur with high frequency in genomic regions called CpG
islands (or CG islands).

o The presence of multiple methylated CpG sites in CpG islands of

promoters causes stable silencing of genes.

o DNA methylation can be divided into 2 classes:

o De novo DNA methylation is mediated by DNMT3A and
DNMT3B,
o Maintenance of DNA methylation happens during DNA
replication and is mediated by DNMT1.

Hemimethylated Symetrically methylated

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DNA Methylation and Hydroxymethylation
o 5-Hydroxymethylcytosine (5hmC) is a modification, by oxidation, of DNA methylation
present in vertebrate DNA. This oxidation is catalyzed by enzymes of the ten–eleven
translocation (TET) family and is relatively abundant in pluripotent cells and neurons.
o 5hmc is
o Less abundant than 5mc
o Differs between cell types and is the highest in neurons and embryonic
stem cells
o 5hmC plays a major role in aging, development and disease,
o Global DNA methylation technologies proved that 5mC & 5hmc are:
o Dynamically deposited and removed,
o Can exist in non-CpG sequence contexts,
o Enriched at the bodies of actively transcribed genes.
o Passive DNA demethylation is caused by a reduction in activity or absence of
DNMTs during DNA replication.
o Active demethylation is independent of DNA replication and happens via
Oxidation pathway or Deamination pathway.

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Heterochromatin
versus
Euchromatin

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Chromatin Remodeling:
Heterochromatin Versus Euchromatin

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 Complexity Of Chromatin
Organization
A general model of genome architecture:
1. Chromosome territories: chromosomes first fold to occupy
distinct territories and positions in the nuclear space.
2. Compartments: Individual chromosomes are then folded into
compartments.
3. TADs: Within compartments, the chromatin is packaged in the
form of topologically associated domains (TADs).
4. sub-TADs: The chromatin is further folded into sub-TADs, the
topologies of which can vary in a tissue-specific manner.
5. Chromatin loops: Loops with anchor points providing physical
contacts between regulatory elements.
6. Nucleosomes: genomic DNA is wrapped around nucleosomes,
which represents the first level of genome folding.

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 Chromatin Remodeling
o Chromatin remodeling is the rearrangement of chromatin from a
condensed state to a transcriptionally accessible state, allowing
transcription factors or other DNA binding proteins to access DNA
and control gene expression.

o Regulation of chromatin in its various active states is controlled

significantly through post-translational modifications of the
histone proteins at the N-terminal tails of these proteins by
phosphorylation, acetylation, methylation, ubiquitination,
SUMOylation.
o Regulation of chromatin by reversible incorporation of phosphate, acetyl
groups, or methyl groups within histone tails are the best understood.
HAT: Histone acetyltransferase
o DNA methylation is also an important epigenetic mark that is known to HDAC: Histone deacetylase
LSD: Lysine specific demethylase
induce chromatin condensation. H3K4me: associated with enhancers
MECP2: Methyl-CpG Binding Protein 2, role in gene silencing

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 Histone Modifications: Methylation
o Methylation is added to the lysine or arginine residues of histones H3
and H4, with different impacts on transcription:
o Arginine methylation promotes transcriptional activation,
o lysine methylation is implicated in both transcriptional
activation and repression depending on the methylation site.

o Lysines can be mono-, di-, or tri-methylated, providing further

functional diversity to each site of methylation:
o H3K4me1 and H3K4me3 are activation markers:
ü H3K4me1 typically marks transcriptional enhancers,
ü H3K4me3 marks gene promoters.
o H3K36me3 is an activation marker associated with transcribed
regions in gene bodies.
o H3K9me3 and H3K27me3 are repressive signals.

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Histone Modifications: Acetylation

o Histone acetylation involves the covalent addition of an

acetyl group to lysine.

o Acetylation adds a negative charge to lysine residues on the

N-terminal histone tails that extend out from the
nucleosome.

o These negative charges repel negatively charged DNA,

which results in a relaxed chromatin structure.

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 Histone Modifications: Phosphorylation
o Histone phosphorylation involves the addition of a phosphoryl
group to histone tails and affects:
o Serine,
o Threonine,
o Tyrosine.

o Phosphorylation occurs on all core histones, with differential effects

on each:
o Phosphorylation of H2AX serves as a recruiting point for DNA
damage repair proteins and is one of the earliest events to
occur after DNA double-strand breaks.
o Phosphorylation of histone H3 and histone H2A are involved in
chromatin compaction and the regulation of chromatin
structure and function during mitosis.
o H2B phosphorylation facilitates apoptosis-related chromatin
condensation, DNA fragmentation, and cell death.

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 Distinctive Chromatin Features of Genomic Elements

Coexisting Marks Marks For Functional Annotation

16
 Non-Coding RNAs
q Non-coding RNAs (ncRNA) are RNA molecules
that are not translated into proteins:

q Short non-coding RNAs (including siRNAs,

miRNAs, and piRNAs),

q Long non-coding RNA (lncRNAs).

q Non-coding RNAs play a significant role in

epigenetic modification and can regulate
expression at the gene level and chromosome
level.

11/6/22 Kumar et al., Cancers, 2020 17

miRNA Regulation of Gene Expression:
Pathway & Mechanisms
q The maturation of miRNAs includes the production of the
primary miRNA transcript (pri-miRNA) by RNA polymerase
II or III and cleavage of the pri-miRNA by the
microprocessor complex Drosha-DGCR8 (Pasha) in the
nucleus.

q The pre-miRNA hairpin is exported from the nucleus by

Exportin-5
q In the cytoplasm, the RNase Dicer in complex with the double-stranded RNA-binding protein transactivation response element RNA-
binding protein (TRBP) cleaves the pre-miRNA hairpin to its mature length.
q The functional strand of the mature miRNA is loaded together with Argonaute (Ago2) proteins into the RNA-induced silencing complex
(RISC), where it guides the RISC to silence target mRNAs through mRNA cleavage, translational repression or deadenylation.

11/6/22 Wu et al., Cellular & Molecular Immunology, 2018 19

Long Non-Coding RNAs & Epigenetic Mechanisms
q lncRNAs can directly interact with the writers, readers and erasers of histone marks, thereby fine-tuning the chromatin structure of
a given target locus.

q lncRNAs roles as epigenetic regulators include:

q H19 blocks DNA methylation by DNMT3B.
q HOTAIR promotes methylation of H3K27me3 and demethylation of H3K4me2.
q TCF7 promotes the activation of gene expression by chromatin remodeling.

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ncRNAs & Epigenetic Changes in a Nutshell

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 The major categories of histone writers and erasers

Modification Writers Erasers

Acetylation Histone Histone
acetyltransferases deacetylases
(HATs) (HDACs)
Methylation lysine Lysine
methyltransferases demethylases
(KMTs) and protein (KDMs)
arginine
methyltransferases
(PRMTs)
Phosphorylation Kinases Phosphatases

• Histone writers, erasers, and readers compose the protein machinery that adds,
Writers, removes or recognizes these post transcriptional modifications.

Erasers and • The balance between these writers and erasers dictates which marks are present
on histones, and at what levels, to ultimately control whether specific genetic

Readers programs and the cellular processes they orchestrate, are turned on or off.

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 Figure 1

Timeline of Sequencing-Based Technologies for Mapping Human Epigenomes

Rivera and Ren Cell 2013

11/6/22
26
Chromatin Immuno-Precipitation (ChIP)
o ChIP-Seq is a powerful method for identifying genome-wide DNA binding sites for
transcription factors and other proteins.

o Advantages of ChIP-seq:

o Captures DNA targets for transcription factors or histone modifications across

the entire genome of any organism,

o Defines transcription factor binding sites,

o Offers compatibility with various target proteins.

o Limitations of ChIP:
o Quality and cross-reactivity of antibodies .

o DNA detection methods

o Primer specificity and efficiency,
o Microarray: specific array design used.

27
11/6/22
MeDIP-seq

q Methylated DNA immunoprecipitation (MeDIP) is a large-scale

(chromosome- or genome-wide) purification technique in molecular biology
that is used to enrich for methylated DNA sequences.

q Limitations of MeDIP:

q Quality and cross-reactivity of antibodies .

q DNA detection methods

q Primer specificity and efficiency

q Microarray: specific array design used

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Bisulfite Sequencing or BS-seq
q Bisulfite sequencing is the use of bisulfite treatment
of DNA followed by routine sequencing to
determine the pattern of methylation.

q Sodium bisulfite deaminates unmethylated C to

uracil (U) and mC remains cytosine (C).

q During subsequent PCR amplification, the U

deamination product templates adenine (A), which
then templates T, resulting in a C to T transition at
unmethylated C.

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Methods For Inferring Chromatin Organization: 3C
q Chromosome conformation capture techniques (3C-based
methods) are a set of molecular biology methods used to
analyze the spatial organization of chromatin in a cell.
q The Spatial and temporal 3D conformation of chromatin is
partially mediated by the physical interactions between DNA
regulatory elements, in cis and in trans, throughout the
genome.
q Method:
q The 3C method uses formaldehyde cross-linking to
covalently link interacting chromatin segments in intact
cells.
q Cross-linked chromatin is solubilized and digested with
an appropriate restriction enzyme.
q Intramolecular ligation of cross-linked fragments.
q Detection by PCR, quantitative PCR or by sequencing.

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 Take home
q The epigenome is the second dimension of the genome and contains key information specific to every type of cells.

q Epigenetic marks functions depend on their chemical nature and locations in the genome.

q Methylation is the most abundant epigenetic mark in the genome.

q Non-coding RNAs play a significant role in epigenetic modification and can regulate expression at the gene level and
chromosome level.

q Histone modifications are added by writers, erasers, and readers that compose the protein machinery that adds,
removes or recognizes post transcriptional modifications.

q Chromatin is tightly compact and organized under chromosome territories, compartments, TADs and sub-TADs.

q Sequencing-based technologies are used to accurately map epigenomes.

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