DNA and RNA

Week 1 - Genetics

DNA - Double Helix Polymer

●​ Deoxyribonucleic Acid.
●​ Organic Chemical composed of a complex molecular
structure found in all prokaryotic and eukaryotic cells as
well as some viruses.
●​ Made up of repeating units or rather monomers called
nucleotides.
●​ These are joined together by covalent bonds.
●​ They form a double helix structure.
●​ The nucleotides are made up of a sugar, a phosphate
group, and a nitrogenous base or compound.
●​ The sugar is commonly called deoxyribose [A FIVE
CARBON SUGAR]

Nitrogenous Bases
Guanine
Cytosine
Thymine
Adenine
 ●​ The double helix structure has sides made of sugars and
phosphates.
●​ The steps are made of a nitrogenous base joined together
by hydrogen bonds. - PURINE AND PYRIMIDINE

Purines ●​ Guanine and Adenine

●​ Double-ringed
Pyrimidines ●​ Cytosine and Thymine
●​ Single Ring

A=T
G=C

●​ DNA is in several parts of the body, but it is mainly in the

nucleus.
●​ It is also in the cytoplasm and chloroplasts.
- ***THE DNA IN THE NUCLEUS COMES FROM THE MOTHER
AND FATHER WHEREAS THE DNA IN THE CYTOPLASM
COMES FROM THE MOTHER ALONE. ***
●​ DNA regulates the synthesis of proteins and enzymes in
the cytoplasm therefore regulating the development of
living things.
●​ GENE – A section of DNA that codes/ encodes for protein.
●​ DNA keeps the number of chromosomes peculiar to each
organism constant from generation to generation. THIS
IS ACHIEVED THROUGH MITOSIS AND MEIOSIS.
●​ ***DNA cannot leave the nucleus if it did it would
become degraded***
●​ So, it sends a messenger also known as the MRNA
[MESSENGER RNA]

RNA
●​ Ribonucleic Acid.
●​ Uses URACIL rather than THYMINE.
●​ Some RNA can self-replicate.
●​ Has a storage and catalytic function.
●​ The 2’ OH functional group increases its reactivity and
reduces the molecule's stability.
●​ RNA is much more unstable than DNA due to its open
hydroxyl (OH) groups.
●​ They are much more open to chemical attacks. [Such as
Hydrolysis]
●​ The similarity between URACIL and THYMINE is
essential for DNA repair mechanisms. [LEARNING
LATER]
●​ DNA uses 3 types of RNA, for the synthesis of proteins
and enzymes in the cytoplasm.

Types of RNA
Messenger RNA - mRNA
Transfer RNA - tRNA
Ribosome RNA - rRNA
Messenger RNA
●​ Carries information from the DNA regarding the synthesis
of specific types of protein.
●​ Formed by Transcription – {CENTRAL DOGMA}
●​ Carries the Information to the Ribosome.
●​ The DNA cannot leave the nucleus, so the mRNA serves
as the genetic template
●​ The only type of coding RNA

In Eukaryotes the mRNA is processed before translation

In Prokaryotes transcription and translation happens at the
same time. They are synchronous.

Transfer RNA
●​ Recognizes special amino acids that are floating in the
cytoplasm and carries them to the synthesis site.
●​ Acts as a link between mRNA and amino acids during
protein synthesis.
●​ They are depicted to have a cloverleaf structure. [3
hairpin loops]
●​ One of these loops contains a sequence called the
anticodon.
 Anticodon
Recognizes and decodes an mRNA codon
The anticodon loop is complementary to the codon
Meaning that is has the opposite sequence
[A-U or G-C]
The accept stem at the top of the structure is charged with a
complementary amino acid.
The anticodon loop and this amino acid are directly linked
So that there is a specific anticodon for every amino acid.

●​ RNA is generally single stranded but tRNAs fold into a

“t” shape.
●​ The tRNA sequence is very similar between organisms.
We can link this to the concept of evolution. **WHY**

Ribosome RNA
●​ The main component of ribosomes along with proteins.
●​ Non-coding RNA [They don’t form proteins]
●​ Cannot be translated.
●​ Has a catalytic function.
●​ Possess the ability to cause reactions but is not an
enzyme.
●​ Takes the amino acids from the tRNAs and attaches it
to the polypeptide sequence.
●​ They trigger amino acids from the charged tRNAs to
polymerase based on the mRNA sequence.
●​ The order in which the tRNAs have the amino acids join is
dictated by the sequence of the mRNA.
This whole situation is catalyzed by the rRNA.
●​ Most of the cellular RNA is ribosomal.
●​ rRNA combines with special proteins to form ribosomes.
●​ These ribosomes then read mRNA to form proteins.
Regulatory RNAs
●​ Modulate the translation (or expression) rate of other
genes.
EXAMPLES
o​ Expression – How much mRNA is being made.
o​ Translation – How much mRNAs are becoming Proteins.
●​ Controls gene expression.
●​ Double-stranded RNA is detected by special proteins
●​ These proteins

●​ They can do this by interfering with translation.

RNA World Hypothesis

●​ Life began as a self-replicating RNA molecule.

DNA RNA

Deoxyribonucleic Acid Ribonucleic Acid

Double Stranded Single Stranded

More structurally Stable Less Stable

Associated with Histone Not bound to proteins

Proteins to form Nucleosomes.

Stores Genetic Info Transfers Genetic Info

Cellular library Synthesizes Protein

 Located in the nucleus Mostly outside of the nucleus

Missing an Oxygen, [DEOXY...] Has an additional Oxygen Atom

***NUCLEOSOMES***
●​ DNA + PROTEIN = NUCLEOSOMES
●​ The basic structural unit of DNA packaging in
eukaryotes.
●​ Small bit of DNA wrapped around a protein called a
Histone.

Similarities between DNA and RNA

Similarities between DNA and RNA

Both have phosphate backbones
Bothe have pentose sugars
Both are formed from nucleotides
Both are linear polymers.
Both contain the 4 nitrogenous bases.
Base pairing rules are the same
[A-T, G-C]
Both have genetic codes.
Why viruses that lack DNA have RNA to carry out their
function
 Combining them

Sugar + Nitrogenous Base ●​ Nucleoside

●​ Ribose + Adenine = Adenosine
●​ Deoxyribose + Thymine = Deoxythymidine
Sugar + Nitrogenous Base ●​ Nucleotide
+ Phosphate ●​ Ribose + Adenine + Phosphate = Adenosine
Monophosphate [AMP]
Nucleoside + Phosphate ●​ Nucleotide

2 phosphate groups added = Diphosphate

3 phosphate groups added = Triphosphate, ATP

ATP
 ●​ There are high energy bonds created by the repulsions of
the negatives in the phosphate group.
●​ SO, ATP > ADP > AMP.
●​ The phosphate group is attached to the sugar and is on
the 5 prime (5’).

Adenosine Triphosphate
●​ ATPase
●​ A group of enzymes that break down ATP.
●​ They break ATP into ADP and then AMP, all whilst
releasing a phosphate ion.
●​ This process is known as dephosphorylation.
●​ During the process energy is released and the ATPase
uses this to power the body's other chemical reactions.

Chemistry Rule
Bond breaking is ENDOTHERMIC.

Bond making is EXOTHERMIC.

 RECAP
●​ DNA is a nucleic acid [ Polynucleotide Structure]
●​ Nucleotide = NUCLEOSIDE + PHOSPHATE
●​ Nucleoside = SUGAR + NITROGENOUS BASE
●​ Nucleotides are bound together by covalent bonds.
●​ The structures of nucleotides determine their hydrogen
bonding potential.
●​ Pyrimidines will always bond with purines through
hydrogen bonds.
●​ This is because they each possess complementary
hydrogen bond donors and acceptor sites.
●​ The different bonds in the base pairs help prevent
mismatched base pairing.
●​ For this base pairing to occur the strands have to be
antiparallel to each other.
●​ DNA has Polarity.
−
●​ The phosphate ends with 0
●​ The negative attracts the hydrogen, so it gives us OH
on both ends thus giving polarity.

2 bonds between T and A

3 bonds between G and C
This makes it more stable because it takes more energy to break the bond.
There are more of these GC bonds so the DNA is more stable.

NOTE
●​ To read DNA start from the 5’ to 3’ and write, replicate and
transcribe.
●​ There are un-bound carbons at the 5’ and 3’ of the DNA
molecules.
●​ The phosphate group binds from the 5’ carbon on one
molecule to the 3’ carbon on the next molecule.
●​ This generates the phosphate backbone of the DNA
molecule.
●​ The Phosphate Backbone makes the DNA and RNA
molecules very negatively charged.
●​ When the backbone is joined together, water is
liberated/released via a condensation reaction.
●​ The nitrogenous bases join together to form an
antiparallel structure through the hydrogen bonds.
●​ The antiparallel structure is a result of the opposing
primes on each end. 5’ to 3’ and 3’ to 5’.
NITROGENOUS NUCLEOSIDE NUCLEOTIDE
BASE
Adenosine AMP ADP ATP @RNA
ADENINE Deoxyadenosine dGMP dGDP dATP @DNA
Guanosine GMP GDP GTP @RNA
GUANINE Deoxyguanosine dGMP dGDP dGTP @DNA
THYMINE Deoxythymidine dTMP dTDP dTTP @DNA
Cytidine CMP CDP CTP @RNA
CYTOSINE Deoxycytidine dCMP dCDP dCTP @DNA

●​ MITOCHONDRIA HAS ITS OWN DNA

●​ It's circular, no histones.
●​ **46 CHROMOSOMES IN EACH SOMATIC CELL OF THE
HUMAN BODY CELL**
●​ Heterochromatin – HEAVY
●​ Euchromatin – LIGHT

Forming a Helix
●​ This is the process by which the polymer structure takes
shape.

Negatively charged phosphate backbones repel and

create a small distance between them

The bases move inside the molecule

They point inwards and stack themselves in top of each

other

So an uneven helix with different space gaps forms to

fit the bases and sugars in the molecule

These spaces are called major or minor grooves.

The strands must be antiparallel for the helix to form.

 If not, the hydrogen bonds don't align properly and the
structure fails.

Central Dogma
●​ Developed in 1957 by James Watson and Francis Crick.
●​ Genetic information flows in one direction, from DNA
to RNA to protein.

STEPS
Replication DNA is copied to make new DNA
Transcription DNA used to make RNA
Translation RNA used to make new proteins or rather
an amino acid sequence.

**IN SOME CASES, RNA CAN BE REVERSED TRANSCRIBED

TO MAKE DNA**
Carbon Nomenclature
●​ In DNA we start numbering from where the
nitrogenous base is bound to the carbon.
●​ The phosphate
●​ Each Nucleotide has a Pentose Sugar [5 CARBON SUGAR],
Phosphate Group and Nitrogenous Base.
●​ RNA has an extra hydroxyl group.
●​ The Nitrogenous bases in RNA are; A, C, U, G.
●​ U – Uracil

RNA Pairs

Adenine and Uracil

Guanine and Cytosine

Protein Structure
●​ A polymer made from a long sequence of monomers
known as amino acids.
●​ A long chain of amino acids can also be called a
polypeptide.
●​ The bonds that connect amino acids are known as
polypeptide bonds.

Amino Acids
●​ The left side with the nitrogen is the end terminal.
●​ The side with the carboxyl group is the c terminal.
●​ Amino acids combine through a
condensation/dehydration reaction.
●​ One molecule of water is lost.
 ●​ A peptide bond is formed.
●​ The peptide bond is also a covalent bond which makes it
very difficult to break.

End Terminal ●​ Left side with nitrogen

C Terminal ●​ Side with carboxyl group

Levels of Protein Structure

●​ There are 4 structures
Primary Structure
●​ It is defined as the sequence of amino acids linked
together to form a polypeptide chain.
●​ Based on the sequence of the amino acids found in the
protein.
●​ This sequence determines the shape and function of
the protein.
●​ So, if one amino acid is replaced or altered then the whole
protein will be affected.

Secondary Structure
●​ Formed because of the properties of the amino acids
within the structure.
●​ Describes the localized shape or localized arrangement of
the protein.
●​ It is defined by the pattern of hydrogen bonds between
the amino acids from the polypeptide backbone.
●​ There are two – Alpha helices and Beta pleated sheet.

Alpha Helices
●​ Tight, ring-handed coils.
●​ Contain about 3.6 amino acids per turn.
●​ Depicted as coiled ribbons in 3d models.
●​ Stabilized by hydrogen bonds.
●​ The NH group of one amino acid interacts with the
carbonyl group of another.
Beta Pleated Sheets
●​ Short regions of the polypeptide chain lie side by side.
●​ Connected and stabilised by hydrogen bonds.
●​ Depicted as parallel or antiparallel rows in models.
●​ The Nh group of one amino acid interacts with the
carbonyl group of another.

Tertiary Structure
●​ 3 dimensional.
●​ Shows the arrangement of the backbone and polypeptide
side chains.
●​ Determined by the interactions of amino acid residue =.
●​ 1 individual Subunit.
Quaternary Structure
●​ Made up of multiple Polymers
●​ Arrangement of multiple polypeptide chains, or subunits.
●​ Haemoglobin is a good example; it has 4 subunits. Two
alpha and two betas.
●​ Haemoglobin has a quaternary protein structure.
DNA replicates by separating into two single strands. Each
of these strand’s function as a template for new strands.

RNA
Week 1 - Genetics
Introduction
●​ Ribonucleic Acid
●​ Made up of monomers called nucleotides.
●​ Nucleotides are held together by Phosphiditer bonds
●​ Sugar Molecule + Phosphate group + Nitrogenous Base =
Nucleotide.
●​ More prone to chemical reaction due to the open
hydroxyl groups on the 2’ carbon.
●​ Much more chemically unstable than DNA.

Nitrogenous Bases

Uracil

Cytosine

Adenine

Guanine

General Function of RNA

●​ Acta as messenger for the DNA.
●​ Carries the genetic information stored in the DNA.
●​ Involved in the process of protein synthesis , regulation
and catalysis of chemical reactions.

Types of RNA

mRNA
●​ Messenger RNA.
●​ Only coding RNA.
●​ Carries the genetic information regarding the synthesis of
specific proteins
 ●​ Also referred to as the Genetic template for DNA.
●​ Made by Transcription.
●​ DNA Replication and Transcription happen in the
nucleus.
●​ The mRNA leaves through the nuclear pores in the
nuclear membrane and goes to find the ribosomes on the
rough endoplasmic reticulum.

NOTE
●​ In Eukaryotes the mRNA is processed before
transcription
-​ The mRNA made before this is called precursor mRNA
also known as Pre mRNA
-​ When it is processed it is then referred to as Mature
mRNA
-​ The mRNA of eukaryotes is Monocistronic

Monocistronic ●​ 1 mRNA yields only one protein.

●​ In Prokaryotes transcription and translation occur at the

same time
-​ The mRNA of prokaryotes is polycistronic , so 1 yields
many proteins.

Polycistronic ●​ 1 mRNA yields many proteins.

tRNA
●​ Transfer RNA
●​ Tiny
●​ Non-coding RNA
●​ Seeks out specific amino acids in the cytoplasm and
brings them to their corresponding mRNA sequence at
the protein synthesis site.
●​ Some say it acts as a link between mRNA and amino
acids.
●​ All have double stranded regions.
-​ The site for binding of the amino acids is on the 3’ region
of the structure - it has a CCA base.
-​ Due to their slightly different base sequences, each tRNA
has a unique shape.
-​ Depicted to have a three leaf clover structure.

-​ Possesses an anticodon loop on the bottom end and an

acceptor stem at the top.
 -​ The anticodon loop matches up with the codon on the
mRNA

Codon ●​ sequence of nucleotides that correspond

with specific amino acids or stop signals

Function of Codon and Anticodon

Ensure the proper amino acid is injected into the

polypeptide bond.

-​ The anticodon loop is complementary to the codon -

they have opposing sequences [A - U and G - C]
-​ This opposing sequence allows for the proper transfer of
genetic information during protein synthesis.
-​ THERE IS A SPECIFIC ANTICODON FOR EACH AMINO
ACID. - And Vice Versa
-​ The amino acid can be found in the acceptor stem of the
tRNA structure.

Activating tRNA
●​ This process requires ATP.
●​ When the tRNA is done delivering the amino acid it needs
to be recharged.
●​ This is done with the help of a specific activating
enzyme.
●​ ATP + AMINO ACIDS + tRNA bind to this site.
●​ Enzymes have a unique shape and structure, so each
one will only accommodate a specific type of tRNA
●​ For every tRNA molecule there is a specific activating
enzyme.
●​ There are 20 tRNA activating enzymes.
●​ In order for the tRNA to attach to this enzyme ATP is
required.
 Function of Codon and Anticodon

Rough endoplasmic Reticulum = Smooth ER +

Ribosomes

rRNA
●​ Ribosomal RNA.
●​ Main component of ribosomes in addition to proteins.
●​ Cannot be transcribed.
●​ Made in the nucleolus of the cell.
●​ Has a catalytic function.
●​ Makes ribosomes which then in turn make the Rough
Endoplasmic Reticulum.
●​ Help catalyze the peptide bond formation between the
amino acids.
●​ Splices out its own introns [NON CODING REGIONS OF
RNA]

Regulatory RNA
●​ MICRO AND SMALL INTERFERING RNA
●​ Modulate the expression and translation of genes.
●​ They do this by interfering with the general process.
●​ They can degrade RNA before they are translated.
●​ To do this they form complexes that suppress the
translation process by cleaving the mRNA.
●​ A good example of the benefits of this process is the
control of the virus pathway

Some viruses fuse their genome with the host's genome.

This allows the virus to be transcribed which leads to

the host being overrun with viruses.
 The regulatory RNA disrupts this process and helps
prevent this.

Micro RNA
●​ Small non-coding RNA that helps modulate gene
expression.
●​ Control the amount and types of protein being produced
●​ They are not translated into proteins.
●​ Involved in processes such as organ development and
cancer.
●​ About 22 nucleotides in length.
●​ Part of an endogenous pathway
●​ The sequences that make up the micro RNA are found in
Introns.
●​ Microrna regulates gene expression through RNA
interference or Gene silencing.

Timeline of Micro RNA

First created in the nucleus as long strands

Strands are cut short and sent into the cytoplasm

Once in the cytoplasms they are trimmed down even

further to become Mature miRNAs

Then they attach to a group of proteins called RISC

RNA inducing silencing complex

This group helps the microRNA find its corresponding

messenger RNA.

If the sequences on both the RNA match the micro RNA

attaches the mRNA.

Once bonded the microRNA can either block the

message on the mRNA.
This would stop it from being used to make proteins.

Or it can destroy the message

Breaks down the mRNA so it cannot be sussed to
make proteins at all.

Synthesis of Micro RNA

miRNA genes are transcribed by RNA polymerase II/ III

into primary miRNA (pri-miRNA)

The pri - miRNA is processed into a precursor miRNA

(pre-miRNA) by an enzyme called DROSHA.

Then the pre-miRNA is exported into the cytoplasm.

An enzyme called dicer cuts the pre-miRNA into mature

miRNA duplex.

One of the strands of the duple load onto the

RNA-induced silencing complex [RISC]

Small Interfering RNA

Also known as short interfering or silencing RNA.

Regulates gene expression.

Typically 20-40 base pairs long.

Double Stranded.
One of the strands acts as a guide to help target the
corresponding mRNA.

Introduced either naturally or synthetically.

siRNAs are a result of the cleavage of double stranded

RNAs by the enzyme known as DICER.