• DNA stands for deoxyribo

nucleic acid

• RNA stands for ribo

nucleic acid

• Both DNA and RNA are

macromolecules like protein

and polysaccharide

• They are polymers

What is a nucleotide
Nucleotide is an organic molecule. It is the building block
of DNA and RNA and is made of three components that
include a phosphate group, a 5-carbon sugar, and
a nitrogenous base. The nitrogenous base can be of four
types or we can say that there are four different
nitrogenous bases in DNA that are adenine, cytosine,
guanine and thymine. However, in RNA instead of
thymine, uracil is present, in other words, thymine is
replaced by uracil. So, it is the nucleotides that make the
DNA (genetic material) of all living organisms.
Structure of Nucleotide:

A nucleotide comprises three units

that are linked through covalent

bonds.

[Link] bases: Purines

(Adenine and Guanine), and

Pyrimidines (Cytosine, Thymine and

Uracil)

[Link] sugar: It can be Ribose

or Deoxyribose sugar.

[Link]: monophosphate,

diphosphate and triphosphate

1) Nitrogenous bases or
Nucleotide Bases:
A nucleotide is defined or
identified by its chemical base.
There are a total of five chemical
bases:
•Adenine
•Cytosine
•Guanine
•Thymine
•Uracil

A nucleotide is named on the basis of the type of base and phosphate residue. For example, an Adenine
nucleotide that has one phosphate group is known as adenosine monophosphate. Adenosine is derived from the
Adenine base of the nucleotide and monophosphate indicates that it has one phosphate group.
A base is represented by a letter and it can be either purine or pyrimidine as described below:
Adenine (A): This base is a purine, which is a family of nitrogenous bases. Its chemical formula is C5H5N5 and it has a double-ringed structure like other purines. A
nucleotide with adenine as a base is called Adeninemononucleotide/adenosinemonophospate. It has two hydrogen bonds that help stabilize the structure of nucleic
acids such as DNA, RNA. In DNA, adenine is bonded with thymine and thus it makes pair with thymine. Whereas, in RNA, it is bonded with uracil.
Cytosine (C): This base is a pyrimidine which is a molecule whose chemical formula is C4H5N3. A cytosine based nucleotide is known as
cytosinemononucleotide/cytidinemonophosphate. Its structure has only one ring and it makes a pair with guanine in both nucleic acids, DNA and RNA. However,
when it is free it may act as a co-enzyme, which helps convert ADP to ATP.
Guanine (G): This base is also a purine, a molecule with a double ring structure and chemical formula C5H5N5. A nucleotide that carries guanine as a base is called
guaninemononucleotide/guanosinemonophosphate. It bonds with cytosine through three hydrogen bonds in both nucleic acids DNA and RNA. Due to the three
hydrogen bonds, it is slightly stronger than the adenine-thymine bond that has only two hydrogen bonds.
Thymine (T): It is pyrimidine base with chemical formula C5H6N2 A nucleotide based on the thymine is called thyminemononucleotide/thmidinemonophosphate.
It pairs or bonds with adenine in nucleic acids that assist in stabilizing the nucleic acid structures.
Uracil (U): Uracil is a pyrimidine base with chemical formula C4H4N2. A uracil-based nucleotide is called uracilmononucleotide/uridinemonophosphate. Uracil is a
demethylated form of thymine and is present in RNA in place of thymine. Demethylation is a chemical process in which a CH3 (methyl group) is removed from a
molecule. These bases can combine with sugars and phosphates to form free nucleotides and can bond with
each another to form nucleic acids like DNA and RNA.
2) Pentose Sugars or Pentose Monosaccharides:
It is one of the three components of a nucleotide that is needed to make this molecule.
It is five-carbohydrate sugar. A nucleotide can have one of the following two sugars:
•Deoxyribose sugar that is found in DNA
•Ribose sugar that is found in RNA
• So, there can be two types of pentose sugars in nucleotides; ribose (C5H10O5)
and deoxyribose (C5H10O4).
• The ribose sugar has a -OH group, whereas, the deoxyribose sugar has -H at
C-2 position.
• The nucleotides that contain ribose are called ribonucleotides or
ribotides and are found only in RNA, whereas, nucleotides that contain
deoxyribose are called deoxyribonucleotides or dexoyribotides.
• DNA is a nucleic acid with a deoxyribose sugar so it is named deoxyribonucleic
acid. Similarly, RNA has ribose sugar so it is named ribonucleic acid.
• A nitrogenous base which is attached to a sugar molecule is called
3) Phosphate Groups:
• A nucleotide can have one, two or three phosphate groups.
• Accordingly, they are known as monophosphate (with one phosphate group), diphosphates
(with two phosphate groups) and triphosphates with three phosphate groups.
• Phosphate is attached to the sugar of nucleoside by an ester bond with the 5-Carbon
hydroxyl group. Thus, a nucleotide is formed from nucleoside.
Formation of Nucleosides:
A nucleoside is formed when a pentose sugar combines with a nitrogenous
base through N-glycosidic base.

The C-1 carbon of pentose sugar is attached to N-9 of a purine or N-1 of a pyrimidine to form a
nucleoside. A nucleoside that has ribose sugar is called ribonucleoside or riboside and a nucleoside that has
deoxyribose sugar is called deoxyribonucleoside or deoxyriboside.
Some examples of ribonucleoside include

1. adenosine (adenine + ribose),

2. guanosine (guanine + ribose),

3. thymidine (thymine + ribose)

4. cytidine (cytosine + ribose)

5. Uridine (uracil+ ribose)

Similarly, some of the corresponding examples of deoxyribonucleosides include

deoxyadenosine, deoxyguanosine, deoxythymidine, deoxycytidine, etc.

 So, a

nucleotide is

required to have

at least one

phosphate

group..
Formation of nucleotides
Nucleotides are formed from nucleoside. They are phosphate esters of nucleosides.
A phosphate is bonded with 5' carbon of sugar of a nucleoside to form a nucleotide or nucleoside
monophosphate.
Some examples of nucleotides include
adenosine monophosphate (AMP), Deoxyadenosine monophosphate (dAMP), Guanosine
monophosphate (GMP), Deoxyguanosine monophosphate (dGMP). These nucleotides have one
phosphate.
The nucleotides that have more than one phosphate group are called higher nucleotides such as
Adenosine Triphosphate (ATP), Adenosine Diphosphate (ADP), Guanosine Triphosphate (GTP), etc. So,
higher nucleotides are actually nucleoside diphosphates and nucleoside triphosphates.
The higher nucleotides occur in a free state and they carry high energy bonds called phosphoanhydride
bonds that exist between phosphates. ATP is the most common energy molecule in the cell that releases
the required energy when it breaks down to form ADP with the release of energy. The hydrolysis of ATP
releases lots of free energy that is required to carry out cellular chemical reactions, e.g. ATP + H O -- >
DNA nucleotides
•The components of a DNA nucleotide are:
• A deoxyribose sugar with hydrogen at the 2′ position
• A phosphate group
• One of four nitrogenous bases – adenine (A), cytosine(C), guanine(G) or
thymine(T)

RNA nucleotides
•The components of an RNA nucleotide are:
• A ribose sugar with a hydroxyl (OH) group at the 2′ position
• A phosphate group
• One of four nitrogenous bases – adenine (A), cytosine(C), guanine(G)
or uracil (U)
•The presence of the 2′ hydroxyl group makes RNA more susceptible to
hydrolysis
• This is why DNA is the storage molecule and RNA is the transport
molecule with a shorter molecular lifespan
Although DNA and RNA nucleotides are very similar, make sure you

know the key differences between them: unlike DNA, RNA

nucleotides never contain the nitrogenous base thymine (in place of

this they contain the nitrogenous base uracil) and unlike DNA, RNA

nucleotides contain the pentose sugar ribose (instead of

deoxyribose).

You don’t need to know the structural formulae of the bases, just

which are purines and which are pyrimidines.

 LINKAGE BETWEEN

NUCLEOTIDES

The phosphate group of a

nucleotide is attached to

the 3rd C-OH group of the

sugar of the other

nucleotide and thus forms

5' - 3' linkage

+ H 2O
Phosphorylated Nucleotides
Structure of ATP & ADP
•All organisms require a constant supply of energy to maintain their cells and stay alive
•In all organisms this energy is required for:
• Anabolic reactions (building larger molecules from smaller molecules)
• Moving substances across the cell membrane or moving substances within the cell
•In animals energy is also required for:
• Muscle contraction – to coordinate movement at the whole-organism level
• The conduction of nerve impulses
•In all known forms of life, ATP from respiration is used to transfer energy in all energy-
requiring processes in cells
• This is why ATP is known as the universal energy currency
•Adenosine Triphosphate (ATP) is a nucleotide
• The monomers of DNA and RNA are also nucleotide
ATP

•Adenosine triphosphate (ATP) is the energy-carrying molecule that provides the energy to drive

many processes inside living cells

•ATP is another type of higher nucleotide and hence it is structurally very similar to the

nucleotides that make up DNA and RNA

•It is a phosphorylated nucleotide

•Adenosine (a nucleoside) can be combined with one, two or three phosphate groups

• One phosphate group = adenosine monophosphate (AMP)

• Two phosphate groups = adenosine diphosphate (ADP)

• Three phosphate groups = adenosine triphosphate (ATP)

THE STRUCTURE OF AMP, ADP AND ATP
 Don’t worry – you are not expected to know the structural

formulae for the nucleotides that make up AMP, ADP and ATP

(as in the diagram above)! You just need to learn the

different groups that they are made up of ( pentose sugars

and nitrogenous bases and how many phosphate groups,).

Remember that adenine is a nitrogenous

base whereas adenosine is a nucleoside (a base – adenine,

attached to a pentose sugar).

 Structure of DNA
•The nucleic acid DNA is a polynucleotide – it is made up of many nucleotides bonded
together in a long chain
•DNA molecules are made up of two polynucleotide strands lying side by side, running in opposite
directions – the strands are said to be antiparallel
•Each DNA polynucleotide strand is made up of alternating deoxyribose sugars and phosphate
groups bonded together to form the sugar-phosphate backbone. These bonds
are covalent bonds known as phosphodiester bonds
• The phosphodiester bonds link the 5-carbon of one deoxyribose sugar molecule to the
phosphate group from the same nucleotide, which is itself linked by another phosphodiester bond
to the 3-carbon of the deoxyribose sugar molecule of the next nucleotide in the strand
• Each DNA polynucleotide strand is said to have a 3’ end and a 5’ end (these numbers relate to
which carbon on the pentose sugar could be bonded with another nucleotide)
• As the strands run in opposite directions (they are antiparallel), one is known as the 5’ to 3’
strand and the other is known as the 3’ to 5’ strand
•The nitrogenous bases of each nucleotide project out from the backbone towards the interior of the
double-stranded DNA molecule
A SINGLE DNA POLYNUCLEOTIDE STRAND SHOWING THE POSITIONING OF THE
ESTER BONDS
Hydrogen bonding
•The two antiparallel DNA polynucleotide strands that make up the DNA molecule are held

together by hydrogen bonds between the nitrogenous bases

•These hydrogen bonds always occur between the same pairs of bases:

• The purine adenine (A) always pairs with the pyrimidine thymine (T) – two

hydrogen bonds are formed between these bases

• The purine guanine (G) always pairs with the pyrimidine cytosine (C) – three

hydrogen bonds are formed between these bases

•This is process is known as complementary base pairing and the pairs are known

as complementary base pairs

A SECTION OF DNA – TWO ANTIPARALLEL DNA POLYNUCLEOTIDE STRANDS HELD TOGETHER BY HYDROGEN
BONDS
Double helix

•DNA is not two-

dimensional as seen in

the diagram above

•DNA is described as

a double helix (this

refers to the three-

dimensional

shape formed by the

twisting of the DNA

molecule)
NOTE: Make sure you can name the different components of a DNA molecule

(sugar-phosphate backbone, nucleotide, complementary base pairs,

phosphodiester bonds, hydrogen bonds) and make sure you are able to locate

these on a diagram.

You must know how many hydrogen bonds occur between the different base

pairs.

Remember that the bases are complementary so the number of A = T and C

= G, as you could be asked to determine how many bases are present in a

DNA molecule if given the number of one of the bases.

DNA Purification

•Practical investigations can be conducted to purify (isolate) DNA via the process of precipitation

•Isolating DNA from cells is an essential starting point for a huge range of other investigations and so is

a key research technique in the field of molecular biology

•A common method used to isolate DNA is known as the ‘Marmur preparation’

• The method is derived from the work of Julius Marmur (1926-1996), an American molecular biologist

who made significant contributions to DNA research

•The Marmur preparation involves three basic steps:

• Breaking (lysing) the cells and disrupting the nuclear membranes to release the DNA

• Using enzymes to denature and remove the proteins (histones) associated with the DNA

• Precipitating the DNA using an organic solvent (e.g. ethanol)

Example practical investigation: extracting DNA from onions
•Onions are good to use for this investigation as their cells contain a relatively large amount of DNA
•Fruits that also have relatively large amounts of DNA in their cells, such as strawberries, bananas and kiwis, can
also be used

Equipment
•Plastic syringe (1 cm³) •Protease enzyme (2-3 drops)
•Plastic funnel •Coffee filter paper (laboratory filter paper
•2 × beakers (250 cm³) not suitable as the liquid takes too long to
•2 × Test tubes pass through)
•Stirrer (e.g. stirring rod or plastic spoon) •Water bath (60 °C)
•Chopping board •Ice-water bath
•Knife (for chopping onion) •Blender or liquidiser
•Onion
•Washing-up liquid (10 cm³)
•Ice-cold ethanol (10 cm³)
•Place the ethanol in a freezer 24 hours before starting the investigation Results
• The ethanol must be ice-cold, it is key to the success of the investigation •The DNA in the resulting white
•Cut up the onion into small pieces (5 mm × 5 mm) precipitate can now be extracted and
•Add the washing-up liquid to 90 cm³ of tap water in a beaker used for analysis or in further
•Add some of the onion pieces to the beaker investigations
•Place the beaker in a water bath at 60 °C for 15 minutes
• The detergent (washing-up liquid) and the heat disrupt the phospholipid bilayer of the onion cell membranes and nuclear
membranes, releasing the DNA
• The heat also denatures enzymes released from the cell that would otherwise begin to digest the DNA
•Cool the mixture in an ice-water bath for 5 minutes, stirring it continually
• Lowering the temperature prevents the DNA itself from breaking down, which would occur if the high temperature from the previous
step was maintained
• Continual stirring ensures the whole mixture is cooled
•Pour the mixture into a blender and blend for 5 seconds
• Blending breaks down the cell walls and cell membranes of the onion cells even further, releasing more DNA
• The mixture is only blended for a very short time to ensure the DNA strands themselves are not broken apart
•Using the filter paper, filter the mixture into another beaker
• Filtering removes cell debris and membrane fragments
• The filtrate now contains the DNA and its associated proteins
•Pour 10 cm³ of the filtrate into a test tube and add 2-3 drops of protease enzyme, mixing well
• The protease denatures and removes the proteins, leaving just the DNA
•Carefully add the ice-cold ethanol to the test tube and wait 2-3 minutes
• Nucleic acids are insoluble in ice-cold ethanol and so the DNA forms a precipitate (white layer) at the top of the test tube mixture
Semi-conservative Replication of DNA
•Before a (parent) cell divides, it needs to copy the DNA contained within it
• Doubling the DNA ensures that the two new (daughter) cells produced will both
receive full copies of the parental DNA
•The DNA is copied via a process known as semi-conservative replication (semi =
half)
• The process is called this because in each new DNA molecule produced, one of
the polynucleotide DNA strands (half of the new DNA molecule) is from the
original DNA molecule being copied
• The other polynucleotide DNA strand (the other half of the new DNA molecule) has
to be newly created by the cell
• Therefore, the new DNA molecule has conserved half of the original DNA and
then used this to create a new strand
The importance of retaining one original DNA strand

•Retaining one original DNA strand ensures there is genetic continuity (i.e. genetic

information is conserved) between generations of cells

•In other words, it ensures that the new cells produced during cell division inherit all

their genes from their parent cells

•This is important because cells in our body are replaced regularly and therefore we

need the new cells to be able to do the same role as the old ones

• Replication of DNA and cell division also occurs during growth

SEMI-CONSERVATIVE REPLICATION

•DNA REPLICATION OCCURS IN PREPARATION FOR MITOSIS, WHEN A PARENT CELL DIVIDES TO PRODUCE TWO GENETICALLY

IDENTICAL DAUGHTER CELLS – AS EACH DAUGHTER CELL CONTAINS THE SAME NUMBER OF CHROMOSOMES AS THE PARENT CELL,

THE NUMBER OF DNA MOLECULES IN THE PARENT CELL MUST BE DOUBLED BEFORE MITOSIS TAKES PLACE

•DNA REPLICATION OCCURS DURING THE S PHASE OF THE CELL CYCLE (WHICH OCCURS DURING INTERPHASE, WHEN A CELL IS NOT

DIVIDING)

•THE ENZYME HELICASE UNWINDS THE DNA DOUBLE HELIX BY BREAKING THE HYDROGEN BONDS BETWEEN THE BASE PAIRS ON THE

TWO ANTIPARALLEL POLYNUCLEOTIDE DNA STRANDS TO FORM TWO SINGLE POLYNUCLEOTIDE DNA STRANDS

•EACH OF THESE SINGLE POLYNUCLEOTIDE DNA STRANDS ACTS AS A TEMPLATE FOR THE FORMATION OF A NEW STRAND MADE FROM

FREE NUCLEOTIDES THAT ARE ATTRACTED TO THE EXPOSED DNA BASES BY BASE PAIRING. THIS METHOD OF REPLICATING DNA IS

KNOWN AS SEMI-CONSERVATIVE REPLICATION BECAUSE HALF OF THE ORIGINAL DNA MOLECULE IS KEPT (CONSERVED) IN EACH OF

THE TWO NEW DNA MOLECULES

•THE NEW NUCLEOTIDES ARE THEN JOINED TOGETHER BY THE ENZYME DNA POLYMERASE WHICH CATALYSES CONDENSATION

REACTIONS TO FORM A NEW STRAND

•THE ORIGINAL STRAND AND THE NEW STRAND JOIN TOGETHER THROUGH HYDROGEN BONDING BETWEEN BASE PAIRS TO FORM THE

NEW DNA MOLECULE

DNA polymerase
•In the nucleus, there are free nucleotides which contain three phosphate groups

• These nucleotides are known as nucleoside triphosphates or ‘activated nucleotides’

• The extra phosphates activate the nucleotides, enabling them to take part in DNA replication

•The bases of the free nucleoside triphosphates align with their complementary bases on each of

the template DNA strands

•The enzyme DNA polymerase synthesises new DNA strands from the two template strands

•It does this by catalysing condensation reactions between the deoxyribose sugar and phosphate groups of

adjacent nucleotides within the new strands, creating the sugar-phosphate backbone of the new DNA strands

•DNA polymerase cleaves (breaks off) the two extra phosphates and uses the energy released to create

the phosphodiester bonds (between adjacent nucleotides)

NUCLEOTIDES ARE BONDED TOGETHER BY DNA POLYMERASE TO CREATE THE NEW COMPLEMENTARY DNA
STRANDS
• Meselson and Stahl experiment gave the experimental evidence of DNA replication to be semi-

conservative type.

• It was introduced by the Matthew Meselson and Franklin Stahl in the year 1958.

• Matthew Meselson and Franklin Stahl have used [Link] as the “Model organism” to explain the

semiconservative mode of replication.

• Matthew Meselson and Franklin Stahl have conducted several experiments after the discovery of

DNA structure (by the two scientists Watson and Crick).

• Watson and Crick’s model is widely accepted to demonstrate the replicative model of DNA.
Meselson-Stahl Experiment
This experiment was performed to prove the semi conservative nature of DNA
replication. Matthew Meselson & Franklin Stahl experimented with bacteria
[Link] in 1958.
Basis of the Experiment
If [Link] was grown in a If [Link] was grown in a
medium with N-15 (isotope of medium with N-14 (more
Nitrogen), the [Link] had DNA abundant isotope of Nitrogen),
with N-15 isotope. the [Link] had DNA with N-14
isotope.
• Cells of [Link] were allowed to divide.

• Sample was taken and DNA was extracted periodically as

cell division continued to check what type of DNA is

being formed now.

• One replication in [Link] takes around 20 minutes.

• So, generation I is formed in 20 minutes.

• Therefore samples are taken after 20 minutes, then

again after 40 minutes.

Results
Conclusion
•Presence of a hybrid/ intermediate density excluded Conservative hypothesis. Had it been
Conservative hypothesis, Generation 1 would have been either Blue(N-15) or Green(N-
14); and not an Intermediate one.
•Presence of N-14 DNA in Generation II excluded Dispersive hypothesis. If it was
Dispersive, each DNA should have had the same density. But, in Generation II, we could
see 50% of the DNA have intermediate density, whereas remaining 50% have N-14
density.
•Semi-conservative hypothesis could explain the entire experimental result. Separation of
strands concept could explain the outcomes of Generation I & II.
Thus, it was proved that DNA replication is Semi-conservative in nature.
NOTE: Therefore, this experiment proves that the DNA replication obeys the semi-conservative
mode of replication in which 50% of the DNA conserve for every next generation in a way like
100%, 50%, 25%, and 12.5% and so on.
VIDEO 1 VIDEO
Mutations
•The replicated DNA molecules must be an exact copy of the parent DNA molecule,
therefore the formation of the complementary strands must be a highly
accurate process
•Although the process is astonishingly accurate considering it is
happening constantly in cells and at a considerable speed, occasional mistakes occur
in the form of:
• Bases being inserted into the complementary strand in the wrong order
• An extra base being inserted by accident
• A base being left out by accident
NOTE:
•TheseMake sureinyou
mistakes thedon’t confuse
process ‘parent cell’ with
of semi-conservative ‘parent organism’.
replication A parent
of DNA result in the
cell is any cell
occurrence in the body
of random, that divides
spontaneous into two cells
mutations and theinterminology
(i.e. errors the genetic is used to
code)
refer to the ‘original’ cell that the DNA came from before it was split and replicated
Nature of the Genetic Code
•A gene is a sequence of nucleotides that forms part of a DNA molecule (one DNA
molecule contains many genes)
•This sequence of nucleotides (the gene) codes for the production of a specific
polypeptide (protein)
•Protein molecules are made up of a series of amino acids bonded together
•The shape and behaviour of a protein molecule depends on the exact sequence of
these amino acids (the initial sequence of amino acids is known as the primary
structure of the protein molecule)
•The genes in DNA molecules, therefore, control protein structure (and as a
result, protein function) as they determine the exact sequence in which the amino
acids join together when proteins are synthesised in a cell
A GENE IS A SEQUENCE OF NUCLEOTIDES THAT CODES FOR THE PRODUCTION OF A SPECIFIC PROTEIN MOLECULE
(POLYPEPTIDE)
The triplet code
•The sequence of DNA nucleotide bases found within a gene is determined by a triplet (three-letter) code
•Each sequence of three bases (i.e. each triplet of bases) in a gene codes for one amino acid
•These triplets of bases are known as codons (each codon codes for a different amino acid – there are 20
different amino acids that cells use to make up different proteins)
•For example:
• CAG codes for the amino acid valine
• TTC codes for the amino acid lysine
• GAC codes for the amino acid leucine
• CCG codes for the amino acid glycine
•Some of these triplets of bases code for start (TAC – methionine) and stop signals
•These start and stop signals tell the cell where individual genes start and stop
•As a result, the cell reads the DNA correctly and produces the correct sequences of amino
acids (and therefore the correct protein molecules) that it requires to function properly
•The genetic code is non-overlapping
• Each base is only read once in which codon it is part of
•There are four bases, so there are 64 different codons (triplets) possible (43 = 64), yet there are
only 20 amino acids that commonly occur in biological proteins
• This is why the code is said to be degenerate: multiple codons can code for the same
amino acids
• The degenerate nature of the genetic code can limit the effect of mutations
•The genetic code is also universal, meaning that almost every organism uses the same
code (there are a few rare and minor exceptions)
•The same codons code for the same amino acids in all living things (meaning that genetic
information is transferable between species)
• The universal nature of the genetic code is why genetic engineering (the transfer of genes
from one species to another) is possible
 NOTE:

Remember – each chromosome in a human cell

nucleus contains one very long DNA molecule.

This DNA molecule is made up of thousands of

specific nucleotide sequences called genes that

code for specific proteins. Even though these

genes are all found within the same DNA

molecule and are therefore all linked up, the cell

knows where individual genes start and stop.

This ensures the cell reads the DNA correctly

and can produce the correct protein molecules

A DNA MOLECULE WITH THE TRIPLET CODE FOR THE CODONS OF THE START
that it requires to function properly.
AMINO ACID (METHIONINE) AND VALINE
Constructing Polypeptides
•A gene is a sequence of nucleotide bases in a DNA molecule that codes for the production of a
specific sequence of amino acids, that in turn make up a specific polypeptide (protein)
•This process of protein synthesis occurs in two stages:
• Transcription – DNA is transcribed and an mRNA molecule is produced
• Translation – mRNA (messenger RNA) is translated and an amino acid sequence is produced
The ‘Central Dogma’ is the process by which the instructions in DNA are converted
into a functional product. It was first proposed in 1958 by Francis Crick, discoverer
of the structure of DNA.
•The central dogma of molecular biology explains the flow of genetic information,
from DNA ?to RNA?, to make a functional product, a protein?.
•The central dogma suggests that DNA contains the information needed to make all
of our proteins, and that RNA is a messenger that carries this information to
the ribosomes?.
•The ribosomes serve as factories in the cell where the information is ‘translated’
from a code into the functional product.
•The process by which the DNA instructions are converted into the functional
product is called gene expression?.
The Genome
•A gene is a length of DNA that codes for a
polypeptide/protein
•A genome is the complete set
of genes present in a cell
•The full genome is present within every
cell of an organism, but not every gene is
expressed in every cell. Which genes are
expressed depends on the cell type
•The proteome is the full range
of proteins that a cell is able to produce
•The proteome is usually larger than the
genome of an organism
• This due to the large amount of post-
translational modification of
proteins (often in the Golgi
apparatus)
• Each gene is also capable of
producing multiple different proteins
via alternative splicing
The Structure of mRNA and tRNA
•Like DNA, the nucleic acid RNA (ribonucleic acid) is a polynucleotide – it is made up of many nucleotides linked together in a long chain
•Like DNA, RNA nucleotides contain the nitrogenous bases adenine (A), guanine (G) and cytosine (C)
•Unlike DNA, RNA nucleotides never contain the nitrogenous base thymine (T) – in place of this they contain the nitrogenous base uracil (U)
•Unlike DNA, RNA nucleotides contain the pentose sugar ribose (instead of deoxyribose)
•Unlike DNA, RNA molecules are only made up of one polynucleotide strand (they are single-stranded)
•Each RNA polynucleotide strand is made up of alternating ribose sugars and phosphate groups linked together, with the nitrogenous bases of
each nucleotide projecting out sideways from the single-stranded RNA molecule
•The sugar-phosphate bonds (between different nucleotides in the same strand) are covalent bonds known as phosphodiester bonds
• These bonds form what is known as the sugar-phosphate backbone of the RNA polynucleotide strand
• The phosphodiester bonds link the 5-carbon of one ribose sugar molecule to the phosphate group from the same nucleotide, which is itself
linked by another phosphodiester bond to the 3-carbon of the ribose sugar molecule of the next nucleotide in the strand
•An example of an RNA molecule is messenger RNA (mRNA), which is the transcript copy of a gene that encodes a specific polypeptide. Two other
examples are transfer RNA (tRNA) and ribosomal RNA (rRNA)
 mRNA

•mRNA is a single-stranded molecule

•It is made up of a sugar-phosphate

backbone and exposed unpaired

bases

•Uracil bases are present instead of

Note: You need to know the difference between DNA
thymine bases (which are found in
and RNA molecules (bases, number of strands, pentose
sugar present).
DNA)
• mRNA accounts for just 5% of the total RNA in the cell. mRNA is the most heterogeneous of the 3 types
of RNA in terms of both base sequence and size.
• It carries complementary genetic code copied, from DNA during transcription, in the form of triplets of
nucleotides called codons.
• Each codon specifies a particular amino acid, though one amino acid may be coded for by many
different codons. Although there are 64 possible codons or triplet bases in the genetic code, only 20 of
them represent amino acids. There are also 3 stop codons, which indicate that ribosomes should cease
protein generation by translation.
• As part of post-transcriptional processing in eukaryotes, the 5’ end of mRNA is capped with a guanosine
triphosphate nucleotide, which helps in mRNA recognition during translation or protein synthesis.
• Similarly, the 3’ end of an mRNA has a poly-A tail or multiple adenylate residues added to it, which
prevents enzymatic degradation of mRNA.
• Both the 5’ and 3’ end of an mRNA imparts stability to the mRNA.
tRNA

•tRNA is a single-stranded molecule

•It has a sugar-phosphate backbone

•It has a folded shape

• There are hydrogen bonds between some of

the complementary bases

•Amino acids bind to a specific region of the

molecule

•The specific anticodon found on the tRNA molecule

is complementary to a specific codon on an mRNA

STRUCTURE OF A tRNA MOLECULE
molecule
tRNA is the smallest of the 3 types of RNA, possessing around 75-95 nucleotides.
tRNAs are an essential component of translation, where their main function is the
transfer of amino acids during protein synthesis. Therefore, they are called transfer
RNAs.
Each of the 20 amino acids has a specific tRNA that binds with it and transfers it to the
growing polypeptide chain.
tRNAs also act as adapters in the translation of the genetic sequence of mRNA into
proteins. Thus, they are also called adapter molecules.
tRNAs have a cloverleaf structure which is stabilized by strong hydrogen bonds
between the nucleotides.
They normally contain some unusual bases in addition to the usual 4, which are
formed by methylation of the usual bases. Methyl guanine and methylcytosine are two
Ribosomal RNA (rRNA)
Ribosomal RNA (rRNA) molecules are the structural components of the ribosome. The rRNAs form
extensive secondary structures and play an active role in recognizing conserved portions of mRNAs
and tRNAs. They also assist with the catalysis of protein synthesis.
In the prokaryote E. coli, seven copies of the rRNA genes synthesize about 15,000 ribosomes per cell.
In eukaryotes the numbers are much larger. Anywhere from 50 to 5,000 sets of rRNA genes and as
many as 10 million ribosomes may be present in a single cell.
n eukaryotes these rRNA genes are looped out of the main chromosomal fibres and coalesce in the
presence of proteins to form an organelle called the nucleolus. The nucleolus is where the rRNA genes
are transcribed and the early assembly of ribosomes takes place.
rRNAs are found in the ribosomes and account for 80% of the total RNA present in the cell. Ribosomes
are composed of a large subunit called the 50S and a small subunit called the 30S, each of which is
made up of its own specific rRNA molecules.

Different rRNAs present in the ribosomes include small rRNAs and large rRNAs, which belong to the
small and large subunits of the ribosome, respectively.
Transcription
•This stage of protein synthesis occurs in the nucleus of the cell
•Part of a DNA molecule unwinds (the hydrogen bonds between the complementary base
pairs break)
•This exposes the gene to be transcribed (the gene from which a particular polypeptide will be
produced)
•A complimentary copy of the code from the gene is made by building a single-stranded nucleic
acid molecule known as mRNA (messenger RNA)
•Free activated RNA nucleotides pair up (via hydrogen bonds) with their complementary (now
exposed) bases on one strand (the template strand) of the ‘unzipped’ DNA molecule
•The sugar-phosphate groups of these RNA nucleotides are then bonded together by the
enzyme RNA polymerase to form the sugar-phosphate backbone of the mRNA molecule
•When the gene has been transcribed (when the mRNA molecule is complete), the hydrogen
bonds between the mRNA and DNA strands break and the double-stranded DNA molecule re-
Template and non-template strands
•In the transcription stage of protein synthesis, the section of the DNA molecule
where the gene is located (the gene coding for a particular polypeptide) unwinds – the
hydrogen bonds between the complementary base pairs break, causing the two DNA
strands to ‘unzip’
•Free activated RNA nucleotides then pair up with the exposed bases on the DNA
molecule but only with those bases on one strand of the DNA molecule
•This strand of the DNA molecule is called the template strand or the transcribed
strand
•This is the strand that is transcribed to form the mRNA molecule (RNA polymerase
binds the RNA nucleotides together to create the sugar-phosphate backbone of the
mRNA molecule)
NOTE:Be careful – DNA polymerase is the enzyme involved in DNA replication;

RNA polymerase is the enzyme involved in transcription – don’t get these

confused.

Note the use of sense and anti-sense strands in transcription has been replaced

with non-transcribed and transcribed (or template) strands respectively.

The mRNA codons have the same base sequence as the non-transcribed strand,

and the tRNA anticodons have the same base sequence as the transcribed

strand except RNA, which has the base Uracil, replacing Thymine.
Eukaryotic Transcription
•The genome within eukaryotic cells contains many non-coding sections
•Non-coding DNA can be found:
• Between genes, as non-coding multiple repeats
• Within genes, as introns
•During transcription, eukaryotic cells transcribe the whole gene (all introns and exons) to produce pre-
mRNA molecules
• pre-mRNA contains the introns and exons of a certain gene
•Before the pre-mRNA exits the nucleus, splicing occurs:
• The non-coding sections are removed
• The coding sections are joined together
• The resulting mRNA molecule carries only the coding sequences (exons) of the gene
• mRNA contains only exons and exits the nucleus before joining a ribosome for translation
Alternative splicing
•The exons (coding regions) of genes can be spliced in many different ways to produce different mature
mRNA molecules through alternative splicing
•This means that a single eukaryotic gene can code for more than one polypeptide chain
•This is part of the reason why the proteome is much bigger than the genome

IMAGE SHOWING THE

ALTERNATIVE SPLICING OF

A GENE TO PRODUCE TWO

DIFFERENT PROTEINS
Translation

•Translation occurs in the cytoplasm of the cell

•After leaving the nucleus via a nuclear pore, the mRNA molecule attaches to a ribosome

•In the cytoplasm, there are free molecules of tRNA (transfer RNA)

•These tRNA molecules have a triplet of unpaired bases at one end (known as the anticodon) and a

region where a specific amino acid can attach at the other

• There are about 20 different tRNA molecules, each with a specific anticodon and specific amino

acid binding site

•The tRNA molecules bind with their specific amino acids (also in the cytoplasm) and bring them to

the mRNA molecule on the ribosome

•The triplet of bases (anticodon) on each tRNA molecule pairs with a complementary triplet

(codon) on the mRNA molecule

•Two tRNA molecules fit onto the ribosome at any one time, bringing the amino acid they

are each carrying side by side

•A peptide bond is then formed (via a condensation reaction) between the two amino acids

•This process continues until a ‘stop’ codon on the mRNA molecule is reached – this acts as

a signal for translation to stop and at this point the amino acid chain coded for by the mRNA

molecule is complete

•The amino acid chain then forms the final polypeptide

NOTE: Make sure you learn both stages of protein synthesis
fully. Don’t forget – transcription occurs in the nucleus but
translation occurs in the cytoplasm! you learn both stages of
protein synthesis fully.

Be careful – DNA polymerase is the enzyme involved in DNA

replication; RNA polymerase is the enzyme involved in
transcription – don’t get these confused.
Ribosomes
•Ribosomes are small organelles that are either free in the cytoplasm (of all
cells) or are attached to the rough endoplasmic reticulum (only in eukaryotic
cells)
•Ribosomes are the site of protein synthesis (where proteins are made)
• They ‘read’ RNA to make polypeptides (proteins) in a process known
as translation
•Ribosomes are themselves formed from RNA and proteins
• The RNA that forms part of the structure of ribosomes is a specific type of
RNA known as ribosomal RNA (rRNA)
• The rRNA in ribosomes has enzymatic properties that catalyse the
formation of peptide bonds between amino acids
•Ribosomes in eukaryotic cells are larger than those in prokaryotic cells. In both cell
types, ribosomes are composed of a small subunit and a large subunit
• 80S ribosomes (composed of 60S and 40S subunits) are found in eukaryotic
cells
• 70S ribosomes (composed of 50S and 30S subunits) are found in prokaryotic
cells, as well as in the mitochondria and chloroplasts of eukaryotic cells
•The large subunit is the site of translation
• The rRNA and proteins of the large subunit hold tRNA molecules (with their
attached amino acids) in place
• rRNA can then catalyse the condensation reactions between amino acids
•mRNA sits between the two subunits and the ribosome moves along it as it
translates it into a polypeptide
•Unlike some organelles, ribosomes are not surrounded by a membrane
A DIAGRAM OF A RIBOSOME, SHOWING THE SMALL AND LARGE SUBUNITS
r
Relating Nucleic Acid & Amino Acid Sequences

•A triplet is a sequence of three DNA bases that codes for a specific amino acid
•A codon is a sequence of three mRNA bases that codes for a specific amino acid
•A codon is transcribed from the triplet and is complementary to it
•An anticodon is a sequence of three tRNA bases that are complementary to a codon
•When comparing the genetic code to amino acid sequences, mRNA codons are often used
•The four bases found in RNA molecules (adenine, uracil, cytosine and guanine) have the ability to
form 64 different codons
•The genetic code is degenerate
• Multiple mRNA codons can encode the same amino acid
• This means that a change in the genetic code doesn’t necessarily result in a change in the
amino acid sequence
• UGU and UGC both code for the amino acid cysteine
•Some send important signals to the transcription machinery
• The START codon initiates the process of transcription and ensure it starts in the
right location (this is always the amino acid methionine in eukaryotic cells, coded for
by the codon AUG)
• STOP codons cause transcription to terminate and do not code for an amino acid
e.g. UAA
•The genetic code is non-overlapping
• Each base is only read once in the codon it is part of
•The number of amino acids in a protein can be calculated using the number of coding
nucleotides in the mRNA molecule and vice versa:
• When given the number of coding mRNA nucleotides, divide by 3 and minus one
(for the stop codon – it is best to state this in your answer too)
• When given the number of amino acids, multiply by 3 and add three (for the stop
NOTE:

In the exam, you may be asked to predict the effect of specific mutations in the

genetic code. Remember that the genetic code is degenerate and non-overlapping! Also

if stop and start codons are inserted into a coding sequence they can have major

effects.

You will not be required to memorise specific codons and the amino acids for which

they code.
 MODFICATION IN ER
SIGNAL SEQUENCE IS CLEAVED AND POLYPEPTIDE IS CORRECTLY FOLDED TO GET SECONDARY AND
TERTIARY STRUCTURES….
PROTEIN TRAFFICKING AS VESICULAR TRANSPORT………
BEYOND ER….
GLYCOSYLATION TAKES PLACE IN GOLGI APPARATUS AS IT MATURES
FROM GOLGI…