Nucleic Acids Bases

 Living cells are capable of producing exact replicas of

themselves
 Cells contain all the instructions needed for making
the complete organism of which they are a part.
 The molecules within the cell that are responsible for
these amazing capabilities are nucleic acids

Friedrich Miescher in 1869

 Isolated what he called nuclein from the nuclei of
pus cells
 Nuclein was shown to have acidic properties, hence
it became called nucleic acid

Nucleic Acids
 Each cell of our bodies contains thousands of
different proteins. Sugars (Monosaccharide)
 How do cells know which proteins to synthesize out RNA contains:
of the extremely large number of possible amino  D-Ribose sugar
acid sequences? DNA contains:
 the transmission of hereditary information took  2-Deoxy-D-Ribose sugar (without O on carbon 2)
place in the nucleus, more specifically in structures
called chromosomes. Nucleoside
 The hereditary information was thought to reside in When a N atom of the base forms a glycosidic bond to C1’
genes within the chromosomes. (anomeric C) of a sugar.
 Chemical analysis of nuclei showed chromosomes
are made up largely of proteins called histones and
nucleic acids.

DNA - stores the genetic information of an organism and

transmits that information from one generation to another.
RNA - translates the genetic information contained in DNA
into proteins needed for all cellular function.
RNA and DNA are unbranched polymers (monomers:
nucleotides).

Nucleotides
A nucleotide is composed of:
 Nitrogen-containing bases (amines)
 Sugars (monosaccharides)
 Phosphate
Primary structure of DNA and RNA Primary structure of DNA and RNA
Polynucleotide A nucleoside = Base + Sugar
A nucleotide = Base + Sugar + Phosphate
A nucleic acid = A chain of nucleotides
 Like amino acids (C-terminal and N-terminal):
Base sequence is read from the C5’ (free phosphate) end to
the C3’ (free hydroxyl) end.

Secondary structure of DNA

 The DNA model is proposed by Watson and Crick in
1953.
 Two strands of polynucleotide form a double helix
structure like a spiral.
 Hydrogen bonds link paired bases:
Adenine-Thymine (A–T)
Guanine-Cytosine (G-C)
 Sugar-Phosphate backbone is hydrophilic and stays
on the outside (bases are hydrophobic).

Sequence of nucleotides.
A Purine base always hydrogen bonds with a pyrimidine.
Each phosphate is linked to C3’ and C5’ of two sugars.

Complementary base pairs

 Chromosome & Gene
 DNA molecules contain several million nucleotides, while
RNA molecules have only a few thousand.
Higher structure of DNA
 DNA is contained in the chromosomes of the nucleus,
 DNA is coiled around proteins called histones.
each chromosome having a different type of DNA.
 Histones are rich in the basic amino acids
 Humans have 46 chromosomes (23 pairs), each made up
 Acidic DNA basic histones attract each other and
of many genes.
form a chain of nucleosomes.
 A gene is the portion of the DNA molecule responsible for
the synthesis of a single protein (1000 to 2000
nucleotides).

Difference between DNA & RNA

DNA has four bases: A, G, C, and T.
RNA has four bases: A, G, C, and U.

In DNA: Sugar is -deoxy-D-ribose.

In RNA: Sugar is D-ribose.

DNA is almost always double-stranded (helical structure).

RNA is single strand.

RNA is much smaller than DNA.

RNA molecules
Transmits the genetic information needed to operate the cell.
1. Ribosomal RNA (rRNA)
Most abundant RNA – is found in ribosomes: sites for protein
synthesis.
2. Messenger RNA (mRNA)
Carries genetic information from DNA (in nucleus) to
ribosomes (in cytoplasm) for protein synthesis. They are
produced in “Transcription” from DNA.
3. Transfer RNA (tRNA)
The smallest RNA. Translates the genetic information in mRNA
and brings specific
Amino acids to the ribosome for protein synthesis.

Functions of DNA
1. It reproduces itself when a cell divides (Replication).
2. It supplied the information to make up RNA, proteins, and
enzymes.
Replication Primases
Separation of the two original strands and synthesis Catalyze the synthesis of primers.
of two new daughter strands using the original strands as  Primers: are short nucleotides (4 to 15).
templates. (By breaking H-bonds)  They are required to start the synthesis of both
daughter strands.
 Primases are placed at about every 50 nucleotides in
the lagging strand synthesis.

DNA Polymerase
It catalyzes the formation of the new strands.
 It joins the nucleoside triphosphates found in the
Leading strand: is synthesized continuously in the 5’ → 3’ nucleus.
direction toward the replication fork.  A new phosphodiester bond is formed between the
5’-phosphate of the nucleoside triphosphate and the
Lagging strand: is synthesized discontinuously in the 5’ → 3’ 3’-OH group of the new DNA strand.
direction away from the replication fork.

Replication is bidirectional: takes place at the same speed in

both directions.

Replication is semiconservative: each daughter molecule has

one parental strand and one newly synthesized one.

Origin of replication: specific point of DNA where replication

begins.

Replication fork: specific point of DNA where replication is

proceeding.

Replication occurs at many places simultaneously along the Ligase

helix. In formation of lagging strand, small fragments (Okazaki) are
join together by ligase enzyme.

Replisomes: assemblies of “enzyme factories”. Protein Synthesis

 Gene expression: activation of a gene to produce a
Helicases specific protein.
Unwinds the DNA double helix.  Only a small fraction (1-2%) of the DNA in a
 Replication of DNA starts with unwinding of the chromosome contains genes.
double helix.  Base sequence of the gene carries the information
 Unwinding can occur at either end or in the middle.  to produce one protein molecule.
 Attach themselves to one DNA strand and cause Change of Sequence –> New Protein
separation of the double helix.

Gene expression
Transcription: synthesis of mRNA (messenger RNA)

Transcription
 Genetic information is copied from a gene in DNA to
make a mRNA.
 Begins when the section of a DNA that contains the
gene to be copied unwinds.
Gene expression
 Polymerase enzyme identifies a starting point to
Overall function of RNAs in the cell: facilitate the task of
begin mRNA synthesis.
synthesizing protein.

The DNA splits into two strands:

 Template strand: it is used to synthesize RNA.
 Coding Strand (Informational strand): it is not used to Genetic code
synthesize RNA. Genetic code: language that relates the series of nucleotides
Transcription proceeds from the 3’ end to the 5’ end of the in mRNA to the amino acids specified.
template.  The sequence of nucleotides in the mRNA
determines the amino acid order for the protein.
 Every three bases (triplet) along the mRNA makes up
a codon.
 Each codon specifies a particular amino acid.
 Codons are present for all 20 amino acids.
When mRNA is released, the double helix of the DNA re-
forms.

Polymerase enzyme moves along the unwound DNA,

forming bonds between the bases.

C is paired with G
T pairs with A
A pairs with U (not T)

Translation
Genetic code Termination
Ribosome encounters a stop condon.
 64 codons are possible from the triplet combination
of A, G, C, and U.
 UGA, UAA, and UAG, are stop signals.
(code for termination of protein synthesis).
 Codons are written from the 5’ end to the 3’ end of
the mRNA molecule

AUG has two roles:

1. Signals the start of the protein’s synthesis (at the beginning
of an mRNA).
2. Specifies the amino acid methionine (Met) (in the middle of
an mRNA).

tRNA (transfer RNA)

 No tRNA to complement the termination codon.
tRNA translates the codons into specific amino acids.
 An enzyme releases the complete polypeptide chain
 It contains 70-90 nucleotides.
from the ribosome.
 The 3’ end, called the acceptor stem and always has
 Amino acids form the three-dimensional structure
the nucleotide ACC and a free OH group that binds a
(active protein).
specific amino acid.
 Anticodon: a sequence of three nucleotides at the
bottom of tRNA, which is complementary to three
bases in an mRNA and it can identify the needed
amino acid.

Protein synthesis
 mRNA attaches to smaller subunit of a ribosome.
 tRNA molecules bring specific amino acids to the
mRNA.
 Peptide bonds form between an amino acid and the
end of the growing peptide chain.
 The ribosome moves along mRNA until the end of
the codon (translocation).
 The polypeptide chain is released from the ribosome
and becomes an active protein.
Sometimes several ribosomes (polysome) translate the same
strand of mRNA at the same time to produce several peptide
chains.
Translation Mutation
There are 3 stages in translation:  A heritable change in DNA nucleotide sequence.
 It changes the sequence of amino acids (structure
and function of proteins).
 Enzyme cannot catalyze.
 X rays, Overexpose to sun (UV light), Chemicals
(mutagens), or Viruses however, some mutations are
random events.

Effect of Mutation

1. Initiation begins with mRNA binding to the ribosome.

Types of Mutations

Point Mutation
2. Elongation proceeds as the next tRNA molecule delivers the
next amino acid, and a peptide bond forms between the two
amino acids.

3. Termination: Translation continues until a stop codon (UAA,

UAG, or UGA) is reached and the completed protein is
released.

Often the first amino acid (methionine) is not needed

and it is removed after protein synthesis is complete.
Frameshift Mutation

Silent Mutation

Recombinant DNA Polymerase Chain Reaction (PCR)

HOW TO Use the Polymerase Chain Reaction to
Amplify a Sample of DNA

Viruses

DNA Fingerprinting
 What is ADE?
ADE occurs when the antibodies generated during an immune
response recognize and bind to a pathogen, but they are
unable to prevent infection. Instead, these antibodies act as a
“Trojan horse,” allowing the pathogen to get into cells and
exacerbate the immune response.

Importantly, when a vaccinated person subsequently gets

infected, this is not automatically evidence of ADE.
Specifically, if a vaccinated person gets infected with the
pathogen against which the vaccine protects, three different
scenarios can occur:

1. Mild illness – In this scenario, the person

may experience some symptoms, but they
Antibody-dependent Enhancement (ADE) and Vaccines
are more of an inconvenience and last only
Immune responses to pathogens involve many cells and
a few days (typically about 1-3 days). For
proteins of the immune system. Early during an infection,
many respiratory and gastrointestinal
these responses are non-specific, meaning that although they
infections (e.g., influenza, COVID-19, and
are directed at the pathogen, they are not specific to it. This is
rotavirus), this is common. These mild
called innate immunity.
symptoms are evidence that the vaccine
worked.
Within a few days, adaptive immunity takes over; this
immunity is specific to the invading pathogen.
2. “Breakthrough illness” – Traditionally, this
Adaptive immune responses include antibodies. A major goal
term has been reserved for vaccinated
of antibodies is to bind to the pathogen and prevent it from
people who get more severely ill, requiring
infecting, or entering, a cell.
hospitalization or experiencing untoward
outcomes, such as disease complications
Antibodies that prevent entry into cells are called neutralizing
(e.g., pneumonia) or death. In this case, the
antibodies. Many vaccines work by inducing neutralizing
vaccine may not have worked at all or it did
antibodies.
not induce high enough levels of immunity
to effectively stop an infection.
However, not all antibody responses are created equal.
Sometimes antibodies do not prevent cell entry and, on rare
ADE – In this scenario, the antibodies that the vaccine
occasions, they may actually increase the ability of a virus to
generated actually help the virus infect greater numbers of
enter cells and cause a worsening of disease through a
cells than it would have on its own. In this situation, the
mechanism called antibody-dependent enhancement (ADE).
antibodies bind to the virus and help it more easily get into
cells than it would on its own. The result is often more severe
illness than if the person had been unvaccinated.

ADE can occur after disease and has on occasion been

identified following vaccination, as described below. Any
vaccine that has been found to cause ADE has stopped being
used or, more recently for dengue vaccine, been
recommended only for those who will not be affected by ADE.
Evidence of ADE has not emerged for COVID-19 vaccines even
though concerns have been raised.