NUCLEIC ACIDS

INTRODUCTION 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 part of
● Nucleic acids: molecules in the cells
responsibilities for each capability
● Transmission of hereditary information takes
place in the nucleus, specifically in the
chromosomes
● Genes where hereditary information resides
within the chromosomes
● Chemical analysis of nuclei showed
chromosomes are made up of largely amount SUGARS
of proteins called histones and nucleic acids

Friedrich Miescher (1869)

● Isolated what he called nuclein from the nuclei
of pus cells
● Nuclein was shown to have acidic properties ->
called Nucleic acids
RNA contains:
NUCLEIC ACIDS ● D-Ribose sugar
DNA contains:
● Backbone of chromosomes
● 2-Deoxy-D-Ribose sugar (without O on C2)
● Contains RNA (Ribonucleic acids) and DNA
(Deoxyribonucleic acids) = unbranched
NUCLEOSIDE
polymers (monomers: nucleotides)
Base + Sugar → Nucleoside
DNA
● Stores the genetic information of an organism
● When a N atom of the base forms a glycosidic
● Transmits the information from one generation
bond to C1 (anomeric C) of a sugar
to another
RNA
● Translates genetic information in the DNA into
proteins needed for all cellular function

NUCLEOTIDES

PRIMARY STRUCTURE (DNA & RNA)

● Nucleoside = Base + Sugar

● Nucleotide = Base + Sugar
+ Phosphate
● Nucleic Acid = Chain of
nucleotides
Composed of:
● Nitrogen-containing bases (Amines) Base sequence is read from the
● Sugars (monosaccharides) C5’ (free phosphate) end to the
● Phosphate C3’ (free hydroxyl) end – ACGU –
 SECONDARY STRUCTURE (DNA & RNA) ● Chromatin Fibers are organized into loops →
provide superstructure of chromosomes
● DNA model was
proposed by Watson CHROMOSOME & GENE
and Crick in 1953
● Two strands of ● DNA molecules contain several million
polynucleotide form a nucleotides, while RNA molecules have a few
double helix structure thousand
like a spiral ● DNA is contained in the chromosomes of the
● Hydrogen bonds link nucleus, each having a different type of DNA
paired bases: ● Humans have 46 chromosomes (23 pairs),
○ Adenine – Thymine each made up of many genes
(A–T) ● A gene is the portion of the DNA molecule
○ Guanine – Cytosine responsible for the synthesis of a single protein
(G–C) (1000 to 2000 nucleotides)
● Sugar-Phosphate backbone is hydrophilic and
stays on the outside (bases → hydrophobic) DIFFERENCES OF DNA & RNA
● Purine base always hydrogen bonds with a
pyrimidine 1. Bases
a. DNA = A, G, C, and T
COMPLEMENTARY BASE PAIRS b. RNA = A, G, C, and U
2. Sugar
a. DNA = 2-deoxy-D-ribose
b. RNA = D-ribose
3. Strands
a. DNA =double-stranded (helical structure)
b. RNA = single strand
4. RNA is much smaller than DNA

RNA MOLECULES
Transmits genetic information needed for cell
operation
HIGHER STRUCTURE (DNA & RNA)
1. Ribosomal RNA (rRNA)
● Most abundant RNA
● Found in ribosomes → site for protein
synthesis
2. Messenger RNA (mRNA)
● Carries genetic information from DNA
(nucleus) to ribosomes (cytoplasm) for
protein synthesis
● DNA is coiled around proteins → histones ● Produced in “Transcription” from DNA
○ Rich in the basic amino acids 3. Transfer RNA (tRNA)
● Acidic DNA basic histones attract each other ● Smallest RNA
and form a chain of nucleosomes ● Translates genetic information (mRNA)
● Brings specific amino acids to the ribosomes
for protein synthesis

FUNCTIONS OF DNA

1. Reproduces itself when a cell divides

(Replication)
2. Supplies information to make up RNA,
Proteins, and Enzymes
● Chromatin: condensed nucleosomes

REPLICATION

● Separation of two original strands

 ● Synthesis of two new daughter strands using
the original strands as templates (breaking
H-bonds)
CHARACTERISTICS
● Replication is bidirectional: takes place at the
same speed in both directions
● Replication is semi-conservative: each
daughter molecule has one parental strand
and newly synthesized one
● Occurs at many places simultaneously along
the helix
PROTEIN SYNTHESIS
Gene Expression: activation of a gene to produce a
specific protein
● Only a small fraction (1-2%) of the DNA in a
chromosome contains genes
Base sequence of the gene carries the information
to produce one protein molecule
Change of sequence → New protein
GENE EXPRESSION

Origin of replication: specific point of DNA where 1. Transcription → synthesis of mRNA

replication begins ● Gene information is copied in DNA to make
Replication fork: specific point of DNA where mRNA
replication is proceeding ● Begins when the section of DNA that
contains the gene to be copied unwinds
● Polymerase enzyme identifies a starting
point to begin mRNA synthesis
● Proceeds from the 3’ end to the 5’ end of the
template

Leading Strand: synthesized continuously in the 5’ →

● When mRNA is released, the double helix
3’ direction towards the replication fork
of the DNA re-forms
Lagging Strand: synthesized discontinuously in the
5’ → 3’ direction away from the replication fork
DNA splits into two strands:
a. Template strand: used to synthesize RNA
REPLISOMES
Assemblies of “enzyme factories” b. Coding strand (Informational strand): not
used to synthesize RNA
1. Helicases → unwinds the DNA double helix
● Replication of DNA starts with unwinding of C is paired with G, T pairs with A, but A pairs with U
the double helix
● Polymerase enzyme moves along the unwound
● Unwinding can occur at either end or in the
DNA, forming bonds between the bases
middle
● Attaches themselves to one DNA strand and
causes separation of the double helix
2. Primases → catalyzes the synthesis of primers
● Primers: short nucleotides (4 to 15)
● Required to start the synthesis of both
daughter strands
Sample Problem
● Placed at about every 50 nucleotides in the
● Write out the mRNA and informational strand
lagging strand synthesis
of the DNA sequence:
3. DNA Polymerase → catalyzes the formation of the
Example strand: 3’ – C T A G G A T A C – 5’
new strands
mRNA: 5’ – G A U C C U A U G – 3’
● Joins the nucleoside triphosphates found in
Information strand: 5’ – G A T C C T A T G – 3’
the nucleus
● A new phosphodiester bond is formed
between the 5’-phosphate of the nucleoside
triphosphate and the 3’-OH group of the new
DNA strand
4. Ligase → joined by ligase enzyme in forming lagging
strand
2. Gene Expression
● Overall functions of RNA: facilitate the task
of synthesizing protein
3. Genetic Code → language that relates the
series of nucleotides in the mRNA to the
specified amino acids
● 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 specified to a
particular amino acid and is present for all
20 amino acids
● 64 Codons are possible from the triplet
combination of A, G, C, and U
● Written from the 5’ end to the 3’ end of the
mRNA molecule
● Stop Signals: UAA, UAG, UGA (code for
termination of protein synthesis)
CODON AUG
● Signals the start of the protein synthesis
(beginning of mRNA)
● Specifies the amino acid Methionine (Met)
(middle of mRNA)
tRNA (transfer RNA)
● Translates codons into specific amino acids
● Contains 70-90 nucleotides
● 3’ end → acceptor stem; always has ACC
and a free OH group - binds a specific
amino acid
● Anticodon: sequence of 3 nucleotides at
the bottom of tRNA
○ Complementary to three bases in an
mRNA and can identify the needed
amino acid
4. Translation
Three Stages
1. Initiation → mRNA binds to the ribosome
2. Elongation → next tRNA molecule deliverers
the next amino acid, peptide bond forms
between the two amino acids
3. Termination → continues until a stop codon
is reached and the completed protein is
released
4. First amino acid (Met) is not often needed
and is removed after protein synthesis is
done
5. Protein Synthesis
● mRNA attaches to a smaller subunit of a
ribosome
● tRNA molecules bring specific amino acids
to the mRNA
● Peptide bonds form between an amino
acid and at the end of the growing peptide
chain
● Ribosomes move along the mRNA until the
end of the codon (translocation)
● 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
6. Termination
● Ribosomes encounter a stop codon: UAA,
UAG, UGA
● No tRNA to complement the termination
codon
● An enzyme releases the complete
polypeptide chain from the ribosome
● Amino acids form 3D structure (active
protein)
7. Mutation
Effect of Mutation:
a. Somatic cell (nonreproductive cell): altered
DNA will be limited to that cell and its
daughter cells → Cancer
 b. Germ cell (reproductive cell): all new DNA
will contain the same default and is passed
on to the next generation → Genetic diseases
Types of Mutation:
a. Point (Substitution) Mutation → most
common
b. Frameshift Mutation
i. Deletion Mutation – occurs when one
or more nucleotides is/are lost from a
DNA molecule
ii. Insertion Mutation – occurs when one
or more nucleotides is/are added to a
DNA molecule
c. Silent Mutation – has a negligible effect to
the organism, because the resulting amino
acid is identical
RECOMBINANT DNA
● Synthetic DNA; contains segments from more
than one source
Three Key Elements:
1. A DNA molecule into which a new DNA
segment will be inserted
2. An enzyme that cleaves DNA at specific
locations
3. A gene from a second organism that will be
inserted into the original DNA molecule
POLYMERASE CHAIN REACTION (PCR)
● Amplifies a specific portion of a DNA
molecule, producing millions of exact copies
Four Elements:
1. The segment of DNA that must be copied
2. Two primers – short polynucleotides that are
complementary to the two ends of the
segment to be amplified
3. A DNA polymerase enzyme catalyzes the
synthesis of a complementary strand
4. Nucleoside triphosphates – the source of the
A, T, C, and G needed to make the new DNA
DNA FINGERPRINTING
● DNA of each individual = unique; used as a
method of identification
● Any type of cell (skin, saliva, semen, blood,
etc.) can be used to obtain a DNA fingerprint
● PCR first amplifies the DNA, and then cut into
fragments by restrictions enzymes
● DNA fragments are then separated by size by
gel electrophoresis
DNA fragments can be visualized on X-ray film after
they have been separated:
VIRUS
● Infectious agent consisting of a DNA or RNA
molecule contained with a protein coating
● Incapable of replicating alone (no enzyme, no
free nucleotide), so it invades a host organism
and makes the host replicate the virus
● Many prevalent diseases like the common
cold, influenza, and herpes are viral in origin
RETROVIRUS → virus with an RNA core
● Invades a host and then synthesizes the
viral DNA by reverse transcription
● The viral DNA can then transcribe RNA,
which directs protein synthesis (new
retroviral particles to infect other cells)
● AIDS (Acquired Immune Deficiency
Syndrome) is caused by the retrovirus HIV
(Human Immunodeficiency Virus)
ANTIBODY-DEPENDENT ENHANCEMENT (ADE)
and VACCINES
● Immune responses to pathogens involve
many cells and proteins of the immune
system
● Early during an infection, these responses
are non-specific - directed at the pathogen,
but not specific to it - Innate Immunity
● Within a few days, adaptive immunity takes
over; this immunity is specific to the
invading pathogen
● Adaptive immune responses include
antibodies. A major goal of antibodies is to
bind to the pathogen and prevent it from
infecting, or entering, a cell.
● Antibodies that prevent entry into cells are
called neutralizing antibodies. Many
vaccines work by inducing neutralizing
antibodies