NUCLEIC ACID
Prepared by: Prof. Nancy D. Buzon
General Education.
NUCLEIC ACIDS
Two Types of Nucleic Acids:
• DNA: Deoxyribonucleic Acid: found within cell nucleus
• Storage and transfer of genetic information
• Passed from one cell to other during cell division
• RNA: Ribonucleic Acid: occurs in all parts of cell
• Primary function is to synthesize the proteins
Nucleic Acids: are polymers in which
repeating unit is nucleotide.
• A Nucleotide has three components:
• Pentose Sugar: Monosaccharide
• Phosphate Group (PO43-)
• Heterocyclic Base
Components of a Nucleotide
Base
Phosphate Sugar
Pentose – 5 C sugar
C5
C4 C1
C3 C2
Pentose Sugar
• Ribose is present in RNA and 2-deoxyribose is
present in DNA
• Structural difference:
—OH group present on carbon 2’ in ribose
—H atom on C 2 in 2-deoxyribose
• RNA and DNA differ in the identity of the sugar
unit in their nucleotides.
Ribose vs. deoxyribose
Nitrogen-Containing Heterocyclic Bases
• There are a total five bases (four of them in
most of DNA and RNAs)
• Three pyrimidine derivatives - thymine (T),
cytosine (C), and uracil (U)
• Two purine derivatives - adenine (A) and
guanine (G)
• Adenine (A), guanine (G), and cytosine (C) are
found in both DNA and RNA.
• Uracil : found only in RNA
• Thymine : found only in DNA.
Stability of purine & pyrimidine bases
• Bases are derivative s of heteroaromatic rings.
• Purine & pyrimidine rings are planar.
• Delocalization of pi electrons in each ring imparts conjugative stability
or aromaticity to the structure.
• Applying 4n + 2 rule of aromaticity, n=whole number.
• 10 electrons are delocalized in the purine ring while 6 electrons in the
pyrimidine ring.
• Rings cannot be readily cleaved.
Purine and Pyrimidine Bases
Phosphate
• Phosphate - third component of a
nucleotide, is derived from phosphoric
acid (H3PO4)
• Under cellular pH conditions, the
phosphoric acid is fully dissociated to
give a hydrogen phosphate ion (HPO42-)
Nucleoside in DNA
Base Sugar Nucleoside
Adenine (A) Deoxyribose deoxyAdenosine
Guanine (G) Deoxyribose deoxyGuanosine
Cytosine (C) Deoxyribose deoxyCytidine
Thymine (T) Deoxyribose deoxythymidine
Nucleosides in RNA
Base Sugar Nucleoside
Adenine (A) ribose Adenosine
Guanine (G) ribose Guanosine
Cytosine (C) ribose Cytidine
Uracil (U) ribose Uridine
Nucleotide Formation
• The formation of a nucleotide from sugar, base,
and phosphate is visualized below.
• Phosphate attached to C-5’ and base is attached to
C-1’ position of pentose
AMP, ADP, ATP
Nucleotide Nomenclature
Give the name and abbreviation for the following and list its nitrogen base and
sugar
Solution
Guanosine 5’-monophosphate (GMP)
nitrogen base: guanine
sugar: ribose
Sugar-phosphate groups are referred to
as nucleic acid backbone -Found in all
nucleic acids
Sugars are different in DNA and RNA
Primary Structure
• A ribonucleic acid (RNA) is a nucleotide polymer
in which each of the monomers contains ribose,
a phosphate group, and one of the heterocyclic
bases adenine, cytosine, guanine, or uracil
• A deoxyribonucleic acid (DNA) is a nucleotide
polymer in which each of the monomers
contains deoxyribose, a phosphate group, and
one of the heterocyclic bases adenine, cytosine,
guanine, or thymine.
Primary Structure of Nucleic Acids
• The primary structure of a nucleic acid is the nucleotide
sequence
• The nucleotides in nucleic acids are joined by phosphodiester
bonds
• The 3’-OH group of the sugar in one nucleotide forms an ester
bond to the phosphate group on the 5’-carbon of the sugar of
the next nucleotide
Reading Primary Structure
• A nucleic acid polymer has a free
5’-phosphate group at one end and
a free 3’-OH group at the other
end
• The sequence is read from the free
5’-end using the letters of the
bases
• This example reads
5’—A—C—G—T—3’-OH
Example of RNA Primary Structure
• In RNA, A, C, G, and U are linked by 3’-5’ ester bonds
between ribose and phosphate
Primary Structure of RNA
The primary structure
of RNA,
• is a single strand of nucleotides
with bases A, C, G, and U.
• is linked by phosphodiester
bonds between ribose and
phosphate.
Example of DNA Primary
Structure
• In DNA, A, C, G, and T are linked by 3’-5’ ester bonds
between deoxyribose and phosphate
Secondary Structure of DNA
Double Helix
bases
sugar-
phosphate
chain
DNA is a double-stranded helix
• James Watson and Francis Crick worked out the three-dimensional
structure of DNA, based on work by Rosalind Franklin
Secondary Structure: DNA Double Helix
• In DNA there are two strands of nucleotides that wind together in a double helix
- a helix structure is like a spiral stair case.
- there are 10 base-pairs per turn of the helix.
- the strands run in opposite directions
- the base pairs are held together by hydrogen bonding
• The pairing of the bases from the two strands is very specific
• The complimentary base pairs are A-T and G-C
- two hydrogen bonds form between A and T
- three hydrogen bonds form between G and C
• Each pair consists of a purine and a pyrimidine, so they are the same width, keeping the two
strands at equal distances from each other
Base Pairing in the DNA Double Helix
PO4
PO4
adenine thymine
PO4
PO4
cytosine guanine
PO4
PO4
PO4
PO4
Double stranded DNA showing 5’
to 3’ and 3’ to 5’ orientation
• Nucleic acids have secondary and tertiary structure
• The secondary structure involves two
polynucleotide chains coiled around each other in a
helical fashion
• The poly nucleotides run anti-parallel (opposite
directions) to each other, i.e., 5’ - 3’ and 3’ - 5’
• The bases are located at the center and hydrogen
bonded (A=T and GΞC)
• Base composition: %A = %T and %C = %G)
• Example: Human DNA contains 30% adenine, ____%
thymine, ____% guanine and _____% cytosine
• DNA Sequence: the sequence of bases on one
polynucleotide is complementary to the other
polynucleotide
• Complementary bases are pairs of bases in a nucleic acid
structure that can hydrogen-bond to each other.
• Complementary DNA strands are strands of DNA in a
double helix with base pairing such that each base is
located opposite its complementary base.
• Example :
• List of bases in sequential order in the direction from the
5’ end to 3’ end of the segment:
• 5’-A-A-G-C-T-A-G-C-T-T-A-C-T-3’
• Complementary strand of this sequence will be:
_______________________________________
Base Pairing
• One small and one large base can fit inside the DNA strands:
• Hydrogen bonding is stronger with A-T and G-C
• A-T and G-C are called complementary bases
Practice Exercise
• Predict the sequence of bases in the DNA strand complementary to
the single DNA strand shown below:
5’ A–A–T–G–C–A–G–C–T 3’
• GENE ----- sentence
• Codon ------ each word
• Letter ------- nucleotide base
• The cat saw the dog
• The bat saw the dog
• The cat saw the hog.
• The cat sat the dog.
RNA
• RNA is much more abundant than DNA
• There are several important differences between RNA and DNA:
- the pentose sugar in RNA is ribose, in DNA it’s deoxyribose
- in RNA, uracil replaces the base thymine (U pairs with A)
- RNA is single stranded while DNA is double stranded
- RNA molecules are much smaller than DNA molecules
• There are three main types of RNA:
- ribosomal (rRNA), messenger (mRNA) and transfer (tRNA)
Types of RNA
Ribosomal RNA and Messenger RNA
• Ribosomes are the sites of protein synthesis
- they consist of ribosomal DNA (65%) and proteins (35%)
- they have two subunits, a large one and a small one
Ri-(rRNA) makes up 2/3 of ribosomes where protein synthesis takes
place.
• Messenger RNA carries the genetic code to the ribosomes
Ribosomal RNA and Messenger RNA
Transfer RNA
• Transfer RNA translates the genetic code from the messenger RNA
and brings specific amino acids to the ribosome for protein synthesis
• Each amino acid is recognized by one or more specific tRNA
• tRNA has a tertiary structure that is L-shaped
- one end attaches to the amino acid and the other binds to the
mRNA by a 3-base complimentary sequence
The Central Dogma of Life
1. DNA to DNA - Duplication/Replication
• Takes place in the nucleus of the cell.
2. DNA to RNA - Transcription
- Takes place in the nucleolus
3. RNA to proteins – Translation
- takes place in the ribosomes
- Use of genetic code.
Exercise
The following section of DNA is used to build mRNA for a protein.
5’—GAA—CCC—TTT—3’-OH
A. What is the corresponding mRNA sequence?
B. What are the anticodons on the tRNAs?
C. What is the amino acid order in the peptide?
Answer
a. 5’- CUU – GGG – AAA - 3’-OH mRNA
b. Anti-codons:
GAA for CUU CCC for GGG UUU for AAA
c. Leu – gly - lys
Genetic Code
The genetic code
-is a sequence of amino acids in a mRNA that determine the amino acid
order for the protein.
• consists of sets of three bases (triplet) along the mRNA called codons.
-has a different codon for all 20 amino acids needed to build a protein.
-contains certain codons that signal the “start” and “end” of a
polypeptide chain.
The Genetic Code: mRNA Codons
Determine the amino acids from the following
codons in a section of mRNA.
1. CCU –
2. AGC-
3. GGA -
4. CUU –
5. AUG –
6. UAA –
7. UAG –
8. UGA -
Thank you for
Listening…
