Nucleic acids

Components of nucleic acids: Adenine, guanine, thymine and Cytosine (Structure only),

other components of nucleic acids, Nucleosides and nucleotides (nomenclature), Structure of

polynucleotides; Structure of DNA (Watson-Crick model) and RNA (types of RNA), Genetic

Code, Biological roles of DNA and RNA: Replication, Transcription and Translation.
 Introduction

• Our traits are all due to the inherited genetic material called genes.

• These genes are segment of giant molecules called DNA (Deoxy ribonucleic acid).

• The other nucleic acid is RNA (Ribonucleic acid).

• In Eukaryotes DNA is present in the form of chromosome, mitochondria and chloroplasts. In Prokaryotes DNA

is largely present in the form of single circular chromosome.

• RNA is distributed through out the eukaryotic cell.

• What are nucleic acids?
• Nucleic acids are polymers of nucleotides.

• What are nucleotides?

• Nucleotides are organic molecules consisting of a nucleoside and a phosphate. Nucleotides contain
carbon ring structures containing nitrogen linked to a 5-carbon sugar (a pentose) and a phosphate
group.

• 5-carbon sugar is either a ribose or a deoxy-ribose making the nucleotide either a ribonucleotide or
a deoxyribonucleotide.

• In the absence of the phosphate group(s), the molecule is called a nucleoside.

• The nitrogenous bases are derivatives of pyrimidine and purine.

Chemical Structure of DNA vs RNA
• Ribonucleotides have a 2’-OH
• Deoxyribonucleotides have a 2’-H
Basic structure of a Nucleotide
Base-Sugar-PO42-
4
3 5N

2 6
O 1
N
5’
O P O C O
O 4’ 1’

3’ 2’

OH

Monophosphate
• Purine and Pyrimidine
• Pyrimidine contains two pyridine-like nitrogens in a six-membered aromatic ring
• Purine has 4 N’s in a fused-ring structure. Three are basic like pyridine-like and one is like that in
pyrrole

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 Major Bases of Nucleic Acids
• Both DNA and RNA contain two major purine bases, adenine (A) and guanine (G).
• Both nucleic acids also contain the pyrimidine base, cytosine (C), and a second pyrimidine base that
is thymine (T) in DNA and uracil (U) in RNA. Only occasionally does thymine occur in RNA or
uracil in DNA.
 Purines

NH2

Adenine N
N
A
N
N
N 6 H
7 5 1N
8
9 4
3
2 O
N N N
NH
G
Guanine N N NH2
H
 Pyrimidines

H3C
Thymine NH
T
N O
4
3 5 N H
2 6 NH2
1
N
N

C
Cytosine N O
H
 Tautomeric Forms of Uracil

• Free pyrimidine and purine bases may exist in two or more tautomeric forms
depending on the pH. Uracil, for example, occurs in lactam, lactim, and double
lactim forms depending on the pH.
• Certain tautomeric forms predominate at neutral pH.
 The Pentoses of Nucleotides
• Nucleotides have two kinds of pentoses. The recurring deoxyribonucleotide units of DNA contain
2’-deoxy-D-ribose, and the ribonucleotide units of RNA contain D-ribose.
• In both types of nucleotides the pentoses exist in their ß-furanose (closed five-membered ring) forms.
• The formation of the ß-D-ribofuranose ring from the straight-chain aldehyde form of D-ribose in solution is
illustrated in the flowing Figure.
• Deoxyribose undergoes a similar interconversion in solution, but in DNA exists solely as
ß-2’-deoxy-D-ribofuranose.
 Phosphate Groups

• Phosphate groups are what makes a nucleoside a nucleotide.

• Phosphate groups are essential for nucleotide polymerization

O P O X

O
 Number of phosphate groups determines nomenclature
O
Monophosphate
O P O CH2
e.g. AMP
O

O O

Diphosphate O P O P O CH2
e.g. ADP
O O

O O O

Triphosphate O P O P O P O CH2
e.g. ATP
O O O
Nomenclature
AMP, ADP and ATP
• Additional phosphate groups can be added to the nucleoside
5’-monophosphates to form diphosphates and triphosphates
• ATP is the major energy source for cellular activity.
 Deoxyribonucleotides of DNA

• The structures and names of the four major deoxyribonucleotides (deoxyribonucleoside 5’-monophosphates)
of DNA are shown below.
• All nucleotides are shown in their free form at pH 7.0. The deoxyribonucleotide units of DNA are usually
symbolized as A, G, T, and C, and sometimes as dA, dG, dT, and dC.
• In their free forms, the deoxyribonucleotides are commonly abbreviated dAMP, dGMP, cTMP, and dCMP.
 Ribonucleotides of RNA
• The structures and names of the four major ribonucleotides (ribonucleoside 5’-monophosphates) of RNA are
shown below.
• All nucleotides are shown in their free form at pH 7.0. The ribonucleotide units of RNA are usually
symbolized as A, G, U, and C.
• In their free forms, the ribonucleotides are commonly abbreviated AMP, GMP, UMP, and CMP.
 Phosphodiester Linkages in the Covalent Backbone of DNA and RNA
• The successive nucleotides in DNA and RNA are covalently linked through
phosphate-group bridges in which the 5’-phosphate of one nucleotide unit is
joined to the 3’-hydroxyl group of the next, creating a phosphodiester linkage.
• Thus, the covalent backbones of nucleic acids consist of alternating phosphate
and pentose residues, and the nitrogenous bases may be regarded as side groups
joined to the backbone at regular intervals.
• The backbones of both DNA and RNA are hydrophilic. The hydroxyl groups of
the sugar residues form hydrogen bonds with water. The phosphate groups, with a
pKa near 0, are completely ionized and negatively charged at pH 7. The negative
charges are generally neutralized by ionic interactions with positive charges on
proteins, metal ions, and polyamines.
• All the phosphodiester linkages in DNA and RNA have the same orientation
along the chain giving each linear nucleic acid strand a specific polarity and
distinct 5’ and 3’ ends. By definition, the 5’ end lacks a nucleotide at the 5’
position and the 3’ end lacks a nucleotide at the 3’ position.
Chargaff's rule:
Chargaff's rules state that DNA from any cell of any organisms should have a 1:1 ratio
(base Pair Rule) of pyrimidine and purine bases and, more specifically, that the amount of
guanine should be equal to cytosine and the amount of adenine should be equal to thymine.
This pattern is found in both strands of the DNA. They were discovered by Austrian born
chemist Erwin Chargaff,
DNA Primary Structure
• In DNA, A, C, G, and T are linked by 3’-5’ ester bonds
between deoxyribose and phosphate
Reference: Lehninger Principles of Biochemistry
 Describing a Sequence
• Chain is described from 5′ end, identifying the bases in order of occurrence,

using the abbreviations A for adenosine, G for guanosine, C for cytidine, and

T for thymine (or U for uracil in RNA)

• A typical sequence is written as TAGGCT

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Properties of a DNA double helix

• The strands of DNA are antiparallel

• The strands are complimentary

• There are Hydrogen bond forces

• There are base stacking interactions

• There are 10 base pairs per turn

 The Double Helix (DNA)
Structural model:
• Model proposed by Watson & Crick, 1953
• Two sugar-phosphate strands, next to each other, but running in
opposite directions.
• Specific Hydrogen bonds occur among bases from one chain to
the other:
A---T , C---G
Due to this specificity, a certain base on one strand indicates a
certain base in the other.
• The 2 strands intertwine, forming a double-helix that winds
around a central axis
Untwisted it • The sides of the ladder are:
looks like this: P = phosphate
S = sugar molecule

• The steps of the ladder are C, G, T, A =

nitrogenous bases
(Nitrogenous means containing the element
nitrogen.)

A = Adenine
T = Thymine
A always pairs with T in DNA

C = Cytosine
G = Guanine
C always pairs with G in DNA
Nucleotide
 Secondary Structure: DNA Double Helix
• In DNA there are two strands of nucleotides that wind together
in a double helix
- the strands run in opposite directions
- the bases are arranged in step-like pairs
- 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
•Model of DNA:
•The model was developed by Watson
and Crick in 1953.

•They received a Nobel prize in 1962

for their work.

•The model looks like a twisted

ladder – double helix.
 17
PO4
PO4 The strands
separate PO4
PO4

PO4 PO4

PO4 PO4

PO4
PO4

PO4
PO4

PO4
PO4

PO4
PO4
 “Base Pairing”

RNA [normally] exists as a single stranded polymer

DNA exists as a double stranded polymer

DNA double strand is created by hydrogen bonds between nucleotides

Nucleotides always bind to complementary nucleotides

A T (2 H-bonds)

G C (3 H-bonds)
Reference: Lehninger Principles of Biochemistry
 Nucleic Acid Structure
Polymerization

P P P P P P
N N
C C
S Phosphodiesterase S

P
+ P P
N
C
(PPi)
S
P P P
N
C
S
Nucleic Acid Structure
The double helix

Minor
Groove

Major
Groove
The Double Helix
• 3.4Å per basepair
• 10 basepairs per turn
• 10-11 in aqueous solution
• 2 anti-parallel strands
https://en.wikipedia.org/wiki/Molecular_models_of_DNA
 Functions of
Nucleotides and Nucleic Acids

• Nucleotide Functions:
• Energy for metabolism (ATP)
• Enzyme cofactors (NAD+)
• Signal transduction (cAMP)

• Nucleic Acid Functions:

• Storage of genetic info (DNA)
• Transmission of genetic info (mRNA)
• Processing of genetic information (ribozymes)
• Protein synthesis (tRNA and rRNA)
 Ribonucleic Acid (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

Type Abbreviation Percentage of total Function in the cell

RNA
Ribosomal RNA rRNA 75 Major component
of the ribosome
Messenger RNA mRNA 5 - 10 Carries information
for protein
synthesis.
Transfer RNA tRNA 10 - 15 Brings amino acids
to the ribosomes
for protein
synthesis.
Messenger RNA (mRNA)
Its sequence is copied from genetic DNA
It travels to ribosomes, small granular particles in the cytoplasm of a cell where protein
synthesis takes place.

Ribosomal RNA (rRNA)

Ribosomes are a complex of proteins and rRNA
The synthesis of proteins from amino acids and ATP occurs in the ribosome
The rRNA provides both structure and catalysis
Transfer RNA (tRNA)

• Transports amino acids to the ribosomes where they are joined

together to make proteins
• There is a specific tRNA for each amino acid
• Recognition of the tRNA at the anti-codon communicates which
amino acid is attached.

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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
https://www.youtube.com/watch?v=aizKUoD-kYk
 Replication

• Before a cell divides, the DNA strands unwind and separate.

• Each strand makes a new partner by adding the appropriate nucleotides.

• The result is that there are now two double-stranded DNA molecules in the

nucleus.

• So that when the cell divides, each nucleus contains identical DNA.

• This process is called replication.

DNA Replication
• Cell division involving mitosis produces 2 daughter cells that are genetically identical to
each other and genetically identical to the parent cell
• Remember that for this to happen, DNA in the parent cell must be replicated (copied) before
the cell divides – this process occurs during Interphase in the cell cycle
 STEP 1

Hydrogen bonds between base pairs

DNA molecule separates into
are broken by the enzyme Helicase complementary halves
and DNA molecule unzips
 STEP 2
Nucleotides match up with
complementary bases

Free nucleotides abundant in nucleus

Mutations occur when copying
errors cause a change in the
sequence of DNA nucleotide
bases
Diagram Examples of DNA Replication:
(You could see DNA replication represented different ways.)
Direction of Replication
• The enzyme helicase unwinds several sections of parent DNA
• At each open DNA section, called a replication fork, DNA polymerase
catalyzes the formation of 5’-3’ester bonds of the leading strand
• The lagging strand, which grows in the 3’-5’ direction, is synthesized in short
sections called Okazaki fragments
• The Okazaki fragments are joined by DNA ligase to give a single 3’-5’ DNA
strand
https://www.youtube.com/watch?v=Qqe4thU-os8
Protein synthesis
 How DNA Works

1- DNA stores genetic information in segments called genes

2- The DNA code is in Triplet Codons (short sequences of 3 nucleotides each)
3- Certain codons are translated by the cell into certain Amino
acids.
4. Thus, the sequence of nucleotides in DNA indicate a sequence of Amino acids in a
protein.
 Protein Synthesis
• Central dogma of biology is often stated as "DNA makes RNA, and RNA makes

protein", although this is not its original meaning.

• The two main processes involved in protein synthesis are

- the formation of mRNA from DNA (transcription)

- the conversion by tRNA to protein at the ribosome (translation)

• Transcription takes place in the nucleus, while translation takes place in the cytoplasm

• Genetic information is transcribed to form mRNA much the same way it is replicated

during cell division

Central Dogma
 Triplet Code: Codons
Universal code: Strong evidence for evolution

3 Nucleotides = 1 amino acid Codon Chart pg. 273

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 Transcription
• DNA mRNA
• Copying of DNA’s
message to mRNA
• Occurs in the nucleus
• Pre-mRNA is processed
into mRNA and then
leaves the nucleus for
the cytoplasm (ribosome)
Transcription Process
• Several turns of the DNA double helix unwind, exposing the bases of
the two strands
• Ribonucleotides line up in the proper order by hydrogen bonding to their
complementary bases on DNA
• Bonds form in the 5′ → 3′ direction,

Based on McMurry, Organic Chemistry, Chapter 28, 6th

58
edition, (c) 2003
Transcription of RNA from DNA

• Only one of the two DNA strands is transcribed into mRNA

• The strand that contains the gene is the coding or sense strand

• The strand that gets transcribed is the template or antisense strand

• The RNA molecule produced during transcription is a copy of the coding strand

(with U in place of T)

59
• Initiation: RNA polymerase binds to DNA at promoter region.

• Promoter is before the gene that is to be transcribed (eukaryotes need transcription factors to help RNA

polymerase bind to the TATA box)

• Determines which strand of DNA to use

• Elongation - adds nucleotides to mRNA strand based on DNA strand in a 5’ 3’ direction (adding only to

the 3’ end).

• Termination – RNA polymerase “falls off” the DNA strand when the termination sequence (terminator) is

reached.

• AAUAAA in eukaryotes, this is now pre-mRNA

RNA Polymerase
• During transcription, RNA polymerase moves along the DNA
template in the 3’-5’direction to synthesize the corresponding mRNA
• The mRNA is released at the termination point
Processing of mRNA

• Genes in the DNA of eukaryotes contain exons that code for

proteins along with introns that do not
• Because the initial mRNA, called a pre-RNA, includes the
noncoding introns, it must be processed before it can be read by
the tRNA
• While the mRNA is still in the nucleus, the introns are removed
from the pre-RNA
• The exons that remain are joined to form the mRNA that leaves
the nucleus with the information for the synthesis of protein.
 Translation

• mRNA protein
• Process of mRNA
converting to a protein
• Occurs in the cytoplasm
– ribosome

63
 tRNA
• Translator of mRNA’s message is tRNA – transfer RNA
• 80 nucleotides long
• Hairpin shape – L shaped
• One end contains an anticodon which pairs with the
codon on the mRNA
• Codons determine which amino acid is coded for by the
DNA
• The other end contains an amino acid attachment
site
• Aminoacyl-tRNA synthetase attaches the correct amino
acid to the tRNA

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tRNA

65
 Ribosomes
• Pair codons on mRNA with anticodons on tRNA
to form polypeptides
• Made of large and small subunits
• rRNA – ribosomal RNA
• Made in the nucleolus
• Contain multiple binding sites
• mRNA binding site
• P site – peptidyl – tRNA site
• A site – aminoacyl – tRNA site
• E site – exit site

66
 Ribosomes

67
 Making a protein
• Initiation
• Small subunit binds to mRNA
• Start codon AUG – methionine at P site
• Elongation
• A site recognizes codon and pairs with correct tRNA
• Peptide bond forms between the carboxyl end of the
polypeptide at the P site and amino acid at the A site
• Amino acid in the A site translocates to the P site
• Termination
• Stop codon is reached at the A site
• UAA, UAG, UGA
• Release factors free the polypeptide from the ribosome

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 Making a Protein

TRANSCRIPTI DN
ON A
mRN
A
Ribosome
TRANSLATIO
N
Polypeptide

Amino
Polypeptide acids

tRNA with
amino acid

Tr Ribosome attached
p
Phe Gly

tRN
C A
C
GC G
A
Anticodon
A A A
U G G U U U G G C

5 Codon 3
mRN s
Figure
A
17.13
https://www.youtube.com/watch?v=GZRwQpb_sdQ
 Questions

1) What are nucleic acids? Give an example.

2) Draw the structures of purine and pyrimidine bases.

3) What is nucleoside ? Give an example.

4) What is nucleotide? Give an example.

5) What is DNA ? Explain Watson and Crick model of DNA.

6) Explain Chargaff’s rule.

7) What are different types of RNA? Write their functions.

8) What is genetic code?

9) What are the three steps involved in transfer of genetic information defined in central dogma?