Introduction

– Each cell of our bodies contains thousands of different proteins.

– How do cells know which proteins to synthesize out of the extremely
large number of possible amino acid sequences?
– The transmission of genetic information took place in the nucleus, more
specifically in structures called chromosomes.
– The genetic information was thought to reside in genes within the
chromosomes.
– Chemical analysis of nuclei showed chromosomes are made up largely
of proteins called histones and nucleic acids.
Nucleic acids
Backbones of chromosomes
Ribonucleic acids (RNA)
Nucleic acids
Deoxyribonucleic acids (DNA)
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).
 Nucleotide
A nucleotide is composed of: I. Nitrogen-containing bases (amines)
II. Sugars (monosaccharides)
III. Phosphate

Phosphate

N H2 O O
Bases 3 N
4

5 N HN
CH3
HN
2 6
N O N O N O N
1
H H H
Pyrimidine Cytosine (C) Thymine (T) Uracil (U)
(DNA and (DNA only) (in RNA only)
some RNA)

6 7
N H2 O
1
N
5 N N N
8
N HN
2
N 4 N9 N N N N
3
H 2N
H H H
Purine Adenine (A) Guanine (G)
(DNA and RNA) (DNA and RNA)
 Sugars (monosaccharide)
RNA contains:
• D-Ribose sugar
DNA contains:
• 2-Deoxy-D-Ribose sugar (without O on carbon
2)
 Nucleoside
When a N atom of the base forms a glycosidic bond to C1’ (anomeric C) of a
sugar.
Base + Sugar Nucleoside
O
uracil O
HN
HN
O N -D-riboside 1
H 5' O N a -N-glycosidic
HOCH2 O bond
ß-N-glycosidic bond
Uracil (U) 1'
4' H H
H 3' 2' H anomeric
HO OH carbon
Uridine
 Nucleoside
To name a nucleoside derived from a pyrimidine base, use the suffix “-idine”.
To name a nucleoside derived from a purine base, use the suffix “-osine”.
For deoxyribonucleosides, add the prefix “deoxy-”.
 Nucleotide
A nucleotide forms with the −OH on C5’ of a sugar bonds
to phosphoric acid.

NH2 NH2
Phosphate ester bond

N N

O O N
O O N 5’
5’
- O- P O CH2
O P OH + HO CH2 O
O O -
O- 1’

OH
OH

deoxycytidine and phosphate A nucleotide

The name cytidine 5′-monophosphate is abbreviated as CMP.
 Nucleotide

The name deoxyadenosine 5’-monophosphate is abbreviated as dAMP.

 Nucleic Acids
• Nucleic acids are molecules that store information for cellular growth
and reproduction
• Chemical Composition:
• Elements: C, H, O, N, and P.
• There are two types of nucleic acids:
- deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
• These are polymers consisting of long chains of monomers called
nucleotides
• A nucleotide consists of a nitrogenous base, a pentose sugar and a
phosphate group:
 Nitrogen Bases
• The nitrogen bases in nucleotides consist of two general types:
- purines: adenine (A) and guanine (G)
- pyrimidines: cytosine (C), thymine (T) and Uracil (U)
 Pentose Sugars
• There are two related pentose sugars:
- RNA contains ribose
- DNA contains deoxyribose
• The sugars have their carbon atoms numbered with primes to
distinguish them from the nitrogen bases
 Nucleic Acids and Nucleotides
• Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are the
chemical carriers of genetic information
• Nucleic acids are biopolymers made of nucleotides, aldopentoses
linked to a purine or pyrimidine and a phosphate

11
 Nucleosides and Nucleotides
• A nucleoside consists of a nitrogen base linked by a glycosidic bond to
C1’ of a ribose or deoxyribose
• Nucleosides are named by changing the the nitrogen base ending to -
osine for purines and –idine for pyrimidines
• A nucleotide is a nucleoside that forms a phosphate ester with the
C5’ OH group of ribose or deoxyribose
• Nucleotides are named using the name of the nucleoside followed by
5’-monophosphate
 Nucleotides and Nucleic Acids
• Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are the chemical carriers
of genetic information
• Nucleic acids are biopolymers made of nucleotides, aldopentoses linked to a purine
or pyrimidine and a phosphate
• RNA is derived from ribose
• DNA is from 2-deoxyribose
– (the ' is used to refer to positions on the sugar portion of a nucleotide)
 Heterocycles in DNA and RNA
• Adenine, guanine, cytosine and thymine are in DNA
• RNA contains uracil rather than thymine
Nucleotides: In DNA and RNA the heterocycle is bonded to C1 of the sugar and The phosphate is bonded to
C5 (and connected to 3’ of the next unit)

Deoxyribo-
nucleotides

Ribon-
ucleotides
 Generalized Structure of DNA

 Nucleotides join together in DNA and RNA by as phosphate between the 5’-
on one nucleotide and the 3 on another

 One end of the nucleic acid polymer has a free hydroxyl at C3 (the 3 end),
and the other end has a phosphate at C5 (the 5 end).
Names of Nucleosides and Nucleotides
 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
 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’
 Example of RNA Primary Structure
• In RNA, A, C, G, and U are linked by 3’-5’ ester 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: 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
Base Pairing in the DNA Double Helix
 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)
  There are three types of RNA in a cell.
Types of RNA :
 Ribosomal RNA (rRNA)
 Messenger RNA (mRNA)
 Transfer RNA ( tRNA)
• Their main function is to make proteins after taking instructions from the DNA.
• They are temporarily present in the cell.
RNA

can be

Messenger RNA Ribosomal Transfer

RNA RNA

also called which functions to also called which functions to also called

Carry Bring
Combine
mRNA instructions rRNA tRNA amino acids to
with
ribosome
proteins

from to to make up

DNA Ribosome Ribosomes

MesseNgeR RNA :
• Also known as mRNA.
• Messenger RNA is a single long chain of nucleotides
• It is a molecule of RNA encoding a chemical "blueprint" for a protein product.
• mRNA is transcribed from a DNA template, and carries coding information to the
sites of protein synthesis: the ribosomes.

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
• Messenger RNA carries the genetic code to the ribosomes
- they are strands of RNA that are complementary to the
DNA of the gene for the protein to be synthesized
 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
 Protein Synthesis
• 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
 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
 The Genetic Code
• The genetic code is found in the sequence of nucleotides in mRNA
that is translated from the DNA
• A codon is a triplet of bases along the mRNA that codes for a
particular amino acid
• Each of the 20 amino acids needed to build a protein has at least 2
codons
• There are also codons that signal the “start” and “end” of a
polypeptide chain
• The amino acid sequence of a protein can be determined by
reading the triplets in the DNA sequence that are complementary
to the codons of the mRNA, or directly from the mRNA sequence
• The entire DNA sequence of several organisms, including humans,
have been determined, however,
- only primary structure can be determined this way
- doesn’t give tertiary structure or protein function
mRNA Codons and Associated Amino Acids
 Reading the Genetic Code
• Suppose we want to determine the amino acids coded for
in the following section of a mRNA

5’—CCU —AGC—GGA—CUU—3’

• According to the genetic code, the amino acids for these

codons are:

CCU = Proline AGC = Serine

GGA = Glycine CUU = Leucine

• The mRNA section codes for the amino acid sequence of

Pro—Ser—Gly—Leu
 Nucleic Acids
• DNA and RNA are chemical carriers of a cell’s genetic information
• Coded in a cell’s DNA is the information that determines the nature
of the cell, controls cell growth, division
• Nucleic acid derivatives are involved as phosphorylating agents in
biochemical pathways
 Base Pairing in DNA: The Watson–Crick Model
• In 1953 Watson and Crick noted that DNA consists of two
polynucleotide strands, running in opposite directions and coiled
around each other in a double helix
• Strands are held together by hydrogen bonds between specific pairs
of bases
• Adenine (A) and thymine (T) form strong hydrogen bonds to each
other but not to C or G
• Guanine (G) and cytosine (C) form strong hydrogen bonds to each
other but not to A or T
• LOCATION:
• It can be found in chromosomes (specifically
nucleus), mitochondria and chloroplast of the cell.
• It is present in every living organism because it
contains genetic material.
• ISOLATION:
• From viruses, bacteria, thymus gland, spleen, blood,
hair, skin, etc
Hydrogen Bonds in DNA
• The G-C base pair involves three H-bonds
• The A-T base pair involves two H-bonds
 DNA Synthesis
• DNA synthesizers use a solid-phase method starting with an attached,
protected nucleotide
• Subsequent protected nucleotides are added and coupled
• Attachment of a protected deoxynucleoside to a polymeric or silicate
support as an ester of the 3 –OH group of the deoxynucleoside
• Step 1: The 5 –OH group on the sugar is protected as its p-dimethoxytrityl
(DMT) ether
DNA Synthesis: Protection
• Step 2: After the final nucleotide has been added, the protecting groups are
removed and the synthetic DNA is cleaved from the solid support
• The bases are protected from reacting

DNA Synthesis: DMT Removal

• Step 2 (Continued): Removal of the DMT protecting group by treatment
with a moderately weak acid
DNA Synthesis: Coupling
• Step 3: The polymer-bound (protected) deoxynucleoside reacts with
a protected deoxynucleoside containing a phosphoramidite group at
its 3 position, catalyzed by tetrazole, a reactive heterocycle

Based on McMurry, Organic Chemistry, Chapter 28, 6th edition, (c) 2003
DNA Synthesis- Step 4: Oxidation and Cycling
• Phosphite is oxidized to phosphate by I2
• The cycle is repeated until the sequence is complete
 DNA Synthesis- Step 5: Clean-up
• All protecting groups are removed and the product is released from
the support by treatment with aqueous NH3