Chapter 10 from TB

The structure and function of DNA and RNA

• Nucleic acids:- Large polymers made of many repeating units called Nucleotides.
• Nucleotides - composed of a Sugar molecule, Phosphate group & one of the four Nitrogenous bases
(i.e. Adenine, Guanine, Thymine, Cytosine).
• RNA has Uracil (U) in place of Thymine.

Structure of Nucleotide
(Monomer of
DNA/RNA)
DNA –Functions
• Store information that determines the characteristics of cells and organisms (hereditary)
• Control the synthesis of RNA
• Control the synthesis of protein
1. Chemically change (mutate) genetic characteristics that are transmitted to future generation.
2. Replicate prior to reproduction by directing the manufacture of copies of itself.

DNA structure:- Scientists identified all its atoms and knew how they were bonded to one another.
Specific 3D arrangement of atoms giving unique properties
Central Dogma DNA ---------→ RNA---------→Protein.
• This unidirectional flow equation represents the Central Dogma (fundamental law) of Molecular Biology.
• Mechanism whereby inherited information is used to create actual products, viz., Enzymes & Proteins

(Structural)

• An exception to the central dogma is that certain viruses ( Retroviruses) make DNA from RNA using the
enzyme Reverse Transcriptase.
 Phosphate
group Nitrogenous base

Sugar Nitrogenous base

(can be A, G, C, or T)
DNA
nucleotide Thymine (T)

DNA
double Phosphate
helix group

Sugar
(deoxyribose)

DNA nucleotide

Polynucleotide
Sugar-phosphate
backbone
Figure 10.1
Difference in
DNA & RNA
sugar
 Watson and Crick’s Discovery of the Double Helix
• Watson and Crick used X-ray crystallography data to reveal the basic shape of DNA.
• Rosalind Franklin produced the X-ray image of DNA.
1.The model of DNA is like a rope ladder twisted into a spiral.
⮚ The ropes at the sides represent the sugar-phosphate backbones.
⮚ Each wooden rung represents a pair of bases connected by hydrogen bonds.

2. DNA bases pair in a complementary fashion:

⮚ adenine (A) pairs with thymine (T) and
⮚ cytosine (C) pairs with guanine (G).

James Watson (left) and Francis Crick

Chemical Structure of DNA

Watson and Crick’s model

James Watson & Francis Crick determined that DNA is a double helix.
• Double helix-ladder twisted into spiral structure
• Base pairing-complementary
• Helical twist DNA backbone
 Photo 51 – The key to discovery of DNA structure

For more info - https://en.wikipedia.org/wiki/Photo_51 (casual reading and information purposes only)
 Linear Polymerization of Nucleotides

Significance of complementary base pairing

• Each strand of DNA can act as template to direct

the synthesis of the other strand - its
complementary strand
• Nucleic acids are uniquely capable of directing
their own self replication.
• The information carried by DNA and RNA direct
the synthesis of specific proteins which control
most cellular activities.

▪ Nucleic acids are formed by Nucleotide Polymers.

▪ Nucleotides polymerize together by phospho-diester bonds
via condensation reaction.
▪ The phospho-diester bond is formed between:
⮚ Hydroxyl (OH) group of the sugar of one nucleotide.
⮚ Phosphate (Po4) group of other nucleotide
 Polymerization of Nucleotides
• The polynucleotide chain is formed of:
• Negative (-ve) charged Sugar-Phosphate backbone.
⮚ Free 5’ phosphate on one end (5’ end)
⮚ Free 3’ hydroxyl on other end (3’ end)
• Nitrogenous bases are not in the backbone
⮚ Attached to the backbone
⮚ Free to pair with nitrogenous bases of other polynucleotide chain

• The polymerization of nucleotides to form nucleic acids occur by

condensation reaction by making phospho-diester bond between
5’ phosphate group of one nucleotide & 3’ hydroxyl group of another nucleotide.

• Polynucleotide chains are always synthesized in the 5’ to 3’ direction, with a

free nucleotide being added to the 3’OH group of a growing chain.
 Denaturing and Annealing* of DNA
The DNA double strands can be denatured if heated (95º C) or treated with chemicals.
• AT regions denature first (2 H bonds)
• GC regions denature last (3 H bonds)
DNA denaturation is a reversible process, as denatured strands can re-annealed again if cooled.

•Every cell contains a DNA cookbook that provides complete information how to make and
maintain the cell.

•When cell grows and divides, two new cells are formed and both these cells need DNA for
their survival.

•Each cell has a means of copying the DNA

•instructions. DNA serves as a template to guide reproduction or replication of the other

strand . (AT-GC)

•Hence the DNA of the parent is copied in a process called as Replication.

 DNA Replication
• When a cell reproduces, a complete copy of the DNA must pass from one generation to the next.
• Watson and Crick’s model for DNA suggested that DNA replicates by a template mechanism.

• Replication of the DNA molecule is semi-conservative

• Which means that each parent strand serves as a template for a new strand and that the
two new DNA molecules each have one old and one new strand.
Parental (old)
DNA molecule

DNA replication requires:

A strand of DNA to serve as a template

Substrates - Deoxyribonucleoside Triphosphates Daughter

(dATP, dGTP, dCTP, dTTP). (new) strand

Enzyme- DNA polymerase - an enzyme that brings the Parental

substrates to the DNA strand template –make covalent bonds (old) strand

between the nucleotides of a new DNA strand

A source of chemical energy to drive this synthesis reaction.

Daughter DNA
molecules
Figure 10.6 (double helices)
DNA Replication: 1. DNA replication begins with an enzyme Helicase -binds to the DNA and separate the two strands of DNA,
forming a replication bubble.
2. Another enzyme, DNA polymerase incorporates DNA nucleotides into the new DNA strand. Nucleotides enter each position according
to base-pairing rules- A pairs with T and G pairs with C.
3. In prokaryotes, this process begins in only one site called the origin of replication. However in eukaryotes, the replication starts at
several places at the same time.
• As the points of DNA replication meet each other, they combine, and a new strand of DNA is formed. The result is 2 identical, DS DNA molecules.

Multiple “bubbles” in replicating DNA

 The process of DNA replication:
https://www.youtube.com/watch?v=TNKWgcFPHqw
 How an Organism’s Genotype Determines Its Phenotype
• An organism’s genotype is its genetic makeup, the sequence of nucleotide bases in DNA.
• The phenotype is the organism’s physical traits, which arise from the actions of a wide variety
of proteins.

The repair of genetic information

• Replication is HIGHLY ACCURATE
• Error (can occur one for every 2 X 109 nucleotides)……. Negligible
• These are corrected by DNA polymerase, removes the incorrect match & replaces it
with the correct match.
• Damage occasionally occur in the DNA helix.
• However, the pairing arrangement of the nitrogenous bases allows damage on one
strand to be corrected by reading the remaining undamaged strand
AGENDA – Structure of DNA • Replication
• Transcription
• Translation
• What are mutations

FROM DNA  RNA  PROTEINS

Genes in DNA contain information to make proteins.
▪ The cell makes mRNA copies of genes that are
needed.
▪ The mRNA is read at the ribosomes in the rough ER.
▪ Protein is produced

How DNA provides instructions to a cell and to an organism

• A sequence of nucleotides in the DNA is transcribed into a

molecule of RNA in the cell’s nucleus.
• The RNA travels to the cytoplasm, where it is translated in
the specific amino acid sequence of a protein.
• Organisms’ physical traits (phenotype) arise from the action
of variety of proteins.
 How an Organism’s Genotype Determines its Phenotype
• DNA specifies the synthesis of proteins in two stages:
1. Transcription, the transfer of genetic information from DNA into an RNA molecule and
2. Translation, the transfer of information from RNA into a protein.

Figure 17.4
 • mRNA carries the information from a gene in DNA.
Key Players • Ribosomes, made of rRNA, consist of subunits and carry out an enzyme-like role.
• tRNA carries specific amino acids to the ribosome.
From Nucleotides to Amino Acids: An Overview
• Experiments have verified that the flow of information from gene to protein is
based on a triplet code.
• A codon is a triplet of bases, which codes for one amino acid.

• The genetic code is the set of rules that convert a nucleotide sequence in
RNA to an amino acid sequence.
• Of the 64 triplets,
• 61 code for 20 amino acids and
• 3 are stop codons, instructing the ribosomes to end the polypeptide.
TRANSCRIPTION Makes RNA from a DNA template,
Only one of the DNA strand is transcribed

Enzyme RNA
polymerase

Transcription: From DNA to RNA

• The enzyme RNA polymerase reads the DNA sequence and follows the base pairing rules to
build a new RNA molecule.
• Transcription begins in the nucleus, when enzymes separate the two strands of the DS DNA.
• Separating the two strands, exposes the nitrogenous bases, so that they can be read and
paired with the RNA nucleotides.
• Only one of the strand of the DNA is read to create RNA for each gene.
• The strand of DNA that serves as a template for the synthesis of RNA is the non coding
strand, while the other is the coding strand.
• i.e: the RNA strand formed has the sequence same as that of the coding strand.
1.Initiation 2.Elongation 3.Termination
• INITIATION- “start transcribing” signal is a nucleotide sequence (promoter), which is
• located in the DNA at the beginning of the gene and
• a specific place where RNA polymerase attaches. RNA polymerase
• The first phase of transcription is initiation, in which
• RNA polymerase attaches to the promoter and DNA of gene
• RNA synthesis begins.
RNA ELONGATION- During the second phase of transcription, called elongation, Promoter
• the RNA grows longer and DNA Terminator DNA
• the RNA strand peels away from its DNA template.
During the third phase of transcription, called TERMINATION,
• RNA polymerase reaches a special sequence of bases in the DNA template Initiation
called a terminator, signaling the end of the gene,
• polymerase detaches from the RNA and the gene, and RNA
• the DNA strands rejoin. RNA nucleotides

RNA polymerase Elongation

Transcription produces 3 types of RNA:
1.mRNA,
Growing RNA
2.r-RNA and
3.t-RNA. Direction of
transcription Termination

Newly Made Template strand of DNA RNA polymerase

RNA
Completed RNA
(a) A close-up view of transcription Figure 10.13 (b) Transcription of a gene
 The Processing of Eukaryotic RNA
• The most significant difference between the prokaryotic & eukaryotic cells is that prokaryotes lack nuclei
• In the cells of prokaryotes, RNA transcribed from a gene immediately functions as messenger RNA
(mRNA), the molecule that is translated into protein.
• The eukaryotic cell
• the RNA produced inside the nucleus undergoes processing before it functions as mRNA.
• modifies, or processes, the RNA transcripts in the nucleus before they move to the cytoplasm for translation by ribosomes.

Pre-mRNA synthesized in Nucleus consists of Introns and Exons

o Exons – coding regions
o Introns – non-coding regions
Pre-mRNA processed before it leaves nucleus

Cap and tail added: Extra nucleotides at ends - which protect the RNA
from attack by cellular enzymes and help ribosomes recognize RNA.

oRNA splicing: Introns are removed

o Allows 21,000 genes to produce many thousand more polypeptides
o Varying the exons that are included in the final mRNA
The Genetic Code: Set of rules converting NUCLEOTIDE sequence in RNA to an AMINO ACID sequence
• The Nucleotides are read in sets of 3 letter alphabets - called Codons. These are the Code words indicate for each amino acid
• Triplets of bases are the smallest of words of uniform length that can specify all amino acids.
• 20 aa - 64 possible combinations.
• AUG – (Met) or Start UAA,UAG,UGA – Stop (Nonsense)
• Universal & Degenerate (or redundant), because a single amino acid may be coded for by more than one codon

• Genetic Code – shared by organisms from simple

bacteria to most complex plants and animals
• Because diverse organisms share common genetic
code – it is possible to program one species to
produce proteins from another species by
transplanting DNA.
• Allows mixing and matching genes from various
species
• Genetic Engineering
Protein synthesis:
DNA and RNA are both required for making proteins
• When RNA is created it carries the code words (for
each amino acid) to the cytoplasm for use in
assembling a protein.
 Translation: The Transfer RNA (tRNA)
Players ✔ acts as a molecular interpreter,
✔ carries amino acids, and
Translation requires ✔ matches amino acids with codons in mRNA using anticodons, a special
⮚ mRNA,
⮚ ATP,
triplet of bases that is complementary to a codon triplet on mRNA.
⮚ Enzymes, ❑To perform the task of interpretation the tRNAs must carry out 2 functions:
⮚ Ribosomes, and ⮚ Pick up the appropriate amino acids
⮚ transfer RNA (tRNA). ⮚ Recognize the appropriate codons in the mRNA
Amino acid attachment site

Hydrogen bond

RNA polynucleotide chain

tRNA
(simplified
Anticodon representation)

tRNA polynucleotide (ribbon model)

Ribosomes
Ribosomes are organelles that
• are made up of two subunits, and
• coordinate the functions of mRNA and tRNA

Each subunit is made up of

• Proteins, and
• a considerable amount of another kind of RNA, ribosomal RNA (rRNA).

A fully assembled ribosome holds tRNA and mRNA for use in

translation

TRANSLATION
- Three stages same as transcription – initiation, elongation,
termination
 Figure 10.20-6 Review: DNA→ RNA→ Protein
RNA polymerase Nucleus In a cell, genetic information flows from
1 Transcription • DNA to RNA in the nucleus and
• RNA to protein in the cytoplasm.

As it is made, a polypeptide -
⮚ coils & folds and
mRNA DNA ⮚ assumes a 3D shape,(its tertiary structure).
Transcription & Translation are how
genes control the structures and
Intron activities of cells.
2 RNA processing Anticodon
Codon
Cap
Tail
mRNA Cytoplasm Polypeptide
Intron
5 Elongation
Translation

Amino acid
A Stop
tRNA Ribosomal
codon
subunits
Anticodon
Enzyme
ATP
4 Initiation of 6 Termination
3 Amino acid attachment translation
• https://www.youtube.com/watch?v=gG7uCskUOrA

https://www.youtube.com/watch?v=8_f-8ISZ164
Mutations- any change in the nucleotide Types of Mutations
sequence of DNA. Mutations within a gene can be divided into two general categories:
• Mutations can change the amino acids in a protein. 1. nucleotide substitutions (the replacement of one base by another) and
2. nucleotide deletions or insertions (the loss or addition of a nucleotide).
• Mutations can involve Insertions and deletions can
✔ large regions of a chromosome or • change the reading frame of the genetic message and
✔ just a single nucleotide pair, as occurs in sickle-cell disease. • lead to disastrous effects.
Figure 10.22a

(a) Base substitution Ala

Me Ph Se Ala
t e r
Mutagens
• Mutations may result from
• errors in DNA replication or recombination or
• physical or chemical agents called mutagens.
• Mutations
• are often harmful but
• are useful in nature as a source of genetic
diversity, which makes evolution by natural
selection possible, and useful in the laboratory
as well
Practice Questions
(i) Of the two strands of nucleic acids (#1 and #2), strand # _____ is RNA and # _____ is DNA. [1M]
(ii) For the DNA strand shown, mention the prime ends from left to right? [0.5M]
(iii) If the 5th base from the left (base A) were deleted from strand #1, what would the new second codon be? [0.5M]
(iv) What would be the effect of this deletion described in (iv) on the protein sequence and why? [2M]
(v) What is the importance of the free 3’-OH group in a deoxyribonucleotide? [1M]
1. Write the sequence of the mRNA transcribed from the following DNA:
5’-ATTGCCTATTCGG-3’
3’-TAACGGATAAGCC-5’
2. Identify the mutation in the given figure: