This document provides an overview of basic molecular biology concepts including: 1) DNA structure including nucleotides, base pairing, and the double helix formation. 2) Genes and genomes, including definitions of a gene, genome size comparisons, and that genes encode proteins. 3) The genetic code and mutations, including how the DNA sequence is translated into proteins and different types of mutations.

1. MIC210
BASIC MOLECULAR BIOLOGY
Lecture 2
Gene Structure
By
SITI NORAZURA JAMAL (MISS AZURA)
03 006/ 06-483 2132
norazura6775@ns.uitm.edu.my

2. OUTLINE
1.
2.
3.
4.
5.
DNA structure and function
Genes and genome
The genetic code and mutation
DNA denaturation and renaturation
Comparative genomics

3. It’s all in the DNA
• Genetic material found in
every living cell
• Contains information to
make proteins

4. 1. DNA Structure & function
• Polymer made of 4 nucleotides : A, C, T, G
• polynucleotide eg. A-G-T-C-C-A-A-G-C-T-T….
• DNA is double stranded - Double-helix
• Complementary base pairing
• Anti-parallel

5. Nucleotides – the building blocks
of DNA
Nucleotide = Sugar + base + phosphate
Nucleoside = Sugar + base
Deoxyribose sugar  5 carbons
Phosphate (PO4) group at carbon no. 5
Hydroxyl (OH) group at carbon no. 3
www.mun.ca/biology/ scarr/Fg10_10rt.gif

6. Fig. 16-1

7. Building a Structural Model of DNA: Scientific Inquiry
• After most biologists became convinced that
DNA was the genetic material, the challenge
was to determine how its structure accounts for
its role
• Maurice Wilkins and Rosalind Franklin were
using a technique called X-ray crystallography
to study molecular structure
• Franklin produced a picture of the DNA
molecule using this technique
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

8. Fig. 16-6
(a) Rosalind Franklin
(b) Franklin’s X-ray diffraction
photograph of DNA

9. • Franklin‟s X-ray crystallographic images
of DNA enabled Watson to deduce that
DNA was helical
• The X-ray images also enabled Watson
to deduce the width of the helix and the
spacing of the nitrogenous bases
• The width suggested that the DNA
molecule was made up of two strands,
forming a double helix
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

10. Fig. 16-7
5 end
Hydrogen bond
3 end
1 nm
3.4 nm
3 end
0.34 nm
(a) Key features of DNA structure (b) Partial chemical structure
5 end
(c) Space-filling model

11. How one nucleotide can be joined to another through the 5’-PO4
(5 prime phosphate) and the 3’-OH (3 prime hydroxyl)

12. Many nucleotides can be joined in such a way to form a
polynucleotide chain  a single stranded DNA

13. The Double Helix
The complete DNA molecule is made up of two complementary strands in
antiparallel directions
http://physicsweb.org/objects/world/16/3/7/pwhux4_03-03.jpg

14. 5’
3’
3’
5’
Complementary base-pairing
• A always pair with T
• C pairs with G
Antiparallel
• each strand of DNA has a “direction”
• at one end, the terminal carbon atom in
the backbone is the 5‟ carbon atom
• at the other end, the terminal carbon
atom is the 3‟ carbon atom
• therefore each DNA strand has a 5’ and a
3’ end
• in a double helix, the two strands are
always antiparallel
The length (or size) of a DNA molecule
is measured in basepairs (bp)
1 kilobase (kb) = 1,000 bp
1 Megabase (Mb) = 1,000,000 bp

15. Chromosomes and DNA
DNA is packaged in the
form of chromosomes in
the nucleus of a cell.
The chromosomes contain
DNA tightly wounded
around proteins.

16. 2. Genes and genomes
The Genome - complete set of DNA for an organism
A comparison of genomes
Organism
Amount of
DNA
No of
Chromosomes
No of genes
3 Gb
46
100,000
Yeast
13 Mb
16
6,000
E.coli
4.5 kb
1
1,000
Human

17. A Gene
• a specific DNA sequence that
contains genetic information
• information required to make a
specific type of protein
• that information is stored in the
sequence on the „sense‟ strand
• we say that a gene encodes a
protein
• thus a DNA molecule can contain
many genes
• the gene sequence is always
written 5‟  3‟
5’ATGCTTGGACGTGATGACATTGGAGGA...
3’TACGAACCTGCACTACTGTAACCTCCT...
‘sense’
‘antisense’

18. 3. The Genetic Code and mutation
– how the DNA (or mRNA) sequence is translated into
the amino acid sequence of a protein

19. Reading frames
• There are 3 ways to read a gene sequence – reading frames
• Each reading frame will give a different result
• Only one reading frame is correct (usually)

20. Gene mutation
• Information coded in the DNA sequence is used to make proteins
• If the DNA sequence is changed, what will happen?
• A change in the genetic information is called a mutation. The outcome
depends on the nature of the „change‟.
• 3 types of DNA sequence mutations

21. Substitution mutations
-change of 1 base
-AAC ATA ACG CCG CGA GAT GAA –
Asn
Ile
Thr
Pro
Arg
Asp Glu
a. Silent mutation
- AAC ATC ACG CCG CGA GAT GAA –
b. Missense mutation
- AAC ATA AAG CCG CGA GAT GAA –
c. Nonsense mutation
- AAC ATA ACG CCG TGA GAT GAA –
What happens to
the amino acid
sequence?
What happens to
the protein?

22. Frameshift mutations
a. Deletion
- AAC ATC AC CCG CGA GAT GAA –
b. Insertion
- AAC AATA AAG CCG CGA GAT GAA –

23. Mutation can also happen due to
-changes in long DNA sequences
-changes in the structure of genes/ chromosomes
-changes in the number of genes/ chromosomes
-e.g. Mutations leading to cystic fibrosis

24. 4. DNA denaturation and renaturation

25. Denaturation – breaking up of the double helix molecule
•
•
•
•
•
hydrogen bonds broken
by heating to > 96oC (and also other conditions)
Tm = the melting point of a DNA molecule
depends on the GC content
higher %GC  higher Tm
Renaturation - if the denatured DNA strands are allowed to
cool slowly
• the can re-anneal with each other and regain the double
helix structure
• reannealing by complementary base-pairing

26. 5. Comparative genomics
• Comparison of whole genome sequences
provides a highly detailed view of how
organisms are related to each other at the
genetic level. How are genomes compared
and what can these findings tell us about
how the overall structure of genes and
genomes have evolved?
• Purpose / benefits?