Gene Structure

MIC210

BASIC MOLECULAR BIOLOGY

By

SITI NORAZURA JAMAL (MISS AZURA)

03 006/ 06-483 2132

norazura6775@ns.uitm.edu.my

Lecture 2

Gene Structure

OUTLINE

1. DNA structure and function

2. Genes and genome

3. The genetic code and mutation

4. DNA denaturation and renaturation

5. Comparative genomics

It’s all in the DNA

• Genetic material found in

every living cell

• Contains information to

make proteins

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

www.mun.ca/biology/ scarr/Fg10_10rt.gif

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

Nucleotides – the building blocks

of DNA

Fig. 16-1

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

Fig. 16-6

(a) Rosalind Franklin (b) Franklin’s X-ray diffraction

photograph of DNA

• 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

Fig. 16-7

(c) Space-filling model

Hydrogen bond 3 end

5 end

3.4 nm

0.34 nm

3 end

5 end

(b) Partial chemical structure (a) Key features of DNA structure

1 nm

How one nucleotide can be joined to another through the 5’-PO4

(5 prime phosphate) and the 3’-OH (3 prime hydroxyl)

Many nucleotides can be joined in such a way to form a

polynucleotide chain a single stranded DNA

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

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

5’

3’

5’

3’

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

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.

Organism Amount of

DNA

No of

Chromosomes

No of genes

Human 3 Gb 46 100,000

Yeast 13 Mb 16 6,000

E.coli 4.5 kb 1 1,000

2. Genes and genomes The Genome - complete set of DNA for an organism

A comparison of genomes

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... ‘sense’

3’TACGAACCTGCACTACTGTAACCTCCT... ‘antisense’

3. The Genetic Code and mutation – how the DNA (or mRNA) sequence is translated into

the amino acid sequence of a protein

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)

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

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?

Frameshift mutations

a. Deletion

- AAC ATC AC CCG CGA GAT GAA –

b. Insertion

- AAC AATA AAG CCG CGA GAT GAA –

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

4. DNA denaturation and renaturation

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

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?