Chap. 1 basic concepts of Molecular Biology

Introduction to Computational Molecular Biology

Chapter 1

1.1 Life IN nature we find both living and nonliving things.

Living things Move, reproduce, grow, ate, and so on.

The main actors in the chemistry of life are molecules called proteins and nucleic acids.

Nucleic acids encode the info. necessary to produce proteins.

1.2 Proteins Most substances in our bodies are proteins.

Enzymes act catalysts of chemical reactions. Usually a given enzyme can help only one kind of

biochemical reaction.

Proteins are polypeptidic chains. The amino group ->The carboxy group

1.3 Nucleic Acids Living organisms contain two kinds of nucleic acids

ribonucleic acid & deoxyribonucleic acid DNA is a chain of simpler molecules.

There are four kinds of bases Adenine(A), guanine(G), cytosine(C), thymine(T)

1.3 DNA DNA molecule having 200 bases or 200

nucleotides. DNA molecules in nature are very long. Based A and T said to be the complement of each

other, or a pair of complementary bases. The 3’ end of one strand corresponds to the 5’ end

of the other strand. DNA is found inside the nucleus and in cell

organelles called mitochondria and chloroplasts.

1.3 RNA In RNA we do not find thymine(T); instead, uracil(U)

is present. RNA does not form a double helix. Sometimes we see RNA-DNA hybrid helices. The mRNA will then be used in cellular structures

called ribosomes to manufacture a protein rRNA

Ribosomes are made of proteins and a form of RNA called rRNA

tRNA Actually implement the genetic code in a process called

translation.

1.4 Genes and the genetic code Each cell of an organism has a few very long DNA

molecules.

Important thing of DNA To encode information for building proteins.

Each nucleotide triplet is called a codon 64 possible nucleotide triplets Special termination codons = STOP Signals the start of a gene = Methionine

1.4 The genetic code mapping codons to amino acidsFirst Position

Second positionThird position

G A C U

G

Gly

Gly

Gly

Gly

Glu

Glu

Asp

Asp

Ala

Ala

Ala

Ala

Val

Val

Val

Val

G

A

C

U

A

Arg

Arg

Ser

Ser

Lys

Lys

Asn

Asn

Thr

Thr

Thr

Thr

Met

Ile

Ile

Ile

G

A

C

U

C

Arg

Arg

Arg

Arg

Gln

Gln

His

His

Pro

Pro

Pro

Pro

Leu

Leu

Leu

Leu

G

A

C

U

U

Trp

STOP

Cys

Cys

STOP

STOP

Tyr

Tyr

Ser

Ser

Ser

Ser

Leu

Leu

Phe

Phe

G

A

C

U

1.4 Transcription, translation, & protein synthesis

Replication

Transcription

Reverse Transcription

Translation

DNA RNA Protein

1.4 CHROMOSOMES The number of chromosomes in a genome is

characteristic of a species. The complete set of chromosomes inside a cell is

called a genome.

SpeciesNumber of

Chromosomes

(diploid)

Genome Size

(base pairs)

Bacteriophage λ (virus)

Escherichia coli (bacterium)

Saccharomyces cerevisiae (yeast)

Caenorhabditis elegans (worm)

Drosophila melanogaster (fruit fly)

Homo sapiens (human)

1

1

32

12

8

46

5 X 104

5 X 106

1 X 107

1 X 108

2 X 108

3 X 109

1.5 How the Genome Is Studied Maps and sequences

A human chromosome has around 108 bps. Locus : the location of a gene in a chromosome.

DNA cloning Recombination

New gene arrangements can form. There are an enormous number of recombination possibilities.

Cutting DNA EcoRI is a restriction enzyme that cuts DNA wherever the

sequence GAATTC is found.

1.5 Maps AND Sequences

CGCACACCGACGTCATTCTCATGTGCTTCTCGGCACA

Clones

Chromosome

Genetic linkage map(works on 107-108 bp range)

Physical map(works on 105-106 bp range)

Sequencing(works on 103-104 bp range)

The different levels at which a genome is studied.

1.5 Specific Techniques Cutting and Breaking DNA

The pair of scissors is represented by restriction enzymes.

Shotgun method DNA molecules can be broken apart by the shotgun method. Each individual molecule breaks down at several random

places, and then some of the fragments are filtered and selected for further processing.

In particular for copying or cloning.

1.5 Specific Techniques Cutting DNA

Using EcoRI (restriction enzyme)

A T C C A G A A T T C T C G G A

T A G G T C T T A A G A G C C T

A T C C A G A A T T C T C G G A

T A G G T C T T A A G A G C C T

CUT

CUT

1.5 Specific Techniques Copying DNA

We insert this piece (given a piece of DNA) into the genome of an organism, a host or vector, and then let the multiplied along with the original DNA.

Popular vectors : plasmids, cosmids, phages,… I.R. is a field that has focused on query and

transaction processing of structured data. Information retrieval and database systems

each handle different kinds of data.

Reading and Measuring DNA Reading is done with a technique known as gel-electrophoresis

1.5 Specific Techniques Copying DNA

Using plasmids for cloning

1.5 Specific Techniques Polymerase Chain Reaction

A way of producing many copies of a DNA molecule without cloning it is afforded by the polymerase chain reaction(PCR).

DNA Polymerase is an enzyme that catalyzes elongation of a single strand of DNA.

PCR consists basically of an alternating repetition of two phases

Double stranded DNA is separated into two single strands by heat.

Each single strand is converted into a double strand by addition of a primer and polymerase action.

1.5 Specific Techniques Polymerase Chain Reaction

Pre-PCR status

Denaturation

Annealing

Extension

1.6 The Human Genome Project The Human Genome Project is a multinational effort,

begun in 1988, whose aim is to produce a complete physical map of all human chromosomes, as well as the entire human DNA sequence.

1.6 The Human Genome Project Schematic view of film produced by gel electrophoresis

GACTTAGATCAGGAAACT

G A T C