chap. 1 basic concepts of molecular biology introduction to computational molecular biology chapter...
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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
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