Chap' 1 basic concepts of Molecular Biology

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Chap. 1 basic concepts of Molecular Biology

• Introduction to Computational Molecular Biology
• Chapter 1

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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.

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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 -gtThe carboxy group

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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)

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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.

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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.

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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

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1.4 The genetic code mapping codons to amino acids
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1.4 Transcription, translation, protein
synthesis
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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.

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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.

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1.5 Maps AND Sequences
Chromosome
Genetic linkage map (works on 107-108 bp range)
Clones
Physical map (works on 105-106 bp range)
Sequencing (works on 103-104 bp range)
CGCACACCGACGTCATTCTCATGTGCTTCTCGGCACA
The different levels at which a genome is studied.
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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.

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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
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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

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1.5 Specific Techniques

• Copying DNA
• Using plasmids for cloning

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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.

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1.5 Specific Techniques

• Polymerase Chain Reaction

Pre-PCR status
Denaturation
Annealing
Extension
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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.

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1.6 The Human Genome Project

• Schematic view of film produced by gel
  electrophoresis

G A T
C
GACTTAGATCAGGAAACT