Lecture 1: Jan. 18, 2006
Introduction and
review
What is Genetics?
• Genetics is the study of inherited traits
• Each organism has its own “Genetic Blueprint” that
makes it different from others.
• This information is stored in the chromosomes
located in the nucleus.
• The genetic information is stored as discrete
instructions called “genes”.
• Their existence was first inferred by Gregor Mendel
in 1866.
History of
Genetics-1
• Serious study of Genetics began in 1902 when
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the work of Mendel was rediscovered.
In the next 20 years genes in many organisms
were studied.
It was discovered that genes are located on
chromosomes.
Changes in genes could lead to inherited
diseases in humans (“Inborn Errors of
Metabolism”)
In the next 20 years, methods for gene
mapping and for experimentally inducing
mutations were developed.
History of Genetics-1
• Starting in 1940, studies using microbes (fungi,
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bacteria and bacterial viruses) began.
Merger of Genetics and Biochemistry led to
“Molecular Genetics”.
Determination of the Structure of DNA in 1953
led to an explosion in molecular studies.
During the 1970s, Gene cloning and DNA
sequencing methods were developed.
Methods for DNA marker analysis, DNA
fingerprinting and Polymerase Chain Reaction
(PCR) were developed in the 1980s.
History of Genetics - 3
• During the 1990s, whole genome sequencing
methods were developed.
• Availability of whole genome sequences led to the
study of all the genes in a genome
(Genomics)and of all the proteins coded by a
genome (Proteomics).
• A merger of Genetics with Physicochemical
methods (such as Mass spectrometry) occurred.
• Fusion of Genetics with Computer Science
created the field of “Bioinformatics”
DNA is the genetic
material - 1
The first hint
came from the
study of genetic
transformation in
bacteria by
Griffith in 1928.
DNA is the genetic material - 2
Avery and coworkers (1944)
showed that the transforming
material was sensitive to DNAdegrading enzyme but not to RNA
or protein-degrading enzymes.
DNA is the genetic material - 3
Hershey and
Chase
in 1952
showed that
P32-labeled
DNA is
passed onto
progeny
phages but
S35-labeled
protein is not.
Structure of
DNA
Watson and Crick
in 1953 proposed
that DNA is a
double helix in
which the 4 bases
are base paired,
Adenine (A) with
Thymine (T)
and Guanine (G)
with Cytosine (C).
Replication of
DNA
Watson and Crick also
proposed that DNA
replicates by the
separation
of the 2 strands and
creation of two daughter
strands by pairing of
template nucleotides with
new nucleotides using the
A:T and G:C pairing rule.
Defective genes can cause
Human Hereditary Diseases
• Many genetic diseases are caused by defective genes.
• Go to http://www.ncbi.nlm.nih.gov/Omim/getmorbid.cgi?
for a current list of hereditary diseases.
• The first such disease (alkaptonuria) was discovered by
Archibald Garrod in 1908.
• The disease results in black urine.
• It is caused by a defective enzyme in the pathway leading to
the breakdown of a protein component, the amino acid
phenylalanine.
• This defect leads to the accumulation of the compound
Homogentisic acid (also called alkapton) which turns black
upon oxidation.
Phenylalanine degradation pathway showing the
steps blocked in various diseases including
Alkaptonuria
Genes code for Proteins with
RNA as an intermediate
Flow of biological information
in a cell (Central Dogma)
Base pairing is involved in both
Transcription and Translation
The Genetic Code
Mutant proteins are created by a base
pair change in a triplet within a gene
Synthesis of normal protein
Synthesis of a mutant protein
Each protein has a distinct 3-dimensional structure
composed of coils, flat sheets and disordered domains
Mutant proteins may have altered structure
leading to faster degradation
DNA fragments can be cut and amplified
(cloned) in a bacterial cell
Structure of the 4 bases found in DNA
Base + sugar is called a nucleoside
Base + sugar + phosphate is called a nucleotide
Nomenclature of deoxynucleotides
Structure of a DNA (polynucleotide) chain
Polynucleotide
chains
have polarity.
One end has
5’-phosphate
and the other end
has 3’-OH
Structure of DNA Double Helix
Ribbon and space-filling diagrams
DNA has grooves of 2 sizes
Structure of A-T and G-C base pairs
Hydrogenbonds
are shown
as dotted
red lines.
A-T base
pairs have 2
and
G-C base
pairs have 3
H-bonds
H-bonds
are shown
as thin
flat white
disks in the
center
DNA strands are anti-parallel
5’
3’
3’
5’
The first proof was provided
In 1961 by measuring the
ratio of different dinucleotides
in DNA. The concentration of
5’AG3’ was equal to 5’CT3’ (as
expected from an antiparallel
orientation) and not equal to
5’TC3’ (as expected from a
a parallel orientation).
DNA sequencing in 1970s
confirmed this conclusion.
Restriction enzymes cleave DNA at a specific
sequence
Properties of restriction enzymes-1
(The next slide shows actual recognition sequences & cuts)
• DNA recognition sequence is usually 4-8 bp.
• The recognition sequence is usually a palindrome.
• The recognition sequence may be ambiguous (for
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example, PuGCGCPy or CCTNAGG).
The enzymes are named after the organisms from
which they were isolated.
The cuts may result in blunt or sticky-ends.
The sticky-ends may have 5’- (EcoRI, for example)or
3’-overhangs (PstI, for example).
The average distance between cutting sites is
determined by how long the recognition sequence is
and the probability of finding each nucleotide.
Properties of restriction enzymes-2
HaeIII
Haemophilus aegiptius
GG/CC
Blunt cut
Sau3A
Staphylococcus aureus
/GATC
5’-overhang
HhaI
Haemophilus haemolyticus
GCG/C
3’-overhang
SmaI
Serratia marcescens
CCC / GGG
Blunt cut
EcoRI
Escherichia coli RY13
G / AATTC
5’-overhang
PstI
Providencia Stuartii
CTGCA / G
3’-overhang
HaeII
Haemophilus aegiptius
RGCGC / Y
Ambiguous
sequence
NotI
Nocardia otitidis
GC /
GGCCGC
8 nt sequence
Size separation of DNA fragments
by electrophoresis in agarose gels
DNA is negatively charged due to phosphates on its surface.
As a result, it moves towards the positive pole.
Distance migrated by a DNA fragment
in a gel is related to log10 of its size
A “Restriction Map” shows the
relative location of DNA fragments
(A) Arrangement of EcoRI fragments (1 to 6) in bacteriophage l DNA
(B) Arrangement of BamHI fragments (1 to 6) in l DNA
Heating of DNA leads to the separation of the
2 strands
Single stranded (SS) DNA can pair with a
complementary strand to regenerate DS DNA
Southern Blotting
DNA fragments separated in a gel can be transferred to a membrane for
hybridization to a SS DNA Prob. The extent of hybridization can be
quantitated by using a radioactive DNA probe and auto-radiography
DNA synthesis is done by an enzyme (DNA
polymerase) adding nucleotides to the 3’-end of a
primer DNA chain
Polymerase Chain Reaction (PCR)-1
A pre-defined DNA
sequence in the
genome can be greatly
amplified by repeated
Polymerization cycles
using 2 primers which
hybridize to the ends
of the target DNA. In
each cycle, the amount of
target DNA
is doubled. After 10, 20
and 30 cycles, there is a
1000-, million- and
billion-fold amplification
respectively.
Polymerase Chain Reaction (PCR)-2
Each PCR cycle
has 3 stepsa. Melting of
DNA
b. Hybridization
of primer
c. DNA synthesis
The amount of DNA, number of genes and DNA
per gene in various organisms
Organism
Genome size
# of genes
DNA/gene
 Haemophilus influenzae
1.8 Mb
~1,700
~ 1 Kb
 Escherichia coli
4.6 Mb
~4,300
~ 1 Kb
(Saccharomyces cerevisiae) 12.1 Mb
~6,000
~ 2 Kb
97 Mb
~18,000
~5.4 Kb
185 Mb
~14,000
~13 Kb
3,000 Mb
~35,000
~ 86 Kb
100 Mb
~25,000
~ 4 Kb
 Baker’s Yeast
 A worm
 (Caenorhabditis elegans)
 Fruit fly
(Drosophila melanogaster)
 Human (Homo sapiens)
 A flowering plant
(Arabidopsis thaliana)
Some terms used in Genetics
Genotype- The genetic constitution of an organism.
Phenotype- The visible appearance of an organism.
Homologous chromosomes- in a diploid organism, the 2 copies
of a chromosome inherited from the mother and the father.
Locus- Location of a gene on a chromosome.
Allelomorph (allele)- different versions of the same gene.
Homozygous- the 2 copies of a gene are identical.
Heterozygous- the 2 copies of a gene are different.
The Missing Link?
Go BRONCOS!!!!!