Human Genetics

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Human Genetics

• DNA Makes RNA Makes Protein

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Terminology Review

• Chromosome
• Threadlike structures in the nucleus that carry
  genetic information
• Gene
• Fundamental unit of heredity
• Inherited determinant of a phenotype
• Locus
• Position occupied by a gene on a chromosome
•  Gene
• sequence of DNA that instructs a cell to produce
  a particular protein
• DNA
• Deoxyribonucleic Acid-the molecule that forms
  genes
• The genetic material
• Allele
• Different DNA sequences possible for the same
  gene location

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• A genetic material must carry out two jobs
  duplicate itself and control the development of
  the rest of the cell in a specific way.
• -Francis Crick

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DNA (deoxyribonucleic acid) is a chain of
nucleotides

• Sugar Deoxyribose
• Phosphate
• Base - one of four types adenine (A),
  thymine (T)
• 
  guanine (G), cytosine (C)

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Which of these are Purine bases?Pyrimidine
bases?

•  A (adenine)
• C (cytosine)
• T (thymidine)
• G (guanine)
• A guy walks into a bar and says "My name's
  Chargaff, and 22 of my DNA is "A" nucleotides.
  I'll bet anyone that they can't guess what
  percentage of my DNA is "C" nucleotides!" You say
  "I'm thirsty, so I'll take that bet!"
  http//escience.ws/b572/L1/L1.htm

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DNA Bases Pair through Hydrogen Bonds

• Erwin Chargaff observed
• of adenine of thymine
• of guanine of cytosine
• Complementary bases pair
• A and T pair
• C and G pair

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What's the difference between DNA and RNA?DNA
contains the sugar deoxyribose while RNA is made
with the sugar ribose. It's just a matter of a
single 2' hydroxyl, which deoxyribose doesn't
have, and ribose does have. Of course, you all
remember that RNA uses the base uracil instead of
thymine too.Cytosine naturally has a high rate
of deamination to give uracil
                                                
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What's the difference between DNA and RNA?

• DNA contains the sugar deoxyribose while RNA is
  made with the sugar ribose. It's just a matter of
  a single 2' hydroxyl, which deoxyribose doesn't
  have, and ribose does have.
• You all remember that RNA uses the base uracil
  instead of thymine too.
• Cytosine naturally has a high rate of deamination
  to give uracil

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If C-U deamination occurs and then is replicated,
the U will pair with an A not the C with a G
DEAMINATION ---------gt
Cytosine Uracil
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If 5-methyl C-T deamination occurs and then is
replicated, the T will pair with an A not the C
with a G
DEAMINATION ---------gt
5 methyl Cytosine Thymine
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DNA is a Double Helix

• X-ray diffraction indicated DNA has a repeating
  structure.
• Maurice Wilkins and Rosalind Franklin
• DNA is double-stranded molecules wound in a
  double helix.
• -James Watson and Francis Crick

G
C
A
T
C
G
T
A
G
C
A
T
C
G
T
A
G
C
A
T
C
G
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DNA Double Helix

• A sugar and phosphate backbone connects
  nucleotides in a chain.
• DNA has directionality.
• Two nucleotide chains together wind into a helix
• Hydrogen bonds between paired bases hold the two
  DNA strands together.
• DNA strands are antiparallel

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Orientation of DNA
The carbon atoms on the sugar ring are numbered
for reference. The 5 and 3 hydroxyl groups
(highlighted on the left) are used to attach
phosphate groups.

• The directionality of a DNA strand is due to the
  orientation of the phosphate-sugar backbone.

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Structure of DNA

• Two nucleic acid chains running in opposite
  directions
• The two nucleic acid chains are coiled around a
  central axis to form a double helix
• For each chain the backbone comes from linking
  the pentose sugar bases between nucleotides via
  phosphodiester bonds connecting via 3 to 5
• The bases face inward and pair in a highly
  specific fashion with bases in the other chain
• A only with T, G only with C
• Because of this pairing each strand is
  complementary to the other
• 5 ACGTC 3
• 3 TGCAG 5
•  Thus DNA is double stranded

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Chromatin DNA and associated proteins
DNA winds around histone proteins (nucleosomes).
Other proteins wind DNA into more tightly packed
form, the chromosome.
Unwinding portions of the chromosome
is important for mitosis, replication and
making RNA.
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Genes molecular definition

• A gene is a segment of DNA
• which directs the formation of RNA
• which in turn directs formation of a protein
• The protein (or functional RNA) creates the
  phenotype
• Information is conveyed by the sequence of the
  nucleotides

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Why is DNA good Genetic Material?

• A linear sequence of bases has a high storage
  capacity
• a molecule of n bases has 4n combinations
• just 10 nucleotides long -- 410 or 1,048,576
  combinations
• Humans 3.2 x 109 nucleotides long 3 billion
  base pairs

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Required properties of a genetic material

• Chromosomal localization
• Control protein synthesis
• Replication

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DNA Replication

• - the process of making new copies of the DNA
  molecules

Potential mechanisms
organization of DNA strands
Conservative old/old
new/new Semiconservative old/new
new/old Dispersive mixed old and new on
each strand
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Meselson and Stahls replication experiment
Conclusion Replication is semiconservative.
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Replication as a process

• Double-stranded DNA unwinds.

The junction of the unwound molecules is a
replication fork.
A new strand is formed by pairing complementary
bases with the old strand.
Two molecules are made. Each has one new and one
old DNA strand.
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Fig 8.14
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Replication in vivo is complex

• Replication requires the coordinated regulation
  of many enzymes and processes
• unwind the DNA
• synthesize a new nucleic acid polymer
• proof read
• repair mistakes

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Enzymes in DNA replication
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Replication
Helicase protein binds to DNA sequences called
origins and unwinds DNA strands.
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Replication
DNA polymerase enzyme adds DNA nucleotides to
the RNA primer. DNA polymerases require an
underlying template (and a primer) and cannot
synthesize in the direction 3' to 5'. That is,
they cannot add nucleotides to a free 5' end.
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Replication
DNA polymerase enzyme adds DNA nucleotides to
the RNA primer.
DNA polymerase proofreads bases added and
replaces incorrect nucleotides.
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Replication
Leading strand synthesis continues in a 5 to 3
direction.
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Replication
Leading strand synthesis continues in a 5 to 3
direction.
Discontinuous synthesis produces 5 to 3 DNA
segments called Okazaki fragments.
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Replication
Overall direction of replication
3
5
3
5
Okazaki fragment
3
5
5
3
3
5
Leading strand synthesis continues in a 5 to 3
direction.
Discontinuous synthesis produces 5 to 3 DNA
segments called Okazaki fragments.
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Replication
3
5
3
5
3
5
3
5
3
3
5
5
Leading strand synthesis continues in a 5 to 3
direction.
Discontinuous synthesis produces 5 to 3 DNA
segments called Okazaki fragments.
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Replication
3
3
5
Leading strand synthesis continues in a 5 to 3
direction.
Discontinuous synthesis produces 5 to 3 DNA
segments called Okazaki fragments.
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Replication
Exonuclease enzymes remove RNA primers.
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Replication
Exonuclease enzymes remove RNA primers.
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Replication
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General rules of conduct for DNA polymerase I
enzymes (like Taq)

• Remember your base pairing rules G goes with C
  and A goes with T.
• The 5' ends are strictly off limits
• There will be no synthesis without a free 3' end
• There will be no degradation without a free 3'
  end

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General rules of conduct for DNA polymerase I
enzymes (like Taq)

• 5. There will be no synthesis without an
  underlying template
• 6. Under no circumstances may you make a
  synthetic addition to the 5 end
• 7. There is no reconstruction of a broken
  phosphodiester bond, unless you have ligase. If
  you are synthesizing DNA and run into an
  obstruction on your template, you must stop and
  leave the nick unrepaired.

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General rules of conduct for DNA polymerase I
enzymes (like Taq)

• 8.If you have been provided with a free 3' end,
  a template, and a substrate molecule that is
  correct, you must add that nucleotide to the
  growing end of the strand (i.e. to the 3' end.)

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PCR Polymerase Chain Reaction

• Selective replication and amplification of
  specific(targeted) DNA sequences. 
• PCR basics
• Know some sequence of the piece of genomic or
  other DNA to be amplified
• DNA primers - short DNA pieces of sequences
  complementary to the DNA sequence to be
  amplified
• Four nucleotide building blocks
• Taq1 - DNA polymerase, Buffer, MgCl2

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Polymerase Chain Reaction (PCR)
DNA template is melted with high heat to
separate strands.
Denaturation
Each DNA primer anneals, binding to its
complementary sequence on the template DNA
Annealing
Extension
DNA polymerase creates a new strand of DNA
complementary to the template DNA starting from
the primers free 3 end.
Multiple rounds of denaturation-annealing-extensio
n are performed to create many copies of the
template DNA between the two primer sequences.
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Polymerase Chain Reaction (PCR)
DNA template is denatured with heat to separate
strands.
3
5
G
A
T
C
A
A
G
C
G
C
T
T
G
A
T
C
G
C
3
5
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Polymerase Chain Reaction (PCR)
DNA template is melted with heat to separate
strands.
3
5
G
A
T
C
A
A
G
C
G
C
T
T
G
A
T
C
G
C
3
5
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Polymerase Chain Reaction (PCR)
DNA polymerase creates a new strand of DNA
complementary to the template DNA starting from
the primer.
3
5
G
A
T
C
A
A
G
C
G
C
T
T
5
3
5
G
C
G
C
T
T
G
A
T
C
G
C
3
5
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Polymerase Chain Reaction (PCR)
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Template Base Pairing

• Requires correct temperature.
• Too hot and nothing can form hydrogen bonds.
• Too cold and the template reforms and the primers
  can form weak hydrogen bonds with sequences that
  are not perfectly complementary.
• http//escience.ws/b572/L3/L3.htm

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Genome and Epigenome vary in Monozygotic Twins

• Identical Twins dont actually have completely
  identical DNA
• http//www.cell.com/AJHG/abstract/S0002-9297(08)00
  102-X
• Bruder et al. Phenotypically Concordant and
  Discordant Monozygotic Twins Display Different
  DNA Copy-Number-Variation Profiles AJHG, Vol 82,
  No, 3, 763-771

http//www.nytimes.com/2008/03/11/health/11real.ht
ml?scp3sqepigeneticsstcse
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