DNA Structure and Variation, Part II

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DNA Structure and Variation, Part II

• Elaine Legras (Hager)
• Molecular Techniques NRES 791

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• Organization of metaphase chromosome
• Hierarchy of coiled coils
• DNA helix
• Histone fiber 11nm in diameter
• 30nm chromatin fiber
• 300nm coiled chromatin fiber
• Coiled coil 700nm in diameter
• Metaphase chromosome 1400nm in diameter

• Reduces 1 meter of DNA into a chromosome 10
  mmeters long

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• DNA - double helix
• Strands held together by hydrogen bonds
• H-bonds base-pairing between complementary
  bases, a linear sequence of A, T, G, and C
• Molecular structure of DNA as a double helix was
  not solved until 1953 (Watson and Crick)

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Alternative DNA structures

• B DNA
• Right-handed double helix
• Bases perpendicular to the main axis
• A DNA
• Right-handed double helix
• Bases are tilted relative to main axis
• More bases per rotation
• Z DNA
• Left-handed double helix
• Backbone zig-zags
• Small DNA mol. with repeating G-C sequences on
  both strands
• May regulate gene expression in eukaryotes

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Nucleotide monomers
Bases are A, G, T , U or C
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Phosphodiester bonds gtgtsugar phosphate backbone
Sugar phosphate backbone Represented as blue
ribbon
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DNA Structure Double Helix
Notice the polarity of the sugar phosphate
backbones
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Base-pairing Rules 5 bases DNA A, T, G, C
RNA A, U, G, C DNA A pairs with T G pairs
with C
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Complementary strands are antiparallelThey have
opposite polarities
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DNA Replication


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DNA Replication
CTGTAGCTGCAGTCTG GACATCGACGTCAGAC
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3
5
3
CTGTAGCTGCAGTCTG CGACGTCAGAC
CTGTAGCTGCA GACATCGACGTCAGAC
5
5
3
3
5
5
3
3
Complementary base pairing allows for accurate
copying of the DNA sequence
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• DNA
• deoxyribonucleotides (dNTs)
• sugar deoxyribose
• RNA
• ribonucleotides (rNTs)
• sugar ribose
• (also, is ss and contains uracil)

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Where are DNA and RNA in the cell?
Nucleus
mRNA
DNA replication followed by cell division
Ribosome
Polypeptide chain Will fold into a 3D structure
Translation of a mRNA into a protein begins at met
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Translation transfer of information from RNA to
protein
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3D conformation of a protein
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A protein consists of 1 or more polypeptides,
folded into the correct 3-dimensional shape
(conformation)
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Proteins

• Perform many roles in cell
• Many are enzymes
• Among other roles
• structural components of membranes
• ionic channels
• receptors

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Gene expression
The processes by which information in the gene is
decoded to synthesize a protein
original Central Dogma of molecular genetics
Genes code for proteins (Including Enzymes)
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Updated Central Dogma
Reverse Transcription RNA replication
Functions of viruses and transposable elements
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One Gene one Enzyme
1908-Garrod studied patients with black urine -
alkaptonuria and identified abnormal excreted
substance homogentisic acid He hypothesized
that there was an inherited defect that blocked
degradation of homogentisic acid and was
hereditary Defect in the gene coding for
homogentisic acid 1,2-dioxygenase Hemoglobin
tetramer 2a 2ß subunits, different loci on 16
and 11 Modified to one gene-one polypeptide
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Breakdown of Phenylalanine
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Mitosis and Meiosis M-phase
(prophase) - chromosome condensation
Interphase nucleus
M-phase
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Overview of mitosis
Mitosis can also occur in most haploid cells (but
not gametes)
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(No Transcript)
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Meiosis - Overview
Interphase DNA is replicated
Pair of homologs
Meiosis I Homologs separate gtgt 1n chromosome
number
Meiosis II Sister chromatids separate.
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Close up of Crossing Over
Centromere
Chromatid
Chiasma
Chiasma
Chiasmata (plural) cross connections between
chromosomes Generated by DNA breakage and
rejoining between non-sister chromatids
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Spermatogenesis
meiocyte 1O spermatocyte
sperm
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Oogenesis - egg formation
Meiocyte 1O oocyte
M-I
M-II
polar bodies
egg
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Homolog pairs are arranged randomly at metaphase
plate, Principle of Segregation
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Mutations

• Mutation refers to any heritable change in a gene
• Any mutation that causes the translation of an
  incorrect amino acid in a protein can impair its
  function
• Base substitutions (changes) alter the genetic
  code which specifies amino acid placement in
  proteins

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Molecular change point mutations

• Base-pair substitution
• Replacement of one bp with a different one.

For example
Consequences missense nonsense silent
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Missense mutation
Effect?
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Nonsense mutation
Effect?
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(c) Silent mutation Changes codon to one for
same aa
e.g., UCU (ser) UCC (ser)
Effect?
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Insertion or deletion Effect?
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Duplication

• Genetic consequences
• In many cases - lethal gene imbalance

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Reciprocal deletions and duplications caused by
unequal crossing over
Occurs in regions of tandem repeats
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Inversions

• Genetic consequences
• Not harmful to individual (except for breakpoint
  within essential gene)
• 2 of humans carry inversions
• Reduced fertility
• Cross-overs in inversion region gtgt unbalanced,
  acentric or dicentric chromosomes
• gtgt zygote lethality

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Location of centromere affects outcome of
cross-over
Paracentric
Inversion does not include centromere
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Paracentric inversion
abc.defghij
abc.dgfehij
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Pericentric inversion
abcde.fghij
abcdgf.ehij
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Mutations

• Transition
• The replacement of a purine or pyrimidine with a
  like base
• i.e. replacement of adenine with guanine
• Caused by a tautomeric shift (movement of H
  between C, N or O and/or replacement of 2 bond)
• Transversion
• The replacement of a purine with a pyrimidine,
  vice-versa
• i.e. replacement of adenine with thymine
• Caused by a tautomeric shift and a base rotation
• Both cause mispairing

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Mechanisms of induced mutation

• Mutagen mimics base
• base analogs
• Mutagen modifies base
• highly reactive chemicals
• UV light
• Mutagen causes DNA strand breaks
• ionizing radiation

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1. Reactive chemicals modify bases and cause a
transition mutation
Example alkylating agents
Alkylating agents are abundant environmental
mutagens (carcinogens)!
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2. UV light cross-links adjacent pyrimidine bases
pyrimidine dimers T-T most common Linkage
brings bases closer together which distorts the
DNA helix blocking both replication and
transcription
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Rates of Mutation

• Mutations are statistically random and
  unpredictable
• Rates are determined by probability
• Mutagens increase rates

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Sequencing the of the genome can give an
evolutionary timeline and insights into human
evolution.
5.4 Myr
2.5 Myr
7.3 Myr
14 Myr
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Le Fin