DNA, chromatin and the nucleus

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DNA, chromatin and the nucleus Lecture 1 -
nucleotides - DNA structure - double
helix - topology - DNA/protein
interactions Lecture 2 - histones - histone
core - histone associated proteins -
chromatin - histone modifications - the
histone code Lecture 3 - nuclear structure -
import/export - organisation Professor N.B. La
Thangue Division of Biochemistry and Molecular
Biology Davidson Building, University of Glasgow,
G12 8QQ. Tel [phone]. Fax [phone]. E-mail
N.LaThangue_at_bio.gla.ac.
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• Information is Stored in the Code Letters of DNA
• All hereditary information is stored in genes,
  which are
• parts of giant DNA molecules
• Genes code for the amino acids of proteins
• DNA is the archival copy of the code- kept in
  nucleus
• where it is protected repaired
• DNA is organized with special proteins into
  chromosomes
• For protein synthesis a working copy of the
  code is made
• from RNA
• Overall scheme DNA -gt RNA -gt protein

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• The Code is Based Upon the Structure of DNA
• DNA has a sugar-phosphate backbone- sugar is
  deoxyribose
• DNA also has 4 types of nucleotide base A, C,
  G, T
• A adenine C cytosine G guanine T
  thymine
• Molecule is a double helix 2 complementary
  strands where A T, C G
• The term"complementary" refers to the fitting
  together of 2 molecules like
• hand and glove
• In DNA complementary bases make good hydrogen
  bonds with one another
• Strands of helix are held together by hydrogen
  bonds between the bases
• This allows DNA to unwind for duplication and
  transcription
• (S sugar P phosphate B base)
•                                                 
                      

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Bases, Nucleosides, Nucleotides
The basic building blocks of nucleic acids are
the nucleotides. Each has three components

• A heterocyclic base
• There are two types of base

There are two purine bases commonly found in
nucleic acids





There are three pyrimidine bases commonly found
in nucleic acids




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Nucleosides and Nucleotides

• A 5 carbon (pentose) sugar
• The sugars are in the furanose (ring) form and
  can be
• deoxyribose (in DNA)
• ribose (in RNA)
• The base is attached to the sugar by a glycosidic
  bond at C1'.

• Phosphate moieties esterified to the C5' of the
  sugar

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The structure of B-DNA The practical
breakthrough in Watson Crick's search for the
structure of DNA
A base pair formed between a guanine nucleotide
and a cytosine nucleotide
A base pair formed between a thymine nucleotide
and an adenine nucleotide
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• Features of the Watson-Crick model of B-DNA
• It is an anti-parallel double helix.
• It is a right-handed helix.
• The base-pairs are perpendicular to the axis of
  the helix.
• The axis of the helix passes through the centre
  of the base pairs.
• Each base pair is rotated by 36 degrees from the
  adjacent base pair.
• The base-pairs are stacked 0.34 nm apart from one
  another.
• The double helix repeats every 3.4 nm, i.e. the
  pitch of the double helix is 3.4 nm.
• B-DNA has two distinct grooves a MAJOR groove
  and a MINOR groove.

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The real structure of B-DNA
Watson and Crick's structure was a just a model
In 1980, Richard Dickerson and Horace Drew
solved the structure of
 5'-CGCGAATTCGCG-3'
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Energetics of B-DNA Three forces are responsible
for the stability of the B-DNA double helix

• Hydrophobic base-stacking interactions (van der
  Waals forces) between adjacent base pairs.
• Hydrogen bonds forming the base-pairs.
• Hydrogen bonds due to the formation of a water
  spine in
• the minor groove.

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Variations in the structures of DNA
poly(A) tracts causes a bending of 18 degrees
palindromes, hairpins, pseudoknots cruciforms
A-DNA there is no water spine minor groove is
about as wide as the resulting major groove.
It is not clear if the A-DNA conformation exists
in vivo.
Z-DNA crystallizing the self-complementary
hexanucleotide, CGCGCG. This particular molecule
adopted a LEFT-HANDED double helix.
Z-DNA seems to form most readily in sequences
that alternate purines and pyrimidine
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Supercoiling and Topoisomerases

• Supercoiling
• The total amount of DNA in any individual cell
  seems very large
• DNA can adopt a compact configuration due to
  supercoiling.
• Supercoiling is a physical rearrangement of the
  DNA double helix that allows it to confirm more
  closely to the ideal B-DNA structure.
• Implications for transcription and replication
  unwinding/unpairing must occur so that mRNA or
  DNA copies can be made.
• Linking Number and Superhelical Density
  Supercoiling in circular DNA molecules is the
  number of times the two phosphodiester backbones
  wrap around one another in a given distance.
• In bacteria, the superhelical density is 0.06.
• Topoisomerases supercoiling is carefully
  controlled by the action of topoisomerases
  Naturally occurring DNA is underwound.

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Topoisomerases
There are two classes of topisomerase Type 1
topoisomerases remove supercoils through a
mechanism that involves breaking only one of the
two phosphodiester backbones.
The best-characterized member of this class in
E. coli is Topoisomerase I. 864 amino-acids in
length and is monomeric encoded by the topA gene.

• formation of a covalent intermediate between a
  tyrosine residue and the
• phosphodiester backbone.
• nucleophilic attack from the hydroxyl group of
  tyrosine to a phosphorus atom
• creates a phosphodiester link between the
  enzyme and the DNA

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• Type 2 topoisomerases
• Both phosphodiester backbone chains are broken
  simultaneously.
• E. coli, Topoisomerase II better known as DNA
  Gyrase.
• E. Coli DNA gyrase is a tetrameric protein
  consisting of two A subunits (875 aas) and two B
  subunits (804 aas).
• Topoisomerases are essential enzymesmutations in
  any of the genes coding for
• topoisomerases are usually lethal. They are
  therefore targets for antibiotics and
• other drugs. Novobiocin, doxorubicin, etoposide.

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Challenges of transcriptional control in a
mammalian cell

• 30,000 genes
• Genome size 3 x 109 base pairs
• DNA organized into chromatin of varying levels of
  compaction
• Developmental requirements
• Homeostatic requirements

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Transcriptional control in eukaryotic cells

• Transcription factors are regulated by
  intracellular and extracellular signals

• Chromatin, sequence specific factors,
  co-activators, co-repressors, and basal machinery
  are all targets of signaling pathways

• Transcription factors work in a combinatorial
  manner to achieve different transcriptional
  outputs

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Sequence-specific DNA-binding Transcription
Factors Are the Apex at the Interface of Genetic
Regulatory Information and Other Transcription
Regulators
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Transcription factors act in a combinatorial
manner to regulate gene expression