schwabe

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5/10/12 Lecture 1 DNA is the genetic material Chemical composition of DNA
FRED GRIFFITH
Investigated streptococcus pneumonia ( in mice )
Two types
Rough ( rippled)
Smooth ( shiny bigger colony ­ made by polysaccharide capsule that coats colony ­shininess)
Smooth ­ pathogenic in mice
Rough ­ non-pathogenic
Smooth ­ heated up ­ bacteria die ­ don't kill mice
In the experiment
Injected mice with dead smooth and live rough = mice die
Fluid contain live smooth bacteria from dead mice ­ transformation of live rough cells by the dead
smooth cell
Concluded Genetic material from killed rough might have incorporated in to genetic material of
smooth
Griffith knew that proteins are denatured when heated- has to be something else
AVERY, MACLEOD & McCarty
crude ( mushed and then homogenised) extract from dead, smooth pneumococci transformed rough
strain put in vitro
done with protein-free extract
Crude extract treated with DNase ­ no longer able to transform
Bacteriologists suspected the transforming factor was some kind of protein. The transforming
principle could be precipitated with alcohol, which showed that it was not a carbohydrate like the
polysaccharide coat itself.
observed that proteases ­ enzymes that degrade proteins ­ did not destroy the transforming
principle
Neither did lipases ­ enzymes that digest lipids. They found that the transforming substance was rich
in nucleic acids, but ribonuclease, which digests RNA, did not inactivate the substance.
transforming principle had a high molecular weight.

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DNA. This was the agent that could produce an enduring, heritable change in an organism
HERSHEY & CHASE
Bacteria: Escherichia coli
Phage T2 ­ virus of bacteria ( smaller than that, which infects eukaryotic cells )
Phage : protein + DNA
T2 infects E.coli
Phage replicates in infected E.coli ­ until E.coli lysis
Progeny ( descendent ) phage released
Experiment
Prepared RADIO ACTIVELY LABELLED phages
Protein 35S
DNA 32 P
Used to infect E.…read more

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TYPES OF BASES: PURINES- nitrogen-containing heterocyclic compounds- TWO RINGED STRUCTURE
Amine
ADENINE 6-aminopurine GUANINE 2-amino-6-oxopurine
Pyrimidine ­ heterocyclic bases ­ ONE RINGED STRUCTURE
THYMINE-5-methyluracil CYTOSINE 2-oxo, 4-amino pyrimidine URACIL 2,4-dioxopyrimidine
When the phosphate is attached to the sugar-base compound its called a NUCLEOTIDE, if its only the
sugar and the base it called a NUCLEOSIDE
Deoxy- adenosine ­ 5'-monophate
dAMP ( nucleotide )
-glycoside bond
chiral carbon ( tetra bonded stereoisomer )…read more

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AMP -Adenosine monophosphate, or AMP, on its own, plays a role in signaling energy depletion in
cells, and in chemical combination forms a component of a number of cofactors
BASE Nucleotide
Adenine A Adenosine
Guanine G Guanosine
Cytosine C Cytidine
Thymine T Thymidine
Uracil U Uridine
Phosphateput in water ( see note book for reference to image )
NUCLEOSIDE ­ BASE COUPLED WITH RIBOSE
Nuclei acids are polynucleotides (polymers of nucleotides )
Polarity ­ one end different to the other 5'prime end and 3' prime…read more

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The four common ribonucleotides of RNA
- adenylate,
- cytidylate,
- guanylate
- uridylate
LECTURE 2 the structure of DNA double helix, packaging cell properties of DNA…read more

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Forces that determine macromolecule structure
1. Covalent bonds
Very strong- single and double
Short C-C = 1.54 Å
Shared electrons
85-175 kcal/mol
2. Non-covalent bonds
-electrostatic interactions
Depends on dielectric constant (resistance that is encountered when forming an electric field in a
medium)- aqueous solutions have a high dielectric constant
Depends on the distance ­ closer = stranger interaction
Weak to strong c.1-50 Kcal /mol
Salt bridge
Repulsive forces form like charges
Hydrogen bonds
Weak 1-5 kcal/mole
Longer than bonds 2.…read more

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The phosphate must be on the outside
Pauling & Corey's unsatisfactory model 3 strands - phosphates on the inside
Bases come in pairs
Relative base composition A=T C=G E. Chargaff
Bases share the same dimension
X-ray diffraction of a DNA fibre ­ DNA is helical- B form of DNA R. Franklin, M.…read more

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What are the physical and functional consequences of DNA supercoiling?
DNA and its constituent nucleotides have similar U.V. absorption spectra with a
maximum around 260 nm. However, the total nucleotides that make up DNA
absorb more strongly than the polymer, so hydrolysis of DNA is accompanied
by a considerable increase in absorbance at 260 nm (HYPERCHROMICITY).
A somewhat lesser hyperchromic effect is observed when DNA is 'melted' i.e.
when the two strands are separated.…read more

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THE CENTRALO DOGMA ----
---- DNA--- CODES---RNA--- CODES--- protein
What are proteins
Polymers of amino acids
Allow enzymes to have wide diversity
Complex 3-d dimension
Structural and functional
What are enzymes
Proteins that catalyse biochemical reactions
Need enzyme to make covalent bond in protein
Enzymes that manipulate DNA
nucleases
ligases
polymerases
kinases & phosphatases
methylases & demethylases
recombinases / topoisomerases
Enzymes that cleave DNA
exonucleases ­ cut the end of DNA
endonuclease ­ cut DNA internally
some cut randomly
some are sequence specific ( break…read more

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DNA as dimers (any molecular structure of any size in
which two initially identical chemical entities have become covalently combined)
Render its DNA immune to the action of its own restriction enzyme(s)
DNA fragments with the same sticky ends can be ligated together (anneal)
regenerate ­ recombinant DNA (fragment of deoxyribonucleic acid (DNA) that has been inserted into
a cloning vector, thereby leading to its use in the isolation of a clone of cells characterized by the
presence of the fragment)
gene cloning
( TAQ)…read more

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