Biochemistry 329

Base is attached to beta hydroxyl group

At 260nm

G>A>C>>U

*The smaller the pKb the stronger the base.

adenosine, guanosine, thymidine, cytidine, uridine

Adenine, Guanine, Thymine, Cytosine, Uracil.

N-9 of a puring, N-1 of a pyrimidine.

Alkaline conditions

*DNA is stable

Isomers of the same organic compound.

10bp; pitch is 34 angrstom, adjacent bp=3.4 A

C-2'-endo

Ethidium brodmide is an intercalator, isert between adjacent base pairs, untise helix; flouresence orange under UV.

The unstacking of base pairs results in an increased absorbance 260.

Different DNA strands of similar sequences can form hybrid duplexes.

N increases Cot 1/2 increases ; more repetitive, Cot 1/2 decreases.

P= 1.660+0.098(G+C) molar fraction in DNA

Tm= 69.3+ 0.41(G+C) molar percent

• Deanimation: C->U
• depurination: hydrolysis of N-glycoscidic bond
• UV damage: form cyclobutane T, Dimer or 6-4 photo product
• nitrate & nitrite can cause de- NH₄
• alkylating agents e.g. (CH₃)₂SO₄

• Topoisomers.
• L is linking number or linkin #. L changes only when covalent bonds are broke as in gyrase strain. T; twist; w: writhe (supercoil)
• L= T+W

• DNA gyrase is a type II topoisomerase, introduced in supercoils
• Type I topoisomerase : increase L by 1x
• Type II decrease L by 2x
• (negative supercoild favor strands seperation)

Circular DNA duplex with supercoiled loops complex with a protein RNA core.

Cleave phosphodiester bonds in DNA.

Cleaves phosphodiester bonds in RNA.

That loops adopts an extended relaxed conformation, super coiling is gone.

A Eukaryotic Chromosome contains a single linear DNA duplex in a highly compacted form known as chromatin that is a complex of DNA and proteins (histones)

Think of beads on a string. The beads are nucleosomes.

• 23s
• /
• 50s---34protein
• E.coli ribosome/
• \ 30s----16s RNA
• 21 proteins

• ATP: energy
• CoA: acyle transfer
• NAD+=H^{- transfer}
• FAD: e^- transfer
• Camp: 2^nd messenger

• S (svedberg)
• -zonal (isophychic) centrifugation with CsCL density gradient.

• 1) General features 1: Growing during replication is bidirectional 2: Growth at replication fork is semi
• leading strand: replicates without a problem
• lagging strand: must replicate with (okazaki fragments)

it is an eznyme containing 3 functions; klenow fragment has the first two functions.

the main replication enzyme, has 10 kinds of polypeptide e.g. beta 2 dimer, the sliding clamp, encircle the template, wake pol III high processive, also has proofreading ability.

Synthesize RNA primer.

Introduce negative supercoils, release torsinal stress.

Unwind DNA duplex, dsDNA --> ssDNA

• 1) initiation: OriC DUE ( DNA unwinding Element)
• 2) Elongation
• 3) Termination

The mutiprotein complex that promotes DNA synthesis at replication fork.

An exyme complex that synthesiszes primers for DNA replication.

Seal nick: use ATP or NAD+ form E. AMP inermediate.

In yeast, ARS: automonous replication sequence is the origin of Rep yes has ~400 ARS, ARS is recognized by ORC ( origin recognition complex) which initiate replication

It is a specialized reverse transcriptase.

• Mismatch repair
• Base excision repair
• Nucleotide excision repair
• Direct repair: repair of mG (methylated G) :mg pair with T rather than C causing GC to AT mutation in Daughter generation.

DNA adenine methylation ezyme methylase. it methylates A of GATC sequence.

• 1)Homologous genetic recombination (general recombination) E.G. in Phase I of meiosis, for "holiday intermediates"
• 2) Site specific recombination: use recombinase which recognize specific sequence for recombination
• 3) Transposition: transposons are transposable elements "jump" from one place to another on chromosomes.

-10: pribnow box : TATAAT -35 TTGACA

• 1) Initiation.
• 2) Elongation
• 3) Termination

• 1) formation of a G:C rich hairpin followed by several U
• 2) Depend on termination factor rho (P) protein: P has helicase and ATP ase activities

RNA Pol II