Biochemistry

• Mitosis: cell division
• Interphase: G0~G1, S, G2
• G1: period of cellular growth preceding DNA synthesis; non-dividing cells like muscles and nerves enter G0
• S: Synthesis of DNA via replication
• G2: Replicated DNA is checked for any errors before cell division

• S phase
• Methotrexate: blocks dihydrofolate reductase
• 5-fluorouracil: blocks thymidylate synthase
• G2 phase
• Bleomycin: used in Hodgkin's lymphoma
• M phase
• Paclitaxel, Vincristine, vinblastine: target mitotic spindle, depolymerize micotubules
• Non-cell cycle specific
• Cyclophosphamide, Cisplatin

• Purines: 2 rings;Adenine, Guanine
• @ Pure As Gold
• Adenine-- deamination by Adenosine deaminase--- forms Guanine
• Amino @ Adenine
• Pyrimidine: single ring; Cytosine, Uracil, Thymine @ CUT
• Cytosine-- deamination with ADA--- forms Uracil
• Uracil-- methylation with Thymidylate synthase--- forms Thymine

• causes SCID
• severe combined immunodeficiency
• AR with complete defect of T and B cells combinedly

• Nucleoside: Sugar + Nitrogen base (covalent link)
• Nucleotide: Sugar + Nitrogen base + Phosphate (1 or more)
• di and tri phosphates are high energy compounds b/o hydrolytic energy a/w acid anhydride bonds

• 1': base
• 2': OH (+ in ribose sugar/- in deoxyribose)
• 5': Phosphate (in nucleotide0

• polymers of nucleotides joined by 3'-5'phosphodiester bonds
• phosphate group links 3' C of a sugar to 5' C of next sugar in chain
• sequence always specified as 5'→ 3' direction from left to right

• if not specified the this is the direction by convention
• eg= TCAG -- 5'-TCAG-3'
• if written backwards, written as= 3'-GACT-5'

• Usually ds DNA and ss RNA 
• exceptions occur in certain viruses where ss DNA and ds RNA genomes maybe present

• in a ds DNA (or ds RNA)
• %purines=%pyrimidines
• %A=%T (%U)
• %G=%C

• B) viral genome
• All options listed are examples of circular ds DNA except C. only a few viruses have single stranded DNA (parvovirus) or ss RNA genomes.

• A always pairs with T with 2 hydrogen bonds: A=T
• G always pairs with C with 3 hydrogen bonds: GΞC
• Thus, GC bond is more stable.
• Most DNA occur as right handed double helical molecule
• aka Watson-Crick DNA or B DNA
• 10 base pairs per complete turn of helix
• Z DNA: left handed double helical form, occurs in GC rich sequences, biologic fun unknown, maybe related to gene regulation

• Disrupt hydrogen bondinga nd base stacking
• No disruption of covalent links
• Agents for denaturation: Heat, Alkaline pH and chemicals like formamide and urea
• Renaturation (or annealing) occurs if denaturing condition is slowly removed.
• Significance: Southern blot and PCR
• Hybridization: When probe DNA binds to target DNAsequqnces of sufficient complementarity
• Probe DNA: DNA synthesized in labs

• Chromatin= DNA+Protein
• Nucleosome=DNA+Histone octamer (specific proteins)
• The basic packaging unit of chromatin is the nucleosome.

• Positively charged proteins
• Rich in l2 positively charged aamino acids lysine and arginine
• Two copies of each histone H2A, H2B, H3 and H4 aggregate to form histone octamer
• H1 is a/w linker DNA found between nucleosomes to help them package to a thick 30 nm fiber
• Further condensation forms chromosomes.

• Euchromatin
• corresponds to nucleosomes (10 nm fibers)
• loosely a/w with each other to form nucleofilaments (30 nm fibers)
• light staining in electron micrograph
• more active (eg: apoptotic cells)
• expressed
• Histone acetylation or phosphorylation 
• -lose the + charge
• -dissociate from DNA
• -favors transcription

• higher order packaging
• dark staining in electron micrograph
• chromatin characteristic of mitotic chromosomes
• less active (eg: barr body)
• not expressed
• DNA methylation
• -inactivates transcription
• -favors heterochromatin

due to phosphates

specialized for ribosome assembly

semiconservative: each parental strand is used as a template for synthesis of new complementary strand.

synthesize nucleic acids by forming phosphodiester (PDE) bonds

• enzymes that hydrolyze PDE bonds
• -Exonucleases: remoe nucleotide from 3' or 5' end of nucleic acid
• -Endonucleases: cut within nucleic acids and release nucleic acid fragments