biochem chapter 1

• produces all the proteins an organism requires
• during transcription RNA copy of only a small portion of DNA is made
• transcription occurs in nucleus throughout interphase
• translation occurs in cytoplasm throughout the cell cycle

• duplicates the chromosomes before the cell division
• DNA copy of an entire chromosome is made
• occurs during S phase of the cell cycle
• replication occurs in nucleus

throughout all phases of interphase

• gap1 phase
• period of cell growth pior to replication
• cells that hav stopped cycling like musc and nerve cells are in G0 phase

• synthesis phase
• DNA replication occurs
• at the end of S phase each chromosome has double DNA content and is composed of two chromatids held together at the centromere

• gap 2 phase
• replicated DNA is checked for errors prior to cell division

• s phase - methotrexate, hydroxyurea, 5FU
• G2 phase - Bleomycin
• M phase - paclitaxel, vincristine, vinblastine
• non cell cycle specific - cyclophosphamide and cisplatin

• produces DNA copies of RNA
• commonly ass with life cycles of retro viruses
• can also occur to a limited extent in humans where it helps to amplify certain highly repetitive sequences in the DNA

• formed by covalently linking a base to the 1` carbon of the sugar
• purine nucleosides - suffix "osine"
• pyramidine nucleosides - suffix "idine"

phos gr added to the 5` carbon of a nucleoside

they are high energy comp due to hydrolytic energy ass with acid anhydride bonds

• polymers of nucleotides linked by 3`-5` phosphodiester bonds
• have distinct 3` and 5` ends and thus polarity
• sequence is always specified from 5` to 3`
• if written backwards the ends must be labelled

• 2 strands are antiparallel
• complementary
• A pairs with T (2 hyd bond)
• G pairs with C (3 hyd bond)
• the amt of A= amt of T
• the amt of G = amt of C
• purines% = pyramidine %
• these are chargaff rules - applicable for ds nucleic acids

• most dna exist as right handed helix 
• also known as watson crick dna or B dna
• there are 10 bases per complete turn of the helix

• a rare left handed double helical dna 
• with G-C rich sequences
• biologic fun is unknown, may be related to gene regualtion

• these are groves between the turns of the helix
• provide binding sites for regulatory proteins

• they are antitumor drugs that are used in rx of leukemias
• act by intercalating between bases of DNA and thus interfer with the activity of topoisomerase II and prevent proper replication of DNA

• used in rx of bladder and lung tumors
• binds tightly to Dna and causes struc distortion and malfunc

• ds dna hydrogen bonds disrupted to give two seperate single strands
• no covalent bonds are broken in this process
• heat, alkaline pH, and chemicals like fomamide and urea are commonly used to denature DNA
• also called melting of the double helix

• denatured Dna can be renatured if the denaturing condition is slowly removed
• this process is also called annealing

• mitochondrial DNA and prokary Dna exist as closed circles
• they may be relaxed circles or supercoiled circles with the helix twisted around itself in 3d space
• supercoiling results from strain on the molecule cause by under or overwinding of the double helix

• formed when DNA is wound more loosely than in Watson crick model
• required for most biological reactions
• topoisomerases can change the amt of supercoiling in DNA 
• they make transient breaks in DNA strands by alternatively breaking and resealing the sugar phos backbone
• in E.coli, the DNA gyrase (DNA topoisomerase II) can introduce negative supercoiling into DNA

when DNA wound more tightly than in watson and crick model

DNA+histones+non histone proteins

lysine and arginine, which confer them positive charge

made of two copies each of H2A, H2B, H3 and H4

• formed when DNA wounds twice around this histone octamer
• series of nucleosomes - beads on a string

ass with linker DNA found between nucleosomes to help package them into a solenoid like struc which is a thick 30nm fibre

• more active --------------------------> less active
• DNA double helix --> 10nm chromatin --> 30 nm fibre --> 30nm arranged into rossettes --> higher order of packaging
• till 30nm in rossettes - euchromatin
• later - heterochromatin

• loosely arranged
• transcriptionally active
• sterically accessible

• highly condensed
• transcriptionally inactive
• sterically inaccessible

metaphase chromosomes

prophase or prometaphase chromosomes

most condensed

the more opened the DNA is the more sensitive it is to enzyme attack

it means that the nucleic acid is a single stranded one