biochem chapter 1

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theapk200
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biochem chapter 1
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2013-09-13 23:43:40
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  1. features of gene experssion
    • 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
  2. features of DNA replication
    • 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
  3. when does gene expression occur
    throughout all phases of interphase
  4. G1 phase
    • gap1 phase
    • period of cell growth pior to replication
    • cells that hav stopped cycling like musc and nerve cells are in G0 phase
  5. s 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
  6. G2 phase
    • gap 2 phase
    • replicated DNA is checked for errors prior to cell division
  7. drugs targeting phases of cell cycle
    • s phase - methotrexate, hydroxyurea, 5FU
    • G2 phase - Bleomycin
    • M phase - paclitaxel, vincristine, vinblastine
    • non cell cycle specific - cyclophosphamide and cisplatin
  8. reverse transcription
    • 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
  9. nucleosides
    • formed by covalently linking a base to the 1` carbon of the sugar
    • purine nucleosides - suffix "osine"
    • pyramidine nucleosides - suffix "idine"
  10. nucleotides
    phos gr added to the 5` carbon of a nucleoside
  11. abt nucleoside di and tri phosphates
    they are high energy comp due to hydrolytic energy ass with acid anhydride bonds
  12. nucleic acids
    • 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
  13. DNA struc
    • 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
  14. B dna
    • 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
  15. Z dna
    • a rare left handed double helical dna 
    • with G-C rich sequences
    • biologic fun is unknown, may be related to gene regualtion
  16. major and minor grooves of double helix
    • these are groves between the turns of the helix
    • provide binding sites for regulatory proteins
  17. daunorubicin and doxorubicin vs DNA struc
    • 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
  18. cisplatin VS dna struc
    • used in rx of bladder and lung tumors
    • binds tightly to Dna and causes struc distortion and malfunc
  19. denaturation of Dna
    • 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
  20. renaturation of DNa
    • denatured Dna can be renatured if the denaturing condition is slowly removed
    • this process is also called annealing
  21. DNA supercoiling
    • 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
  22. negatively supercoiled DNA
    • 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
  23. positively supercoilied DNA
    when DNA wound more tightly than in watson and crick model
  24. chromatin
    DNA+histones+non histone proteins
  25. histones are rich in what aminoacids
    lysine and arginine, which confer them positive charge
  26. histone octamer
    made of two copies each of H2A, H2B, H3 and H4
  27. nucleosome
    • formed when DNA wounds twice around this histone octamer
    • series of nucleosomes - beads on a string
  28. H1 histone
    ass with linker DNA found between nucleosomes to help package them into a solenoid like struc which is a thick 30nm fibre
  29. DNA packaging in a eukaryotic cell
    • 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
  30. euchromatin
    • loosely arranged
    • transcriptionally active
    • sterically accessible
  31. heterochromatin
    • highly condensed
    • transcriptionally inactive
    • sterically inaccessible
  32. karyotype analysis uses which chromosomes
    metaphase chromosomes
  33. banding tech utilize which chromosomes
    prophase or prometaphase chromosomes
  34. mitotic DNA level of packaging
    most condensed
  35. which chromatin will be more senstive to enzymatic action
    the more opened the DNA is the more sensitive it is to enzyme attack
  36. if chrgaffs rules are not applicable what does it mean
    it means that the nucleic acid is a single stranded one

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