Biochemistry

  1. Stages of cell cycle
    • 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
  2. Chemotherapeutic agents targeting specific phases of cell cycle
    • 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
  3. Nitrogenous bases
    • 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
  4. Deficiency of ADA
    • causes SCID
    • severe combined immunodeficiency
    • AR with complete defect of T and B cells combinedly
  5. Nucleoside vs Nucleotide
    • 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
  6. Attachments of sugar molecule
    • 1': base
    • 2': OH (+ in ribose sugar/- in deoxyribose)
    • 5': Phosphate (in nucleotide0
  7. Nucleic acids
    • 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
  8. Chargaff's rule
    • in a ds DNA (or ds RNA)
    • %purines=%pyrimidines
    • %A=%T (%U)
    • %G=%C
  9. Suppose a sample of DNA has 10% A and 50%G. What is the significance?




    • A) 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.
  10. DNA Structure
    • 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
  11. Denaturation and Renaturation of DNA
    • 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
  12. Nucleosomes and Chromatin
    • Chromatin= DNA+Protein
    • Nucleosome=DNA+Histone octamer (specific proteins)
    • The basic packaging unit of chromatin is the nucleosome.
  13. Histones
    • 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.
  14. Euchromatin vs Heterochromatin
    • 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

  15. Heterochromatin
    • 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
  16. Negative charge in DNA
    due to phosphates
  17. Nucleolus
    specialized for ribosome assembly
  18. DNA replication
    semiconservative: each parental strand is used as a template for synthesis of new complementary strand.
  19. Polymerase
    synthesize nucleic acids by forming phosphodiester (PDE) bonds
  20. Nucleases
    • 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
Author
Binita
ID
342191
Card Set
Biochemistry
Description
Central dogma of molecular biology and enzyme kinetics
Updated