biochem

• Nucleic acids


  Polynucleotides (formed by the polymerization of nucleotides)

  
• Nucleic acids

  • Biopolymers essential to all forms of life
  • Cells have ability to produce exact replicas of themselves
  • Cells contain all instructions needed for making a complete organism
• Deoxyribonucleic acid (DNA)


  Primary function is the storage and transfer of genetic information

  
• Ribonucleic acid (RNA)


  Primary function is the synthesis of proteins

  
• Nucleotide


  Three subunit molecule; pentose sugar bonded to both phosphate group and a nitrogen-containing heterocyclic base

  
• Nucleoside


  Molecule without phosphate group
• Nitrogenous bases


  • Purines (adenine, guanine)
  • Pyrimidines (thymine, cytosine, uracil)

  
• Phosphate group


  Under cellular pH conditions, the phosphoric acid loses two of its hydrogen atoms to give a hydrogen phosphate ion HPO42-

  
• Nucleoside


  Composed of a nitrogenous base and a sugar

  
• Glycosidic bond


  Bond between base and sugar in a nucleoside

  
• Nucleosides of RNA and DNA

  • Adenosine, guanosine, cytidine, uridine
  • Deoxyadenosine, deoxyguanosine, deoxycytidine, deoxythymidine

  
• Nucleotide


  Phosphate ester of a nucleoside

  
• Nucleotides of RNA

  • Adenosine 5'-triphosphate (ATP), guanosine 5'-triphosphate (GTP), cytidine 5'-triphosphate (CTP), uridine 5'-triphosphate (UTP)

  
• Nucleotides of DNA


  • Deoxyadenosine 5'-triphosphate (dATP), deoxyguanosine 5'-triphosphate (dGTP), deoxycytidine 5'-triphosphate (dCTP), deoxythymidine 5'-triphosphate (dTTP)

  
• Differences between DNA and RNA

  • Location (nucleus, mitochondria, chloroplasts vs nucleolus, chromosomes, cytoplasm)
  • Composition (pyrimidine bases, purine bases, sugar, acid)
  • Structure (double helix vs single stranded)
  • Function (storage and transfer of genetic information)

  
• Primary nucleic acid structure

  Sequence in which nucleotides are linked together in nucleic acid

  
• Nucleic acid backbone


  Alternating sugar-phosphate chain

  
• Phosphodiester bond


  Linkage between two nucleotides
• DNA is wrapped tightly around histones and coiled tightly to form chromosomes
• In normal human cells, DNA is contained in the nucleus, arranged in chromosomes
• DNA


  Deoxyribonucleic Acid, the genetic material of all cellular organisms and most viruses, the gigantic molecule which is used to encode genetic information for all life on Earth

  
• DNA

  • Have a 5' end and a 3' end
  • Each nucleotide can be thought of as a single letter taken from the first letter of the name of the base (A,G,T,C, & U) creating a base sequence written in the 5' → 3' direction

  
• DNA strand


  • 5'ACTTTCAGACCTG3'
• RNA strand


  • 5'GUCAAGCCGAUC3'
• DNA & RNA chain


  A fragment of
• Function of DNA


  • Storage of genetic information
  • Transmission of genetic information
• Eukaryotic organisms


  • Store their DNA inside the cell nucleus
• Prokaryotes


  • Their DNA is found in the cell's cytoplasm
• In normal human cell DNA contained in the nucleus, arranged in 23 pairs of chromosomes
• 1. DNA


  Right-handed helix, exhibits a larger diameter (2.6nm), with 11 bases/turn of the helix, bases are stacked closer in the helix (0.25nm apart)
• 1. DNA


  The most dominant form, the base pairs are stacked 0.34 nm apart, 10bp/turn of the right handed double helix, diameter of approx, 2nm

  
• 1. DNA


  Left-handed, bases seem to zigzag, One turn spans 4.6 nm, comprising 12 base pairs, DNA molecule with alternating G-C sequences in alcohol or high salt solution tends to have such structure

  
• B and A DNA

  • Reveal the presence of a major groove and a minor groove, these grooves particularly the minor groove contain many water that interact with the amino and keto groups of the bases

  
• Complementary base pairing


  • Adenine – Thymine base pair (forms 2 H-bonds)
  • Guanine – Cytosine base pair (forms 3 H- bonds)

  
• Chargaff's Rule: Adenine must pair with Thymine, Guanine must pair with Cytosine, their amounts in a given DNA molecule will be about the same

  
• DNA Double Helix

  • Strands connected by Hydrogen bonds between bases
  • Bases extend inward
  • Strands antiparallel

  
• Factors that make DNA stable: Covalent bonds linking the individual nucleotide subunits, Noncovalent interactions (hydrophobic, H-bonds, electrostatic), Planar structure of bases, Base stacking, Positive reactions between DNA & proteins

  
• Types of RNA


  • Messenger RNA (mRNA)
  • Transfer RNA (tRNA)
  • Ribosomal RNA (rRNA)
• Messenger RNA (mRNA)


  Carries DNA sequence information to ribosomes
• Transfer RNA (tRNA)


  Provides linkage between mRNA and amino acids, transfers amino acids to ribosomes