Chapter 3: Gene to proteins

• DNA


  The genetic blueprint of life
• It's in our genes


  Refers to the genetic basis of differences between organisms
• Gene variation is responsible for most of the differences between organisms
• Epigenetic modifications of DNA nucleotides and alternative splicing of RNA account for plenty of differences too

  
• DNA in bacteria


  Located in the cytoplasm, circular in prokaryotes
• DNA in eukaryotes


  Located in the nucleus, linear and contained within chromosomes
• Genes are composed of DNA
• Chromosomes are composed of proteins (has 20 different types of Amino acids)
• DNA molecule


  Composed of genes - individual segments containing instructions for a single polypeptide
• Not all genes coded for by an organism's DNA are expressed as protein. Some genes code for functional RNA molecules

  
• Nucleic acids


  Polymers of nucleotides, which include bases
• Purines


  • A
  • G
• Nucleotides


  Consist of a nitrogen base, a monosaccharide (ribose), and at least one phosphate
• Pyrimidines


  • C
  • T
• RNA contains uracil rather than thymine

  
• DNA contains A, C, G, and T
• RNA contains A, C, G, and U
• DNA and RNA


  Contain sugar groups, with the sugar atoms numbered with primes

  
• Nucleoside


  A nitrogen base and ribose sugar

  
• Nucleotide


  A nucleoside with a phosphate group
• Phosphates


  Can attach to the sugar of the nucleotide, usually at C5'

  
• Nucleotides


  Serve as building blocks for RNA and DNA, involved in energy transduction, intracellular signaling, regulation of enzyme activating

  
• Coenzyme A


  Contains adenosine, carriers of other molecules during their synthesis and degradation, useful for capturing free energy

  
• NAD


  Contains adenosine, undergoes oxidation and reduction
• FAD


  Contains adenosine, oxidation and reduction occurs at riboflavin group (AKA vitamin B2)

  
• Nucleotide linkage


  Via sugar in phosphodiester backbone, read sequence of bases from 5' to 3'

  
• RNA primary structure


  Nucleotides linked 5' to 3' by phosphodiester bonds, sugar-phosphate backbone is constant, nitrogen bases are variable (5'-ACGU-3')

  
• DNA base pairing


  A and T have two hydrogen bonds, C and G have three hydrogen bonds

  
• DNA double helix


  • Strands are antiparallel, has a large groove and a small groove, sugar-phosphate outside exposed to solvent and negatively charged

  
• DNA is negatively charged
• 1. T and C-G base pairs are complementary
• 1. DNA


  The natural, right-handed form of the DNA helix
• RNA


  Single-stranded, has greater conformational freedom than DNA, can fold back on itself
• RNA-DNA hybrid helix


  Composed of one RNA and one DNA strand, different from standard DNA helix due to two -OH groups in RNA
• DNA stability


  • Depends mostly on stacking interactions, can also depend on hydrogen bonding

  
• DNA denaturation


  Unstacking of bases and separation of strands, occurs with increasing temperature
• GC bond is more stable than AT because it has three hydrogen bonds, thus it has a higher melting point
• DNA renaturation


  Separate strands can re-form a double helix by reestablishing hydrogen bonds and restacking base pairs, occurs with decreasing temperature

  
• Evolution occurs due to favorable changes in the sequence of nitrogen bases in the DNA over time
• The sequence of nitrogen bases in the DNA of identical twins is the same