SU 5

• 20 amino acids


  • Diverse number of proteins
• Amino acids


  Make up proteins
• Proteins are the agents of biological function
• At neutral pH


  NH3+ and COO-
• pH at which this occurs

  Isoelectric point
• Central carbon


  Alpha carbon
• Amino acids


  • Chiral: 4 different groups attached
  • Asymmetric

  
• Side chain


  Gives the molecule its identity
• All (except glycine) amino acids are asymmetrical/chiral
• Asymmetrical/chiral


  • 4 different types of atoms or groups of atoms or groups linked to central carbon
  • Non-superimposable mirror images
  • 2 configurations (L and D)
  • All amino acids in protein are of the L-configuration

  
• Spectroscopic properties


  Aromatic rings absorb UV light
• Classification based on polarity side chains

  • Charged polar hydrophilic side chains: protein surface
  • Hydrophobic side chains buried in the core of the protein (no water contact)
  • Nonpolar: important in processes that drive protein folding
  • Polar uncharged: R groups form hydrogen bonds with water (amide+OH groups), nucleophilic roles in enzyme reactions soluble in water
  • Acidic: R group = carboxyl groups
  • Basic

  
• Polymerize via peptide bond


  • Due to amino and carboxyl groups
  • Water lost
  • Amide/peptide bond formed
  • At equilibrium: hydrolysis favoured
  • Bond formation require energy input

  
• A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule releasing a molecule of water H2O

  
• Amino and carboxyl groups

  Can ionized in solution depending on pH
• Henderson-Hasselbach


  Used to understand ionization
• pKa


  pH where you have equal amounts of the protonated and unprotonated forms

  
• Buffers


  • Resist changes in pH
  • Max buffering capacity at specified pKa
• Application


  • Estimates charge of amino acids
  • Calculate concentration of [A-] or [HA] or both
  • Similarly, pH of solution can be calculated

  
• Amino acids

  • Weak polyprotic acids (contain min of 2 dissociable hydrogens)
  • Groups don't dissociate easily
  • Dissociation is pH dependent
  • Low pH: increased [H+]; protonated
  • High pH: increases OH, less [H+]; deprotonated
• In trying to understand how nucleotide sequences in mRNA are translated to amino acid sequences, one has to understand the genetic code

  
• Genetic code


  • Code that allows for translation of this information
  • 4 letter nucleotide language translated to 20 letter language
  • No affinity between bases and amino acids
  • Structural/stereochemical connection between polynucleotides and amino acids
  • Molecules are polar and asymmetric
  • Sense/direction
  • The order of building blocks specifies information
  • Letters make up words
  • Information can inturn be extracted/retrieved from the structure of molecules
  • For retrieval recognition is required
  • Recognition → interaction → physiological activity
  • Recognition mediated via weak forces
  • Complementarity aspect

  
• Francis Crick postulated adaptor molecules to read and interact with mRNA and amino acids

  
• Amino acid attached to 3' OH group at 3' CCA end of tRNA

  Forming amino acyl tRNAs

  
• Process is catalyzed by amino acyl tRNA synthetase


  1 enzyme per amino acid

  
• Each amino acyl tRNA synthetase loads its amino acid only onto a tRNA designed to carry it

  
• In turn tRNA will recognize unique specific sequences of bases in the mRNA through complementary base pairing

  
• Secondary structure of tRNA

  Linear sequence of ~85 nucleotides of the polynucleotide chain from the 5' to the 3'-OH CCA terminal with a universal 3'-OH CCA terminal end

  
• Genetic code


  • Triplet code continuously read from a start point in mRNA
  • Codons are triplets of bases in mRNA that specifies amino acids
  • Consecutive, non-overlapping
  • All codons have meaning (61 of 64 = amino acids, 3 stop/nonsense codons)
  • Unambiguous (1 codon/amino acid)
  • Degenerate (1 amino acid specified by different codons)
  • Codons representing the same or chemically similar amino acids tend to be similar in secuence
  • Universal

  
• It was recognized that bases specify a.a sequences
• Codons with pyrimidine as second base


  Yields amino acids with hydrophobic chains

  
• Codons with purine as second base


  Yields amino acids with polar or charged amino acids

  
• Codons representing same/similar amino acids


  Are similar in sequence, 3rd base irrelevant = 3rd base degeneracy

  
• Degeneracy


  Protective against mutational disruption
• Secondary genetic code


  Code which each aminoacyl-tRNA synthetase matches an amino acid to tRNAs so that tRNAs can interact with codons specifying the amino acid

  
• How amino acid is matched with its tRNA

  1. mRNA has codon specifying amino acid sequence

  2. Amino acid added at 3'OH of CCA end of tRNA, process catalyzed by amino acyl tRNA synthetases (1 enzyme per amino acid)

  3. Each amino acyl tRNA synthetase loads its amino acid only onto a tRNA designed to carry it

  4. In turn tRNA through its anticodon will recognize unique specific sequences of bases in the mRNA through complementary base pairing

  5. Reaction serves to activate the amino acid so it can form a peptide bond, bridges codon-amino acid formation gap, ensures proper amino acid loaded onto tRNA, mNA translated with fidelity, information transfer is accurate

  
• Codon-anticodon interaction


  • Protein synthesis dependent on codon-direction binding of proper aminoacyl tRNA
  • Ensures amino acid is aligned according to the mRNA undergoing translation
  • Codon-anticodon pairing achieved
  • Degeneracy (different codons yield a particular amino acid) in the genetic code at the 3rd base resolved by increasing specificity: 1 anticodon for each of those codons, fewer anticodons so that 1 anticodon recognizes more than one codon (yielding the same amino acid)
  • Crick noted: some organisms have less than 61 tRNA
  • More at play at 3rd base of codon at 1st base of anticodon, bp less stringent, more than 1 codon for most amino acids
  • tRNAs of particular amino acid (whether the 1 amino acid is coded by 5 plus codons) will have 1 synthetase
  • Bais in codon usage e.g. codons specifying Leu. CUG used more than 48000 time vs UUA (6000 times), greater bias to use CUG
  • When mutations alter codon to nonsense codon protein synthesis is terminated, incomplete polypeptide yielded, not always deletions, can confer advantages

  
• Activation of amino acids

  • tRNA synthetase has to recognize amino acids and discriminate the various tRNAs
  • No universal structural features that allows amino acyl synthetases to recognize a specific tRNA, unique combination of sequences elements allows for recognition: 1 base in the anticodon, 1st free bp after 3'CCA, 1 or more of the 3bp in the acceptor stem
  • 2nd genetic code is an operational code, amino acyl synthetases have to recognize varying sequence and structural features of the different tRNAs during aminoacyl tRNA synthesis

  
• Image shows identity elements within the tRNA that are recognized by its specific aminoacyl-tRNA synthetase

  
• Synthetase enzyme


  Relies on anticodon for selecting tRNA for loading, altering anticodon specifies whether tRNA would be loaded or not and also with which amino acid, although recognition features reside in the anticodon recognition is not limited to the anticodon