Biochemistry

• R groups affect the amino acids:

  • size
  • polarity
  • name
• General structure of an amino acid

  A) R group

  B) Amine group

  C) carboxyl group

  
• Effect of the environment on amino acids:

  Acidic conditions: all amine groups accept a proton becoming NH3+

  Alkaline conditions: All carboxyl groups donate an proton becoming COO-

  Neutral: Exist in their zwitterion form
• Properties of Amino acids:

  High melting points

  soluble in water

  Reason: Because of their charged groups on their zwitterions
• Naming amino acids

  To find the IUPAC name for an amino acid: 

   

  1. Identify the longest carbon chain to write the root.
  2. Identify all the functional groups and substituents.
  3. Use the highest priority functional group to write the suffix.
  4. Number the longest carbon chain.
  5. Add the prefix, including all additional substituents.
• The r group of zwitter ions remain unchanged whilst the amine and carboxyl group change to their charged form
• A bond between 2 amino acids is called a peptide link and occurs between the amine group and carboxyl group
• individual amino acids that are joined together are called amino acid residues
• The joining of 2 amino acids is an example of a condensation reaction as it produces a molecule of water
• polypeptides can be split up via hydrolysis
• a peptide bond is formed when the hydrogen of an amine group reacts with the hydroxyl group of the carboxyl group of another amino acid forming water and leaving the C=O forming a bond NH
• all but one amino acids have a chiral carbon
• Enzymes are proteins that act as a biological catalyst. They speed up chemical reactions without being used up.
• The substances that react with enzymes are called substrates
• The enzyme model theory used in chemistry is the lock and key theory where the shape of the substrate is complementary to the shape of the enzymes active site hence fits into the lock
• Enzymes are stereospecific meaning only a single enantiomer from a pair can bind to its active site
• Enzyme inhibitors are molecules that bind to the active site of an enzyme and prevent the substrate from binding

  some antibiotic drugs are designed for this purpose, for example to prevent the breakdown of a poison to its harmful components
• Competitive inhibition occurs when there is competition between the substrate and the inhibitor for the same active site on the enzyme
• Bonds between R groups consist of hydrogen bonding, covalent bonding between 2 Sulfur of cystine groups called disulfide bridges
• The components of DNA:

  2-deoxyribose sugar

  nitrogenous bases

  Phosphate ions
• DNA exists as a double helix structure
• Cytosine forms 3 hydrogen bonds with Guanine
• Adenine forms 2 hydrogen bonds with Thymine
• A single strand of DNA (deoxyribonucleic acid) is a polymer of nucleotides linked by covalent bonds between the phosphate group of one nucleotide and the 2- deoxyribose of another nucleotide. This results in a sugarphosphate-sugar-phosphate polymer chain with bases attached to the sugars in the chain
• The anti-cancer drug to know is called cisplatin. It is a platinum complex that is used to treat cancer.
• Cisplatin works by a ligand replacement reaction where chlorines are replaced with a bond forming between platinum and a nitrogen on guanine and prevents DNA replication
• A side effect of cisplatin is hair loss as when ingested it affects all of your body but more so towards cells that replicate more frequently which involves hair