amino acids, proteins and DNA

• amino acids

  -organic compounds that contain a basic amino group (NH2) and an acidic carboxylic acid (-COOH)

  -amphoteric due to presence of both a basic and acidic group
• naturally occurring amino acids

  -2-aminocarboxylic acids have -NH2 bonded to C atom next to COOH

  -these make up building block that make up proteins

  -R group can be acidic, basic or neutral
• acid/base properties of amino acids

  -can interact intramolecularly to form a zwitterion

  -ion with both +ve (-NH3+) and -ve (-COO-) charge

  -due to charges - strong intermolecular forces of attraction between amino acids - therefore are soluble crystalline solids
• Isoelectric point

  -a soln of amino acids will exist as zwitterions with both acidic and basic properties

  -act as buffer solutions - can resist changes in pH

  -if an acid is added - COO- will accept H+ to reform COOH - zwitterion to become +ve charged ion

  -is base is added - NH3+ will donate H+ to reform NH2 - zwitterion becomes -ve charged ion

  -pH can be slightly adjusted to reach a point at which neither -ve or +ve charged ions dominate - exists as neutral - isoelectric point
• peptide bond

  The chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid
• primary structure of proteins

  -the sequence of amino acids bonded by covalent peptide bonds

  -primary structure is specific for each protein
• secondary structure of proteins

  -when weak -ve charged N and O interact with weak +ve charged H to form H bonds

  -most fibrous proteins have secondary structures

  -only relates to H bonds forming between amino group and carboxyl group

  -H bonds can be broken at high temps and pH changes
• alpha helix

  A spiral shape constituting one form of the secondary structure of proteins, arising from a specific hydrogen-bonding structure.
• beta pleated sheet

  One form of the secondary structure of proteins in which the polypeptide chain folds back and forth, or where two regions of the chain lie parallel to each other and are held together by hydrogen bonds.
• tertiary structure of proteins

  -additional bonds forming between R groups

  -additional bonds are:

  hydrogen bonds between R groups

  Disulphide bonds between cysteine amino acids

  ionic bonds between charged R groups

  weak hydrophobic interactions between non polar R groups

  -more common in globular proteins
• hydrolysis of proteins

  -peptide link is broken and water is added

  -polypeptides are broken down to amino acids

  -conc HCl is the reagent used and the mixture is boiled for many hours as the reaction is slow

  -with enzyme, reaction occurs at room temp
• identifying amino acids

  -after hydrolysis amino acid components can be identified using TLC

  -R group changes overall polarity of the molecule so amino acids will rise up TLC at different rates
• enzymes

  -biological catalysts

  -speed up the rate of chemical reactions w/out being used up

  -globular proteins

  -extreme heat or pH can change shape of active site - denaturation

  -substrates collide with enzyme active site at the correct orientations and speed in order for reaction to occur
• enzyme specificity

  -result of the complementary nature between shape of active site and its substrate

  -specificity determined by complex tertiary structure

  -chain of amino acids held together by peptide bonds

  -order of amino acids determines the shape

  -if order is altered, the shape changes

  -stereospecific - one substrate can bind
• Drug-Receptor Interactions

  -receptors are proteins found on enzymes, membranes or DNA

  -drugs work by their ability to bind to receptors stopping their normal activity and interrupting the development of disease

  -bind using intermolecular forces or ionic bonds

  -stronger interaction = more effective drug activity
• drug receptor interactions: enantiomers

  -many naturally occurring organic molecules consist of enantiomers - only one is biologically active

  -drugs also have enantiomers - only one form is active

  -site drug binds to can only accept one orientation - said to be stereoselective
• polynucleotide

  A polymer consisting of many nucleotide monomers in a chain; nucleotides can be those of DNA or RNA.
• nucleotide

  A building block of DNA, consisting of a five-carbon sugar covalently bonded to a nitrogenous base and a phosphate group.
• structure of DNA

  -polynucleotide made up of alternating deoxyribose sugars and phosphate groups bonded - forms sugar-phosphate backbone

  -bonds are covalent bonds AKA phosphodiester

  -DNA molecules made up of two polynucleotide strands running in opp directions - antiparallel

  -nitrogenous base project out from backbone
• hydrogen bonding in DNA

  -antiparallel polynucleotides held together by H bonds between nitrogenous bonding

  -always occur between the same bases

  -AT CG - complementary base pairing
• anticancer drugs - cisplatin

  -works by binding to nitrogen atoms on bases in DNA

  -cisplatin passes through cell membrane and undergoes ligand exchange where Cl replaced by H2O

  -N is a better ligand than H2O and forms dative bonds with CP

  -distorts shape of DNA preventing it from replicating
• adverse effects of cisplatin

  -binds to healthy cells as well as cancerous ones - affects cancer cells more because they are fast replicating

  -fast replicating healthy cells like hair follicles are also effected by cisplatin

  -hair loss of often a side effect of cancer treatment

  -cisplatin is a highly effective drug