Amino acids, proteins, DNA

• What are amino acids?


  Compound with an amino group and carboxyl group.

  Amphoteric (acid and base properties).

  They all except glycine have a side chain where R is a hydrogen.

  Amino acids except glycine are chiral molecules.
• Naming amino acids?


  Find longest carbon chain.

  No. the carbons.

  No. where the NH2 group lies.

  Name any other groups attached.
• Zwitterions?


  A molecule with both + and - ions.

  They only exist at the amino acids isoelectric point (pH where overall charge is 0).

  At low pH COO- accepts a H+.

  At high pH NH3+ loses a H+.

  
• TLC?


  Allows us to separate amino acids as they have varying solubility.

  Stationary phase is a silica/alumina metal plate.

  Place plate in solvent once pencil line and amino acid mixtures are added.

  Leave it until solvent is near top of plate. Remove and mark solvent front.

  We identify amino acids based on their solubility in the solvent.
• Identifying amino acids?


  Amino acids are colourless compounds. They can be seen using:

  Fluorescent dye and UV light. The colourless spots block glow from the dye so you can draw round them.

  Iodine (locating agent). Place chromatogram in sealed jar with iodine crystals. Iodine vapour sticks to chromatogram, dying them purple.
• Calculating rf values?


  no. spots on plate= no. amino acids in mixture.

  Distance travelled by spot/ distance travelled by solvent.

  rf values are fixed for each amino acids HOWEVER this changes if temp/solvent/make up of tlc plate changes.
• What're proteins?


  Amino acids joined by a peptide link.

  Chain can be broken via hydrolysis.

  2 amino acids form a dipeptide molecule
• How does further substitution occur in protein?

  -COOH and -NH2 at either end of dipeptide can undergo further substitution to make a polymer chain.
• What does hydrolysis require?


  6moldm-3 HCL

  110 degrees

  Reflux for 24 hours
• Primary protein structure?


  Shows the individual amino acid sequence that makes up a protein.
• Secondary protein structure?


  Hydrogen bonds exist between peptide link in chains. This pulls a straight chain into a coiled or pleated sheet.
• Tertiary protein structure?


  Protein chain is long and coils itself up.

  Additional bonds hold long coiled chain together.
• Forces in secondary/tertiary proteins?

  Intermolecular forces create a twisting feature and give the proteins a specific 3D shape.

  Temp/pH change the shape by affecting hydrogen bonding and the disulphide bond formation.
• Bonds holding a protein shape?

  Disulphide bonds:

  Cysteine has a thiol group (-SH). They lose the H atom and the sulfur atoms bond forming disulphide (S-S).

  Hydrogen bonding:

  Exists between highly electronegative atoms eg -OH, -NH2.
• Whatre enzymes?

  Proteins and biological catalysts that speed up chemical reactions.

  They catalyse metabolic reactions within living organisms.
• Whats a substrate?

  Molecules that enzymes interact with to speed up reactions.

  Enzymes only bind with specific substrates as their active sites have a fixed shape.
• Chiral carbon enzymes?

  Enzymes have chiral carbons as they are made up of amino acids.

  This means only 1 enantiomer in the substrate will fit into the active site.

  Active sites are stereospecific.
• What are inhibitors?

  A substance that has a similar shape to the substrate and fits into the enzymes active site, blocking it.

  This can slow the rate of reaction.
• The higher the conc of an inhibitor?

  The more active sites are blocked, so the rate of reaction decreases.
• The more strongly an inhibitor is binded to the active site?

  The more reduced the rate of reaction.
• Drugs as inhibitors?


  Some drugs block an enzymes active site that is responsible for making a bacteria's cell wall. If a cell wall can't be made, the bacteria will burst and die.
• Drug development?

  Requires trial and error.

  To speed p drug development, scientists use computer modelling to test how a drug will respond by enzymes without making the drug.

  This method is cheaper and quicker.
• What is DNA?

  Deoxyribonucleic acid is a polymer made up of nucleotide monomers.
• DNA nucleotides?

  Made from a phosphate, sugar and a base.
• How are polynucleotide chains formed?

  By joining nucleotides together.

  Phosphate on one nucleotide covalently bonds to a sugar on another. This creates a sugar-phosphate backbone formed via condensation polymerisation.
• Condensation polymerisation DNA?


  A phosphodiester bond is formed and water is eliminated.

  OH groups on phosphate/sugar can react further to extend the polymer chain.

  
• How is DNA formed?

  2 polynucleotide strands twist together to form a double helix.

  Strands are held via hydrogen bonds between bases.

  Adenine bonds with Thymine.

  Cytosine bonds with Guanine.
• polynucleotide strands?

  Hydrogen bonds form when delta positive hydrogen reacts with an electronegative element at the correct distance apart.

  No other pairings can occur as the partially charged ions would be too close and repel.

  
• Why is DNA a twisted double helix?

  To allow bases to align perfectly to form hydrogen bonds.
• What is Cis-Platin?

  An anti cancer drug.

  Square planar complex with a platinum metal ion, 2 ammonia ligands and 2 chloride ion ligands.

  
• Cis-platin Cl groups?

  They are always next door to eachother.

  Trans-platin has Cl ions opposite eachother and has a different bodily effecy.
• Formation of cancer?

  Cells that multiply to form a tumour by replicating its DNA.
• How does Cis-platin prevent cancer?

  Cis-platin binds to DNA in cancer cells and prevents the cell reproducing through cell division. The cell dies and cant repair itself.
• Cis-platin binding to DNA?

  The Cl ions are easily displaced. The pt bonds to a nitrogen atom on the guanine base in DNA.

  As it bonds to DNA, it creates a distortion and the strand can;t unwind or be copied.
• Cis-platin negatives?

  Prevents healthy cells from reproducing eg prevents hair cell regeneration.
• Reducing cis-platin side effects?

  Give lower dosages and using more targeted delivery to reduce attack of healthy cells.

  Still used in chemotherapy due to the long term benefits of eliminating cancer.
• Explain the origin of interaction from the dotted lines?

  Nitrogen and oxygen are very electronegative. Therefore C=O and N-H are polar. This results in a hydrogen bond forming between the oxygens lone pair of electrons and the delta positive hydrogen atom.

  
• How can cis-platin be administrated to reduce the side effects of preventing healthy cells from replicating?

  Use in very small amounts.

  Target the application to the tumour.
• TLC essential steps?

  Wear plastic gloves- prevents contamination from hands to plate.

  Add solvent to a depth of 1cm3- Ensures mixture from plate won't dissolve from it being too deep.

  Allow plate to dry in fume cupboard- the solvent is toxic.
• Outline the steps needed to locate the positions of the amino acids on the TLC plate and to determine their Rf values?

  Use UV light. Measure distance from baseline to spots. And distance from baseline to solvent front. rf value= spots/solvent.