Proteins and Enzymes

• What is the general structure of an amino acid?

  Every amino acid has a central carbon atom, an amino group(NH2), a carboxyl group(COOH), a hydrogen atom, a variable group(R) which is different for each amino acid. There are 20 naturally occurring amino acids.

  
• How are dipeptides formed?

  A condensation reaction between 2 amino acids where an OH$^-$ ion from the carboxyl group of 1 amino acid, and the H$^+$ ion from the amino group from another amino acid form a water molecule. A peptide bond is formed between the carbon of the -C=O group and the nitrogen of the -N-H group.
• What is the diagram for the formation of a dipeptide?


  As shown.

  
• How are polypeptides formed?

  Polypeptides are formed by polymerisation which is a serious of condensation reactions where many amino acids from a polypeptide chain, bonded together by many peptide bonds.
• How are proteins formed?

  Proteins are formed by bonding within the polypeptide chain to form a primary structure, secondary structure, tertiary structure and quaternary structure.
• What are the functions of proteins?

  Transport- haemoglobin in the blood carries oxygen

  Hormones - which have many different uses in the body

  Structural proteins - collagen in skin

  Movement - muscles

  Enzymes - to catalyse chemical reactions

  Glycoprotein - receptors on outside of cell, cell recognition.
• What is the biochemical test for proteins?

  1.add a sample to the test tube

  2. add an equal volume of biuret reagent/sodium hydroxide solution

  3. add a few drops of dilute copper(II) sulphate solution and mix gently

  positive-purple/lilac negative-blue
• What is the primary structure of proteins?

  The sequence of amino acids that is determined by DNA forming a polypeptide chain, it determines the ultimate shape and hence function of the final protein. A single change in the sequence may prevent it from carrying out its function due to a proteins function being very specific to its shape.
• What is the secondary structure of a protein?

  Hydrogen bonds are formed causing the polypeptide chain to twist into a coil either a alpha-helix or a beta pleated sheet. They hydrogen bonds are weak and are formed from the hydrogen on -NH group and oxygen of -C=O group.
• What is the tertiary structure of a protein?

  A complex 3D shape where bonds such as disulphide bridges, hydrogen bonds, ionic bonds cause alpha-helix and beta pleated sheets to fold and twist into the 3D shape. The 3D structure of a protein is very important for it to perform its function.
• What are the bonds in the tertiary structure of a protein?

  Disulphide bridges: between sulphur atoms which are fairly strong and are not broken easily.

  Ionic bonds: formed between carboxyl and amino groups not involved in peptide bonds, easily broken by changes in pH.

  Hydrogen bonds: formed between R groups of amino acids, many of them but individually they are weak and are easily broken
• What is the quaternary structure of proteins?

  Two or more polypeptide chains linked together in various ways. May contain a prosthetic group (non-protein). Even though 3D structure is important, the sequence of amino acids determines this 3D structure in the first place.
• What is denaturation?


  Denaturation - when a protein is subject to drastic changes in temperature or pH causing bonds to break meaning the tertiary structure has changed therefore the protein cannot perform its function and has been denatured. Hydrogen bonds break first, then ionic bonds, then last disulphide bridges as they are stronger and can withstand higher temperatures.
• What is the definition of a globular protein?

  They are soluble, spherical and are involved in chemical reactions. A hydrophobic R-group turns inwards and a hydrophilic R-group turns outwards forming the spherical shape. Example: enzymes.
• What is the definition of a fibrous protein?

  They have a structural function and form fibres, most have regular repetitive sequences of amino acids, usually insoluble. Example: collagen.
• What is the structure of collagen?

  Primary structure - unbranched polypeptide chain.

  Secondary structure - chain is very tightly wound, alpha - helix.

  Tertiary structure - chain is twisted into a second helix.

  Quaternary structure - made up of 3 such polypeptide chains wound together as individual fibres like a rope.
• What is the function of collagen?

  It is found in tendons, they join muscle to bone. The point where one collagen molecule ends and the next begins is spread out through out the fibre rather then being in the same position throughout.
• What is an enzyme?

  A globular protein that acts as a biological catalyst that speeds up the rates of chemical reactions, by lowering the activation energy of the reaction, without undergoing permanent changes meaning they can be reused repeatedly.
• What is activation energy?

  The minimum amount of energy needed to activate the reaction.
• What is the diagram that shows an enzymes affect on a reaction?

  Enzymes lower the activation energy required.

  
• What do enzymes lower in a reaction?

  They lower activation energy, they lower the temperature allowing metabolic processes to occur rapidly at 37 degrees Celsius in the body.
• What is the structure of an enzyme?

  A globular protein with a specific 3D tertiary structure. It contains a functional active site, it is made up of a relatively small number of amino acids. It forms a small depression with a specific shape within the much larger enzyme.
• What is the induced fit model of enzyme action?

  The active site is complementary to the shape of a substrate but not specific. It is flexible therefore when the enzyme and substrate interact the functional active site moulds around it, to form an enzyme-substrate complex. This puts strain on the bonds within the substrate, weakening the bonds. This lowers the activation energy of the reaction as less energy is required to break the bonds of the substrate.
• What is the structure of an enzyme-substrate complex?

  The substrate and enzyme interact where the substrate fits into the active site of the enzyme, forming an enzyme-substrate complex. It is held together temporarily by hydrogen and ionic bonds between certain amino acids of the active site and groups of the substrate molecule.
• What are the similarities and differences between the induced fit model and the lock and key model?

  Similarities: Enzyme and substrate are complementary, enzyme lowers substrate activation energy, forms enzyme-substrate complex, both catalyse reactions.

  Differences: active site is flexible and functional and moulds around substrate, active site distorts bonds in substrate, not an exact specific fit between enzyme and active site, enzymes does not have a rigid structure.
• What is the effect of temperature on enzyme action?

  As temperature first increases, kinetic increases causing enzymes and substrates to move around more rapidly resulting in more collisions and formation of more enzyme-substrate complexes, rate of reaction increases. This continues until an enzyme reaches its optimum temperature.

  Past the optimum temperature bonds begin to break slightly changing the shape of active site, rate of reaction slows down.

  At a certain temperature enzyme is disrupted so much it no longer works and is denatured.
• At what temperatures do each stage of effects of temperature usually occur?

  In the human body the optimum temperatures of enzymes is usually 40 degrees the body however is 37 degrees as any other temperature increase due to illness would cause denaturation, past 40 degrees enzymes found in the body begin to break down. At 60 degrees they are said to be denatured.
• What is the effect of pH on enzyme action?

  Each enzyme has an optimum pH and any change away from the optimum will decrease the rate of reaction. If the change in pH is extreme the enzyme will be denatured. A change in pH causes a change in charges of the active site meaning substrates cannot bind. Active site determined partly by bonds between -NH group and -C=O group a change in H$^+$ions affect this bonding. Bonds may break. Less enzyme-substrate complexes form, rate of reaction decreases.
• What is pH and how is it calculated?

  pH - measure of concentration of H$^+$ions.

  pH=-log10(H$^+$)
• What is the effect of enzyme concentration on the rate of reaction?

  Once an active site has acted on a substrate it can be used again on another substrate. As long is there is excess substrate when enzyme concentration increases so will rate of reaction. As more substrates can be acted on and form more enzyme-substrate complexes. If substrate is limiting the rate of reaction will level off when all substrates are being used by existing enzyme molecules.
• What is the effect of substrate concentration on enzyme action?

  If the concentration of enzymes is fixed, when substrate is increased the rate of reaction increases as more enzymes can be acted on, until the point when all enzymes are in use. The rate of reaction at its maximum (Vmax). After this point the addition of more substrates will have no effect on rate of reaction.
• What are competitive inhibitors and how do they work?

  Competitive inhibitors - bind to the active site of enzymes preventing substrates from binding. They are a similar shape to substrate, they are not permanently bound and can leave. It is the difference between concentration of inhibitor and substrate that determines the effect it has. If substrate concentration increases the effect of inhibitor decreases. When the inhibitor leaves another molecule takes it place that could be a substrate molecule is the concentration is high.
• What are non-competitive inhibitors and how do they work?

  Non-competitive - bind to an enzyme at a position other than the active site(allosteric site). This alters the shape of the enzyme and thus its active site. Substrate molecules can no longer occupy the active site. An increase of substrate concentration does not decrease the effect of inhibitor as they are not competing for the same site.
• What is the graph showing the comparison of competitive and non-competitive inhibitors?


  As shown below.