Proteins and Enzymes

• Amino acid


  A molecule consisting of a central carbon atom attached to an amine group, a hydrogen atom, a carboxyl group and an 'R' group which is different in each amino acid
• Proteins


  Polymers of amino acids joined together by peptide bonds
• Amino acids


  • 20 different amino acids that our body needs to stay healthy
• Amino acid structure


  • Central carbon atom
  • Amine group
  • Hydrogen atom
  • Carboxyl group
  • R group (different in each amino acid)
• Identity of the R group


  Influences how the amino acid interacts with other amino acids, therefore influencing protein folding
• Peptide bond formation:

  Peptide bond formation involves the removal of water in a condensation reaction. The water is formed by removing a hydrogen atom from the amine group and a hydroxyl (-OH) group from the carboxylic acid. What’s left behind is a peptide bond (-CONH) which can be broken with the addition of water in a hydrolysis reaction.
• Primary structure


  Peptide bonds have formed between amino acids to form a long, straight chain (polypeptide)
• Secondary structure


  1. Hydrogen bonds form between nearby amino acids (from the amine group on one amino acid to the carboxyl group of another) to form either an alpha helix or a beta pleated sheet

  2. Proteins which form neither of these two structures will form a random coil
• Tertiary structure


  1. More bonds form between the different R groups to give the protein a 3D structure

  2. R-group interactions involve hydrogen bonds, disulfide bonds, ionic bonds and polar interactions
• If proteins are made of a single polypeptide chain, this is their final overall structure
• Quarternary structure


  The structure formed from the interaction of multiple polypeptide chains held together by bonds
• Protein with quaternary structure


  • Haemoglobin
• Haemoglobin


  • Consists of four polypeptide chains (two alpha chains and two beta chains) bonded together
  • Each chain surrounds an iron-containing haem group
• Haem group


  Non-protein components which are required for protein function
• The haem group is referred to as a prosthetic group
• Globular proteins


  Spherical and arranged with their hydrophobic amino acids tucked inside and the hydrophilic amino acids exposed on the outside. Soluble and can be transported easily from one part of the cell to another. Perform functional roles like enzymes, hormones or proteins like haemoglobin. Unravel and denature when the temperature or pH deviates from optimum levels.
• Fibrous proteins


  Long and thin, with a primary structure consisting of a repetitive sequence of amino acids. Perform structural roles so they are strong and insoluble. Examples include collagen, keratin and elastin. Collagen consists of three polypeptide chains wrapped tightly around each other to form a stable quaternary structure held together by numerous hydrogen bonds. Found in connective tissue, such as skin, muscle and bone. Less sensitive than globular proteins to changes in temperature and pH.
• Protein categories


  • Globular proteins
  • Fibrous proteins
• Globular proteins


  • Enzymes (such as amylase)
  • Hormones (such as insulin)
  • Haemoglobin
• Fibrous proteins


  • Collagen
  • Keratin
  • Elastin
• Enzymes


  Biological catalysts that speed up the rate of chemical reactions happening inside our body
• Enzymes


  • They work by reducing the activation energy of a reaction
  • Activation energy is the minimum amount of energy needed for a reaction to happen
  • If less energy is needed, then reactions can take place at lower temperatures than would be needed without an enzyme
  • Without enzymes in our bodies, the reactions that happen inside of us would not be possible at normal body temperature
  • Enzymes are unchanged at the end of a reaction which means they can be reused
• Types of enzymes


  • Intracellular (catalyse reactions inside cells)
  • Extracellular (catalyse reactions outside of cells)
• Enzymes


  • All enzymes are globular proteins and have regions called active sites
  • The active site of an enzyme has a specific shape and allows the substrate to bind
  • Enzymes may have regulatory regions where an inhibitor can bind, which we refer to as the allosteric site
• Mechanism of enzyme action


  Scientists have two ideas to explain the way in which enzymes work: the 'lock-and-key' model and the 'induced-fit' model
• Lock and Key model


  1. Substrate binds to the enzyme's active site, forming an enzyme-substrate complex (ES complex)

  2. The enzyme converts the substrate into product, forming an enzyme-product complex (EP complex)

  3. The product is released from the enzyme's active site
• Lock and Key model


  • The substrate fits into the enzyme's active site in the same way in which a key fits into a lock
  • The shape of the substrate and the active site are perfectly complementary to each other
• The Induced Fit model

  The induced fit model suggests that the shapes of the enzyme’s active site and its substrate are not exactly complementary, but when the substrate enters the active site, a conformational change (change of shape) occurs which induces catalysis. The induced fit model can be broken down into the following stages:

  1. The substrate enters the enzyme’s active site, forming an ES complex.
  2. The enzyme undergoes a conformational change which causes the conversion of substrate intoproduct, forming an EP complex.
  3. The product is released from the enzymes active site.
• Lock-and-key model


  Explains why most enzymes display high specificity to their substrates
• Induced fit model


  • Able to explain how enzymes can bind to a variety of lipids
  • Able to explain how catalysis actually occurs through conformational changes that place stress on bonds within the substrate
• The induced fit model is the more widely accepted model of the two
• Enzyme concentration


  • As enzyme concentration increases, the rate of reaction increases since more active sites will be available to bind to substrate molecules
  • A point will be reached when increasing enzyme concentration does not result in further increases in reaction rate, as something else has become a limiting factor, such as the availability of substrate
• Substrate concentration


  The amount of substrate molecules available for the enzyme to bind to
• As substrate concentration increases

  The rate of reaction increases
• Saturation point


  The point where all of the enzyme's active sites are occupied with substrate molecules, so the addition of more substrate molecules will have no effect on the rate of reaction
• Vmax

  The maximum rate of reaction, where the reaction is proceeding as fast as possible
• To increase the reaction rate beyond Vmax


  The only way is to increase enzyme concentration
• At low temperatures


  The rate of reaction will be slow
• As the temperature is increased


  The number of collisions increases
• Increased number of collisions


  Increases the formation of ES complexes