protein and enzyme

• Protein

  Macromolecules important for the functioning of a cell and organisms
• Subunit

  Amino acid
• Amino acid


  An organic molecule with a central C-atom attached to an amino group, a carboxyl group, a H-atom, and a variable side chain (-R)
• Elements in proteins

  • Carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur
• Factors determining protein structure

  • Primary structure: Sequence of amino acids in the polypeptide chain
  • Secondary structure: Coiled (𝛼 helix) or pleated (𝛽 pleated) due to hydrogen bonds
  • Tertiary structure: Folding, pleating, and coiling due to side chain interactions
  • Quaternary structure: Complex structure from bonding of two or more polypeptide chains
• Proteins are made up of more than one polypeptide chain folded into a specific three-dimensional shape
• A change in the three-dimensional shape of a protein is caused by denaturation, rendering it unable to carry out its function
• Sequence of amino acids in the protein chain determines its folding, giving it a specific shape and function
• Nearly all proteins function by recognizing and binding to their specific substrate
• Fredrick Sanger sequenced the first protein with 51 amino acids, the hormone insulin


  1958
• Protein structure

  1. Primary structure: Sequence of amino acids held together by peptide bonds

  2. Secondary structure: Coiled or pleated due to hydrogen bonds

  3. Tertiary structure: Folding, pleating, and coiling due to side chain interactions

  4. Quaternary structure: Complex structure from bonding of two or more polypeptide chains
• Functions of proteins

  • Structural
  • Catalyse reactions
  • Contraction
  • Transport
  • Defence
  • Coordination
  • Storage
• Examples of protein functions


  • Actin and tubulin in the cytoskeleton
  • Enzymes
  • Fibres in muscles
  • Carrying oxygen (haemoglobin), transport proteins in membranes
  • Antibodies produced by white blood cells (immunoglobulins)
  • Hormones and receptor proteins
  • Albumin in eggs, ferritin
• Examples of proteins with specific shapes

  • Enzymes, some hormones, receptor proteins, antibodies
• Protein specificity, function, and application

  • Enzymes: Active site complementary to specific substrate
  • Regulatory proteins: Activators or inhibitors allowing RNA polymerase to bind to DNA segment coding for a gene
• Alcohol binds to dehydrogenase

  Regulatory proteins
• Regulatory proteins

  • Activators or inhibitors which allow RNA polymerase to bind to DNA segment that codes for a gene
  • Increase gene expression by enhancing RNA polymerase attachment to the promoter site of gene
  • Decrease gene expression by blocking polymerase to the promoter site of gene
• Troponin

  • Regulatory protein which binds to Cu ion to activate myosin synthesis and concentration
• Hormones

  • Chemicals that bind to complementary site on a receptor protein
  • Hormone receptor protein complex binds to bring about change in internal cell mechanism
  • Insulin binds to the insulin receptor to form hormone receptor complex to increase transport of glucose in blood into cell
• Glucose conversion into glycogen

  Insulin binds to the insulin receptor to form hormone receptor complex to increase transport of glucose in blood into cell
• Antibody and antigen

  • Antigen binding site on Y-shaped antibodies are complementary to specific non-self-antigen found on other cells, bacteria, and virus
  • Antigen-antibody complex which is eliminated by phagocytosis or toxin to form T-cells as an immune response
  • Antibodies for hepatitis B vaccines can bind to hepatitis B antigens to destroy the virus
• Explain why the three-dimensional shape of a protein is critical to its function
• Many human genetic diseases are due to the person’s cells producing proteins which have an abnormal 3D structure
• Genetic diseases

  • Tay-Sachs disease: faulty enzyme beta-hexosaminidase results in neurological disorder, an enlarged head, and death in early childhood
  • Phenylketonuria (PKU): faulty enzyme phenylalanine hydroxylase results in severe mental retardation
  • Type A insulin: faulty insulin receptor results in impaired blood sugar regulation and leads to diabetes mellitus
  • Sickle cell anaemia: production of haemoglobin with an incorrect shape results in red blood cells having a fragile “sickle” shape, leading to anaemia
  • Cystic fibrosis: faulty channel protein in the membranes of mucus-producing cells in the respiratory system and intestine results in the production of very thick and sticky mucus giving rise to lung infections and impaired digestion
• Enzymes are specific for their substrate
• Enzymes are globular proteins, and each cell produces its own enzymes
• Every enzyme is specific for a particular reaction
• Majority of enzymes catalyse reactions within cells and are called intracellular; although some enzymes are produced by cells, act outside cells are called extracellular enzymes
• Each enzyme has a region on its surface with a specific shape called active site; for the enzyme to function, it must combine with the substrate
• The reaction will occur if the active site of the enzyme is complementary to the shape of the substrate molecule
• Even a slight change in the structure of enzymes may prevent this recognition, resulting in enzymes losing their ability to catalyse this reaction
• Induced-fit model of enzyme-substrate binding

  1. Substrates bind to the active site of the enzyme forming an enzyme-substrate complex

  2. This interaction between the enzyme and its substrate is called an induced fit

  3. Enzyme-substrate complex then undergoes the reaction far more readily than the substrate would have if there were no enzymes present
• Model of enzyme-substrate binding

  1. Substrates bind to the active site of the enzyme forming an enzyme-substrate complex

  2. This interaction between enzyme and its substrate is called an induced fit

  3. Enzyme-substrate complex then undergoes the reaction far more readily than the substrate would have if there were no enzymes present

  4. Product molecules then break away from the enzyme, which is now free to combine with another substrate molecule and repeat the process
• Enzymes

  • Have specific functions
  • Are affected by factors including temperature, pH, presence of inhibitors
• Temperature

  1. Human enzymes work best at 37℃; enzymes of certain algae that live in hot springs might work best at temperatures between 60℃ to 80℃

  2. This high temperature would be sufficient to alter the shape of most proteins

  3. If the shape of the enzyme is altered, it will cease the function as its active site will be altered
• pH

  1. Different enzymes work best at different pH levels

  2. Example: salivary amylase has an optimum pH of about 7; whereas the optimum pH of pepsin is about 2
• Inhibitor

  1. A substance with a molecular shape similar to that of a substrate may bind with the active site, thus blocking it from the substrate

  2. 2 types of inhibitors: competitive inhibitor and non-competitive inhibitor

  3. Competitive inhibitor: If the inhibitor were to bind permanently in the way, then the enzyme molecule would be rendered (mimic) completely ineffective

  4. Non-competitive inhibitor: a molecule may bind to the enzyme without blocking the active site, but its presence may distort the shape of the enzyme molecule so that the active site no longer has the complementary shape to the substrate
• The rate of an enzyme-controlled reaction is affected by concentration of reactants and enzymes

  • For the same enzyme concentration, increasing the concentration of the reactant (substrate) molecule will result in an increase in the rate of reaction until all active sites of the enzyme molecule are occupied
  • Rate of reaction will remain constant
  • For the same substrate concentration, increasing the concentration of enzyme molecules will result in an increase in the rate of reaction until all substrate molecules have bound to the active site of the enzyme molecules
  • Any further increase in enzyme concentration will not increase the rate of reaction
• Enzymes increase reaction rates by lowering activation energy


  1. Biological enzymes have evolved to speed up the rate of chemical reactions by lowering the activation energy needed to start the process

  2. Ways to lower activation energy: Bringing reactants together in the same orientation, binding to a substrate molecule in a way that puts a strain on its chemical bonds, making the reaction happen in several small steps which require only a small amount of activation energy

  3. Managing a large amount of heat energy released is also achieved by carrying out the overall reaction in several small steps as each step requires only a small amount of energy

  4. Some of this energy is stored as chemical energy, while the rest is lost as heat