3 Proteins

• Proteins

  • Play a variety of roles in structural, transport, enzymatic, and signalling functions
  • Structure of a protein is related to its function
  • Number of proteins found in the natural world is enormous
  • Proteins are specific to each species unlike carbohydrates
• Haemoglobin proteins in crocodiles differ from those in humans, affecting their ability to hold their breath underwater
• References: 'Reece, K., Jane, B. Taylor, Martha, R., Simon, Eric, J., Dickey, Jean, L., Hogan (2020) Campbell Biology (12th Edition) (Pearson Higher Education) ISBN-10 0135188741<|>Raven, P., Johnson, G., Mason, K., Losos, J. and Duncan, T. (2022) Biology (13th Edition) (McGraw-Hill) ISBN-10 1264097859<|>Alberts, B., Heald, R., Johnson, A., Morgan, D., Raff, M., Roberts, K. and Walter, P. (2022) Molecular Biology of the Cell (7th Edition) (W. W. Norton & Company) ISBN-10 0393884821'
• Structures of proteins can influence their functions


  Proteins determine characteristics of a species
• Proteins, rather than fats or carbohydrates, determine characteristics of a species
• The 20 amino acids differ from each other only in their R groups, which determine the uniqueness of each amino acid
• Acidic amino acids have negatively-charged R groups due to the presence of a carboxyl group which dissociates to form COO- at cellular pH
• Amino acids can buffer against changes in the pH of their environment when a small amount of acid or alkali is added, important in biological systems where a sudden change in pH can adversely affect the activity of proteins such as enzymes
• Acidic and basic amino acids are hydrophilic and able to form interactions with water
• Proteins - Introduction

  • Proteins consist of carbon, hydrogen, oxygen, nitrogen, and sulphur (in some proteins)
  • The basic structural units or monomers of proteins are called amino acids
  • There are 20 amino acids used in the biosynthesis of proteins in cells
• Amino acids exist in the form of zwitterions, which are generally soluble in water and become ionized
• Electrically neutral amino acids have non-polar, hydrophobic R groups or polar, hydrophilic R groups
• Amino Acids


  An amino acid consists of an α-carbon atom covalently bonded to 4 groups: a hydrogen atom, an amino group (-NH2), a carboxyl group (-COOH), and a variable R group or side chain
• Basic amino acids have positively-charged R groups due to the presence of an amino group which accepts H+ to form NH3+
• All amino acids have carboxyl and amino groups; the terms acidic and basic in this context refer only to the groups within the R groups/side chains
• In zwitterion form, amino acids act as buffers in biochemical reactions by being amphoteric, able to act as an acid or base, thereby serving as buffers in biochemical reactions
• Hydrolysis reaction


  The reverse reaction resulting in the breaking of the peptide bond, requiring a water molecule
• Peptide Bond Formation

  Joining amino acids via a condensation reaction that links the carboxyl group of one amino acid to the amino group of another, with the elimination of one water molecule (H2O)
• The H+ from NH3+ neutralises the OH-


  Prevents a change in pH of the solution
• A polypeptide folds into a protein with a specific three-dimensional shape/conformation
• A protein's function is determined by its conformation, which is dictated by its amino acid sequence
• Amino acids join together to form linear polymers called polypeptides during the process of translation in cells
• The sequence of amino acids of the polypeptide chain determines the type and location of the chemical interactions, and hence the pattern of folding of the polypeptide
• Primary structure refers to the number, sequence, and type of amino acids in a single polypeptide chain
• EJC H2 Biology

  2023
• When alkali (OH-) is added to the solution

  NH3+ of zwitterion loses a H+ and becomes NH2
• Peptide Bond


  The bond formed between 2 amino acids via a condensation reaction resulting in the removal of 1 water molecule
• Polypeptides

  • Dipeptide
  • Tripeptide
  • Oligopeptide
  • Polypeptides
• The primary structure of a protein is specified by nucleotide sequences in genes
• Polypeptide chain


  • Has directionality with N-terminus having a free amino group at the start and C-terminus having a free carboxyl group at the end
• Levels of organisation in the structure of proteins

  • Primary
  • Secondary
  • Tertiary
  • Quaternary
• Proteins interact only with specific molecules due to complementary surfaces and clefts that can only fit with specific molecules
• 5.2 Secondary Structure

  EJC H2 Biology 2023
• A protein interacts only with specific molecules
• Secondary structure of proteins

  Maintained by hydrogen bonds at regular intervals between the C=O and -NH groups of the polypeptide backbone
• β-pleated structure is formed when two or more regions/segments of a single polypeptide chain lying side by side are linked by hydrogen bonds
• There are 3.6 amino acid residues per turn of the α-helix
• α-helix is made of a single polypeptide chain wound into a regularly coiled helical structure
• Tertiary structure

  • Maintained by 4 types of intramolecular interactions (hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bonds) formed between R groups of amino acid residues
• 5.3 Tertiary Structure

  EJC H2 Biology 2023