proteins and enzymes

• formation of peptide bond

  • Amino acid monomers combine to create dipeptides via a condensation reaction, where a water molecule is removed.
  • links the carboxyl group (-OH) of one amino acid with the amino group (-H) of another, forming a peptide bond between the carbon and nitrogen atoms.
  • the peptide bond is broken by hydrolysis
• structure of amino acid

  • amino group (-NH2)
  • carboxyl group (-COOH),
  • hydrogen atom (-H)
  • R (side) group, has 20 versions
• primary structure- polypeptide

  • condensation reactions, multiple amino acid monomers can undergo polymerization, which forms polypeptide chain
  • primary structure determines the protein's overall shape and function
• How can a change in a single amino acid affect protein function?

  • A change in shape can affect function
• secondary structure

  • The folding or coiling
  • to create a β pleated sheet or an α helix
  • held in place by hydrogen bonds
• tertiary structure

  • The further folding, to create a unique 3D shape
  • complex, 3D structure of a protein
• What are the types of bonds involved in maintaining the tertiary structure?

  • Disulfide bridges are strong,
  • ionic bonds are weaker and easily broken by pH changes
  • Hydrogen bonds are numerous but easily broken.
• quaternary structure

  • More than one polypeptide chain in a protein

  
• enzyme structure

  • globular proteins, 3D shape determined by sequences of amino acid
  • active site= functional region
• enzyme substrate complex

  • forms when an enzyme and substrate collide and bind
  • resulting in a lowered activation energy
• induced fit model

  • The enzyme active site is not initially complementary to the substrate
  • active site changes its shape, it puts strain on the substrate molecule, lowering the activation energy needed to break bonds
• enzymes as catalysts lowering activation energy

  • Activation energy is the minimum amount of energy required to initiate a reaction
  • the substrates must collide with sufficient energy to alter their arrangement to form the products
  • free energy of products must be lower than substrates
• effect of temperature on controlled reaction

  • At low temperatures, there is not enough kinetic energy for successful collisions between the enzyme and substrate
  • too high a temperature, enzymes denature, the active site changes shape and enzyme-substrate complexes cannot form
• effect of pH on enzyme controlled region

  • Too high or too low a pH will interfere with the charges in the amino acids in the active site
  • This breaks the ionic and hydrogen bonds holding the tertiary structure in place
  • therefore the active site changes shape and the enzyme denatures
  • Different enzymes have a different optimal pH
• effect of substrate concentration on enzyme controlled reaction

  • At low substrate concentrations, there will be fewer collisions between the enzyme and substrate
  • At high substrate concentrations, the rate plateaus
  • because all the enzyme active sites are saturated
• effect of enzyme concentration on enzyme controlled reaction

  • At low enzyme concentrations, there will be fewer collisions between the enzyme and substrate
  • At high enzyme concentrations, the rate plateaus
  • because there are more enzymes than the substrate, so many empty active sites.
• whats a competitive inhibitor

  • A molecule that is the same/similar shape as the substrate
  • binds to the active site
  • prevents enzyme-substrate complexes from forming
• whats a non competitive inhibitor

  • A molecule that binds to an enzyme at the allosteric site
  • causing the active site to change shape
  • preventing enzyme-substrate complexes from forming
• end product inhibition

  • Metabolic pathways are regulated to prevent overproduction of specific products
  • Reversible inhibitors (end-products of metabolic reactions), act as regulators
  • When an end-product binds to an alternative site on the enzyme, it alters the shape of the active site, slowing down the reaction
  • As product levels decrease, the enzyme resumes catalysis, creating a continuous feedback loop
  • This tight control ensures balanced metabolic reactions
• Why are globular proteins generally soluble in water?

  • Their solubility in water allows for easy transport around organisms and involvement in metabolic reactions.
• What are globular proteins?

  • compact, roughly spherical, and soluble in water
• Why do globular proteins form a spherical shape when folding into their tertiary structure?

  • their non-polar hydrophobic R groups are towards the center of the protein, away from the aqueous surroundings, while their polar hydrophilic R groups are on the outside
• what are the functional roles of globular proteins?

  • have specific shapes due to the interactions between R groups
  • enabling them to catalyze specific reactions (enzymes) or respond to specific antigens (immunoglobulins)