1.4 Proteins Flashcards
What are amino acids
- The monomers that form proteins.
- Contain an amino group (NH2) and a carboxylic acid group (-COOH) and a variable R group (different for each amino acid.
- They are joined by peptide bonds formed in a condensation reaction.
Describe the primary structure of a protein
- The order and number of amino acids.
- The primary structure contains the initial sequence of amino acids which will determine the proteins overall 3D shape, and therefore its function.
Describe the secondary structure of a protein
- The shape that the chain of amino acids make (either alpha helix or beta pleated sheet).
- The hydrogen in the -NH has a slight positive charge and the oxygen in the -C=O has a slight negative charge.
- This causes weak hydrogen bonds to form, leading to alpha helices or beta pleated sheets.
When do alpha helices occur
When hydrogen bonds form between every 4th peptide bond.
When do beta pleated sheets occur
When the protein folds so that 2 parts of the polypeptide chain are parallel to each other, enabling hydrogen bonds to form.
How are hydrogen bonds broken
By high temperatures or changes in the pH.
Describe the tertiary structure of a protein
- The 3D shape of the protein, formed from further twisting and folding which leads to interactions between R groups.
- This structure is maintained by 3 bonds: hydrogen bonds, disulfide bridges and ionic bonds.
Properties of hydrogen bonds and how are they formed
- Numerous and easily broken.
- Formed by the hydrogen in the -NH and the oxygen on the -C=O.
Properties of disulfide bridges and how are they formed
- Interactions between the sulfur in the R group of the amino acid cysteine.
- Strong and not easily broken.
Properties of ionic bonds and how are they formed
- Form between the carboxyl and amino groups that are not involved in the peptide bond.
- Easily broken by pH and are weaker than disulfide bridges.
What is a globular protein (SAFES)
- Shape: roughly spherical
- Amino acid sequence: irregular and wide range of R groups.
- Function: physiological/ functional
- Examples: haemoglobin, enzymes
- Solubility: (generally) soluble in water
Why are globular proteins generally soluble in water
Their non-polar hydrophobic R groups are orientated towards the centre of the protein (away from the aqueous surroundings) and the polar hydrophyllic R groups orientate themselves outside the protein.
What is a fibrous protein (SAFES)
- Shape: long strands of polypeptide chains that have cross-linkages due to hydrogen bonds.
- Amino acid sequence: repetitive with a limited range of R groups
- Function: structural
- Examples: collagen, keratin
- Solubility: (generally) insoluble in water
Why are fibrous proteins generally insoluble in water
They have many hydrophobic R groups.
What is the biochemical test for proteins
- The biuret test tests for the presence of peptide bonds.
1. Place a sample to be tested in a test tube and add an equal volume of sodium hydroxide solution at room temperature.
2. Add a few drops of very dilute (0.05%) copper (II) sulfate solution and mix gently.
3. A purple colouration indicates the presence of a peptide bond and hence a protein (negative result - solution remains blue).
What are enzymes and how do they increase ROR
- 3D structured globular protein.
- They increase the ROR by providing an alternative reaction pathway with a lower activation energy.
What is the active site
- An area of the enzyme that is made up of only a few amino acids and forms a small depression in the overall enzyme.
- The active site is specific to the substrate in which it binds to, and they form an enzyme-substrate complex.
Describe the induced fit model of the enzyme
- When the enzyme and substrate bind, they form an enzyme-substrate complex.
- The structure of the enzyme is slightly altered so that the active site of the enzyme fits around the substrate.
How does temperature affect the rate of enzyme-controlled reactions
- Rate increases up to the optimum temperature as the kinetic energy of the enzyme increases.
- Above the optimum temperature, ROR decreases as the enzyme becomes denatured (as bonds disrupted in the tertiary structure which has changed the shape so it is no longer complementary to the substrate).
How does pH affect the rate of enzyme-controlled reactions
- The pH can disrupt bonds in the tertiary structure of the enzyme.
- Enzymes have different optimum pH’s, most work best at neutral.
How does enzyme concentration affect the rate of enzyme-controlled reactions
- Increases as enzyme concentration increases as there are more active sites for substrates to bind to.
- Increasing beyond a certain point has no affect on the ROR as there are more active sites than substrates, so substrate concentration becomes the limiting factor
How does substrate concentration affect the rate of enzyme-controlled reactions
- As concentration of substrate increases, ROR increases as more enzyme-substrate complexes are formed.
- However, beyond a certain point, the ROR no longer increases as enzyme concentration becomes the limiting factor.
What is a competitive inhibitor
A molecule with a similar shape to the substrate, so competes with the substrate in order to bind to the enzymes active site.
What is a non-competitive inhibitor
A molecule that attaches to an allosteric site on the enzyme which changes the shape of the active site of the enzyme, so the substrate can no longer bind.
