Protein Structure Flashcards
What is the basic structure of amino acids?
Central CH bonded to COOH (carboxyl group, C double bonded to O and single to OH), variable R group and H2N (amine group)
How do amino acids join together?
In a condensation reaction between the carboxyl group of one amino acid and the amino group of another, forming a peptide bond + a water molecule
What molecules bond in the reaction between two amino acids?
CO from carboxyl group and NH from amine group; OH and H form water
Describe the primary structure in proteins
Specific order of amino acids in a polypeptide chain; helps determine the final 3D shape of the protein and determined by DNA sequence of the gene that codes for it
Describe the secondary structure of proteins
Chain begins to fold, as the positively-charged H attracted to negatively charged O, forming a hydrogen bond across polypeptide chain
- can be either alpha helix or beta pleated sheet
Describe the tertiary structure of proteins
Overall final folded 3D shape of polypeptide; critical for how protein functions
Describe quaternary structure of proteins
When proteins are made up of several polypeptide chains called sub-units; may also contain non-protein molecules called prosthetic groups which help proteins carry out their function (those with are called conjugated proteins)
Give an example of a conjugated protein
Haemoglobin, has 4 prosthetic groups called haem made of iron, which is where oxygen attaches
Which bonds are involved in primary, secondary, tertiary and quatenary structure?
primary = peptide
secondary = hydrogen
tertiary = side chains, ionic, disulphide bridges (if R groups have sulfur), hydrophobic/philic reactions, hydrogen
quaternary = all of the above
What are the properties of globular proteins?
Have compact, spherical shape, soluble due to hydrophilic amino acids being on the surface and hydrophobic in the centre
Describe an example of a globular protein
Haemoglobin; has 4 polypeptide chains and carries oxygen around the body so must be soluble; has iron containing haem groups which bind to oxygen
Describe properties of fibrous proteins
- Made up of long polypeptide chains tightly coiled to form rope-like shape
- Insoluble due to many hydrophobic amino acids
- Often have structural roles due to strength from many bonds, e.g tendons, bones, arteries
Describe an example of a fibrous protein
Collagen is found in skin, ligaments and tendons; made up of 3 polypeptide chains twisted into a triple-helix
- Every 3rd amino acid is glycine a/ R group hydrogen, allowing polypeptide chains to wrap tightly with hydrogen bonds
- Staggered molecules to avoid weak spots
What are enzymes?
“Biological catalysts” which speed up the rate of reaction without being used up, by reducing activation energy
What type of molecule are enzymes?
Globular proteins
What are intracellular and extra cellular enzymes?
- Intracellular = produced and function inside the cell
- Extracellular = secreted by cells and catalyse reactions outside cells
Give examples of intracellular and extracellular enzymes
Intracellular - Catalase; converts harmful hydrogen peroxide to water and oxygen
Extracellular - Amylase; involved in carbohydrate digestion as it hydrolyses starch into simple sugars, secreted by salivary glands + pancreas
What is activation energy and how do enzymes lower it?
Minimum amount of energy needed by the substrate to become unstable enough for a reaction to occur; enzymes offer an alternate reaction pathway and reduce stability of bonds in reactant
What is the lock and key model?
States shape of active site is exactly complimentary to the substrate
What is the induced-fit model?
States the active site changes shape slightly to fit around the substrate
How does changing temperature affect enzymes?
- as temperature increases, rate of reaction increases as kinetic energy is higher so more collisions and E-S complexes formed
- however once an enzymes optimum temperature is reached, increasing temperature further decreases rate of reaction as bonds holding tertiary structure in place break and active site may change shape and become denatured
Describe how changing pH affects enzyme concentration
Rate of reaction is optimum at each enzymes optimum pH (usually pH7), going above or below this means H (alkali) and OH (acidic) ions disrupt the ionic and hydrogen bonds in its tertiary structure
What are competitive inhibitors?
Molecules other than the substrate which bind to the active site; lower rate of reaction by preventing substrate from binding
What are non-competitive inhibitors?
Molecules which bind to the allosteric site, changing the shape of the active site of the enzyme permanently and stopping rate of reaction
Compare similarities of globular and fibrous proteins
Similarities —> both amino acids joined by peptide bonds
Give differences of globular and fibrous proteins
Properties - globular = soluble, fibrous = insoluble; globular = reactive (can have molecules added/removed, fibrous = unreactive; globular = not strong, fibrous = high tensile strength
Structure - globular = hydrophilic R groups on surface, fibrous = hydrophobic R groups on surface ; globular = spherical + compact, fibrous = long chains; globular = have tertiary or quatenary structure, fibrous = little or no tertiary structure
