Book Two Flashcards
Which 4 factors affect enzyme activity and in what way?
- Substrate concentration - enzymes are ‘saturated’ when the level of substrate is high. Lower Km value indicates that the enzymes work efficiently at a lower substrate concentration. 2. Temperature - enzymes work most efficiently at their optimum temperature range. Increasing temperature increases the energy in the system but too hot and the protein structure is compromised as non-covalent interactions breakdown - the enzyme is denatured. 3. pH - enzyme surface side chains are at risk of ionisation/deionisation at pH levels other than their optimum. 4. Cofactors - are required by approximately one third of all enzymes and are involved in catalysis - receiving or donating molecules.
Which two types of inhibitor and two other mechanisms regulate the activity of enzymes?
Competitive inhibitors - bind to the active site and block substrate. Vmax is unaffected but greater [S] is required Non-competitive inhibitors - bind to a different site and alter the conformation of the active site which reduced the efficiency of the enzyme (binding between substrate and enzyme is weakened). The enzyme still functions but at a reduced rate - Vmax is lowered, Km is unaffected. Allosteric reaction - binding of a ligand results in a change to the binding site(s) of other ligands. Can be positive (promoting further ligand binding) or negative (reducing affinity for other ligands) Reversible covalent modification - temporary covalent changes increase/decrease the efficiency of the enzyme. A efficient means of temporary increasing/decreasing the level of product. Eg. phosphorylation - addition of a phosphate group.
Describe the use and components of the Michaeli-Mentens equation v= Vmax [S] / Km + [S]
A means of working out the initial reaction rate of an enzyme-catalysed reaction by looking at the relationship between the maximum reaction rate and the substrate concentration. v = initial reaction rate Vmax = maximum initial rate of reaction [S] = initial substrate concentration Km = michaelis constant (the substrate concentration that gives half the maximum reaction rate, Vmax)
What makes enzymes specific to substrates?
A specific region of the protein - the active site - is where enzyme substrate interactions occur. The active site must be complementary in shape, three-dimensional structure and chemistry (especially regarding charged groups)
What are cofactors and give an example of one?
Cofactors are non-protein molecules that become associated into polypeptides as they fold and are often critical to the function of the protein. eg. haem - which associates with each of the globin subunits of haemoglobin.
a) What are the differences between the way small and large proteins fold? b) What happens to misfolded proteins?
a) Small single-domain proteins often have polypeptide chains capable of spontaneously folding. Larger and/or multimeric proteins require specialised chaperon proteins that prevent unwanted interactions and recover and refold misfolded proteins. b) They are ‘tagged’ with ubiquitin proteins and broken down by proteases (enzymes)
a) What are the four levels of protein structure and give examples of common motifs (where applicable)? b) What are the substructures within a protein called? They usually have distinct functions.
a) primary structure (composed of amino acid residues) secondary structure (α-helices, β-sheets and random coils) tertiary structure (β-barrel fold, Rossman fold) quaternary structure (assembly of individual subunits to make a multimeric protein - not applicable for all proteins) b) Domains
a) Amino acid R-groups can be chemically categorized into what four groups? b) What tertiary structure folding patterns do some of the groups follow?
a) negatively charged, positively charged, uncharged polar, non-polar. b) +/- charged groups - ionic interactions non-polar - hydrophobic interactions with other non-polar side chains. various groups - hydrogen bonds cysteine amino acids - disulfide bridges
a) Describe the chemical structure of an amino acid b) Describe the reaction that occurs during the formation of a peptide bond
a) Amino acids have a central alpha carbon Cα An amino group NH2 A carboxyl group COOH and a varying side chain (R Group) b) A condensation reaction occurs (water is released) between the amino group of one amino acid and the carboxy group of another. A peptide group is formed with a covalent C-N bond (a peptide bond)
What are the three non-covalent interactions that stabalise the tertiary structure of proteins and drive the formation of protein-ligand interactions?
- Hydrogen bonds 2. Ionic interactions 3. Hydrophobic interactions
What are ligands and what is their function?
Ligands can be: ions, small organic and inorganic molecules, macromolecules (proteins / lipids / polysaccharides / nucleic acids), cofactors or other proteins. They bind with proteins and are necessary for proteins to carry out their specific function.
Describe the basic process of endcytosis and the three specific types of endocytosis
A bud is formed in the membrane in a region lined with small proteins called clatherin which form a ‘coat’ around the forming vesicle. The vesicle is ‘pinched-off’ and the coat disassembes. The vesicle fuses with early endosomes and is either returned to the membrane (for exocytosis) or delelops into a late endosome which is either returned to the Golgi Apparatus for reycling or taken to the lysosome for digesting.
- Pinocytosis - extracellular fluid is taken in with the vesicle.
- Receptor-mediated endocytosis (RME) - macromolecules bind to receptors on the extracellular surface and the receptor-molecule complex is engulfed along with the membrane into the vesicle.
- Phagocytosis - larger molecules are engulfed so larger areas of the membrane form the vesicle.
a) What are the 2 processes in which macromolecules are transported across the membrane?
b) Describe the process where macromolecules are transported out of the cell?
a) Exocytosis (secretion of substances)
Endocytosis (intake of substances)
b) Exocytosis: a vesicle containing molecules destined for secretion fuses with the cell membrane. The contents of the vesicle are realeased outside the cell. The vesicle membrane is incorporated into the cell membrane.
Constitutive exocytosis = occurs all the time
Regulated exocytosis = triggered by extracellular signal
a) Identify the parts of the lipids labelled a - h
b) What types of lipid are 2 and 3?
c) What varieties of lipid are 1 and 2/3?
d) State if 1,2 and 3 are saturated or unsaturated
a) a - hydrophilic head b - sphingosine
c - saturated fatty acid tail d - polar group
e - phosphate f - glycerol
g - unsaturated fatty acid tail h - sugar residue
b) 2 is a phospholipid and 3 is a glycolipid
c) 1 is a sphingolipid and 2 and 3 are glycerolipids
d) 1 and 3 are saturated, 2 is unsaturated.
a) What are the three ways that solutes can diffuse into the cell?
b) By which other process can macromolecules enter the cell?
a) 1. Passive diffusion
- no energy requirements and no transport proteins - unregulated
- small molecules diffuse through the lipid bilayer until equilibrium is reached.
2. Facilitated diffusion
- no energy requirements, carrier and channel tranport proteins
- solutes enter the cell via transmembrane proteins - can be regulated but is subject to concentration/electrochemical/osmotic gradients.
3. Active transport
- requires an energy input and carrier protiens
- solutes are transported into or out of the cell by carrier proteins working against a conertration gradient.
b) endocytosis
