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6. Molecular Interactions in Cell Events:

All references made are to the unit 1 Scholar book. Page numbers may vary each year as different versions of the book are released.

Activation energy Active site Globular protein

You should know these words, and be able to explain these effects from Lock and key Higher and theory Standard Grade

Effect of enzyme and substrate concentration


Coenzymes/ cofactors Effect of temperature and pH Substrate

Names of enzymes describe their function. Copy and complete table p.114 of scholar book Enzyme Group

Protease ATPase Phosphatase Nuclease

Reaction Catalysed Hydrolysis of peptide bonds to break down protein Hydrolysis of ATP Removal of phosphate (hydrolysis) Breakdown of nucleic acids (hydrolysis


Transfer of phosphate to another molecule


Join 2 molecules by dehydration synthesis


Joining molecules in a chain (e.g. DNA synthesis)

Enzyme Activity •Cofactors (e.g. copper, zinc, iron) increase the effectiveness of an enzyme •Organic cofactors also called coenzymes (e.g. vitamins, NAD) •Lock and key theory has been replaced by the induced fit hypothesis Substrate changes the shape of active site to allow perfect binding.

Allosteric enzymes • 2 forms – active and inactive • change shape in response to a regulating molecule • molecule binds to enzyme’s allosteric site • positive modulator (activator) stabilises active form • negative modulator (inhibitor) stabilises inactive form •Figure 6.5 p.121

Control of Enzyme Activity • control no. enzyme molecules in cell (What will control this?) Genes • compartmentalise enzymes (what does this mean?) Enzymes for specific functions are stored in membrane-bound organelle. E.g., digestive enzymes for phagocytosis in lysosome, respiratory enzymes in mitochondria

• competitive inhibition – inhibitor competes with substrate for active site - reversible, increase substrate concentration to outcompete inhibitor • non-competitive inhibition – inhibitor attaches to part of enzyme altering shape of active site • activators and inhibitors bind to allosteric site of enzyme to stabilise in/active form

• covalent modification – adding, modifying removing, chemical groups to or from an enzyme • shape of enzyme is changed • e.g. glycogen phosphorylase breaks down glycogen to glucose-1-phosphate when sugar is needed by muscles • enzyme is normally in a non-phosphorylated inactive form Which class of enzyme adds phosphate to make enzyme active?

• phosphorylase kinase adds phosphate to glycogen phosphorylase to produce active form

Which type of enzyme removes phosphate to store enzyme in an inactive form?

• phosphatase removes phosphate after muscular activity slows down • glycogen phosphorylase can also be controlled allosterically • glucose and ATP inhibit the enzyme, and AMP (adenosine monophosphate) activates it Which hormones will also stimulate/inhibit glycogen phosphorylase?

• covalent modification can also occur by proteolytic cleavage – breaking of peptide bonds in proteins • this is used to turn the secreted inactive form of an enzyme into its active form • e.g. trypsinogen and chymotrypsinogen are inactive in the pancreas. • converted to active form in duodenum • trypsinogen into trypsin by enteropeptidase • chymotrypsinogen into chymotrypsin by trypsin

• end-product inhibition – the end product of a metabolic pathway inhibits the first enzyme of the pathway by binding to allosteric site • this is also a type of negative feedback •Figure 6.7 p.123

Which process maintains the concentration gradient of sodium and potassium in the cell? Active Transport What are the requirements for this process? (4 things!) ATP, respiratory substrate (glucose), oxygen, suitable temperature

Sodium-potassium Pump • 3 Na+ ions pumped out for every 2 K+ ions pumped in • creates an electrochemical gradient – cytoplasm more negatively charged than outside cell • provides energy for active transport of sugars and amino acids into cell => electrogenic pump

• 3 Na+ ions attach to pump activating phosphorylation of pump by ATPase • pump changes shape affecting affinity of binding sites, causing release of Na+ out of cell • change in shape allows 2 K+ ions from outside of cell to bind • this releases phosphate group, causing shape of pump to change • K+ released inside cell, and cycle continues • Figure 5.4 p.105

• allows communication between cells and co-ordination without contact • ensures activities occur in the right cell at right time, and in co-ordination with other cells • what structures allow signals to pass between plant cells?

i) Plant Cells • communicate by perforations in cell wall called plasmodesmata (plasmodesma) • membranes are continuous between cells • allows transport of water, small solutes, proteins and RNA • along fibres of cytoskeleton

ii) Animal Cells • ligand (signal molecule) is sent by signalling cell to the target cell • in most cells, receptor protein on target cell detects the ligand • ligand joins with receptor protein to activate target cell (ligand is small molecule which binds to a large molecule)

• after the ligand reaches the target cell, the signal needs passed on • transfer of a molecular signal in a cell is called transduction • original signal molecule not passed on, causes information to be passed • at each stage the signal is changed to a different form until there are a large number of activated molecules • known as a signal transduction pathway

• proteins play major role in signal transduction • signal transduction brought about by: Calcium ions are second messengers in blood clotting and muscle contraction • cyclic AMP signals breakdown of glycogen to glucose • phosphorylation of proteins by protein kinases or phosphatases

Extracellular Hydrophobic Cell Signalling • diffusion of signal molecule through membrane of target cell • e.g. steroid hormones (sex hormones, thyroxine, hydrocortisone) • hormones activate regulatory proteins which regulate transcription of certain genes • slow process as relying on hormone circulating in blood then diffusion

Extracellular Hydrophilic Cell Signalling • proteins on outside of membrane receive signal, as signals too large to pass through membrane • receptor proteins convert binding into intracellular signal • 3 types of receptor protein:

1.Enzyme receptors – generate enzyme-linked reaction on cytoplasmic side of protein to activate intracellular proteins Figure 7.2 p.132

2. G-protein-linked receptors – activate GTPbinding protein to start transduction (e.g neurotransmitter and odour receptors) G-protein is usually inactive with GDP bound Ligand attaches, and GDP becomes GTP, activating the G-protein, which then activates an enzyme Figure 7.3 p.134

3. Ion-channel-linked receptors – open in response to ligand, allowing ions to move through channel, change in ion concentration initiates cell response Figure 7.4 p.135

6+7 Catalysis,Pumps+Signalling