Cell Membranes and Signalling Flashcards
state what it is meant by the key term - ligand
a ligand is any molecule, or ion, that is bound to a protein by electrical attractions or hydrophobic forces
state, and explain, the two forces in which ligands can be bound to proteins
- electrical attractions between oppositely charged ionic or polarised groups on the ligand and protein
- weaker attraction due to hydrophobic forces between non polar forces on the two molecules
state, and explain, what it is meant by the key term - binding site (4 points)
- the point on the protein which the ligand binds to
- not covalent + easily reversible
- binding causes a conformational change in the shape of the protein
- then proteins specific function is then activated/inactivated
state what it is meant by the key term - chemical specificity
the ability of a protein binding site to bind specific ligands (in order to bind correctly, they must have a complementary shape)
state 2 facts about binding sites
- conformation determined by sequence of amino acids in the primary protein structure
- some binding sites are only complementary in shape / specific to one ligand, and some to several
state what it is meant by the key term - affinity
the strength of a ligand-protein binding - affinity determines how easily binding occurs and releases
state the definitions for the three type of binding in relation to affinity
- strong binding - site containing a positively charged amino acid side chain
- less strong bonding - a site which has the same shape but not a positively charged amino acid side chain
- weaker bonding - different shape and no positively charged amino acid side chain
state what it is meant by the key term - saturation
the percentage total ligand binding sites that are occupied at one point in time
state the two determinants of percentage saturation
- concentration of unbound ligands in solution
2. ligand affinity to ligand binding site
state the two ways to control protein activity
- change the protein shape - alters ligand binding ability
2. regulating protein synthesis and degradation
there are two mechanisms in cells which can selectively alter protein shape. name these two mechanisms
- allosteric modulation
2. covalent modulation
state what it is meant by the key term - allosteric modulation
occurs when a protein has two binding sites and the binding of a protein to one of the binding sites alters the shape of the other binding site
state the names of the two binding sites on a protein (allosteric modulation)
- functional/active site - carries out the proteins physiological functions
- regulatory site
state what it is meant by the key term - modulator molecules (allosteric modulation)
modulator molecules are ligands that bind to regulatory sites. it’s binding modulates the shape, and therefore activity, of the active site/functional unit of the protein
state what it is meant by the key term - cooperativity
when a ligand binds to the first of several active/functional sites on a molecule and induces a change that increases the affinity of the other active/functional sites
state what it is meant by the key term - covalent modulation
the covalent bonding of charged chemical groups to some of the protein side groups
explain what kinase and phosphatase is (covalent modulation)
- kinase - an enzyme that adds a phosphate group to another molecule
- phosphatase - an enzyme that removes the phosphate group from another molecule
metabolism consists of two aspects. state and explain these two aspects
- anabolism - the synthesis of organic molecules
2. catabolism - the breakdown of organic molecules
state what it is meant by the key term - 1 calorie
1 calorie = the amount of heat required to raise the temperature of 1 g of water by 1’c
state what is is meant by the key term - 1 kcal
1 kcal = the amount of heat required to raise the temperature of 1000 g of water by 1’c
state the 4 determinants of reaction rate
- reactant concentration
- activation energy
- temperature
- catalyst (present or not)
state what it is meant by the key term - activation energy
the energy required to overcome the mutual repulsion from electrons surrounding the atoms that need to bump into each other
state what it is meant by the key term - reaction rate
how many molecules of a product are formed per unit of time
state what it is meant by the key term - ‘law of mass action’
the concentration of reactants, or produce, can determine the direction at which the net reaction proceeds (forward reaction, backward reaction, reversible reaction)
state 3 facts about enzymes
- they lower the activation energy
- to function, an enzyme must come into contact with reactants
- reactants bind to the active site of the enzyme
state 3 facts about cofactors
- most enzymes are inactive without cofactors
- many cofactors are trace metals
- binding of a metal to an enzyme alters it’s conformation so that it can bind to the substrate (allosteric regulation)
state 3 facts about coenzymes
- the term coenzyme is used to describe an organic molecule
- it directly participates as one of the substrates in the reaction
- coenzymes are usually derived from vitamins
give two examples of coenzymes
- nicotinamide adenine dinucleotide (NAD) - derived from Niacin from green veg, meat, poultry, fish and eggs
- flavine adenine dinucleotide (FAD) - derived from Riboflavin from milk, meat, eggs, nuts and green veg
regulation of enzyme mediated reactions: (3 things)
- substrate concentration
- enzyme concentration
- enzyme activity
state what it is meant by the key term - maximal rate
maximal rate of reaction is reached when all the active sites are occupied by substrates
state what it is meant by the key term - metabolic pathway
the sequence of enzyme mediated reactions leading to the formation of a particular product
state what it is meant by the key term - ‘the rate limiting reaction’
as all enzymes have different concentrations and activities, it is likely that one of the enzymes in the chain will be slower than the others - ‘the rate limiting factor’
state 2 facts about ‘rate limiting enzymes’
- often the site of allosteric of covalent modulation
2. control of enzymes via modulation can be important in regulating the direction of reversible/irreversible reactions
state the difference between agonists and antagonists when talking about receptors and cell signalling
- antagonists - drugs that act as inhibitors
2. agonists - drugs that mimic the messenger
state what it is meant by the key term - receptor
a specific protein that a chemical messenger binds with, thereby invoking a biologically relevant response in that cell
state what it is meant by the key term - specificity
the ability of a receptor to only bind to one, or a limited number, of structurally related types of chemical messengers
state what it is meant by the key term - saturation
the degree to which receptors are saturated by messengers
state what it is meant by the key term - affinity
the strength with which a chemical messenger binds with it’s receptor
state what it is meant by the key term - competition
the ability of different molecules to compete with a ligand for binding to it’s receptor
state what it is meant by the key term - antagonist
a molecule that competes with a ligand for binding to it’s receptor but does not activate signalling normally associated with the natural ligand. therefore preventing the natural ligands actions
state what it is meant by the key term - agonist
a chemical messenger that binds to the receptor and triggers a cell response
state what it is meant by the key term - down-regulation
a decrease in the number of target cell receptors for a given messenger
state what it is meant by the key term - up-regulation
an increase in the total number of target cell receptors for a given messenger
state what it is meant by the key term - increased sensitivity
the increased responsiveness of a target cell to a given messenger
state what it is meant by the key term - first messenger
the intercellular chemical messenger that reaches the cell and binds to it’s receptor
state what it is meant by the key term - second messenger
substances that enter, or are generated, in the cytoplasm as a result of receptor activation
state what it is meant by the key term - protein kinases
transfer a phosphate from ATP to a protein and is often how a signal is transferred
binding of a ligand to a receptor leads to 1 of 5 cell responses. state these 5 cell responses
- the permeability, transport properties, or electrical state of the cell
- metabolism
- sensory activity
- rate of proliferation and/or differentiation
- contraction
state 4 facts about water soluble messengers
- broad range of receptors
- receptors activate intracellular signalling cascades which effect cell function
- receptors can activate downstream mediators which effect DNA transcription and other effects
- faster response and less sustained that lipid soluble messengers
