TOPIC 1-6 OBJECTIVES Flashcards
- Define the concepts of a biochemical pathway and cellular metabolism
Biochemical pathway – In a pathway, the product of one reaction serves as the substrate of the subsequent reaction – these are classified as either catabolic or anabolic. Metabolism is best understood by examining its component pathways. Each pathway is composed of multienzyme sequences, and each enzyme, in turn, may exhibit important catalytic or regulatory features
Cellular metabolism – collectively network of pathways is called metabolism
- Explain the difference between catabolism and anabolism
Catabolic – where complex molecules are broken down into simple molecules
Anabolic – where simple molecules are used to build larger more complex molecules
- Explain the concepts of the transition state and activation energy, indicating the effect that enzyme catalysis has on these parameters
Have substrate on left and to go from substrate to product – go through a transition state – activation energy
Activation energy (AG‡) is the amount of energy required to bring all of the molecules in 1 mole of substrate to the transition state
This is critical to life, without it high energy compounds would be too unstable to exist
- To increase rate of reaction, we either need to:
1. Add more energy to the system
2. Decrease AG‡ - we use a catalyst to do this
- Define the terms Vmax and Km as related to the Michaelis-Menten model of enzyme kinetics and explain what these terms tell us about the relationship between an enzyme and its substrate
Vmax – maximum velocity, The rate of an enzyme-catalyzed reaction increases with substrate concentration until a maximal velocity (Vmax) is reached. The leveling off of the reaction rate at high substrate concentrations reflects the saturation with substrate of all available binding sites on the enzyme molecules present.
Km – is the substrate concentration at which the reaction rate is half maximum (Vmax)
- Derive Vmax and Km values from the Lineweaver-Burk plot
To determine Km and Vmax, it is easier to transform the Michaelis-Menten equation
We take the reciprocal (1/v) of both sides:
- Define the five main ways in which enzyme activity is regulated
- Enzyme production
- Transcription or translation is switched on or off
- e.g. production of specific cytochrome P450 enzymes in the liver - Compartmentalization
- This confines specific metabolic pathways to different parts of the cell
- e.g. enzymes for b-oxidation of fatty acids are only found in the mitochondria - Post-translational modification - e.g. phosphorylation and glycosylation
- e.g. phosphorylation of glycogen synthase helps control blood sugar levels - Environment
- Some enzymes are only active in certain environments
- e.g. chymotrypsin is produced in the pancreas but only activated by acidic conditions in the stomach - Activation and inhibition
- Specific molecules can bind to enzymes and switch them on or off
- This is a common target for drug development
- This is known as allosterism
- Explain the concept of substrate regulation of enzyme activity
At low [S], when one substrate molecule binds to the enzyme, it makes it easier for the next to bind
- This is referred to as homotropic interaction
This tells us that there is more than one active site per enzyme molecule
There is interaction (co-operation) between these active sites
- Distinguish between positive, negative, homotropic and heterotropic allosteric interactions
homotropic interaction - At low [S], when one substrate molecule binds to the enzyme, it makes it easier for the next to bind
heterotropic interaction - regulation of an enzyme by the binding of an effector molecule at the protein’s allosteric site
Positive allosteric effectors (activators) enhance enzyme activity
Negative allosteric effectors (inhibitors) decrease enzyme activity
- Compare and contrast reversible and irreversible enzyme inhibitors
irreversible (binds to enzyme covalently) or reversible (noncovalently)
- Interpret a Lineweaver-Burk plot to demonstrate the effect of competitive, non-competitive, and uncompetitive inhibitors on enzyme kinetics
Competitive
inhibitor binds at same site where substrate would usually bind – competitive and can be overcome by increasing [S], as [S] required for Vmax increases so does [S] required for 1/2Vmax so Km increases
1. effect on Vmax – unchanged
2. effect on Km – increased, more substrate is needed
3. effect on Lineweaver Burk plot
Non-competitive
causes decrease in Vmax
inhibitor and substrate bind at different sites on the enzyme, inhibition cannot be overcome by increase [S], enzyme-substrate complex cannot convert substrate to product, so enzyme concentration is effectively reduced
1. effect on Vmax – decrease, inhibitor cannot be overcome by increasing the substrate concentration
2. effect on Km – unchanged, no interference with binding
3. effect on Lineweaver Burk plot
Uncompetitive
uncompetitive inhibitors can only bind to ES complex and not to free enzyme
inhibition cannot be overcome by high concentrations of substrate
enzyme-substrate-inhibitor complex cannot convert substrate to product, so enzyme concentration is effectively reduced
binding of inhibitor to ES complex means that takes longer for substance to leave active site
1. effect on Vmax – decreased
2. effect on Km – decreased
3. effect on Lineweaver Burk plot
- Define the five central themes of metabolism
1) Fuel molecules are degraded (catabolism) and large molecules made (anabolism) step-by-step in a series of linked reactions called metabolic pathways
2) The energy currency of all life is ATP
3) The oxidation of pre-existing carbon molecules drives the formation of ATP
4) There are only a limited number of types of reactions in metabolism
5) Metabolic pathways are tightly regulated
- Relate bond formation and breakage to energy capture and release
1) Breaking bonds = releases energy
2) Making bonds = consumes energy
- Understand the central importance of ATP in metabolism
1) Adenosine triphosphate (ATP), energy-carrying molecule found in the cells of all living things. ATP captures chemical energy obtained from the breakdown of food molecules and releases it to fuel other cellular processes.
2) When ATP is hydrolysed, energy is released
3) Adenosine triphosphate is used to transport chemical energy in many important processes, including:
- Aerobic respiration (glycolysis and the citric acid cycle)
- Fermentation
- Cellular division
- Photophosphorylation
- Motility (e.g., shortening of myosin and actin filament cross-bridges as well as cytoskeleton construction)
- exocytosis and endocytosis
- Photosynthesis
- Protein synthesis
- Relate oxidation and reduction to electron transfer reactions
- An oxidation–reduction or redox reaction is a reaction that involves the transfer of electrons between chemical species (the atoms, ions, or molecules involved in the reaction).
- During a redox reaction, some species undergo oxidation, or the loss of electrons, while others undergo reduction, or the gain of electrons.
- Understand the role of NAD+ and FAD in metabolism
- Nicotinamide adenine dinucleotide (NAD+) and flavin adenine dinucleotide (FAD+) are two cofactors that are involved in cellular respiration. They are responsible for accepting “high energy” electrons and carrying them ultimately to the electron transport chain where they are used to synthesize ATP molecules.
- NAD accepts just one hydrogen a single hydrogen and an electron pair is transferred, and the second hydrogen is freed into the medium reduced to NADH
- FAD can accommodate two hydrogen reduced to FADH2
- Calculate concentrations by mass and by moles and use appropriate prefixes to convert concentrations in biological systems
- Concentration by mass : concentration = amount in mass/ volume
- Concentration by moles or molarity = moles/ volume
- Common prefixes
o 10^-3 M = 1 mM = 1 mmole/litre (1 millimolar)
o 10^-6 M = 1 µM = 1 µmole/litre (1 micromolar)
o 10^-9 M = 1 nM = 1 nmole/litre (1 nanomolar)
- Define the three broad classes of hormone
1) Peptide hormones are hormones that are made of small chains of amino acids, water soluble – e.g. prolactin, insulin, glucagon
2) Steroid hormones are steroids that act as hormones, lipid soluble– e.g. progesterone, testosterone, estradiol
3) Amino acid derivatives are hormones derived from amino acids (tyrosine and tryptophan), are water soluble – e.g. adrenaline, thyroxine, triiodothyronine
- Distinguish between the ways in which hormones can exert their effects
1) Those that act at the level of the cell surface – outside
a. Peptide hormones and the catecholamines
b. Growth factors
c. Water-soluble and unable to cross the membrane
d. They exert their effects on the target via intracellular secondary messengers
2) Those that enter the cell to exert their effects – inside
a. Steroid hormones and the thyroid hormones
b. Lipid soluble and can readily penetrate the membrane
c. They exert their effects from within the target cell
- Explain the mechanism of action of G protein-coupled receptor using cAMP as a secondary messenger
- For those agents acting at the cell surface, it has been shown that an essential target in their mode of action is the generation of an identifiable intracellular second messenger
o This acts to notify the cell that the first messenger (hormone/ growth factor) has bound
o The first second messenger/ most important to be identified was cyclic AMP - Cyclic AMP-mediated response:
o Hormone outside cell binds to receptor – causing change in shape of receptor which activates G protein (GNP) which interacts with GTP and this eventually activates a membrane bound enzyme called adenylate cyclase – which is able to take ATP and convert it into a circular molecule cyclic AMP – this is then able to allosterically activate protein kinase A within in cell – can then phosphorylate enzymes (switch them on or off) because it is a protein
- Distinguish between the terms hypo- and hyperglycemia
Hyperglycemia
Excessive blood glucose in circulating plasma
Generally classified as BG > 10 mM
Has widespread effects on the body: CNS; heart; immune system; skin; vision
Can be caused by diabetes; eating disorders; some drugs; some diseases; and physiological stress
Hypoglycemia
Lower than normal level of circulating blood glucose
Generally classified as BG < 3.6 mM
Has wide-ranging effects: adrenergic system; CNS; neuroglycopenia
In adults, it can be caused by: diabetes’ immunological disorders; problems with the adrenal and pituitary glands; tumours
- Explain why blood glucose levels need to be regulated
- Glucose is the primary source of energy for all cells of the body
- Some cells can only metabolise glucose, so it is required in the body at all times
- Blood glucose levels in the body are tightly regulated within a range of 4 to 6 mM
- Describe the basic structure and site of synthesis of Insulin
- A dimer consisting of two peptide chains (A and B), held together by disulphide bonds
o 51 amino acids, MW 5808 Da
o Synthesised in the pancreas
- Explain how insulin release is controlled
Stimulation of insulin secretion - Insulin is stored in granules in the cytosol
- Secretion of insulin and glucagon are tightly regulated to maintain glucose levels
- B-cells transport glucose via GLUT2 and phosphyorylate it via glucokinase
- As levels of phosphorylated glucose increase, it signals release of insulin and decreases release of glucagon
Inhibition of insulin secretion - Insulin secretion is inhibited by lack of dietry fuel or during stress (e.g. infection)
- This is mediated via adrenaline
- Regulated via the sympathetic nervous system
- Allows the body to override glucose-dependent insulin production during emergencies
Insulin: mechanism of action - When insulin binds the alpha-subunits, tyosine kinase is activated and phosphorylates cellular proteins
- Describe the major effect of insulin on metabolism
- Increases glucose uptake into muscle cells and adipocytes - GLUT4 transporters are translocated form the intracellular vesicles to the cell membrane allowing more glucose to be transported from blood to muscle cells
- Increases glycolysis – because will use more glucose
- Decreases hepatic gluconeogenesis – because wont be producing glucose at a time we are trying to decrease it
- Increases glycogen synthesis, decreases glycogenolysis – so glucose isnt being released
- Increases triglyceride synthesis (in adipocytes) – so cells use glucose instead
- Decreases lipolysis
- Increases protein synthesis – so its not available as a feul source, same as trigs
- Decreases protein degradation
- Describe the basic structure and site of synthesis of glucagon
- A single polypeptide chain, unlike insulin
- 29 amino acids, MW 3485 Da
- Similar to insulin, it is synthesised as a large precursor
- This is serially cleaved to produce active glucagon
- Explain how glucagon release is controlled
Inhibition of glucagon secretion - Glucagon is inhibited by elevated blood glucose
Glucagon: mechanism of action - Glucagon acts through a G protein-coupled receptor
- Binding of glucagon causes an increase in cAMP, which activates protein kinase A
- This activates a cascade of other enzymes that affect carbohydrate and lipid metabolism
- Describe the major effect of glucagon on metabolism
- Decreases glycolysis – want glucose in blood
- Increases hepatic gluconeogenesis – want increase glucose in liver
- Decreases glycogen synthesis, increases glycogenolysis (in liver not muscle) – don’t want to be packaging it away
- Decreases triacylglycerol synthesis – want to use this as a energy fuel instead of glucose, same for protein below
- Increases lipolysis (in adipose tissue)
- Decreases protein synthesis
- Increases protein degradation
