Metabolic Regulation 2024 PDF

Metabolic Regulation Nov 2024 MD138: 24_25 LOC 1 http://www.genome.ad.jp/kegg/pathway/map/map01100.html Typical cell has a capacity to make...

Metabolic Regulation Nov 2024 MD138: 24_25 LOC 1 http://www.genome.ad.jp/kegg/pathway/map/map01100.html Typical cell has a capacity to make  30,000 proteins  Catalyze thousands of different reactions  Metabolites shared by one or more ‘pathway’  4,000 genes (~ 12%) of all genes encode regulatory proteins  Receptors  Regulators of gene expression  500 different protein kinases MD138: 24_25 LOC 2  Metabolism – the feat! Regulate interlocking metabolic processes simultaneously – Right product – Right concentration – Right time Despite major changes external to the cell (e.g., supply of nutrients, oxygen) Generate no leftovers MD138: 24_25 LOC 3  Factors affecting the activity of enzymes By altering (1-6 in diagram) a) the number of molecules or b) the effective activity in a subcellular compartment 7-10 in diagram by modulating the activity of existing molecules MD138: 24_25 LOC 4  Alteration of enzyme activity Response to hormone or growth factor – Number of molecules in cell Rate of synthesis Rate of degradation Time scale hours to days – Changes in catalytic activity Allosteric control – Covalent modification – Time scale seconds to hours Liver is the most adaptable tissue – Change in diet from high carbohydrate to high fat Effects transcription of hundreds of genes and hence proteins MD138: 24_25 LOC 5 MD138: 24_25 LOC 6 Some of the genes regulated by Insulin Enzymes essential for glycolysis, which consumes glucose for energy PPP – produces NADPH – essential for conversion of glucose to lipids MD138: 24_25 LOC 7  > 150 genes are transcriptionally regulated by insulin Humans have at least 7 general types of insulin response elements (REs - IRE) – each recognized by a subset of transcription factors activated by insulin under various conditions MD138: 24_25 LOC 8  The regulatory input into genes is complex The PEP carboxykinase promoter region, showing the complexity of regulatory input into the gene for this enzyme MD138: 24_25 LOC 9  A priority for the cell - Maintenance of [ATP] 1. Protection of DNA (1st priority) 2. Maintain a constant supply and concentration of ATP [ATP] ~ 5 - 10 mM 3. Ratio of [ATP]/[ADP], [NADH]/[NAD+] and [NADPH]/[NADP+] are critical for reactions which use these cofactors – [AMP] is a sensitive indicator of the cell’s energy – [AMP] < 0.1 mM Adenylate kinase – ATP ADP then 2ADP AMP + ATP – AMP dependent protein kinase (AMPK) Increases glucose transport, glycolysis,  oxidation MD138: 24_25 LOC 10 The levels of ATP and AMP are a sensitive reflection of a cell’s energy status. Important mediator of regulation by AMP = AMP-activated protein kinase (AMPK) -phosphorylates key proteins and thus regulates their activities MD138: 24_25 LOC 11  Adenine Nucleotides and Metabolic Regulation Many ATP-using enzymes have Km values between 0.1 and 1 mM ATP conc in a typical cell is approx 5 mM If [ATP] drops – enzymes rates of hundreds of reactions would fall Very little chance of surviving this scenario MD138: 24_25 LOC 12  Many regulatory processes linked to regulation by AMP One of the most important is AMP-activated protein kinase (AMPK) MD138: 24_25 LOC 13 AMPK is activated by elevated [AMP] or decreased [ATP], by exercise, by the sympathetic nervous system or by peptide hormones produced in adipose tissues When activated, AMPK phosphorylates target proteins and shifts metabolism in a variety of tissues away from energy –consuming reactions in a tissue specific manner MD138: 24_25 LOC 14  Overview of AMPK signaling pathway https://www.youtube.com/watch?v=4G56m9fyNWY 6:57 min MD138: 24_25 LOC 15  General regulatory mechanisms Prevent simultaneous operation of pathways in opposite directions – Glycolysis and gluconeogenesis Partition metabolites between pathways – Glycolysis and Pentose phosphate pathway Use fuel best suited for immediate needs – Glucose, fatty acids, glycogen, amino acids Shut down biosynthetic pathways when their products accumulate Errors (see glycogen storage diseases) MD138: 24_25 LOC 16  Coordinated Regulation of pathways Glycolysis and Gluconeogeneis If both occurred at same time, then ATP would be consumed without any biological or chemical work = Futile cycle ATP + fructose 6-phosphate ADP + fructose 1,6 bisphosphate Fructose 1,6 bisphosphate + H2O Fructose 6-phosphate + Pi Overall reaction ATP + H2O ADP + Pi + heat Need coordination MD138: 24_25 LOC 17  Allosteric regulation Very rapid (milliseconds) Triggered locally by changes in [metabolite] – Substrate – Product – Key cofactor – Examples already given (Glycolysis, TCA cycle, Fatty Acid synthesis, -oxidation) MD138: 24_25 LOC 18  Covalent modification Most common is phosphorylation and dephosphorylation – Kinases and phosphatases Effects of phosphorylation – Electrostatic features – Cause movement of an inhibitor out of active site – Alter interaction with other proteins – Force conformational changes MD138: 24_25 LOC 19  Isoenzymes The distribution of different isozymes of a given enzyme reflects at least 4 factors 1. Different metabolic patterns in different organs 2. Different locations and metabolic roles for isozymes in the same cell 3. Different stages of development in embryonic or fetal tissues and in adult tissues 4. Different responses of isozymes to allosteric modification MD138: 24_25 LOC 20  Isoenzymes Isoforms generally differ in – kinetic or regulatory properties (Km differences for hexokinase) – In the cofactor they use (NADH/NADPH for dehydrogenase isozymes) – Subcellular distribution (soluble or membrane-bound) – Amino acid sequences E.g Hexokinase isoenzymes Lactate Dehydrogenase (LDH) MD138: 24_25 LOC 21  Compartmentation PHYSICAL SEPARATION e.g. FA synthesis and Degradation RAISES METABOLITE CONCENTRATIONS REDUCES DIFFUSION BARRIERS ALLOWS EUKARYOTIC CELLS MAINTAINENCE OF DIFFERENT ENVIRONMENTS REQUIRED TO ACCOMMODATE e.g pH and potential gradients for ox phos ASSISTS METABOLIC CONTROL: keeps enzymes, substrates and regulators in separate locations with only intermittent access between them MD138: 24_25 LOC 22  Location-dependent functions of metabolic enzymes a) ATP citrate lyase (ACL) and b) PDH complex (PDC) contribute to histone acetylation, thus regulating gene expression c) the glycolytic enzyme PK activates transcription of glycolytic enzymes when relocated to the nucleus d) GAPDH acts as an RNA-binding protein in the absence of glycolytic substrate- reducing translation of cytokines Metabolic enzymes can perform nonmetabolic functions dependingMD138: on their subcellular 24_25 LOC location 23