Cellular metabolism (Higgins) Flashcards
(31 cards)
define exergonic and endergonic
exergonic will have a negative delta G, remember that a reaction can only occur spontaneously if its negative
endergonic will have a positive delta G, so the reaction requires energy input
state why we need to produce energy in our cells, with examples
many biological processes are endergonic, energy is required for:
- mechanical work (muscle contraction) using ATP to ADP for Ca2+
- active transport (neurotransmission)
- synthesis of complex biomolecules from simple precursors
- signal transduction (environmental response), generation of light (fire flies) and electricity (eels)
describe the currency of energy transfer in the body
stage 1: large molecules broken down into smaller units, no useful energy captured
stage 2: small molecules degraded into a few simple units that play a role in central metabolism, some ATP generated
stage 3: ATP produced from the complete oxidation of simple units by the final common pathways for oxidation of fuel
ATP is the currency, energy rich molecule with high phosphoryl transfer potential, contains two phosphoanhydride bonds on its triphosphate unit
describe the 4 main functions of metabolism and compare anabolic and catabolic metabolism
metabolism has 4 main functions:
obtain energy
convert nutrients into own characteristic molecules
polymerise monomeric precursors (polysaccharides)
synthesise and degrade molecules required for special cellular functions (intracellular messengers)
catabolic - transfer fuels into unstable cellular energy
degradative, produces ATP, negative free energy, produces reducing potential, generates NADH and FADH2
anabolic - utilise the useful energy formed by catabolism to generate complex structures from simple ones
synthetic, requires ATP, positive free energy, requires reducing potential, uses NADPH
explain why metabolic regulation is required
human body requires energy to function
body does not have a constant external supply of energy
energy intake is intermittent (3 or 4 times a day)
yet energy expenditure is continuous with occasional extra outbursts
needed to tore energy and release it when required
energy and exercise increase metabolic rate, the body needs to recognise these situations and regulate the release of energy
list 3 principle ways metabolism is controlled
levels and accessibility of substrates (thermodynamics and compartmentation)
amounts of metabolic enzymes (rate of transcription and degradation)
modulation of catalytic activities of enzymes (allosteric regulation, covalent modification, association with regulatory proteins)
outline allosteric regulation of enzyme, using adenylate control as an example
energy charge ranges from 0 (all AMP) to 1 (all ATP)
ATP generating pathways are inhibited by a high energy charge
ATP utilising pathways are stimulated by high energy charge
control of pathways has become buffered (narrow limits)
ATP-generating catabolic:
glycogenolysis
glycolysis
beta-oxidation
ATP-utilising anabolic:
glycogenesis
gluconeogenesis
lipogenesis
purine and pyrimidine syntheses
outline covalent modification
attachment of a functional group covalently to an AA side chain, attachment is selective and enzyme catalysed induces conformational change
quicker than changing levels of enzyme
the types include;
adenylation
methylation
phosphorylation (common) - or dephosphorylation alters protein so Vmax or Km changes, sensitivity to substrate, sensitivity to inhibitors or activators, protein locked in new conformation, reversible, triggered by external amplification signal
describe the mode of uptake of glucose into cells (brief)
stage 1: trapping and destabilising glucose in order to produce 2x 3C molecules and energy is required (2ATP’s per glucose molecule)
stage 2: oxidation of 3C molecules to pyruvate and energy is generated (4 ATP’s and 2NADH per glucose molecule)
discuss the role of isoenzymes and hormonal control in glucose uptake
step 1: using HexoKinase - phosphorylates hexose sugars, induced fit enzyme action, equilibrium strongly favours glucose 6-phosphate
negative feedback system so inhibited by glucose 6-P
step 3: phosphofructokinase
triose phosphate isomerase (TIM) - accelerates isomerisation, kinetically perfect enzyme the rate limiting step is the diffusion-control encounter of substrate and enzyme, so 2 molecules of G-3-P from F1,6-bisP
step 6: glyceraldehyde 3-P dehydrogenase - oxidation of the aldehyde to a carboxylic acid by NAD+, joining of orthophosphate to the carboxylic acid
step 8, 9 and 10: pyruvate kinase - irreversible transfer of phosphoryl group form ATP, substrate level phosphorylation, regulatory enzyme activated by fructose 1,6bis-p and inhibited by ATP and alanine
outline the steps in stage 1 of glucose breakdown
stage 1 trapping and destabilising:
step 1: glucose enters cells via facilitated diffusion, glucose trapped by phosphorylation, the negative charge of glucose 6 means it cannot freely diffuse out of the cell and begins destabilisation
step 2: isomerisation of glucose 6_P to fructose 6-P is reversible reaction carried out by phosphate isomerase, convert one isomer to another by tautomerisation
step 3: second phosphorylation reaction, phosphofructokinase used in this step, allosteric enzyme (tetramer) sets pace of glycolysis, inhibited by ATP, citrate and H+, stimulated by AMP, ADP and Fruc 2,6bisP
step 4 and 5: cleavage of fructose 1,6bisP is catalysed by aldolase to yield 2 triose phosphates, readily reversible under normal physiological conditions
outline the steps in stage 2 of glucose breakdown
stage 2: energy generation
step 6: G3-P and phosphorylated enzyme G3 dehydrogenase, transfer high energy electrons from complex organic molecule to NAD+ to form NADH (formation of high energy bond)
step 7: ATP generation from 1,3-bisPglycerate, substrate level phosphorylation, remember: glucose yields 2x3C intermediates so 2 ATPs generated per glucose molecule
steps 8,9 and 10:
generation of additional ATP and pyruvate formation, phosphoryl group on 3-pglycerate shifts position followed by dehydrogenation and formation of a C=C bond, increases transfer potential of phosphoryl group
identify the regulatory enzymes of glycolysis
hexokinase
phosphofructokinase
pyruvate kinase
describe the metabolic fate of pyruvate
3 routes:
ethanol formation: yeast and some other microorganisms through an anaerobic process - pyruvate to acetaldehyde by decarboxylation then producing ethanol by NADH + H+ to NAD+
lactate formation: pyruvate to lactate by NADH to NAD+
pyruvate to acetyl CoA by decarboxylation to then undergo further oxidation
indicate the importance of glucose as a fuel and the finite store available in the body
synthesis of carbohydrate containing molecules relies on a source of activated monosaccharides
glucose is the primary source of fuel for the brain and the only fuel for RBA
160g glucose daily req
recognise the requirement for a route for glucose production from a non-carbohydrate source, identify the precursors
gluconeogenesis occurs in the liver, helps maintain blood glucose levels so brain and muscle can extract it
precursors first converted to pyruvate or enter pathways further along (oxaloacetate or DHAP)
major precursors:
lactate - skeletal muscle when glycolysis exceed oxidative metabolism
AA - diet or during starvation (not leucine or lysine)
glycerol - hydrolysis of TAG yields glycerol and FA
outline the gluconeogenic pathway
converts pyruvate into glucose (not the reverse of glycolysis)
in the liver
bypass 1:
step 1: carboxylation of pyruvate to oxaloacetate by pyruvate carboxylase - anaplerotic reaction (fill up)
step 2: decarboxylation and phosphorylation of oxaloacetate by phosphoenolpyruvate carboxykinase, GTP required, enzyme located both in cytosol and mitochondria, mitochondrial phosphoenolpyruvate carboxykinase used if lactate is glucogenic precursor (lactate to pyruvate yields NADH), cytosolic phosphoenolpyruvate carboxykinase used if pyruvate is glycogenic precursor (used if reducing equivalents low, NADH needed)
bypass 2:
PEP is metabolised by enzymes of glycolysis but in reverse until Fructose 1,6-bisP is formed
reactions near equilibrium, when conditions favour gluconeogenesis driven in direction of fructose 1,6-bisP, PFK catalyses irreversible step fructose1,6-bisP to fructose6-P using fructose 1,6bisphosphatase (allosteric enzyme to catalyse hydrolysis of c1 phosphate group)
bypass 3:
most tissue conversion of fructose6-P to glucose6-P is end of gluconeogenesis
tissues responsible for maintaining blood glucose homeostasis such as kidney and liver need to convert glucose 6-P to glucose, muscle cannot directly increase blood glucose, takes place in ER
identify the key enzymes in gluconeogenesis
pyruvate carboxylase in step 1
phosphoenolpyruvate carboxykinase in step 2
glyceraldehyde 3-phosphate dehydrogenase in terms of phosphoenolpyruvate carboxykinase
fructose 1,6-bisphospahte in bypass 2
discuss the reciprocal regulation of glycolysis and gluconeogenesis particularly in the liver
to initiate glycolysis fructise6-phosphate to be converted to fructose 1,6-bisphophate uses phosphofructokinase
fructose 1,6 bisphosphate to phosphoenolpyruvate to pyruvate uses pyruvate kinase
to initiate gluconeogenesis pyruvate to phosphoenolpyruvate required oxaloacetate
then to fructose 1,6bisphosphate to fructose 6-phospahte requires fructose 1,6bisphosphatase
describe the cori cycle and glyoxylate cycles
the cori cycle:
lactate formed by active muscle is converted to glucose by the liver - lactic acid production due to anaerobic activity, NADH is oxidised by transfer of electrons to pyruvate to form lactate
lactic acid dissociates into lactate and H+, causing a decrease in pH, muscle pain and failure to contract so activity decreases and causes oxygen debt
lactate can be converted into pyruvate which enters the TCA cycle, excess lactate is converted to glucose to maintain blood glucose levels
glyoxylate cycle:
plants convert FA into glucose
acetyl CoA generated by beta-oxidation is converted to glucose via glyoxylate cycle and gluconeogenesis
decarboxylation of TCA cycle bypassed so the carbon on acetyl CoA is assimilated, isocitrate cleaved to glyoxylate and succinate (metabolised by TCA enzyme to OA then to glucose by gluconeogenesis)
glyoxylate condenses with another acetyl CoA to generate malate which is oxidised to generate OA for another round of the cycle
explain the importance of having a finite carbohydrate store
glucose is only fuel for the brain under non-starvation conditions
glucose from glycogen is readily mobilised, good source of energy for sudden, strenuous activity
can provide energy under anaerobic conditions (unlike FAs)
outline the synthesis of glycogen
conversion of glucose to glucose 6-P, hexokinase traps it within the cell and the product inhibits the enzyme
glucokinase
glucose6-p converted to glucose1-P by phosphoglucomutase
glucose1-p becomes activated by UDP-glucose pyrophosphorylase to rpoduce UDP-glucose which is a reversible reaction
glycosyl units added to the non-reducing end of glycogen molecule to form alpha 1,4-glycosidic bonds catalysed by glycogen synthase
a primer called glycogenin is required due to the enzyme only adding glycosyl units if polysaccharide chain is greater than 4 residues
identify the key regulatory enzyme in the synthesis of glycogen and the other relevant enzymes for the production of glycogen
hexokinase
glucokinase - found in the liver and is not inhibited by glucose 6-P, high Km (lower affinity than hexokinase), provides glucose6-P for synthesis of glycogen and formation of FAs
phosphoglucomutase
UDP-glucose
pyrophosphorylase
glycogen synthase - this is the regulatory enzyme for glycogen synthesis, regulated by covalent modification of PKA by phosphorylation, converts active a from of the enzyme into inactive b form, insulin counteracts phosphorylation to signal body to synthesise glycogen, at high levels of glucose6-P can allosterically activate the b form
catalysation of 1,6-glycosidic bond are catalysed by a branching enzyme by removing 7 glucose units from end chain at least 11 residues long, reattaches at more interior site and must be at least 4 residues away from a branch point
outline the breakdown of glycogen
glycogen phosphorylase cleaves alpah1,4-glycosidic binds by addition of orthophosphate (removal at non-reducing end)
release of glucose 1-P
full reversible under physiological conditions [Pi]/[Glucose1-P] greater than 100
alpha 1,6 linkages cannot be broke down by glycogen phosphorylase and instead requires an enzyme that acts as a transferase and has alpah1,6-glucosidase activity (debranching enzyme)
activity of debranching enzyme allows further cleavage by glycogen phosphorylase
glucose1-P is converted to glucose6-P by phospholucomutase and due to its negative charge, it cannot exit the cell, hydrolytic cleavage of glucose6-P to glucose means that it can then enter the blood
