Metabolism Flashcards
What are the three stages of metabolism?
Step 1 = breakdown of macromolecules
- Occurs outside of cells
- Macromolecules –> subunits
Step 2 = glycolysis & krebs’ cycle
- Occurs in the cytosol (final step in the mitochondria)
- Production of ATP + NADH
Step 3 = oxidative phosphorylation
- Occurs in the mitochondria
Define anabolic and catabolic metabolism
Anabolic - construct molecules from smaller units (i.e. use energy)
Catabolic - breakdown molecules from larger units to produce energy (often referred to as “useful” metabolism)
Define the following type of metabolic reaction:
- Oxidation-reduction
- Ligation (req. ATP cleavage)
- Isomerisation
- Group transfer
- Hydrolytic
- Addition/Removal of functional group
REDOX = electron transfer
Ligation = formation of covalent bond (eg: C-C)
Isomerisation = re-arrangement of atoms (i.e. forms isomers)
Group transfer = transfer of functional group from one molecule to another
Hydrolytic = cleavage of blond + addition of water
Addition/Removal of functional group = to double bond
Where does ATP carry its energy?
Energy is carried within the phophate bonds (anhydride bonds)
Define free energy
Free Energy (G) is defined as the amount of energy within a molecule that could perform useful work at a constant temperature (units = kJ/mole)
What is ∆G?
∆G is negative, leading to an increase in disorder of the system, release of heat.
What is the main way of generating ATP?
Glucose combustion
Give the formula/equation for glucose combunstion
C6H12O6 + 6O2 –> 6CO2 + 6H20
What is a coupled reaction? Why is it within the cell’s interest to have coupled reactions?
Many cellular reactions required energy (i.e. they are energetically unfavourable) therefore they are coupled with energetically favourable reactions (i.e. reactions that form energy). This ensures that overall, the cell is energetically neutral
What are the two main ways of making ATP (within the cell)?
- Substrate Level Phosphorylation - the direct transfer of one phosphate group from an intermediate substrate to ADP throughout a biochemical pathway (eg: glycolysis)
- Electron Transfer - energy derived from the ETC is used to produced ATP (eg: oxidative phosphorylation)
What is NAD? Describe its role
- NAD+ (Nicotinamide adenine dinucleotide) is a co-enzyme
- Critical co-factor for dehydrogenase reactions
- Catalyses the dehydrogenation of substrates
- Acceptor of one hydrogen atom and two electrons
- Note - it has no effect on its own but functions only after binding to a protein.
What is glycolysis?
Glycolysis is the anaerobic metabolic pathway that converts glucose into pyruvate
What is the net yeild of glycolysis?
Net Yeild = 2 x ATP, 2 x NADH
(Total = 4 x ATP, 2 x NADH)
What are the three general phases of glycolysis
- Energy Investment (steps 1 - 3)
- Glucose → Fructose 1,6-bisphosphate
- Energy Usage (steps 4 - 5)
- Fructose 1,6-bisphosphate → Glyceraldehyde-3-phosphate
- Enegy Release (steps 6 - 10)
- Glyceraldehyde-3-phosphate → Pyruvate
Outline the 10 steps of glycolysis
(i.e. give the 10 molecules involved)
- Glucose
- Glucose-6-Phosphate
- Fructose-6-Phosphate
- Fructose-1,6-Bisphosphate
- Glyceraldehyde-3-Phosphate
Dihydoxyacetone-Phosphate - Glyceraldehyde-3-Phosphate
- 1,3-Bisphosphoglycerate
- 3-Phosphoglycerate
- 2-Phosphoglycerate
- Phosphoinol-Pyruvate
- Pyruvate
How many reactions are involved in glycolysis?
10
Glycolysis: Reaction 1
Reaction 1: Phosphorylation
Reaction: Glucose –> Glucose-6-Phosphate
Enzyme: Hexokinase
Energy: 1 x ATP –> ADP (i.e. requires energy)
This is the first phosphorylation event and is irreversible
Glycolysis: Reaction 2
Reaction 2: Isomerisation
Reaction: Glucose-6-Phosphate à Fructose-6-Phosphate
Enzyme: Phosphoglucose Isomerase (shuffling of phosphate forming open chain form)
Product: Water
Glycolysis: Reaction 3
Reaction 3: Phosphorylation
Reaction: Fructose-6-Phosphate –> Fructose 1,6-bisphosphate
Enzyme: Phosphofructokinase
Energy: 1 x ATP –> ADP (i.e. energy usage)
Glycolysis: Reaction 4
Reaction 4: Cleavage
Reaction: Fructose 1,6-bisphosphate –> glyceraldehye-3-phophate + dihydroxacetone phophate
Enzyme: Aldolase (2x 2C molecules formed)
Glycolysis: Reaction 5
Reaction 5: Reduction/Fixation
Reaction: glyceraldehye-3-phophate fixation
Enzyme: **Triose phosphate isomerase **
Glycolysis: Reaction 6
NB: reaction 6 = 2 parts - hydrogenation + phosphorylation
Reaction 6: **Hydrogenation **
Reaction: 2 x glyceraldehye-3-phophate
Enzyme: **Triose phosphate dehydrogenase **
Product: 2 x NAD –> 2 x NADH (hydrogenation of NAD)
2 molecules created as the pathway splits in two at this point - i.e. from this point, everything happens twice
Reaction 6: **Phosphorylation **
Reaction: glyceraldehye-3-phophate –> 1,3-bisphophoglycerate
Enzyme: glyceraldehyde 3-phosphate dehydrogenase
Product: ADP –> ATP (i.e. energy generation) (2 in total - one produced in each branch)
Glycolysis: Reaction 7
Reaction 7: Phosphorylation (relocation of C bond)
Reaction: 1,3-bisphosphoglycerate –> 3-phosphoglycerate
Enzyme: Phosphorglycerate Kinase
Glycolysis: Reaction 8
Reaction 8: Dehydration
Reaction: 3-phosphoglycerate –> 2-phosphoglycerate
Enzyme: Phosphoglycerate Mutase
Glycolysis: Reaction 9
Reaction 9: Transfer
Reaction: 2-phosphoglycerate –> phosphoinol-pyruvate
Enzyme: Mutase
Glycolysis: Reaction 10
Reaction 10: Phosphorylation
Reaction: phosphoinol-pyruvate –> pyruvate
Enzyme: pyruvate kinase
Product: ADP –> ATP (one produced in each branch, 2 in total)
Pyruvate Kinase transfers high energy phosphate group to ADP forming ATP
phosphoinol pyruvate becomes pyruvate
How many possible fates does pyruvate have?
Three
(two anaerobic - alcoholic fermentation & generation of lactate, one aerobic - acetyl coA)
What is the general purpose of the anaerobic fates of pyruvate?
Generation of Lactate/Alcohol Fermentation enable the regeneration of NAD+ which allows glycolysis to continue, even in situations of oxygen deprivation
Discribe alcoholic fermentation of pyruvate
- one of two anaerobic fates of pyruvate
- product = ethanol
- biproduct = water + carbon dioxide
- co-factor = NADH –> NAD+ (purpose of the reaction)
- Not major reaction in humans
Describe the generation of lactate
- the major anaerobic fate of pyruvate
- reaction occurs in the liver
- pyruvate is fermented to lactate
- There is no oxidant therefore the cell recycles NADH converting pyruvate into lactate
- lactate can be converted back to glucose
- occurs during intense exercise (anaerobic metabolism - oxygen is limiting factor)
- generates free NAD+ which is needed by the muscle for other reactions.
- lactate diffuses from the muscle into the blood stream and is picked up by the liver, where the high levels of NAD+ can be used by lactate dehydrogenase to regenerate pyruvate.
How can LDH be used diagnostically?
LDH = lactate dehydrogenase
- Function = catalyses lactate –> pyruvate
- Distribution = various body tissues (heart, muscle, liver etc.)
- Elevated levels = indicator of several disorders therefore testing is a useful diagnostic tool
- Heart attack
- Stroke
- Liver disease
How can creatine kinase be used diagnostically?
A large reservoir of creatine phosphate is on hand to buffer demands for phosphate in the following reaction:
CP + CK –> Creatine + ATP
CK can be used diagnostically - because, when a muscle is damaged, creatine kinase leaks into the bloodstream. Elevated levels suggest:
- Heart attack
- Chest pain
- Duchenne’s
Describe the generation of acetyl coA
- The only aerobic fate of pyruvate
- Pyruvate enters the Krebs Cycle where it is oxidised (final product = acetyl coA which then enters TCA cycle)
- Occurs in the mitochondria
What is the committed step of the Krebs’ Cycle
The first step - the conversion of pyruvate to acetyl coA (by the pyruvate dehydrogenate complex)
What is the Pyruvate Dehydrogenase Complex?
- Not a single enzyme but a complex of three enzymes
- 5 co-factors involved
- Thiamine pyrophosphate (TPP)
- lipoamide
- FAD
- CoA
- NAD+
Describe the key features of the major co-factors of the PDC (TPP, lipoamide & FAD)
TPP
- Derived from Vit. B
- Forms carbanion which attacks pyruvate
Lipoamide
- Functional group capable of REDOX reactions
FAD
- Accepts and donates 2 e- + 2 H+
- Forms FADH
Outline the steps involved in the PDC reaction
- Decarboxylation of pyruvate to give hydroxyethyl TPP (by TPP)
- Oxidation & transfer to lipoamide to give acetylipoamide (by lipoamide)
- Transfer of the acetyl group to CoA to give acetyl CoA
- Regeneration of oxidised lipoamide.
- Regeneration of oxidised FAD, generating NADH
*This is a cyclical reaction *
What is the krebs’ cycle
The Krebs Cycle occurs in the mitochondria - it is the aerobic metabolic pathway to generate energy (ATP) from Acetyl CoA
What is the overall energy production from the Krebs Cycle?
around 12 ATPs per Krebs Cycle
Every cycle produces 3 x NADH + 1 x GTP + 1 x FADH2 (plus 2 x CO2 as waste)
- Every NADH molecule produces 3 ATPs
- Every FADH molecule produces 2 ATPs
- FAD produces less ATP because it is accepted complex II (no H+)
Where are the krebs’ cycle enzymes located?
In the mitochondrial matrix space
EXCEPT - succinate dehydrogenase (which is an integral membrane protein)
Outline the Krebs Cycle
(i.e. list the molecules)
- Acetyle CoA (2C)
- Citrate (6C)
- Isocitrate (6C)
- α-Ketone Gluterate (5C)
- Succinyl CoA (4C)
- Succinate (4C)
- Fumerate (4C)
- Malate (4C)
- Oxaloacetate (4C)
Krebs Cycle: Step 1
Reaction 1 = transfer reaction
- Acetyl CoA (2C) enters cycle from pyruvate dehydrogenase complex
- Combines with oxaloacetate (4C) in the presence of citrate synthase forming citrate (6C) (aka: citric acid)
Krebs Cycle: Step 2
Reaction 2 = isomerisation
- Citrate isomerisation reaction via aconitase to form isocitrate (first dehydration [release H2O] then hydration [take up H2O])
Krebs Cycle: Step 3
Reaction 3 = decarboxylation
- Oxidative decarboxylation of isocitrate forming α-ketone gluterate (5C) via **DH dehydrogenase **
- H+ released forming NADH (NAD + H+ –> NADH = energy carrying)
- H+ released and rebound to free C from CO2 formation (CO2 released)
Krebs Cycle: Step 4
Reaction = *decarboxylation *
- Oxidative decarboxylation of α-ketone gluterate into succinyl coA (4C) via **co-enzyme A **
- H+ released forming NADH (NAD + H+ –> NADH = energy carrying)
- H+ released and rebound to free C from CO2 formation *(CO2 released) *
- CoA displaced by phosphate molecule and transferred to GDP (GDP + Pi –> GTP = energy carrying)
Krebs Cycle: Step 5
- Succinic thiokinase breaks high energy bond converting succinyl coA into succinate (4C)
- _GTP & CoA released _
Krebs Cycle: Step 6
Reaction = oxidation
- Oxidation of succinate into fumerate (4C) via **succinate DH **
- 2 H+ released forming FADH2 (FAD + 2H+ –> FADH2 = energy carrying)
Krebs Cycle: Step 7
Reaction = hydration
- Hydration of fumerate C=C to C-C + OH- in malate (4C) via **fumerase **
Krebs Cycle: Step 8
Reaction = oxidation
- Malate oxidation via malate DH forming oxaloacetate (original 4C compound)
- H+ released forming NADH (NAD + H+ –> NADH = energy carrying)
Define transamination
Transamination = amine group transfer from one aa to a keto acid forming new pair of amino acid and keto acids
Describe the conversion of alanine to acetyl coA
Alanine (C3) undergoes transamination by the action of the enzyme alanine aminotransferase
What is the overall purpose of oxidative phosphorylation?
Oxidative phosphorylation works to create energy via the re-oxidisation the reduced co-factors
(NADH + FADH2) via molecular oxygen from the Krebs Cycle (total = 12 ATPs)
NADH + H+ + ½ O2 à NAD+ + H20 = 3 ATPs per NADH
FADH2 + ½ O2 à FAD + H20 = 2 ATPs pet FADH2
Define chemiosmosis
Chemiosmosis is the movement of ions (H+) across a selectively permeable membrane, down their electrochemical gradient to produce ATP
What are the two major steps involved in oxidative phosphorylation?
- The translocation of protons from within the matrix of the mitochondria. This is controlled by the electron transport chain (ETC)
- The pumped protons are allowed back into the mitochondria through a specific channel (ATP synthase), which is coupled to an enzyme which can synthesise ATP
How is ATP created during chemisomosis
The second step of oxidative phosphorylation (flow of protons back into mitochondria) is coupled to ATP synthesis
Define proton motive force
- The force that drives the H+ back into the matrix space.
- It consists of a pH gradient and a t_ransmembrane electrical potential _
How does NADH enter the mitocondria?
- NADH is produced by glycolysis (therefore needs to move from the cytosol to the mitochondria)
- Note - it is the high energy electrons (carried by NADH) not the molecule itself that is transported to the mitochondria
- This is done by two shuttles
- Glycerol Phosphate Shuttle – skeletal muscle & brain
- Malate Aspartate Shuttle – liver, kidney & heart
Describe the glycerol phosphate shuttle
- Cytosolic glycerol 3-phosphate dehydrogenase transfers electrons from NADH to glycerol 3-phosphate.
- A membrane bound form of the same enzyme transfers the electrons to FAD.
- These then get passed to co-enzyme Q, part of the electron transport chain.
Describe the malate aspartate shuttle
- Uses two membrane carriers (alpha-ketoglutarate transporter & glutamine/aspartate transporter) & four enzymes:
- A hydride ion (H-) is transferred from cytoplasmic NADH to oxaloacetate to give malate
- Malate can be transported into the mitochondria where it is rapidly re-oxidised by NAD+ to give oxaloacetate and NADH (catalysed by mitochondrial MDH).
List the 3 membrane complexes and 2 mobile carriers involved in the ETC
Membrane Complexes
- NADH Dehydrogenase Complex (complex I)
- Complex II = succinate dehydrogenase (integral membrane protein)
- Cytochrome b-c1 Complex (complex III)
- Cytochrome Oxidase Complex (complex IV)
Mobile Carriers
- Ubiquinone (Co-Enzyme Q)
- Cytochrome C
Outline the overall progression of the ETC
Outline the steps involved in oxidative phosphorylation
- NADH moves from the matrix to the inner membrane space
- NADH donates electrons to NADH Dehydrogenase (complex I)
- NADH Dehydrogenase donates electrons to Ubiquinnone
- Ubiquinnone donates electrons to Cytochrome b-c1 (complex III)
- Ubiquinnone donates electrons to Cytochrome C (complex (IV)
- Cytochrome C donates electrons to Cytochrome Oxidase (complex 3 – 4 e, must be full)
- Cytochrome Oxidase donates electrons to oxygen (forming 2 x H2O molecules)
Describe the structure of ATP synthase
ATP synthase = mutlimeric enzyme
- Membrane bound part (F0) – three subunits: F0 = a, b, c
- Catalytic Subunit = Projection to the matrix (F1) – three subunits F0 = α, β, γ
Describe how the structure of ATP synthase helps in the formation of ATP
- H+ flows the enzyme (membrane anchored) via pore
- C subunit (membrane bound portion) rotate (γ-subunit (catalytic portion) rotates with it)
- α- and β-subunits (catalytic) are fixed (no rotation) by B subunit (membrane)
- β-subunits = conformational change causing rotation (this drives catalysis)
- Catalysis alters affinities for ATP and ADP
- Torsional energy flows from the catalytic subunit into the bound ADP and Pi to promote the formation of ATP.
The direction of proton flow determines whether ATP of ADP is formed - which way is which?
- Protons into matrix = ATP synthesis
- Protons into cytosol = ATP hydrolysis
Discuss the effects of the following poisons:
- Cyanide
- Carbon Monoxoide
- Malonate
- Oligomyin
Cyanide
- Few drops = fatal
- Binds with high affinity to the ferric (Fe3+) form of the haem group in the cytochrome oxidase complex
- Blocks flow of electrons through ETC
- No ATP production
Carbon Monoxide
- Similar to CN
- Binds to the ferrous (Fe2+) form of the haem group, also blocking the flow of electrons.
- No ATP production
Malonate
- Structurally similar to succinate
- Acts as a competitive inhibitor of succinate dehydrogenase
- Slows flow of electrons from succinate to ubiquinone by inhibiting oxidation of succinate to fumerate
Oligomyin
- Antibiotic produced by Streptomyces
- Inhibits oxidative phosphorylation by binding within the “stalk” of ATP synthase
- Blocks the flow of protons, ATP synthesis inhibited + build up of protons in intermembrane space
Define amphiphatic
Molecules which contain both hydrophilic (polar) and lipohilic structures
What is the difference between a saturated and non-saturated fatty acid?
Unsaturated fats have a C=C (double bond) causing a kink(s) in the chain (the number of double bonds depends on the fat). These are stored as plant oils
Saturated fats only have C-C (single bonds) therefore the fat is straight. These are stored as animal fats.
Define catabolism
Catabolism is faty acid metabolism
What is β-oxidation?
β-oxidation is fatty acid metabolism.
It occurs in the mitochondria in several stages, resulting ultimately in the generation of acetyl CoA (which enters the Krebs Cycle)
Where is β-oxidation initiated?
On the outer mitochondrial membrane
Describe the inititation of β-oxidation
β-oxidation is initiated through the generation of Acyl coA from a fatty acidwhich requires the enzyme acyl coA synthetase
What is the carnitine shuttle?
- The carnitine shuttle transports the acyl coA into the mitochondrial matrix
- Acyl coA is coupled to carnitine forming acyl carnitine.
- Carnitine and acyl carnitine are moved to and from the matrix by a translocase.
- Acyl coA is created in the process
Outline the steps involved in β-oxidation
- β-Oxidation (yields FADH2)
- Hydrolysis
- β-Oxidation (yields NADH)
- Cleavage (yields Acetyl CoA)
What are the products of β-Oxidation of fatty acids?
- Acetyl Co-A (enters the TCA/Krebs Cycle)
- NADH (enters the ETC - part of the TCA/Krebs Cycle)
- FADH2 (enters the ETC - part of the TCA/Krebs Cycle)
What is a ketone?
Ketone bodies are not lipids however they are derived from them - soluble form of energy derived from lipids in starvation (extreme fasting) conditions
What are the key differences between lipid metabolism and lipid synthesis?
Lipid Metabolism
- Occurs in the mitochondria
- Involves acyl coA species
- Reducing power is FAD/NAD+
Lipid Synthesis
- Occurs in the cytosol
- Involves acyl carrier protein
- Reducing power is NADPH
Outline lipogenesis
Lipogenesis = fatty acid synthesis
- Product = palmitate (the only de novo fatty acid, all others are produced via modifications)
- Two enzymes are invovled:
- **Acetyl CoA Carboxylase **
- Fatty acid synthase
The reaction:
- Acetyl coA carboxylase catalyses Acetyl coA –> malonyl coA (req. ATP)
- Fatty acid synthase catalyses further reactions
- Palmitate produced
- Fatty acid modifications (to produce other fats)
Where does cholesterol biosynthesis occur?
sER of liver cells (hepatocytes)
Outline the major steps in the cholesterol biosynthetic pathway
- Acetyl CoA (from metabolism) + Acetoacetyl CoA enter pathway and are converted to HMG CoA by HMG CoA Synthase
- HMG CoA is converted to mevalonate by HMG CoA Reductase (this is the rate limiting step, inhibited by statins)
- Series of sequential steps lead to the formation of Cholesterol
What are bile salts?
Bile salts are the major breakdown products of cholesterol
Name the two primary bile salts
- Glycocholate
- Taurocholate.
From what do all steroid hormones derive?
Choleterol
What are lipoproteins?
Lipoproteins are a mechanism of transporting lipids around the body (i.e. an alternative method of cholesterol excretion)
Describe the composition of lipoproteins
Lipoproteins are composed of a phopholipid monolayer containing cholesterol and proteins known as **apoproteins. **
Packed within the core of the lipoprotein are a mixture of cholesterol esters and triacylglycerols
Name the 5 types of lipoproteins
- Chylomicrons (CM)
- Very low density lipoproteins (VLDL)
- Intermediate density lipoproteins (IDL)
- Low density lipoproteins (LDL)
- High density lipoproteins (HDL)
How is insulin involved in metabolism?
Metabolism is regulated by insulin - it signals a “fed” state:
- Signals enzymes (glycogen synthase) to store fat
- Switches on glycolysis
- Switches off gluconeogenesis
- Switches off ketogenesis
What happens during starvation?
After 36 hours of no food, glucose and fat stores are essentially worn down therefore ketogenesis kicks in.
Ketone bodies can be used as an energy source for some period of time however, they can cause ketoacidosis - without respiratory compensation (hyperventilation) this will cause metabolic issues (common issue with diabetics)
