Metabolism Flashcards
what are the primary sources of energy in cells?
- photosynthesis (plants and some bacteria)
- metabolism (2 types)
what is catabolic metabolism?
- Reactions that generate energy
- Reactions that generate energy from fuels such as fats and carbohydrates
- Breakdown of large complex molecules into smaller molecules
what is anabolic metabolism?
- Building up of larger molecules from smaller ones
- Eg building up of protein from amino acids
- Reactions that require energy → performance of mechanical work, active transport, synthesis of larger biomolecules
what is meant by metabolism is circular?
- catabloic reactions fuel anabolism
- energy released from catabolic is used for anabolic
what are the stages of catabolism?
- Break down complex dietary substrates into simple organic molecules (digestion)
- Monomers enter different pathways which results in the production of Acetyl CoA, feeds into the cells main energy production paths (small amount of energy produced)
- The TCA cycle and oxidative phosphorylation generating most of the cells energy
what is the universal energy currency?
ATP - free energy that the cells trade in
how is energy produced?
Break down our dietary substrates which generates energy captured in the form of ATP
describe the breakdown of ATP?
- coupled to an energy required reaction
- used in an anabolic reaction
- in the presence of water ATP is broken dow into ADP and a free phosphate group
what is ATP?
- adenosine triphophosphate
- Consists of adenosine (adenine and ribose) and 3 phosphoryl groups
- The final phosphoanhydride bond is a high energy bond which releases energy when broken which can then be harnessed by a living system to fuel anabolism
what is a hydrolysis reation?
water is needed
what is the free energy change for ATP?
large and negative (-30.5)
how do ATP and ADP compare?
ATP is at a much higher state than ADP → going from a high energy to low energy therefore releasing a lot of energy
why does ATP have such a high phosphoryl potential?
high energy molecules → wants to get rid of a phosphate group to be in a lower energy state → more stable → good phosphate donor
Electrostatic repulsion → negative charges of phosphate groups in ATP repel each other → 3 negative charges next to each = very unstable
Resonance stabilisation → ADP and phosphate have more resonance structures which results in a more favourable state compared with ATP → double bond is shared between the oxygen atoms
Water can bind more easily to ADP and phosphate resulting in stabilisation → reactions take place in an aqueous environment
describe ATP in the body
- at rest about 24kg/day (vary depending on basal metbaolism)
- during exercise 0.5kg/minute
- body only contains 100g of ATP at any one time
- ATP is made as we need it → constantly generated by catabolic pathways
what are electron carriers?
- NADH, NADPH and FADH
what is an acyl carrier?
coenzyme A
what happens to substrates in metabolism?
- oxidised
- generating energy
why are electron carriers needed?
- glucose is oxidised oxygen become an electron acceptor
- final electron acceptor in that metabolic reaction
- electrons aren’t transferred directly but they go through the carriers NADH and FADH first
- act as intermediates → act as an electron acceptor and then oxygen becomes the electron acceptor and they become reduced
what are the features of NAD?
- At one end of the molecule there is a reactive site
- This can accept an hydrogen atom it also accepts electrons
- Reduced form carrying electrons
Has ADP
what are the features of FAD?
- Has 2 reactive sites and so can accept 2 hydrogen atoms and at the same time accepts electrons
- Has ADP
what are the features of coenzyme A?
- Has ADP
- Reactive group is a beta mercaptoethylamine unit which has a sulfur atom and this sulfur atom can accept and acyl group
- This is important in using fatty acids, need acyl groups to be transferred in order for fatty acids to move into the cell
apart from ATP what are some other phosphate carriers?
Phosphoenolpyruvate
1,3 - Bisphosphoglycerate
Creatine phosphate
what can happen if the phosphate carriers have higher energy than ATP?
can donate their phosphate group onto ADP to create ATP
what phosphate carriers can phosphorylate ADP?
PEP and 1,3 BPG are used during glycolysis
when is creatine phosphate used?
acts as an energy store in muscle, used during strenuous exercise to replenish ATP
Muscles are most likely to have a very high and very rapid increase need for energy
Amount of creatine phosphate in the muscle only lasts a few seconds and then you go on to breaking down substrates/stored energy
what is group transfer?
One group from one reactant is transferred to another reactant
Transfer of phosphate groups or acyl groups for example
describe group transfer with phosphates?
- kinases
1. Creatine phosphate for example donates its phosphate group onto ADP generating ATP
2. Phosphate group of the ATP is transferred onto a molecule of glucose forming glucose-6-phosphate (hexokinase) → activates the glucose and primes it ready for the next stage of processing
what are redox reactions?
- oxidation and reduction
- transfer of electrons
- occur simultaneously
what is oxidation?
electrons are lost. oxygen is a good electron acceptor as it is highly electronegative
what is reduction?
when electrions are gained. hydrogen is a good electron donor
what is isomerisation?
When groups change places without a net gain or loss of atoms
Eg glucose to fructose or citrate to isocitrate
Can primes a molecules for the next stage of a process
what is hydrolysis?
Bonds cleaved by the addition of water
Breakdown of ATP to generate energy
Can also be used in the breakdown of large molecules
describe the creation or breakage of carbon-carbon bonds?
- Aldol condensation
- Aldolase
- have bonds removed or added by the addition or the removal of CO2
what is aldol condensation?
we get two 3 carbon molecules to form one 6 carbon molecules → creation of a new carbon-carbon bond
what is aldolase?
when a six carbon molecules is broken down into 2 3 carbon molecules
which are the key substrates that we oxidise for energy?
glucose and fatty acids
descibe ooxidation of glucose?
Glucose = 6 carbon molecules
Glucose and oxygen equals carbon dioxide and water
Full process of glucose oxidation results in a lot of free energy being produced
Equivalent to 94 ATP molecules but biological oxidation only produces 38 ATP molecules → results in an efficiency of about 40% lots of ATP/energy is lost
describe oxidation of fatty acids
Lots of different types of fatty acids → 16 carbon chain
Eg palmitate → most common fatty acid you’d be oxidising → generates much more free energy compared with the oxidation of glucose
Biological oxidation produces 129 ATP
why do fatty acids generate more energy than oxygen?
When substrates are oxidised they lose electrons → these electrons are then used to fuel ATP production
The substrate that produces the most electrons will be the substrate that generates the most ATP
Palmitate generates more electrons than glucose
how is the total oxidation state of glucose determined?
Carbons of glucose that become oxidised → total oxidation state of carbons
When a carbon is bound to an oxygen → oxygen is more electronegative → steals electrons away from carbon
When carbon is bound to a hydrogen → carbon is more electronegative so steals the electrons away from hydrogens
Oxygen steals away 2 electrons → carbon and oxygen together it has an oxidation state of +2
Carbon bound to hydrogen the oxidation state is -1
what is the overall oxidation state in glucose?
6 oxygens bound so there would be an oxidation state of +12
There are 12 hydrogens they are donating one of the electrons and so give the carbons an oxidation state of -12
So overall there is an oxidation state of 0
Carbons in carbon dioxide → 2 oxygen are stealing 2 electrons and so the oxidation state here is +4
Complete oxidation of glucose results in 6 carbon dioxides which gives a total oxidation state of +24
Generates 24 electrons → can be fed into the electron transport chain
what is the overall state in palmitate?
There are a lot less electrons in a molecules of palmitate has an oxidation state of -28
This means that palmitate is in a more reduced state to begin with
When palmitate is oxidised there is 16 carbon dioxides
Gives an oxidation state of +64
Generates 92 electrons
what is the inovlvement of NADH and DAFH2?
- cells redox currencies
- electrons carried by electron carriers
- get passed to oxygen
- reactions produce energy via the electron transport chain
outline the key features of glycolysis?
- does not require oxygen
- universal
- turns glucose into pyruvate
- need 2 ADP, 2 phosphate, 2 NAD+
what are the products ofglycolysis?
pyruvate 2 ATP and 2 NADH are also produced
what is stage 1 of glycolysis?
- activation stage
- use energy to generate an intermediate
- requires ATP
- converts glucose to fructose 1,6 bisphopshate
what is stage 2 of glycolysis?
- 6 carbon compound is broken into 2 3 carbon compounds
- glyceraldehyde 3 phosphate
what is stage 3 of glycolysis?
- glyceraldhyde 3 phosphate is processed to generate pyruvate
- get some generation of energy
- this happens twice as there are 2 3 carbon compounds
how many reactions make up glycolysis?
10
what is step 1 of glycolysis?
- glucose converted to glucose 6 phosphate
- requires ATP to transfer the phosphate group
- catalysed by hexokinase
- non0bonding pair of electrons that attacks the final phpsphate group of ATP
- left with ADP
what is step 2 of glycolysis?
- glucose 6 phosphate is being cinverted into fructose 6 phosphate
- carbonyl group changes positiion
- vital to get it ready for thenext stages of the reaction
- isomerisation
what is step 3 of glycolysis?
- requires energy
- another phosphate group is added to the hydroxyl group
- phosphate transfer reaction
- catalysed by a kinase in this case its phosphofructokinase
- phosphate group from ATP transferred to the hydroxyl group
- creates a bisphosphate molecule that is symmetrical
what is step 4 and 5 of glycolysis?
Fructose 1,6 bisphosphate converted by aldolase to 2 3 carbon compounds: dihydroxyacetone phosphate and glyceraldehyde 3 phosphate
Aldolase → breakage of a carbon-carbon bond
It’s glyceraldehyde 3 phosphate that is used
Dihydroxyacetone can be converted glyceraldehyde 3 phosphate
Good to split into 3 you can use the same reactions and same enzymes each time → its more efficient → less steps twice over
what is step 6 of glycolysis?
Oxidation of GAP
Glyceraldehyde 3 phosphate is oxidised
Results in the production of NADH which can then be used to generate energy
Formed NADH because the electrons and hydrogens have been transferred onto the NAD+
This results in the formation of 1,3 bisphosphoglycerate → high energy compound → requires phosphate but not ATP
Under aerobic conditions NADH is used to generate ATP via the electron transport chain
what is step 7 of glycolysis?
The high energy intermediate 1,3 bisphosphoglycerate can transfer its phosphate onto ADP in order to generate ATP
what are steps 8-10 of glycolysis?
First goes through an isomerase reaction → changes the position of the phosphate group
Converted to a different intermediate through a dehydration reaction → loses water
Phosphophenol Pyruvate → donate its phosphate group to ADP generating ATP
Another ATP is made through the high energy PEP intermediate
This results in the formation of pyruvate
This is happening twice over
how does hexokinase work?
Works because of induced fit which ensures specificity
Consists of 2 lobes
When glucose binds causes a conformational change in the enzyme and it wraps around the substrate
When ATP binds it means that the reaction occurs within that enzyme therefore preventing any water getting into the reaction
Want the oxygen of glucose not the oxygen of water
how does phosphofructokinase work?
Control of this enzyme is via an allosteric mechanism → controlled by the binding of regulating at a site that is distinct from its catalytic site
In the presence of the activator ADP, arginine is placed in the catalytic site which attracts the negative charge of F6P
ADP levels will be high when ATP levels will be low → energy depleted site
In the presence of the inhibitor PGC, glutamine is placed in the catalytic site which repels the substrate → PGC linked to pyruvate → helps to prevent excessive glycolysis
what is the net production of ATP from glycolysis?
2 ATP
how many enzymes are involved in glycolysis?
10 enzymes
what is standard free energy?
energy under standard conditions → assuming equal substrates (reactants) and products → not realistic as to how reactions take place in the body
what are the values for hexokinase?
Hexokinase → -33.5 → far away from 0 → non reversible → reaction is driven towards creating product
what are the values for Phosphofructokinase?
-22.2
what are the values for Pyruvate kinase?
-16.7
what happens if the reactions are far away from 0?
reaction can proceed even if the substrates become dramatically depleted → strong driving reaction from left to right
Strongly driven towards generating the product
what is the purpose of the 3 key reactions in glycolysis?
prevent glycolysis from flipping and going in the reverse direction
There are times where we want glycolysis to function in reverse for example if we are low on glucose
why is gluconeogenesis important?
it is the reverse pathway of glycolysis
what is gluconeogenesis?
formation of glucose from non-carbohydrate sources
Glucose is generated using the reverse pathway of glycolysis
Pyruvate to PEP is high endergonic and therefore requires energy
The intermediate oxaloacetate has high energy content allowing synthesis of PEP
how is the reaction by pyruvate kinase ‘reversed’?
This 1 reaction is replaced by 2 reaction
The reaction goes from pyruvate to phosphoenolpyruvate through the intermediate of oxaloacetate
describe the reverse reaction of the pyruvate kinase stage
First part of the reaction is catalysed by pyruvate carboxylase, going from pyruvate to oxaloacetate → energy requiring reaction → adds an additional carbon atom
Conversion of oxaloacetate to phosphoenolpyruvate which is catalysed by phosphoenolpyruvate carboxykinase → an energy requiring reaction → remove the carbon that has been added and the addition of the phosphate group
We need to go through the intermediate is to allow the generation of the high energy compound phosphoenolpyruvate → make it energetically feasible
what are the 2 atp consuming reactions in glycolysis replacted by?
ATP independent phosphate reaction
what is phosphofructokinase replaced by?
fructose 1,6 bisphosphate - remove a phosphate group through the addition of water
what is hexokinase replaced by?
glucose 6 phosphate - remvoe a phosphate through the addition of water
what do the irreversible steps in glycloysis and gluconeogensis do?
regulate the pathways
why does gluconeogenesis need to be regulated?
generating glucose → want this to take place when there’s a lack of glucose → don’t want this to take place if we need energy
what is gluconeogenesis inhibited by?
- ADP
- high ADP represents a low energy status
- ADP and AMP inhhibit the enzymes and therefore glucogenesis
what activates gluconeogenesis?
acetyl CoA and citrate
if these are high means energy is being generated and don’t need much more
what are the different dietary sugars?
monosaccharides and disaccharides and polysaccharides
what are some examples of monosaccharides?
- glucose
- fructose
- galactose
what are some examples of disaccharides?
- maltose
- sucrose
- lactose
what are some examples of polysaccharides?
starch - main dietary substrate
in what way is lactase activity regulated in mammals?
- developmentally
- lactase acitve in infants and then downregulated
- human populations evolution has selected for the reactivation of lactase
- 2/3 of adults are lactose intolerant down to regulation of lactase
what is the result of lactase inactivity?
- accumulation of lactose in the colon
- fermented by bacteria
- results in CO2 and H2 production
where does fructose enter?
- different entry point depending on location
- majority = fructose directky cibverted in fructose 6 bisphosphate (hexokinase)
- liver = enters further down the pathway either to DHAP or GAP (np hexokinase)
why does fructose enter the pathway at a different stage in the liver?
does not have the hexokinase enzyme → has a different form that can process glucose and fructose independently → liver plays a key role in glycolysis and gluconeogenesis → because of this it needs more control over this pathway so has a specific glucokinase
how does galactose enter glycolysis?
converted directly to glucose 6 phosphate
how is glycogen used in the body?
- gluocse storage
- liver and skeletal muscle
- has different functions
describe the function of glycogen in the liver
regulates blood glucose level, acts like a master store for the entire body, ensure that glucose is adequately supplied to all organs of the body
describe the function of glycogen in skeletal muscle
only for its own benefit, becomes a fuel source for skeletal muscle contractions, particularly important during times of exercise
why is it important to regulate glucose levels?
Changing glucose levels can be dangerous
Needs to be in a narrow range or can be life threatening
The brain can only use glucose as a substrate → brain is so important → essential we maintain glucose levels so that the brain can function
why do we need glycogen?
not constantly eating but we need a constant energy source
when is glycogen broken down?
Regulated by the ‘fight or flight’ hormone adrenaline
Adrenaline causes the breakdown of glucose so you can do more activity
Conversion of glycogen into glucose doesn’t require oxygen
Provides a glucose source that can fuel glycolysis → which also doesn’t require oxygen
what catalyses the breakdown of glycogen?
- glycogen phosphorylase
how does glycogen phosphorylase work?
Cleaves the alpha 1-4 glycosidic bond
The product of this reaction is glucose 1 phosphate and a glycogen chain that is one unit shorter
Requires the addition of a phosphate group → energy requiring reaction
The phosphate group ensures the glucose stays within the cell → shuttles it into the glycolytic pathway
describe the strutcure of glycogen
Has both 1,4 and 1,,6 bonds which creates a highly branched molecule
This structures is much more effective for storage
Need additional enzymes for the 1,6 bonds
what does transferase do?
transfers glucose units from the side branch to the main linear chain
what is the role of Alpha1,6 glucosidase?
breaks alpha 1,6 glycosidic bonds → this reaction generates a glucose molecule
what is amount of glucose produced?
10%
- rest is converted to gluocse 1 phosphate converted to glucose 6 phosphate and enters glycolysis
what are the 2 forms of glycogen phosphorylase?
Phosphorylase B and Phosphorylase A
what are the features of phosphorylase B?
- have an active and inactive form
- found in the muscle
- more to do with fuelling energy → allow muscle contraction → glycogen phosphorylase B is inhibited or activated by energy status → most often in the inactive form
what are the features of phosphorylase A?
- have an active (R) and an inactive form (T)
- in the liver
- inhibited by glucose
- liver glycogen is a master control of all organ use → if blood glucose levels are high than you’d want to inhibit glycogen phosphorylase A → mainly in the active form
what is an activator of phosphorylase B?
high AMP levels
describe the strutcure of fatty acids?
- hydrocarbon chains
- carboxyl group at the end
- vary in length
- different numbers of carbons
what forms do fatty acids exist in?
- saturated = single carbon-carbon bonds
- unsaturated = at least one double carbon=carbon bonds
what is the structure of triacylglycerol (TAG)?
- 3 fatty acid cahins
- attached to glycerol backbone
- break down to liberate fatty acids
what is TAG?
main dietary form that we ingest lipids in our diet, also the form in which we store fatty acids → broken down to liberate the fatty acids
what is the structure of phospholipids?
they are structural lipids and they’re part of membranes, body doesn’t break down phospholipids because it would be destructive
what are the functions of fatty acids?
signalling molecules - steroid hormones. fuel - energy or storage
what are the functions of TAGs?
- efficient way to store energy
- breakdown of fat produces double the amount of energy as glycogen
what would be the result of the oxidation of palmitate?
- C16
- produces 129 ATP
- high molecular weight
how are fatty acids generated?
lipid droplets in adipose tissue
- TAG forms lipid droplets
what are lipid droplets?
membrane bound cell organelles with lipid rich core
how is TAG broken down?
- enzyme lipase
- produces free fatty acids and glycerol
- lipase acts on triglycerides to produce fatty acids
describe the process of TAG being broken dowm
- liberate one fatty acid, creates DAG
- another fatty acid broken off, creates MAG
- all the way 3 fatty acid chains and a glycerol
what happens to the fatty acids after being released?
- travel in the bloodstream bound to albumin
- to target tissues
- broken down to produce ATP
why is storing fat for energy good?
- in theory can store an unlimited amount
- if we need more simply put on more fat tissue
- compare this to glycogen
- stored in the liver which we can’t just make bigger
- evolutionary speaking it is an advantage
- obesity is a problem
what needs to happen for fatty acids to enter oxidation?
activation. ultimately activated to acyl coenzyme
what are the stages of activation?
- fatty acids react with ATP to form acyl adenylate
- oxygen of fatty acid attack the first phosphate of ATP
- cleaves off 2 phosphate groups which are released as pyrophosphates
- sulfhydryl group of coenzyme A attacks acyl adenylate form Acyl-CoA and AMP
what is needed for activation?
- catalysed by enzyme acyl CoA synthetase
- takes place in the outer membrane of mitochondria
- these fatty acids need to enter the mitochondria in order for beta oxidation to take place
what is the mitochondria role in oxidation?
- final oxidation of fuels happens
- perform fatty acid degradation, the TCA cycle and the electron transport chain
- majority of energy producing reactions happen here
- beta oxidation → in the matrix
- have to pass through the 2 mitochondrial membranes
how do fatty acids pass through the 2 mitochondrial membranes?
- activated fatty acids easily pass through the outer membrane
- inner membrane is not permeable
- have to use the carnitine shuttle
how does the carnitine shuttle move fatty acids through the inner mitochondrial membrane?
- reacts with carnitine molecules
- CoA swapped for a cartine results in a acylcarnitine and a free CoA molecule
- acyl carnitine can be transported across the inner mitochondrial membrane which has specific carriers for carnitine
what is needed for the carnitine shuttle to function?
addition of carnitine catalysed by enzyme carnitine palmitoyltransferase I
what happens after the acyl carnitine is inside the inner mitochondrial membrane?
- needs to be converted back to acyl CoA
- reverse reaction happens
- CoA swaps places with carnitine
- free carnitine is shuttle back out
- catalysed by carnitine palmitoyltransferase II
outline the process of beta oxidation
- a cycle so final product will by acetyl CoA
- 4 reactions to reduce the fatty acid by 2 carbon units
- 2 carbons cleaved off in the form of acetyl CoA
- acetyl CoA can then enter a fruther pathway
what is the first reaction of beta oxidation?
- OXIDATION
- Acyl CoA oxidised
- lose electrons from 2 carbon atoms
- this generates a double bond
- electrons transferred to FAD → get FADH2
- enter the electron transfer carrier chain to generate energy
what is the second reaction of beta oxidation?
- HYDRATION
- add a water molecule
- breaks the carbon double bond
- adds 2 hydrogen and a oxygen atom
what is the third reaction of beta oxidation?
- removes hydrogen atoms and electrons
- transfer to NAD → generates NADH → feeds into the electron carrier chian
- creates a carbon=oxygen double bond → carbonyl group
- called the beta carbon (start counting from this group)
- carbonyl oxygen is generated as the same molecule as the first molecule
- can be regenerated
what is the fourth reaction of beta oxidation?
- THIOLYSIS
- carbon carbon bond is broken generating a 2 carbon molecule
- addition of Coenzyme A
- breaking of 2 carbons generating acetyl CoA
- other molecule is acyl CoA which can be regenerated
what are the classical experiments of Franz Knoop?
- labelled fatty acids with benzene ring
- trace where the breakdown products end up
- fed to dogs with different length chains (even and odd)
- analysed the urine
- difference in excretion products in the dogs fed the odd and even chains
what was the breakdown from the odd chains?
gives us a breakdown with only one carbon present
what was the breakdown from the even chains?
have 2 carbons which were originally in the fatty acid molecules
what is the conclusion of the Franz Knoop experiments?
must happen in 2’s. carbons removed 2 at a time. know now its as acetyl CoA products
how much energy may be produced from beta oxidation?
- fatty acids have to be preceded by toher steps
- acetyl CoA and electron carriers also produce energy in later steps
how much energy is produced form the beta oxidation of a palmitate molecules (C16) ?
8 acetyl CoA → ATP = 96 → every cycle you are cleaving of 2 carbons
7 FADH2 → ATP = 14 (each produce 2 so makes 14)
7 NADH → ATP = 21 (each produce 3 so makes 14)
Activation = -2
Overall 129 ATP produced
what are the problems with unsaturated fatty acids?
Have a double bond → at some point the double bond will mess up the 4 stages of beta oxidation
After 3 cycles the trans double bond at C3-C4 prevents the formation of a double bond at the beta carbon
Degrading unsaturated fatty acids produces a reduced amount of energy → miss out on a step which gives electrons to an electron to carrier to shuttle it to the electron transport chain
how do unsaturated fatty acids go through the beta oxidation cycle?
First 3 cycles happen the same way → 3 acetyl CoA molecules → cleave off 6 carbons
The double bond between C3-C4 is shifted to between C1-C2 → this is an isomerisation → isomerase enzyme → this allows further processing
You now have the correct format → dont need the first oxidation reaction → double bond is in the right position → can carry on
what does the TCA cycle do?
completes the oxidation of glucose
what does pyruvate need to be converted into in order to go into the TCA cycle?
acetyl CoA
how is pyruvate converted into acetyl CoA?
- decarboxylation → carbon is removed → goes from a 3C molecule to a 2C molecue
- generation of acetyl CoA → transfer of acetyl to CoA → acetyl group attached to CoA
- oxidation → transfer of electrons from the carbonyl group to NAD+ → becomes NADH
what enzyme catalyses the conversion of pyruvate in acetyl CoA?
pyruvate dehydrogenase
what are the products of the reaction converting pyruvate into acetyl CoA?
- generates energy
- acetyl CoA
- electron carriers
what would it mean if the reaction converting pyruvate into acetyl CoA was reversible?
if this reaction was reversible then you could have the beta oxidation producing acetyl CoA and then this reaction going in the reverse and producing glucose
- would mean fatty acids could generate glucose
what is the impact of the reaction converting pyruvate into acetyl CoA not being reversible?
If we are starved of glucose we can’t use fatty acids → important consequence if we are starved → the brain can only really use glucose
can glucose generate fatty acids?
yes beta oxidation is reversible
what is PDH?
- giant multienzyme complex
- catalyzes 3 reactions
- one of the largest
- requires cofactors NAD+ and CoA
- requires 3 catalytic cofactors: TPP, Lipoic acid, FAD
describe the structure of PDH
In the core you have an E2 unit
Surrounding this you have an E3 unit and E1 units
These make up PDH
There are 3 different subunits → are each responsible for catalysing one of those 3 reaction which make up the larger combined reaction
what are the 2 main sources of the TCA cycle?
- beta oxidation
2. glycolysis
why is acetyl CoA a high energy molecule?
- Free energy = -31.5 kJ/mol
- Due to the thioester bond → between the sulfur of CoA and the acetyl group
- When broken generates huge amounts of energy
what are the 3 main stages of the TCA cycle?
- Formation of citrate:
- oxaloacetate combines with acetyl CoA
- gives us citrate (C^) - Lose 2 carbons
- released as CO2
- citrate to succinate - Succinate to oxaloacetate
- so it can accept the next CoA
what is the impact of TCA cycle being a cycle?
ccycle will constantly run as long as acetyl CoA is being fed in. can become limited. very efficient.
how many reactions make up the TCA cycle?
8
what is reaction 1 of the TCA cycle?
- Entry of acetyl CoA
- Oxaloacetate combines with acetyl CoA
- combine to form citrate
- removal of the CoA group
- get a 6C compound
- catalysed by citrate synthase
- hydrolysis of the high energy thioester bond drives the reaction
- lots of free energy
what is reaction 2 of the TCA cycle?
- Aconitase and isocitrate dehydrogenase I
- conversion of citrate into isocitrate
- change position of hydroxyl group
- isomerase reaction
- allows further processing
what is reaction 3 of the TCA cycle?
- Aconitase and isocitrate dehydrogenase II
- generates an electron carrier NADH
- isocitrate is converted into alpha-ketoglutarate
- isocitrate is being oxidised
- coupled to the removal of a carbon as CO2
- 5C compound generated
- catalysed by isocitrate dehydrogenase
what is reaction 4 of the TCA cycle?
- Alpha-Ketoglutarate Dehydrogenase
- conversion of alpha-ketoglutarate to succinyl CoA
- lose another carbon atom as CO2
- oxidation reaction
- generation of NADH
- catalysed by a dehydrogenase
- now a 4C moelcule
what is reaction 5 of the TCA cycle?
- Succinyl CoA synthase
- succinyl CoA is a high energy intermediate (thioester bond)
- energy can be used to phosphorylate GDP creating GTP which is converted to ATP
- energy when bond is broken
what is reaction 6 of the TCA cycle?
- Formation of oxaloacetate I
- succinate to fumarate
- oxidation reaction
- succinate dehydrogenase
- generating electron carriers (FADH2)
what is reaction 7 of the TCA cycle?
- Formation of oxaloacetate II
- hydrolysis reaction
- breaking double bond formed in the previous reaction
- generates malate
what is reaction 8 of the TCA cycle?
- Formation of oxaloacetate III
- oxidation reaction
- form NADH
- able to form the carbonyl group
- forms oxaloacetate so the cycle can begin again
why does the TCA cycle need to be regulated?
- depends on energy needs of the cell and substrate availability
- amount of CoA being fed
- energy status of the cell
which enzymes play key roles in TCA cycle regulation?
- Pyruvate dehydrogenase
- Citrate synthase
- Isocitrate dehydrogenase
- Alpha - ketoglutarate dehydrogenase
what does each round of the TCA produce?
3 NADH
1 FADH2
2 CO2
1 GTP
what are inhibitors of the TCA cycle?
ATP, acetyl CoA and NADH
what are activators of the TCA cycle?
ADP and pyruvate
why is oxygen needed?
- oxygen is the final electron acceptor
- involves electron carriers to generate energy
what are the 3 main stages of catabolism?
- digestion of dietary substrates to be absorbed into the bloodstream
- generation of acetyl CoA, fatty acids go through beta oxidation to produce acetyl CoA, glucose forms acetyl CoA through glycolysis and pyruvate dehydrogenase reaction
- citric acid cycle and oxidative cycle
what process can be used if there is not oxygen?
fermentation
what is fermentation?
- removes NADH and FADH2
- prevents inhibition of downstream reactions
- produces ethanol or lactate
- takes pyruvate away from the TCA cycle
- allows glycolysis to continue
- anaerobic process
why is it important not to produce electron carriers when there is no oxygen?
- NADH and FADH2 can’t enter the electron transport chain as there is no final acceptor
- they will inhibit the previous reaction if it builds up
- no energy will be produced
when is lactate produced?
during strenuous exercise the oxygen becomes limited in muscle and lactate is produced
in humans what is pyruvate converted into?
lactate
why is lactate produced?
- don’t have sufficient oxygen to fuel ATP production
- (don’t ever have a full lack of oxygen or we would die)
- rely on ATP from glycolysis
how does lactate affect the body?
- reduces the pH of the muscles
- causes cramps and aching
what is ethanol?
yeast produces ethanol during anaerobic fermentation
- process is exploited in industry
what is NADH converted into in fermentation and why?
- NAD+
- removes inhibition from NADH build up
- no oxygen = NADH buildup
why dont we want to inhibit glycolysis?
only part that produces ATP without oxygen
how do we get from pyruvate to lactate?
Removing excess of NADH → NAD+
Pyruvate is reduced → carbonyl group is changed to a hydroxyl group
Reduced by NADH → donates electrons to pyruvate
Pyruvates gains electrons and accepts hydrogen atoms → one from NADH and a free proton
When it accepts the hydrogens it produces a hydroxyl group forming lactate
This converts NADH into NAD+
Using the enzyme lactate dehydrogenase → it is a reversible reaction
what is the role of lactate dehydrogenase?
to regenerate NAD+ when oxidative phosphorylation is inhibited due to a lack of oxygen
what is the pentose phosphate pathway?
alternative route for glucose instead of glycolysis
what is generated through the pentose phosphate pathway?
NADPH
pentoses
what is NADPH use for?
- NADH is used for ATP production, NADPH is the redox currency for anabolic
- Fatty acid biosynthesis, cholesterol biosynthesis, neurotransmitter biosynthesis, nucleotide biosynthesis
- Detoxification → reduction of oxidised glutathione, cytochrome P450 monooxygenases
what is glucose converted into to enter the pentose phosphate pathway?
glucose 6 phosphate
what is the oxidative phase of the pentose phosphate pathway?
Glucose 6 phosphate is converted (oxidised) into ribulose 5 phosphate
This generates NADPH
Also generates carbon dioxide → lost a carbon
Glucose 6 phosphate is losing electrons which is accepted by NADP and forms NADPH
what is the non-oxidative phase of the pentose phosphate pathway?
The ribulose 5 phosphate is converted into 2 other 5 carbon sugars
The 5 carbon sugars combine and can produce several glycolytic intermediates
Generation of NADPH and the formation of glycolytic intermediates
Isomerisation reactions → getting the swapping of the positions of functional groups
2 5 carbon groups → ribulose 5 phosphate and xylulose 5 phosphate
The ribulose 5 phosphate sugar is really important for DNA synthesis
By combining the 2 5 carbon sugars you’ve got 10 carbons to play with
Could get a 3 carbon and a 7 carbon or into a 6 carbon and a 4 carbon
Glycolytic intermediates → can therefore generate energy
is the pentose phosphate pathway reversible?
yes
what does it mean if the pentose phosphate pathway is reversible?
direct intermediates anywhere depending on what the cell needs
what is the small intestines role in metabolism?
uptake the nutrients which we can then turn into energy
Dietary substrates broken down into monomers
Through digestion
Get absorbed into the bloodstream
what is the kidneys role in metabolism?
Waste products need to be excreted
A main product of reactions to be excreted is water
what is the lungs role in metabolism?
get rid of carbon dioxide
what is the pancreas role in metabolism?
regulation Produces digestive enzymes Secrete into the small intestine to help with digestion and absorption Also produce hormones Insulin and glucagon
what is the brains role in metabolism?
Accounts for 20% of glucose usage at rest
The brain is constantly active → even during sleep → regulates sleep
Bodily functions needed at all times
Has no energy stores (no glycogen or TAG) → relies on adequate blood supply to ensure a delivery of energy substrates
Cannot use fat for fuel due to the highly selective blood brain barrier (BBB)
what is the muscles role in metabolism?
usage
Especially when performing exercise
what is the livers role in metabolism?
- storage of glycogen
- metabolic control of the body
what is the adipose tissues role in metabolism?
Cells that make up the tissue are adipocytes
Adipocytes store triacylglycerol for energy (white fat)
In contrast to brown fat tissue which is involved in heat generation
Limited in the amount of glycogen you can store → adipose tissue can just grow and grow and grow and can store unlimited energy
what is the blood brain barrier?
protective membrane - stops any toxins entering the brain cells
what can the brain use as fuel apart from glucose?
- ketone bodies if there is low glucose supply
- requires a constant supply of glucose
describe muscle as an energy store?
large energy store
¾ of the body’s glycogen is found in muscle → muscle is the primary store of glycogen
Muscles are very active
Need a rapid supply of energy
what is the consequence of muscle lacking the enzyme glucose-6-phosphotase?
catalyses the reverse of the first reaction of glycolysis
When glucose 6 phosphate is turned back into glucose
Can’t generate glucose → any glucose 6 phosphate generated stays in that form
More glucose 6 phosphate remains and stays with muscle cells
The muscle can use this to provide it with energy
how is lactate produced in muscles?
Muscles are good at anaerobic respiration
Muscle expresses the enzyme lactate dehydrogenase
Allows glycolysis to keep on running and ATP to be supplied even in times of low oxygen
describe triacylglycerol as and energy source/store?
broken into glycerol and fatty acids
Fatty acids → beta oxidation → generates energy through the TCA cycle
Glycerol
Converted into a glycolytic intermediate
Dihydroxyacetone Phosphate → inserted around halfway through glycolysis
This can either be converted into pyruvate → generating energy
Can be converted into glucose through gluconeogenesis
Glycerol is important in times when fatty acids cannot be used
how does the liver control fuel use?
- glycogen is stored
- liver breaks down the glycogen to ensure the blood sugar levels remain constant
- transported to organs such as the brain
how is glucose processed in the liver?
turns glucose in glucose 6 phosphate, different fates:
- Acetyl CoA (fatty acid synthesis)
- NADPH (biosynthesis)
- Glucose (bloodstream)
- Glycogen (storage)
describe how the liver goes through different processes depending on what the body needs
If there is plenty of glucose and glycogen stores are full then the glucose is shunted into fatty acid synthesis → high sugar diet increases fat stores
Can enter the pentose phosphate pathway → NADPH
Converted back into to glucose → leave the liver and enter the bloodstream
Converted into glycogen → will happen until a capacity is reached
what happens in the muscle cell during exercise?
Glucose oxidised to carbon dioxide and water or to lactate
Glucose form the bloodstream or from the breakdown of stored glycogen
what happens in the liver cell during exercise?
Glucose is oxidised
Glycerol and amino acids can be converted into pyruvate → from glucose through gluconeogenesis
what happens in the cardiac muscle cell during exercise?
Glucose oxidised
Don’t generate huge amounts of lactate
Use glucose but oxidise right the way through
what are the important reactions during exercise?
Glycolysis Gluconeogenesis Lactic acid fermentation Citric acid cycle Oxidative phosphorylation Glycogen breakdown Fatty acid oxidation Amino acid oxidation
what are the key features of fuel use in a sprint?
- ATP stores - any ATP present is used
- Creatine Phosphate
- Anaerobic glycolysis
how is creatine phosphate used in a sprint?
→ phosphate carriers that has a higher energy compared with ATP
→ they can donate a phosphate group to ADP
→ bigger store of creatine phosphate in muscles compared to ATP
→ don’t need to break down substrates
→ limited supplies
how is anaerobic glycolysis used in a sprint?
→ breaks down glycolysis
→ can’t oxidise glucose all the way through because the demand is high
→ pyruvate is converted to lactate
→ much quicker supply of ATP
→ only a limited amount of ATP that can be generated as lactate would be used
This wouldn’t be able to fuel anything longer than sprint
→ lactate builds up
→ pH lowers
→ muscles start to cramp
what are the key features of fuel use in a marathon?
- Muscle glycogen
- Glucose from liver - glycogen break down
- Fatty acids from fats
describe muscle glycogen in a marathon?
- deplete all glycogen stores first from muscle
- have more stored
- these are the muscles that are active
why don’t you want anaerobic production during a marathon?
- don’t want lactate to build up
- can afford to produce ATP at a slower rate
- body prefers ATP faster
- prevents switch to fatty acids (get a slump in performance - slower rate of ATP production)
what happens when lactate builds up?
Goes through the Cori Cycle Lactate is recycled back to glucose Catalysed by lactate dehydrogenase After lactate has been produced → it enters the bloodstream and is transported to the liver → regenerate back to glucose Also known as gluconeogenesis
what is starvation?
animals have a period of fasting - dont continuously eat
starved-fed cycle
need to ensure brain is supplied with glucose
what happens when its been 6h - 1day since the last meal?
- Liver glycogen is exhausted
- Glucose comes from → glycerol form TAG breakdown and amino acid catabolism from muscle protein
- Problem with this → start breaking down muscle can lose around 75g/day
- Muscle uses fatty acids for fuel → brain can’t use fatty acids
what happens when its been 3 days since the last meal?
- Get the production of ketone produced by the liver
- Make up 30% of brain fuel
- This reduces muscle loss now 20g/day
- Ketone bodies can be quite damaging → don’t want to many of them around
what happens when its been 40 days since the last meal?
- Brain fuel is now 75% ketone bodies
- Fat reserves determine survival time
- After fat is exhausted, protein degradation accelerates
- Death by liver/kidney/heart failure → start breaking down your organs
when do ketone bodies take over?
when there is low glucose
why can breaking down muscle be detrimental?
for animals that have to hunt/escape predators - would die quickly
what happens to lipids if there is a high energy demand?
- Breakdown of fatty acids to acetyl CoA and then ketone bodies
- Through beta oxidation
- Fatty acids can help with low glucose → brain is primary organ that needs taking care
- Ketone bodies → generated from fatty acids
what happens to lipids if there is a low energy demand?
- Fatty acids shunted into different pathways
- Repackagaed and stored as triacylglycerol
- FA synthesis
- Formation and secretion of lipoproteins
describe PEP
highly endergonic and requires energy
what allows the synthesis of PEP
high energy intermediate oxaloacetate
what are the two irreversible steps in glycysis
- fructose 6 phosphate to fructose 1,6 bisphosphate
2. phosphoenolpyruvate to pyruvate
how is glycolysis inhibited in times of high energy production?
high ATP inhibits phosphofructokinase kinase and pyruvate kinase
what enzyme catalyses fructose 1 6 biisphosphate to fructose 6 phosphate?
fructose 1 6 bisphosphatase
how are the pentose pathway and glycolysis linked?
conversion of pentose to glycoltic intermediates eg xylulose 5 phosphate and ribulose 5 phosphate can combine to make GAP and another substance
