biochem s2 Flashcards
what do catabolic pathways do
catabolic pathways release energy and involve the breakdown of molecules
what do anabolic pathways do
Anabolic pathways require energy and are involved in the synthesis of complex molecules from simpler molecules
what are the 2 functions that oxidative catabolism of glucose serve
Serves 2 functions:
-1-The production of free energy in the form of ATP
-2-The production of intermediates from glycolysis and the TCA cycle to provide material for other metabolic pathways
what is oxidative metabolism
Oxidative metabolism-A chemical process in which oxygen is used to make energy from carbohydrates (means the same thing as aerobic respiration)
what is the standard Gibbs free energy change
its the change in Gibbs free energy at pH 7.0 under standard conditions
what does the standard Gibbs free energy change provide information on
Provides information about what happens to the free energy during a chemical/biological reaction
if delta G is negative is the reaction exergonic or endergonic
exergonic
if delta g is positive is the reaction endergonic or exergonic
endergonic
what is the equation for Kc
Kc=conc of products/reactants
if Kc is small what does this mean in terms of products and reactants
Reaction lies to the left
Large amount of reactants
Small amount of products
If Kc is large what does this mean in terms of reactants and products
Reaction lies to the right
Small amounts of reactants
Large amounts of products
what is the equation for Gibbs free energy change
=-RT In K
R=gas constant
T=temperature
K = equilibruim constant
if Gibs free energy change is positive is the reaction endergonic or exergonic
endergonic
if Gibs free energy change is negative is the reaction endergonic or exergonic
exergonic
if Kc is small is the reaction exergonic or endergonic
endergonic
if Kc is large is the reaction endergonic or exergonic
exergonic
what is delta G dependent on
dependent on two parts:
-a constant term whose value depends only on the reaction taking place
-A variable term that depends on the concentration of the reactants and products
what are the standard conditions for delta G
-pH=0
-Temp=25
-pressure= 1atm pressure
-1.0M
if the delta g is negative what side of the equilirbuim is in favour
the equilibruim lies in favour of the products
if the delta g is positive what side of the equilibrium is in favour
the equilibruim lies in favour of the reactants
if delta G is large and negative what does this mean for the equilibruim
The reaction equilirbuim is irreversible
if delta g is large and positive what does this mean in term of the reaction
the reaction wont proceed
what is le chateliers principle
-Is the idea that any deviation from the equilibrium stimulates a process that tends to restore the system to equilibrium (comes back to equilibrium)
-If the substrate increases , the reaction proceeds to the right (more products)
if the overall delta G is negative will the pathway proceed
yes
are metabolic pathways reversible or irreversible
irreversible
what does hexokinase do
(Hexokinase is an enzyme thats phosphorylates glucose , fructose and mannose)
what does feedback inhibition consist of
The end product (feedback inhibition ) goes back and can bind to the allosteric site on the enzyme and cause inhibition of the enzyme (this occurs hexokinase)
what is control of flux based on
Control of flux is based on the amount of key enzymes and the presence of tissue specific isoenzymes and their regulation once made
what are the two ways to regulate metabolic pathways
1-Gene regulation
This is a slower form of control as it required additional copies of the enzyme to be produced.It can enhance the amount of final product
2-End product feedback inhibition
This is quick, if the end product is not rapidly used then the complete pathway is slowed as the first enzyme is inhibited
what is the structure of glucose
Glucose structure=hexose sugar with an aldehyde group at position 1.All of the hydroxyl groups are then on the right apart from position 3 which is flipped to the left hand side
draw the structure of glucose
does glucose have an aldehyde at the top
yes
how does glucose cross the membrane
-glucose cant cross the membrane by itself
-It uses transport proteins to move from high to a low conc
-Doesn’t require energy
-Phosphorylation prevents the glucose from returning
write out the 10 steps of glycolysis
how many irreversible steps are in glycolysis
3
what is the role of coenzymes
-A non protein component of an enzyme is called the cofactor
-If the cofactor is organic its called a coenzyme
-Coenzymes are derived from vitamins
-Their role is to deliver chemical groups or atoms (hydrogen ions /phosphate)to and from the active site
-The coenzyme nicotinamide adenine dinucleotide is involved in the transfer of protons
-The coenzyme adenosine triphosphate (ATP)is involved in the transfer of phosphate groups
what is oxidation
-loss of electrons
-gain of oxygen
-loss of hydrogen
-results in many c-o bonds
-results in compounds with lower potential energy
what is reduction
-Gain of electrons
-loss of oxygen
-gain of hydrogen
-results in many c-h bonds
-results in compounds woth higher potential energy
what does dehydrogenase mean
-Dehydrogenase means it is an oxidation step in which an aldehyde is converted to a carboxylic acid
are phosphorolyation reactions endergonic or exergonic
endergonic
are dephosphorylation reactions energonic or exergonic
exergonic
is carboxylation endergonic or exergonic
enderogonic
are oxidation reactions exergonic or energonic
exergonic
what is glycolysis
Glycolysis is where the 6 carbon molecule is broken down into pyruvate to extract energy
The complete oxidation of glucose has a =-2834 kJ/mol of free energy that can be used to meet the cells energy requirements
why is all of the free energy produced from glucose metabolism not all used up
The whole 2834 is not released as heat due to :
1-biological systems cant utilise heat as a source of energy
2-No single reaction of metabolism requires this amount of energy to be released in one step
3-Always needing to overcome the activation energy.Enzymes are capable of effecting only small changes when they catalyse reactions , releasing energy in steps
This is why during the catabolism of glucose the molecule is broken down in small steps and energy is released in small amounts in the form of chemical energy with ATP being the energy carrier
what are the products of glycolysis
2 pyruvate
2 ATP
2 NADH and 2H+
what is the structure of glycerol-description not diagram
-has a 3 carbon backbone that fatty acids attach to
-metabolized readily into an intermediate in glycolysis , dihydroxyacetone phosphate , which may be converted into pyruvic acid
-Dihydroxyacetone may be used in gluconeogenesis to make glucose-6-phosphate for glucose to the blood
draw the structures of an aldehyde,carboxylate and a ketone
what do kinases do
-kinases phosphorylates enzymes
what does phosphatases do
-phosphatases dephosphorylates substrates
draw the process of glycolysis
what is the energy balance sheet of glycolysis (what are the energy inputs and outputs involved in the process of glycolysis)
-2 ATPs used to prime glycolysis
-4 ATPs produced from the glycolytic pathway as a result of substrate level phosphorylation (step 7+10)
-2 NADHs generated
-8 ATPs net gained from the conversion of glucose to pyruvate and the re-oxidation of the 2 NADHs produced
describe the overall process of glycolysis
-series of 10 reactions that extract energy from glucose by splitting it into two three-carbon molecules called pyruvate
-Glycolysis includes two distinct phases-energy investment and the energy generation phase
-The total amount of energy produced is 8 ATPs
-2 ATP(investment)+2 NADH (6 ATPs payoff ) + 4 ATP(payoff)
is ATP an energy transducer
yes
what does ATP do
ATP is an energy transducer
-Transfers energy between reactions
-Not a store of energy
-Produced on demand by the phosphorylation of ADP and pi
what does endergonic mean
chemical process accompanied by or requiring the absorption of energy, the products being of greater free energy than the reactants.
describe the action of a coenzyme and what makes a cofactor a coenzyme
Coenzyme has to be bound before the substrate
-Coenzyme is bound tightly so that the group to be transferred is properly oriented to allow catalysis to occur
-Once bound to a chemical group the structure of the coenzyme is changed , coenzymes can be considered as the second substrate of the enzymes , hence they are called co-substrates
-Coenzymes need to regenerate in order to participate in the reaction again
-A non protein component of an enzyme is called the cofactor
-If the cofactor is organic its called a coenzyme
-Coenzymes are derived from vitamins
-Their role is to deliver chemical groups or atoms (hydrogen ions /phosphate)to and from the active site
-The coenzyme nicotinamide adenine dinucleotide is involved in the transfer of protons
-The coenzyme adenosine triphosphate (ATP)is involved in the transfer of phosphate groups
what is the fate of pyruvate in aerobic conditions
-Glycolysis requires the continual supply of NAD+
-Under aerobic conditions this requirement can be met by the oxidation of NADH by the ETC
-Also under aerobic conditions , pyruvate can enter the mitochondria and be consumed in the tricarboxylic acid cycle (TCA) to generate even more NADH
-pyruvate must leave the cytoplasm
-entry of pyruvate into the mitochondria results in its complete oxidation by the reactions of the tricarboxylic acid (TCA) cycle
-The outer membranes of mitochondria contains porins- proteins that allow small molecules like pyruvate to enter the intramembranous space
-A pyruvate transporter (MPC) transports pyruvate across the impermeable inner mitochondrial membrane
-The conversion of pyruvate to acetyl occurs in the matrix
what does the Mitochondrial pyruvate carrier (MPC) facilitate in the transport of
-MPC faciliates the transport of the pyruvate
what does coenzyme A do
Coenzyme A-another coenzyme
-CoA is an acetyl carrying group group to active sites
When there is excess glucose , coenzyme A is used in the cytosol for synthesis of fatty acids
what is the fate of pyruvate in anaerobic conditions
-Anaerobic conditions: oxygen limiting conditions
-Under anaerobic conditions the cell must still generate NAD+ from NADH
-One example is the conversion of pyruvate to lactate
-All pyruvate has to converted to lactate under anaerobic conditions for ATP synthesis to continue
how many ATP are produced for every glucose , in anaerobic conditions
-Under anaerobic conditions, only 2 ATP are produced for every glucose molecule that is converted to lactate or alcohol
-NADH is recycled and not used to make more ATP
In prokaryotic cells where does glycolysis , TCA,ETC and fermentation occur
Glycolysis:cytoplasm
TCA cycle:cytoplasm
ETC:Cell membrane
Fermentation :cytoplasm
In eukaryotic cells where does glycolysis , TCA,ETC and fermentation occur
Glycolysis:cytoplasm
TCA cycle:mitochondria
ETC:mitochondrial membrane
Fermentation:cytoplasm
what is fermentation
The production of lactic acid or ethanol under anerobic conditions
what are the pyruvate oxidation steps (same as the link reaction)
step 1 - a carboxyl group is snipped of pyruvate and released as a molecule of CO2, leaving behind a 2 carbon molecule (acetate)
step 2 - the 2 carbon moelcule is oxidised and the electrons lost are picked up by NAD+ to form NADH
step 3- The oxidised 2 carbon molecule (acetyl group) is attached to coenzyme A , to form acetyl CoA
what is the job of Acetyl CoA
To carry the acetyl group to the citric acid cycle
summary of pyruvate oxidation
-molecules of pyruvate converted into two molecules of acetyl CoA
-2 carbons are released as c02 , out of the six originally present in glucose
-2 NADH are generated from NAD+
what does the link reaction do
connects glycolysis with the TCA cycle
where is pyruvate dehydrogenase located for eurokaroytes
in the mitochondrial matrix
what are the similarities between mitochondria and bacteria
Similarities between mitochondria and bacteria (as mitochondria believed to derive from symbiotic bacteria):
-Size and shape
-Both replicate by fission
-Both contain circular DNA plasmids
-The ribosomes that mitochondria have to make proteins are more similar to bacterial ribosomes than to eukaryotic cell ribosomes
draw the structure of glucose , pyruvate and glycerol
draw the structure of glucose
draw the structure of pyruvate
draw the structure of glycerol
what is the fate of pyruvate in aerobic conditions
-The porins in the mitochondria allow small molecules like pyruvate to enter the intermembrane space
-A pyruvate transporter (MPC) transports pyruvate across the impermeable inner mitochondrial membrane
-The conversion of pyruvate to acetyl occurs in the mitochondrial matrix , with the loss of 1 carbon in the form of CO2
where does the TCA cycle occur (eukaroytes)
in the matrix
what does TPP stand for
Thiamine pyrophosphate
what does TPP do - Thiamine pyrophosphate
The reaction with TPP chemically changes the acetyl group.It is this compound that is oxidised back to acetyl while transferring to the lipoamide
what are the three enzymes that pyruvate dehydrogenase uses
-TPP(thiamine pyrophosphate)
-Reduced lipoamide
-Flavin adenine dinucleotide (FAD)
where does the oxidation of pyruvate occur (in eukaroytes)
matrix-mitochondria
what does pyruvate dehydrogenase use TPP , thiamine pyrophosphate , for and what does dihdrolipoyl transacetylase use lipoamide , FAD and coenzyme A for
E1:Pyruvate dehydrogenase which uses thiamine pyrophosphate (TPP) as its prosthetic group
E2:Dihydrolipoyl transacetylase which uses lipoamide and coenzyme A as its prosthetic groups
E3:Dihydrolipoyl dehydrogenase which uses flavin adenine dinucleotide (FAD) and nicotinamide adenine dinucleotide (NAD+)as its cofactors
Note:Prosthetic groups are molecules that are tightly bound to an enzyme or protein
what are the prosthetic groups in pyruvate dehydrogenase
For pyruvate dehydrogenase these include:
TPP-thiamine pyrophosphate - required for pyruvate decarboxylation
Lipoate-required for th transfer of the acetyl group to coenzyme A
FAD-flavin adenine dinucleotide - required for the regeneration of the oxidised form of lipoate
what is a prosthetic group
-Tightly bound , non-polypeptide unit required for enzymatic activity
Why do enzyme complexes exist?
-To speed up reactions because the products of one reaction can be passed directly to the next enzyme without the newly formed substrate having to diffuse to the next enzyme
what does the citric acid cycle generate
-3 NADH,1 FADH2 and 1 GTP(=ATP)
-Relases 2 CO2
how many oxidation/reduction steps in the citric acid cycle
-4 oxidation/reduction steps
what are the glycogen stores in the liver mainly used for/used by
the brain
what is the composition of glycogen
6 carbons
-made of alpha 1,4 and alpha1,6 glycosidic bonds
what is the linkages for the main chain and side chain for glycogen( 1-4 or 1-6)
-Branched polymer of glucose
-Main chain alpha(1-4) linkage (carbon 1 joined to carbon 4)
-Side chain alpha (1-6) linkage (carbon 1 joined to carbon 6)
what is the structure of glycogen
Helical
12-14 glucose residues
Branch occurs every 8-12 glucose
3D branching structure
Up to 120,000 glucose per glycogen molecule
10-40 nm diameter
how is glycogen stored , the percentage of it in liver mass and muscle
Glycogen granules (20-40 molecules)
Up to 10% of liver mass (more as liver has to supply the whole body)
1-2% of muscle
what does catabolism mean in terms of glycogen
catabolism=break down glycogen into glucose = glycogenolysis
define glycogenolysis
catabolism=break down glycogen into glucose = glycogenolysis
what does Phosphoglucomutase do
Phosphoglucomutase turns 1 glucose into 6 glucose
what does Glycogen phosphorylase do
Glycogen phosphorylase adds a phosphate
what is meant by phosphorolysis
Using phosphate to break bonds = phosphorolysis
what is step 1 in glycogenolysis , glycogen catabolism
-Glycogen reacts with phosphate in step 1 , using the enzyme glycogen phosphorylase
why do we use phosphorolysis in glycogenolysis rather than hydrolysis
-We use phosphorolysis to avoid wasting ATP
is phosphorylase an enzyme
yes
what is the prosthetic group for phosphorylase
-Has a prosthetic group , pyridoxal phosphate , which is required to work
what are the 3 isozymes of phosphorylase
3 isozymes of phosphorylase(3 different versions of the enzyme)for the :
-Muscle (mGP)
-Brain (bGP)
-Liver (lGP)
what does PLP stand for
pyridoxal phosphate
what does PLP do (pyridoxal phosphate) in the catabolism of glycogen
PLP (pyridoxal phosphate) holds phosphate in place using hydrogen bonds
what occurs in the phosphorylase mechanism
PLP (pyridoxal phosphate) holds phosphate in place using hydrogen bonds
-We make a positively charged glucose unit
-positively charged intermediate attracted to negatively charged phosphate
-Processive means it doesn’t let go of the substrate
-Works its way along the chain = processive
-Stays attached to the glycogen so doesn’t need to rebind
-Progression branched structure=rapid mobilization of Glycogen
-Each brand tip is a source of glucose release
phosphorylase is processive , what does this mean
that it works its way along the chain
what cant phosphorylase do-ie what bonds can it not break
phosphoroylase cant:
Break 1-6 bonds (ie it stops when it reaches a branch)
Break 1-4 bonds within 4 units of branch point
what do you get from one round of the phosphoroylase mechanism
-multiple G-1-P and limit dextrins
what does the debranching enzyme contain , that moves the glucose from one part of the glycogen to another part of the molecule
-Transferase
-Debranching enzyme has transferase which moves the glucose from one part of glycogen to another part of the molecule
what does Alpha-1,6 Glucosidase do
-Alpha-1,6 Glucosidase brakes the 1,6 bond which forms the side chain
what does a mutase enzyme do
-rearranges the molecule
what is the glycogen in the muscles used for
Muscle glycogen-> glycolysis->ATP
-Glycogen in muscles is broken down into glucose , which then undergoes a process called glycolysis.This is where glucose is converted into pyruvate and ATP is produced.
what is glycogen in the liver used for
Liver glycogen->Glucogenesis>Blood glucose increases
-The liver produces glucose through glucogenesis and this glucose is then released into the bloodstream , helping to raise blood glucose levels
what is meant by anabolism
-Anabolism= creating glycogen molecule=Glycogenesis
what is meant by glycogenesis
-Anabolism= creating glycogen molecule=Glycogenesis
explain what occurs in glycogensis , glycogen anabolism
-The phosphoglucomutase step is reversible so this stays the same , just the other way around (hence its reversible)
-UDP is attached = activated form of glucose , activate molecules that we want to start sticking together
-Glycogen synthase used find the tip of an existing glycogen chain and then creates a 1-4 glycosidic bond, UDP and hydrogen ion then released :
what does UDP-Glucose pyrophosphoroylase do to glucose 1 phosphate
-UDP is attached = activated form of glucose , activate molecules that we want to start sticking together
-It is now UDP-glucose
what does glycogen synthase do to UDP-Glucose
-Glycogen synthase used find the tip of an existing glycogen chain and then creates a 1-4 glycosidic bond, UDP and hydrogen ion then released
what does glycogenin do
1)Glycogenin:
-Builds initial 8 unit primer chain
-Primer extended by Glycogen synthase
what does the branching enzyme do
2)Branching enzyme:
-Binds to chain 11+ units long
-Cuts of heptamer of glucose units
-Reattaches heptamer via a (1-6) bond
-Reattachment site >4 units from existing branch
what does glycogen synthase do
-Makes the chain longer
What does lysis mean
-Breaking down
Why do eukaryotic cells physically separate glycolysis and TCA while in prokaryotes it all takes place in the cytoplasm?
-Prokaryotic cells are a lot smaller than eukaryotic cells , so prokaryotic rely on diffusion
-So eukaryotic can’t rely only on diffusion , hence they have this compartmentalisation
Similarities between mitochondria and bacteria (as mitochondria believed to derive from symbiotic bacteria):
-Size and shape , both rod shaped
-Both replicate by fission
-Both contain circular DNA plasmids
-The ribosomes that mitochondria have to make proteins are more similar to bacterial ribosomes than to eukaryotic cell ribosomes
what is the fate of pyruvate in aerobic conditions
In the presence of oxygen , the NADH can be oxidised back to NAD+ by the ETC
In the presence of oxygen , pyruvate is now free to enter the TCA cycle which will be broken down to CO2 and H20 while releasing energy
-The porins in the mitochondria allow small molecules like pyruvate to enter the intermembrane space
-A pyruvate transporter (MPC) transports pyruvate across the impermeable inner mitochondrial membrane
-The conversion of pyruvate to acetyl occurs in the mitochondrial matrix , with the loss of 1 carbon in the form of CO2
what happens to the pyruvate in aneorbic conditions
In anaerobic conditions , absence of oxygen , pyruvate has to be converted to either lactate or ethanol .So that the NADH cycle can be maintained in order to keep making ATP via glycolysis
where does the TCA cycle occur
in the matrix
where does the oxidation of pyruvate occur
-The oxidation of pyruvate occurs in the mitochondria of the cell .
what does Dihydrolipoyl transacetylase use lipoamide and coenzyme A for
Dihydrolipoyl transacetylase which uses lipoamide and coenzyme A as its prosthetic groups
what does Dihydrolipoyl dehydrogenase use flavin adenine dinucleotide (FAD) and nicotinamide adenine dinucleotide (NAD+) for
Dihydrolipoyl dehydrogenase which uses flavin adenine dinucleotide (FAD) and nicotinamide adenine dinucleotide (NAD+)as its cofactors
whats a prosthetic group
Prosthetic groups are molecules that are tightly bound to an enzyme or protein
what are the enzymes TPP , thiamine pyrophosphate , lipoate and FAD flavin adneine dinucleotide used for (two seperate uses)
TPP-thiamine pyrophosphate - required for pyruvate decarboxylation
Lipoate-required for the transfer of the acetyl group to coenzyme A
FAD-flavin adenine dinucleotide - required for the regeneration of the oxidised form of lipoate
Give a brief overview of the TCA cycle (krebs cycle/citric acid cycle )
1-acetyl-CoA (2) and oxaloacetate (4c) combine into citrate
2-citrate (6) isomerised into isocitrate
3-Isocitrate converted into alpha-ketoglutarate ( by removing the carboxylic acid from isocitrate) , releasing C02 and generating NADH
4-Alpha-ketogultarate converted into Succinyl-CoA (4c) , releasing C02 and generating NADH
5-Succinyl-CoA makes GTP , then converted into succinate
6-Succinate makes some FADH2, loses 2 protons, and converted into Fumarate
7-Water comes in allowing another hydroxyl to be added which enables the NAD+ to be reduced into NADH and H ,Fumarate converted into Malate
8-Malate makes NADH and is then converted into oxaloacetate , to make the 6c compound again by combining oxaloacetate with acetyl-CoA to make citrate(6)
explain what occurs in step 1 of the TCA cycle
Citrate synthase-uses water to converted acetyl-CoA and oxaloacetate into citrate , and releases the CoA
Reaction type:condensation.the first reaction is a synthase reaction , called this because a new molecule is made but ATP is not used (the latter is called a synthetase)
The high free energy difference gained by the hydrolysis of this thioester to drive the reaction
-Large negative value
Explain what occurs in step 2 of the TCA cycle
-Tertiary alcohol moved from the second position to the first position, creates a secondary alcohol doing so
-Isomerisation reaction catalysed by enzyme -Aconitase
-Uses cofactor Fe-S complex
Explain what occurs in step 3 of the TCA cycle
Enzyme-Isocitrate dehydrogenase reduces NAD+ into NADH , which in doing so makes the oxalosuccinate which is an intermediate reaction.The isocitrate c=dehydrogenase will then remove the carboxylic acid group to release C02 ,generating the alpha -ketoglutarate
Reaction type:oxidative decarboxylation(this is the first of our 4 reduction reactions) .This is the first carbon loss as CO2, from C6 to C5
Cofactor:NAD+ is reduced to NADH + H+
Note:two step reaction , intermediate is oxalosuccinate
Explain what occurs in step 4 of the TCA cycle
-Alpha-Ketoglutarate converted into Succinyl-CoA, using the enzyme alpha-ketoglutarate dehydrogenase
-Carboxylic acid group released as C02
-NAD+ turned into NADH + H+ (this is our second reduction step)
Explain what occurs in step 5 of the TCA cycle
Enzyme-Succinyl CoA synthetase breaks the thioester bond which allows us to generate the phosphoanhydride bond in for GTP , Coenzyme A is released -A thioester bond is a high energy bond, we can use it to generate GTP from GDP
Reaction type:the energy released from the hydrolysis of the thioester bond provides the energy for the formation of the phosphoanhydride bond of GTP
A substrate level phosphorylation
Cofactor: GDP+Pi=GTP.The GTP can be used to form ATP (nucleoside diphosphate kinase, which is able to converted GTP into ATP)
ATP and GTP are energetically equivalent ( they’re the same )
how is step 5 in the TCA cycle substrate level phosphorylation
The enzyme involves an enzyme-succinyl phosphate intermediate
what occurs in step 6 of the TCA cycle
Enzyme -Succinate dehydrogenase which reduces the NAD into NADH2, generating fumarate
Reaction type:Oxidative dehydrogenation of succinate to fumarate (this is the third of our reduction reaction out of the 4 reduction reactions that occur in the TCA cycle)
Cofactor:FAD is reduced to FADH2
Important note :The succinate dehydrogenase is the only enzyme contained within the inner mitochondrial membrane out of the Krebs enzymes used
what occurs in step 7 of the TCA cycle
Enzyme: Fumarase acts on fumarate to make Malate , needs water to do this , producing a hydroxyl group
Reaction type:Catalyses a stereospecific trans addition of a hydrogen atom and a hydroxyl group
what occurs in step 8 of the TCA cycle
Enzyme : Malate dehydrogenase catalyses the conversion of Malate intoOxaloacetate
Reaction type:Oxidative dehydrogenation of malate to oxaloacetate
Cofactor:NAD+ is reduced to NADH + H+
draw the structures of acetate,aceyl-CoA and pyruvate
write the energy balance sheet for glycolysis (products)
-2 ATPs used to prime glycolysis
-4 ATPs produced from the glycolytic pathway as a result of substrate level phosphorylation
-2 NADHs generated
-8 ATPs net gained from the conversion of glucose to pyruvate and the re-oxidation of the 2 NADHs produced
write the energy balance sheet for the complete catabolism of pyruvate
-1 NADH for the production of acetyl-CoA
-3 NADHs from one turn of the TCA cycle
-1 FADH2 from TCA
-1 GTP directly from TCA cycle
=30 ATP in total
what is the Balance sheet for the complete oxidation of glucose(how much ATP does glycolysis and TCA cycle produce)
-Glycolysis generates 8 ATP
-TCA cycle generates 30 ATP for 2 pyruvates entering the TCA cycle
Total=38 net ATPs
describe the process starting with glucose , then glycolysis , into pyruvate , then anaerobic or aerobic pathway (TCA cycle) in simple form
-Glucose comes in , Glycolysis occurs
-Glycolysis generating the pyruvate , pyruvate has two choices
-In aerobic systems its fermented which enables us to regenerate the NAD+ we need in glycolysis , completing the cycle , lactate produced
-Pyruvate in our aerobic conditions enters the mitochondria , through a porin and a Mitochondrial Carrier , in the mitochondrial matrix its converted into acetyl-CoA through the link reaction and enters the TCA cycle , which generates all the reduced factors
what are the 10 enzymes in glycolysis
-hexokinase
-phosphoglucose isomerase
-phosphofructokinase
-aldolase
-triose phosphate isomerase
-GAP dehydrogenase
-phosphoglycerate kinase
-phosphoglycerate mutase
-enolase
-pyruvate kinase
The glycerol-phosphate shuttle and the malate-aspartate shuttle are two key mechanisms that do what
The glycerol-phosphate shuttle and the malate-aspartate shuttle are two key mechanisms that cells use to transfer electrons from NADH produced in the cytoplasm (during processes like glycolysis) into the mitochondria, where oxidative phosphorylation occurs. This is necessary because NADH cannot directly cross the mitochondrial membrane, so these shuttles provide a means of transporting the electrons in a way that facilitates ATP production in the mitochondria.
describe the malate-asparate shuttle , during oxidative phosphorolyation (page 51)
-Two specific mitochondrial transporters-malate and aspartate
-Results in the electrons and protons from the cytoplasm NADH being transferred to the NAD+ in the mitochondrial matrix
-Any NADH made using the malate-aspartate shuttle will result in the production of 3ATP per NADH
-Occurs in tissues where the energy requirements is low (such as the liver)
-A different mechanism is used in metabolically active tissue such as neurons and muscle
describe the glycerol-phosphate shuttle , to do with oxidative phosphorolyation
Used in metabolically active tissue such as neurons and muscles
-What this does is that it uses dihydroxyacetone phosphate to oxidise the NADH, producing glycerol 3-phosphate which is then used by the enzyme-mitochondrial glycerol 3-phosphate dehydrogenase and it reduces the FAD into FADH2,FADH2 is then able to donate those electrons and protons to the ubiquinone to produce the ubiquinol(in yellow)
There are two glycerol-3-P dehydrogenase enzymes (cytosolic and the other mitochondrial bound with the active site on the intramembranous side)
-The glycerol-3-phosphate is produced in the cytoplasm and can easily move into the intermembranous space of the mitochondria
-The DHAP can pass back into the cytoplasm and be used in glycolysis
-The one less ATP ensures that this reaction is not able to reverse as it decouples the matrix NADH from the cytoplasmic NADH
-The oxidation / reduction cycle produced FADH2 hence using this glycerol-phosphate shuttle produces a total of 2 ATP per NADH
what is the energy balance sheet for the glycerol-phosphate shuttle and the malate-aspartate shuttle
Energy balance sheet =glycerol -phosphate shuttle
Glycolysis generates 6 ATP and TCA cycle generates 30 ATP for 2 pyruvates entering the TCA cycle using only the glycerol phosphate shuttle
Energy balance sheet=malate-aspartate shuttle
Glycolysis generates 8 ATP and the TCA cycle generates 30 ATP for 2 pyruvates entering the TCA cycle using only the malate-aspartate shuttle
Total net ATP ranges from 36 (using the glycerol-phosphate shuttle) to 38 (using the malate-aspartate shuttle)
where does oxidative phosphorylation take place
-within the mitochondria
how does pyruvate go into the intermembarnous sace within the mitochondria (what part of the mitochondria )
-pyruvate comes into the intermembraneous space through a porin and then into the matrix via the mitochondrial pyruvate carrier
how does pyruvate get from the intermembraneous space in the mitochondria then into the matrix (in mitochondria)
-pyruvate comes into the intermembraneous space through a porin and then into the matrix via the mitochondrial pyruvate carrier
the inner membrane of the mitochondria is highly impermeable this means what are required
specific transporters
what do the porins in the mitochondria allow NADH access to where
-Porins allow the NADH access to the intermitochondrial space for small molecules
what enzyme makes FADH2
-FADH2 is made on the inner membrane and its made by the succinate dehydrogenase enzyme which is the enzyme that turns the succinate into fumarate
-The succinate dehydrogenase sits in the inner membrane and is also a component of the electron transport chain
decsribe the structure of succinate dehydrogenase
Succinate dehydrogenase= 4 subunit protein, protein complex , large region stretches out into the matrix
describe the electron transport chain
-NADH and FADH2 pass their electrons to transmembrane protein complexes within their inner membrane
-At each step the electrons are passed to the next carrier in the chain - that carrier has a slightly higher affinity for electrons than the previous carrier
-Ultimately , the electrons are passed to molecular oxygen to produce water
are oxidation reactions exergonic or endergonic
exergonic
the electron transport has how many complexes
5
complex 1 , complex 2 ,complex3,complex4,complex 5
complexes 1,3,4 in the electron transport chain are what type of pumps
1,3,4 are proton pumps , they transport H from the matrix into intramembranous space
describe the structure/function of the proton pump during oxidative phosphorylation
-consist of 2 gates , gate 1 opens on matrix side , proton comes in and binds to negatively charged AA as they’re positively charged and it will associate tightly with them
-Close the gate
-Open the intramembranous space gate (the bottom one)
-need to dissociate proton,as the electrons travel through the protein complex they provide energy and this energy is used to dissociate the protons from the protein complex to position them into the intramembranous space
describe complex 1 of the electron transport chain (what does it do, where does it pass the electrons to - what complex next )
-Also known as NADH ubiquinone reductase / NADH-Q reductase
-Oxidises NADH and transfers 2 electrons through protein structure(the mobile carrier ubiquinone) , it provides the energy thats needed to pump 4 protons from matrix side into intramembranous space, these electrons and protons combine with ubiquinol to produce reduced ubiquinone
-Reduced ubiquinone called ubiquinol (QH2) is free to move throughout the inner membrane
-Ubiquinol transfers these electrons to complex 3
-The transfer one of the electrons through complex 1 will result in two protons from the matrix into the intermembraneous space
describe complex 3 of the electron transport chain (what is it called ,what does it do )
-Called Q-cytochrome-c oxidoreductase
-Transfers two electrons between two mobile electron carrier
-It receives them from the QH2 (ubiquinol) and transfers them to the soluble cytochrome-c located in the intramembranous space
-1 electron is transferred to 1 cytochrome-c (an electron acceptor)with the transfer of approximately 2H+.The second electron is first stored internally and then transferred to a second cytochrome c which results in two additional H+ being transferred from matrix to intramembranous space
-There are a total of 4H+ transferred ,2 from QH2 and 2 from the matrix
-cytochrome carries electron so we need two of these (have two cytochrome-c)
what does complex 4 do in the electron transport chain
-Also called cytochrome oxidase
-This transfers the 2 electrons from the 2 cytochrome-c proteins to the mitochondrial matrix
-This is accompanied by the transfer of 2H+ to the intramembranous space and reducing oxygen on the matrix side to produce water
-Hence the oxidation of one NADH results in the transfer of approximately 10 H+ (4 from complex 1 , 4 from complex 3 and 2 from complex 4) to the intermembraneous space
what occurs in complex 2 of the electron transport chain
-It is complex 2 that in the conversion of succinate to fumarate , FAD is reduced to FADH2
describe the ATP synthase protein
-ATP synthase
-Protons from from intermembraneous space through the protein , and the rotor rotates quickly , generating ATP quickly
-If the ATP synthase has stopped using the protons then at some point the proton gradient will be so high that the proton transfer stops
how many beta subunits are in the ATP synthase protein , and what are the three forms of the beta subunits
-Beta subunits can be in three forms : open state , lose state and tight state
The rotation in ATP synthase drive ATP synthesis , how (how is ATP produced)
-page 60
-ADP and Pi binds to open state of Beta subunit , gamma subunit rotates and as this rotates it turns into the loose confirmation , the gamma subunit rotates again and forms the closed complex , which forces the ADP and Pi together to produce ATP
-the return of the H+s causes rotation of the spindle of the ATP synthase (rotor)
-The rotor is asymmetric and causes conformational changes in the head group subunits that make up the stator
-These conformational changes in the stator ( the stationary part fo the enzyme complex) are involved in the driving the synthesis of ATP from ADP and Pi
-It is not the synthesis of ATP but the unbinding that requires energy
ATP can only leave the matrix if its replaced by an ADP , what transporter does this
-We have this transporter , ATP-ADP translocase in the inner mitochondrial membrane which recognises ADP and ATP and swaps the places of them
-It is the voltage gradient that drives ATP/ADP movements as -4 charge on ATP prefers to move out while -3ADP moves into the matrix
what happens when there is a demand for ATP
-ADP level rises
-ADP enters the matrix and ATP leaves
-ADP can now be phosphorylated by the ATP synthase using the proton motive force
-The proton motive force is reduced
-The electron transport chain starts up again to rent the proton motive force
-Hence ATP is only produced on demand
are lipids hydrophobic or hydrophilic
hydrophobic
what are fatty foods rich in
triglycerides
are fats and oils solid or liquid at RT (two different)
fat=solid at RT
oil=liquid at RT
what is the structure of a triglyceride
3 fatty acids are ester-linked to glycerol backbone
are triglycerides insoluble or soluble
insoluble
do triglycerides tend to clump together
yes
what is the structure of a fatty acid
-long chain (between 12 and 24 carbons ) hydrocarbons
-Methyl group at one end , COOH (carboxyl ) group at one end
-0 or more double bonds (none at all or several )
-no double bonds = saturated=higher melting point
-unsaturated = several double bonds= lower melting point
what does a monounsaturated and polyunsaturated fatty acid mean
Polyunsaturated = more than 1 double bond
monounsaturated= one double bond
-The double bonds change the properties
-More double bonds you turn fats into oils (lower melting temp)
describe a cis and a trans fatty acid
cis= same side , has a kink in it , cant pack as closely together , lowers the MP
Poly-cis = bend becomes more curled
Trans = opposite side (across) , linear
what are the three ways of naming a fatty acid
-common name EG-Oleic acid
-Systematic name - cis octadecenoic acid
-omega or n system - C18:1 (n-9)
-omega is the position of the first double bond
what does elongases and desaturases do in terms of fatty acids
Elongases -increase chain length by 2 carbons
Desaturases-add double bonds
We cant make fatty acids less than omega 9
The human body cant make omega 3 or omega 6 so where do they come from
-Humans don’t have the right desaturase to add double bonds lower than omega 9
-Omega 3 / omega 6 fatty acids therefore have to come from the diet and are termed essential
-Omega 3 + omega 6 can be elongated and further desaturated
why do we alter fatty acids
-no need for energy storage purposes
-membrane phospholipids
Fatty acid length increases bilayer thickness
Degree of saturation increases membrane fluidity
Tissue-specific membrane composition
Some fatty acids are precursors to signalling molecules
what does pancreatic lipases do in terms of triglycerides
triglycerides digested by pancreatic lipases
why are triglycerides digested
-majority of lipid in food is triglycerides
-digested by pancreatic lipases
-water come in and split the ester bond , water added
-Triglycerides are too big to be absorbed as they are , so this is why this occurs
-can now cross membrane into intestinal cells
describe how triglycerides are absorbed and assimilated
-digested triglycerides are re-esterified in gut mucosa
-Fatty acids have to be activated first using Coenzyme A
-Triglycerides are packaged into lipoproteins for transport in the blood to the tissues as they are too hydrophobic otherwise
why are triglycerides packaged into lipoproteins
-Triglycerides are packaged into lipoproteins for transport in the blood to the tissues as they are too hydrophobic otherwise
what is a lipoprotein
Lipoprotein
-mixture of lipid and protein
-phospholipid and chlol (OH group )outer layer
-tylerglericde and chol ester core
-transport from gut to tissues uses chylomicrons
describe the structure of a lipoprotein
Lipoprotein
-mixture of lipid and protein
-phospholipid and chlol (OH group )outer layer
-tylerglericde and chol ester core
-transport from gut to tissues uses chylomicrons
how are triglycerides taken up by adipose tissue
-Endothelial cells have Lipoprotein lipase attached on the lumenal side
-endothelial cells coated with an enzyme
-lipoprotein lipase cleaves off fatty acids when enter cells
-When chylomicron has offloaded most of the TG it is called a remnant and is removed from circulation by the liver
-all three fatty acids cut off
-chylomicron offloads the triglycerides
describe triglyceride synthesis in adipose tissue
White adipose tissue (WAT)
White adipose tissue = storage
-Tg synthesis here is different from intestinal synthesis
-all 3 FA need to be activated again
-Glycerol-3-phosphate comes from DHAP (glycolysis)
Use NAD+ to add on a hydrogen
provide a summary of triglyceride metabolism
-triglycerides come in , in the food
-In the gut they are broken down into 2 fatty acids and 1 monoacylglycerol
-in the gut lining they are turned back into a triglyceride
-then loaded onto lipoproteins to travel around the body
-Then broken down again into 3 fatty acids and glycerol
-then turned again back into triglycerides
Why do we metabolise fatty acids?
-They contain lots of energy , more than glucose (glucose = 17 , fatty acids= 38 )
-Makes a better source than glucose as when glucose stored as glycogen , there is a high mass of water
-They form a dense energy store
-Fatty acids form a pure droplet of triglycerides so not wasting space with water
what is adipose tissue speciliased for
-Specialised for storing triglycerides
-Each fatty acid droplet has a shell of protein around it
-Protein shuts off the droplet
what are the three enzymes used in lipolysis
-The three enzymes used in lipolysis are : Adipose triglyceride lipase (ATGL), hormone-sensitive lipase (HSL) and Monoacylglycerol ( MGL)
-Coat is open after phosphorylation
-Set of 3 enzymes
-Each enzyme is recognised and cleaves a different fatty acid
what do the three enzymes in lipolysis (hydrolsis of a triglercide)
-The three enzymes used in lipolysis are : Adipose triglyceride lipase (ATGL), hormone-sensitive lipase (HSL) and Monoacylglycerol ( MGL)
-ATGL is the enzyme that is responsible for the initial step in lipolysis , it cleaves the fatty acid from the triglyceride , converting it into a diacylglycerol (DAG) and free fatty acid (FFA)
-After ATGL acts on the triglyceride , HSL further breaks down the diacylglycerol (DAG) , it cleaves the second fatty acid , resulting in a monoacylglycerol (MAG) and another free fatty acid
-The first step of lipolysis involves MGL (monoacylglycerol ) which cleaves the remaining FA from the MAG producing glycerol and a free fatty acid
-Coat is open after phosphorylation
-Set of 3 enzymes
-Each enzyme is recognised and cleaves a different fatty acid
Triglycerides can be only broken down in one type of tissue , which is what
The breakdown is only in adipose tissue so needs to be transported in the blood to somewhere else
-HSA carries the fatty acids in the blood
-Delivered to areas of the body with low conc
what carriers the fatty acids into the blood
-HSA carriers the FA into the blood
-delivered to areas of the body with low conc
-target within the cell is the outer membrane of the mitochondria
-FA are released from HSA and travel to the outer membrane of a mitochondrion where theyre activated
describe the process of fatty acid cataboism
-When they reach the surface they attach to coenzyme A , to make Acyl CoA
-This consumes ATP which is catalysed by an enzyme called Acyl CoA synthetase
-Synthetase means it consumes ATP
-No energy cost for the next step
-2 step process
-Carboxylic group reacts with ATP , we attach AMP to the end , releasing pyrophosphate (pp)
CoA must be swapped for what , in order to cross the inner mitochondrial membrane
-CoA must be swapped for carnitine to cross the inner mitochondrial membrane
Acycl-cartitine is transported across the bilayer by what type of antiporter
-Acyl-carnitine is transported across the bilayer by a Translocase antiporter
in triglyceride catabolism , how does the Acycl-CoA cross the mitochondria
-Acyl-CoA can cross the outer mitochondrial membrane
-CoA must be swapped for carnitine to cross the inner mitochondrial membrane
-Acyl-carnitine is transported across the bilayer by a Translocase antiporter
-Acyl chain is reattached to CoA once in the matrix
-Need to get across 2 membranes in the mitochondria the inner and outer membrane
-Fatty acids comes in and binds to protein acyl-CoA synthetase then goes through the membrane
-Goes from being attached to CoA to being attached to carnitine
-Carnitine swaps with the carintine attached to the fatty acid
-Allows two separate pools of fatty acids , one in the cytoplasm and one in the mitochondria
what does acyl-CoA do in terms of the triglyceride catabolism
acyl CoA - can chop off 2 carbons at a time from the acyl CoA ( 2 carbons removed from Acyl CoA then becomes the acetyl CoA) to feed it into the TCA cycle
-Acetyl CoA is a mini fatty acid that can be made from a full sized fatty acid
in terms of fatty acid catabolism , what does beta oxidation involve
-Breaking the bond will release Acetyl CoA
-Going from an attacked fatty acid to acetyl CoA= Beta oxidation
-Only 2C are ever removed at one time
-Bond in pink is the one that is broken which releases an acetyl CoA
(page 73)
describe step 1 in fatty acid catabolism
Step 1 - removed hydrogen from beta and alpha to make C-C double bond , FAD picks up the hydrogens , breaks a double bond , get 2 ATPs out
-Oxidation of alpha and beta carbons
describe step 2 and step 3 in beta oxidation - fatty acid catabolism
-Can use water to add oxygen to the H to create an OH group and then 2 more H to create a single bond between the carbon
-Creates a carbonyl group on the beta carbon
-(step 3)Two hydrogens removed , by the dehydrogenase, one goes to NADH , the other goes to the ETC
-No energy has been consumed yet
revise fatty acid catabolism
what are the products of beta oxidation-fatty acid catabolism
-each cycle produces
-1 acetyl CoA
-1 FADH2
-1 NADH
what is the equation needed to work out the number of cycles in beta oxidation
-The number of cycles needed = number of carbons / 2 - 1
for one turn of the TCA cycle , how many ATP do we get
12 ATP
why arent excess of aa excreted
Excess amino acids arent stored
Excess of aa arent excreted , not lost in urine , because there is energy in them and theyre useful molecules
what is the amino acid pool , and how does it work
Aa have nitrogen atoms within them , there is an aa pool in the body , this is the free aa in the blood so cells can take the ones they need
250 new body protein made a day , aa leave the aa pool and make body protein
Constantly recycling proteins in the body
Same amount each day broken down or turned into something
there are three destinations for amino acids in the amino acid pool what are these
1-Protein synthesis
2-Direct use / minor modification
3-Breakdown and redeployment
list the aa used to make neurotransmitters
AA used to make neurotransmitters
Direct use:
Neurotransmitters
Glutamate , Aspartate and Glycine
Glutamate used to make GABA
Tyrosine - Dopamine , Noradrenaline , Adrenaline
Tryptophan used to make Serotonin
Arginine used to make NO
Hormone
Tyrosine-Thyroxine
Tryptophan - Melatonin
how are aa broken down in the amino acid pool
-amino group chopped off , problem is its ammonia which is toxic to cells , so is a partial solution
-a carbon skeleton is left(lost amino group)
- can be turned into c02 and water , by breaking down carbon skeleton , to produce ATP
-carbon skeleton can be the starting point to make other useful molecules in the body
how does the body detoxify and handle the aa
-need to detoxify the amino
-amino group is therefore stuck on alpha ketoglutarate and made into glutamate
-no energy cost
-Deamination is the removal of the amino group , into ammonia
-ammonia converted to urea , easier to get rid of now
-this is a funnelling effect
-the carbon skeleton can go round again for another amino group to attach to , cycle will continue
-page 91
what is meant by
Transamination
Transamination- an amino acid from one amino acid is transferred to a keto acid ( alpha-ketoglutarate) to form a new amino acid
explain the process of transamination
-family of enzymes called aminotransferase
-swap oxygen for NH2
-alanine gets converted into pyruvate
-turn aa into something that can or is already into the TCA cycle
-This is the livers job to do this process
-use water to break double bond , release ketoacid
-alphaketoglutuarte comes in
-reverse this process
-water released
-rearrangement of double bond
-amino group now on a different carbon skeleton
-no energy cost to do this
page 92
what is deamination
Deamination-process of removing the amino group from an amino acid
describe the process of deamination
-glutamate reacts with water hydrolysis reaction , releases ammonia
-glutamate dehydrogenase catalysis this producing NADH,generating ATP
-enzyme highly regulated , inhibited by GTP,activated by ADP
describe the process of urea synthesis
-c02 , ammonium , ATP and water react
-Produce carbamoyl phosphate-Cycle of AA different to ones found in protein apart from arginine
Citrulline reacts with aspartate to produce arginino succinate
-this is split into arginine and fumarate
-arginine is hydrolysed to release urea and regenerate into ornithine
what do extraheptic tissues catabolise aa into
-catabolise aa to ammonia but cant make urea
carbon skeletons all end up as one of
list them all
Carbon skeletons all end up as one of :
Pyruvate
Acetyl CoA
Acetoacetyl CoA
Alpha Ketoglutarate
Succinyl CoA
Fumarate
Oxaloacetate
provide an overview of fatty acid anabolism - what is the starting point and endpoint of it
Overview of fatty acid anabolism
-starting point is Acetyl CoA (2c)
-endpoint if Palmitic acid (16c)
-process is almost a reverse of beta oxidation (beta carbon being reduced)
(due to the use of NADPH rather than NADH and the use of Malonyl CoA as a basic unit - not Acetyl CoA)
revise how sulphurous amino acids are disposed of-page 96
how is Malonyl-CoA formed from Acetyl-CoA (synthesis of fatty acids)
Synthesis of fatty acids through fatty acid biosynthesis
Step 1 Carboxylation of Acetyl-CoA to Malonyl-CoA:
-start with acetyl CoA , ATP and HCO3 react with each other first, Acetyl coA carboxylase is adding a carboxy to something
-The enzyme is highly regulated, stimulated by the presence of citrate in the cell ,insulin stimulates this pathway , the palmitic acid is a negative inhibitor (negative feedback loop), Glucagon and adrenaline inhibit Acetyl CoA carboxylase
describe step 2 in fatty acid anabolism - fatty acid synthesis elongation
Step 2:Fatty acid synthesis elongation
-Chain grows by 2c at a time
-Acetyl-CoA and malonyl-CoA are transferred to fatty acid synthase (FAS)
-one of the carbons is released as carbon dioxide, release of CO2 drives the reaction
-make a 4 carbon molecule
where are FAS (fatty acid synthase) and Acetyl CoA located in the cell
-both in the cytoplasm
why do we need shuttles in fatty acid anabolism
-Both FAS and Acetyl CoA carboxylase are in the cytoplasm
-All acetyl CoA are in the mitochondria
-We need to have some shuttles
-Starting point is a build up of Acetyl CoA , reacts with citrate , we then have a transporter for citrate which moves citrate into the cytoplasm
-citrate is converted back to Acetyl CoA and back to oxaloacetate
what does the first step of fatty acid synthesis involve
-The first step of fatty acid synthesis involves the binding of acetyl-CoA to the acyl carrier protein (ACP) domain of fatty acid synthase
-Acetyl-CoA then reacts with the sulfhydrl group of ACP , creating the acetyl-ACP complex
-FAS is a huge enzyme , with 6 different active sites
-The bold part is not a polypeptide , but the rest is
-page 83
revise fatty acid anabolism page 84
describe step 1,2,3,4 of fatty acid anabolism -page 84
-step 1 is the first two domains, forms the bond and joins them together, making C-C bond is step 1
a)Acetyl group transferred to KS via ACP and MAT
KS= beta ketoacyl-ACP synthase
MAT=Malonyl/Acetyl CoA-ACP Transacylase
b) Malonyl transferred onto ACP by MAT
c)KS joins the Acetyl and Malonyl (loss of co2)
Step 2 , 3 and 4 we need to get to a CH2 group
Step 2 - carbonyl to CHOH, reduction gets rid of carbonyl
Step3-single carbon bond to double carbon bond , dehydration gets rid of oxygen
Step 4-Adds hydrogen to CH to make CH2, reduction makes it into CH2, the goal is to use NADPH to remove the oxygen and add 2 hydrogens
describe fatty acid elongation
-the 4c chain is transferred back to KS to start off step 1
-teh cycle is repeated 6x until enough 2c have been added to make palmitic acid (16c) which is then released (thioesterase)
-Cycle continues until enough carbonyl are added
-Ends up on flexible arm but needs to be cut off to make it a free FA which can then be attached to glycerol to form a triglyceride
in the anabolic state , what will new fatty acids be converted to
-In anabolic state , new FA will be converted to TG and stored
-If synthesised in the liver , lipoproteins used to export TG to adipose and other tissues
what is a lipoprotein made up of
phospholipids,cholesterol,triglyceride,cholesteryl ester
what are the 5 types of lipoproteins
VLDL- very low density lipoprotein
IDL-intermediate denisty lipoprotein
LDL-low density lipoprotein
HDL-high density lipoprotein
-5 types of chylomicrons
-Theres a density gradient
-As they get smaller they get more dense
what happens to excess AA in the body
Excess amino acids arent stored
Excess of aa arent excreted , not lost in urine , because there is energy in them and theyre useful molecules
describe the amino acid pool
Aa have nitrogen atoms within them , there is an aa pool in the body , this is the free aa in the blood so cells can take the ones they need
250 new body protein made a day , aa leave the aa pool and make body protein
Constantly recycling proteins in the body
Same amount each day broken down or turned into something
list the three desinations of AA in the amino acid pool
1-Protein synthesis
2-Direct use / minor modification
3-Breakdown and redeployment
list the uses of AA , specifically the ones used to make neurotransmitters
AA used to make neurotransmitters
Direct use:
Neurotransmitters
Glutamate , Aspartate and Glycine
Glutamate used to make GABA
Tyrosine - Dopamine , Noradrenaline , Adrenaline
Tryptophan used to make Serotonin
Arginine used to make NO
Hormone
Tyrosine-Thyroxine
Tryptophan - Melatonin
describe how amino acids are broken down into a carbon skeleton
-amino group chopped off , problem is its ammonia which is toxic to cells , so is a partial solution
-a carbon skeleton is left(lost amino group)
- can be turned into c02 and water , by breaking down carbon skeleton , to produce ATP
-carbon skeleton can be the starting point to make other useful molecules in the body
provide an overview of AA breakdown (transamination , deamination)
-need to detoxify the amino
-amino group is therefore stuck on alpha ketoglutarate and made into glutamate
-no energy cost
-Deamination is the removal of the amino group , into ammonia
-ammonia converted to urea , easier to get rid of now
-this is a funnelling effect
-the carbon skeleton can go round again for another amino group to attach to , cycle will continue
Transamination- an amino acid from one amino acid is transferred to a keto acid ( alpha-ketoglutarate) to form a new amino acid
describe transamination
an amino acid from one amino acid is transferred to a keto acid ( alpha-ketoglutarate) to form a new amino acid
describe the process of transamination -page 91
-family of enzymes called aminotransferase , they transfer amino groups from one thing to another
-swap oxygen for NH2 , becoming glutamate
-Swapping carbonyl for an amino , becoming an alpha keto acid
-bidirectional
what prosthetic group does Aminotransferase use to do the amino group transfer in transamination when breaking down AA-page 92
Aminotransferases use a Vit B6-derived prosthetic group called pyridoxal phosphate (PLP) to do the amino group transfer
Picture on P92:
-use water to break double bond , release ketoacid
-alphaketoglutuarte comes in
-reverse this process
-water released
-rearrangement of double bond
-amino group now on a different carbon skeleton
-no energy cost to do this
what is meant by deamination
Deamination-process of removing the amino group from an amino acid
describe the process of deamination -page 93
-glutamate reacts with water hydrolysis reaction , releases ammonia
-glutamate dehydrogenase catalysis this producing NADH,generating ATP
-enzyme highly regulated , inhibited by GTP,activated by ADP
describe the urea cycle -page 94
-all AA
-Cycle of AA different to ones found in protein apart from arginine
Citrulline reacts with aspartate to produce arginino succinate
-this is split into arginine and fumarate
-arginine is hydrolysed to release urea and regenerate into ornithine
what is extraheptic tissue
Extrahepatic tissues refers to all the tissues and organs in the body outside the liver
extraheptic tissue catabolize AA , what is the product they release
ammonia (NH3)
list the things that all carbon skeletons can end up as
Pyruvate
Acetyl CoA
Acetoacetyl CoA
Alpha Ketoglutarate
Succinyl CoA
Fumarate
Oxaloacetate
revise how sulfurous amino acids are disposed of
-page 96
-M converted to SAM
-SAM changed into S
-Then changed into homocysteine
-VitB6 , reaction with serine produces cystathionine
-Overall product is succinyl CoA
how can purines be synthesized from scratch
by combining carbon skeletons from three AA
what is meant by gluconeogenesis
Gluconeogenesis= new glucose creation , make glucose
what are the key steps of gluconeogensis -page 99 diagram
-Three in pink cant be reversed
-Need alternative routes , pyruvate to oxaloacetate to EP , 2 ATP consumed
-get rid of phosphate on fructose 1-6 bisphosphate , hydrolyse the bond back into fructose 6 phosphate
-chop of phosphate from glucose 6 phosphate into glucose
-all other arrow can run in either direction
-lower part has to run twice
-6 ATP used
Pyruvate cant go back to PEP
Need an alternative pathway
-pyruvate carboxylase - movies round carboxyl groups
-add co2 onto pyruvate to make oxaloacetate
-This is in the mitochondria
-Either the malate or aspartate shuttle transfers OAA to cytoplasm
PEPCK- moves carboxyl group
-CO2 added on
-simple hydrolysis
-fructose 1-6 bisphosphate hydrolysed into fructose 6 phosphate
-glucose 6 phosphate hydrolysed into glucose
-Glucose 6 phosphate cant cross the plasma membrane , so only when converted to glucose it can cross the membrane
There isnt a store of pyruvate readily available to support gluceogensis , what are the solutions for this
lactate via the cori cycle and glucogenic amino acids
pruvate cant go back to PEP-Page 99 , what is the alternative pathway
Need an alternative pathway
-pyruvate carboxylase - movies round carboxyl groups
-add co2 onto pyruvate to make oxaloacetate
-This is in the mitochondria
-Either the malate or aspartate shuttle transfers OAA to cytoplasm
describe the cori cycle
-conversion of lactate
-uses LDH - lactate dehydrogenase
-Lactate travels through the body to the liver, the liver turns the lactate into pyruvate and then joins 2 pyruvates together to make glucose
what does glucogenic amino acids mean-105
Glucogenic AA- means AA that can be used in gluconeogenesis
describe the steps of the alanine cycle
-muscle proteins are broken down into AA
-muscles undergo transamination , a process where amino groups are transferred from AA to form glutumate and pyruvate , allowing for the release of alanine
-in the liver , alanine is converted back into pyruvate via the action of the enzyme alanine aminotransferase (ALT)
-the amino group of alanine is transferred to alpha-ketoglutarate which forms glutamate
-pyruvate formed in the liver is then used in gluconeogensis to synthesize glucose
-10 ATPs everytime we do this
-Only the liver does this
-describe the steps in gluconeogensis
-glycerol phosphoroylated by glycerol kinase to form glycerol-3-phosphate , consumes 1 ATP
-glycerol-3-phosphate oxidised by glycerol-3-phosphate dehydrogenase to form dihdryoacetone phosphate, produces 1 NADH
-1 ATP consumed , 1 NADH created
revise pictures on page 108
is the rate limiting step the slowest reaction in pathway and does it determine overall flux through the pathway by acting as bottleneck
yes
what is a metabolic pathway
-the enzymatic route that a metabolite molecule takes
how can you identify the RLS of an equation = rate limiting step
1-measure Vmax for enzymes in pathway , lowets = RLS
2-compare Keq and mass action (MAR)
-If reaction is close to equilibrium in the cell MAR=Keq
-If reaction is rate-limiting in the cell MAR<Keq
For RLS:MAR is usually 100-1000 times < Keq
Products/reactants at equilibrium
Products/reactants within cell
What are the three ways to identify the rate limiting step of a reaction-page 110
1-measure Vmax for enzymes in pathway , lowets = RLS
2-compare Keq and mass action (MAR)
3-Test if at crossover point (-To see whether its an enzyme that changes activity when u change the conditions
-stimulation may be enzyme
-before enzyme D substrate levels drop and after product levels increases
-D slows down the whole pathway)
what is the need to control the regualtion of metabolism , list the points
To ensure a given metabolic pathway is active when its product is needed
Ensure competing pathways arent simultaneously active ie dont want to make and break down glycogen at same time
Ensure co-ordinated activity in multiple related pathways , ensuring the right things are on and off at the right time
why dont we want futile cycling
-we dont want futile cycling , it wastes ATP
-Waste energy comes off as heat
Brown adipocytes deliberately use futile cycling
what are the types of enzyme regulation
Intrinsic control by metabolites : allosterism / inhibitors
Fast extrinsic control via hormones (not influenced by whats going on inside the cell ): covalent modification -EG-phosphorylation
Slow extrinsic control via hormones : gene expression
describe the control by metabolites for the control of enzyme regulation-page 112
-A=product inhibition:
-hexokinase joins a phosphate to glucose = glucose 6 phosphate
-These then go back into the active site and prevent any further production
-a product can inhibit its own production
-B=Allosterism -example for fructose e,6-bisphosphate
-phosphofructokinase adds a phosphate to a different place
-This then stimulates the PDK-1 enzyme to break down the build up of F-6-P faster
-ADP and ATP are also going to have a feedback effect
–citrate building up is a signal you have plenty pf ATP , inhibiting glycolysis , stimulating gluconeogenesis
-If you have lots of ATP you dont need to to glycolysis , ATP inhibits the PFK-1 enzyme
-AMP levels should never build up in the cell , if it does its a signal the cell is starving
-The liver should not release glucose therefore , it should be doing glycolysis and stimulates the PFK-1 enzyme
-PFK-2 is inhibited by citrate and PEP but not ATP , activated by Pi
-page 113
-ATP will inhibit the pyruvate kinase step
-ADP inhibits both of the steps on the left (negative sign)
-Acetyl CoA build up stimulates gluceogenic pathway
-Alanine inhibits pyruvate kinase
-Alamine suggest we are breaking down the muscle due to short glucose
-Glycolysis is heavily regulated
What are the enzymes that are activated by ADP but inhibited by ATP
-PFK1
-Pyruvate kinase
-Pyruvate dehydrogenase
-Citrate synthase
-Isocitrate dehydrogenase
-Alpha ketogluturate dehydrogenase
-All of these enzymes are inhibited by ATP
-Lots of ATP means we dont need to do the metabolic pathway
-ADP/AMP activate and stimulate the enzymes in the pathway
how can hormones regulate enzymes
hormones can alter : the actvitity of enzymes (rapid , via phosphorylation , short lived effect) and number of enzymes (slow , via gene expression changes, longer-lived effect)
-Hormones can change the number of enzyme molecules present as well as the activity of the enzymes
how are enzymes controled by phosphorylation
phosphorylation=conformational change = activation / inactivation = phosphorylation ovverides allosterism
-3 amino acid side chains that contain a phosphate
-Kinase adds a phosphate , phosphatase removes a phosphate , this causes a conformational change
-This is a permanent change that overrides the allosteric step
phosphorylase is regulated in two ways what are these
-metabolites
-phosphorylation
-phosphorylase exists in two forms , what are these
inactive form phosphorylase B and an active form phosphorylase A
what are the allosteric regulators in the muscle and liver for phosphorylase
-In the muscles its stimulated by AMP , inhibited by ATP and G-6-P
-In the liver its inhibited by glucose
-In both cases (both B and A ) serine 14 can be phosphorylated it can then become active
glycogen synthase has lots of phosphorylation sites , how many does it have in the muscle and the liver
-muscle = 9
liver = 7
-six different kinases = inhibtion
-Glycogen synthase has lots of phosphorylation sites , activating and stimulating the breakdown of glycogen and inhibits the synthesis of glycogen
-6 different kinases that all add a phosphate to glycogen synthase , all inhibit it
how does phosphorylation control glycogen metabolism -page 116
-Both adrenaline and glucagon will bind to a receptor and activate a G protein
-The G protein will cause the production of cyclic AMP
-cyclic AMP then activates a protein kinase
-This activated protein kinase then phosphorylates other enzymes
-Phosphorylase kinase is activated , this attaches a phosphate onto phosphorylase making it active , this is the one that breaks down the glycogen
-add a phosphate to glycogen synthase its inactive
-add a phosphate to phosphorylase alpha = activated
-protein phosphatase removes phosphate
-Insulin makes glycogen
-We end up with protein Kinase B , adds a phosphate to glycogen synthase kinase
-Here we are switching off a deactivation
-Phosphorylation of glycogen synthase kinase 3 stops it phosphorylating glycogen synthase and switching off glycogen synthase
-PP1 (protein phosphatase 1 ) removes a phosphate to activate G.synthase
-Adrenaline stimulates phosphorylation of things
-Insulin stimulates dephosphorylation of things
-page 117
if you add a phosphate to glycogen synthase does it become active /inactive
-inactive
does insulin promote dephosphorylation or phosphorylation
-Insulin promotes dephosphorylation
explain how lipid metabolism is controlled by phosphorylation in terms of insulin-118
-Insulin promotes dephosphorylation
-the hormone lipase(hormone sensitive lipase ) isnt very active when its dephosphorylated
-perpilipin is in the way of the triglycerides
explain how lipid metabolism is controlled by phosphorylation in terms of adrenaline/glucagon-118
-On the other side (right side ) we see everything is the opposite , when high levels of adrenaline everything becomes phosphorylated so now the perilipin move out of the way and allow access to the triglycerides and the hormone sensitive lipase is now fully active and starts breaking them down , FA released from this store
What happens to fructose-6-phosphate (F-6-P) in its dephosphorylated state?-page 119
In its dephosphorylated state, fructose-6-phosphate (F-6-P) is converted into fructose-2,6-bisphosphate (F-2,6-P2) by the enzyme PFK-2. This activates PFK-1, stimulating glycolysis.
What effect does adrenaline have on the phosphorylation state of PFK-2 and its activity?-119
When adrenaline is dominant, it causes PFK-2 to become phosphorylated. This phosphorylation inactivates PFK-2’s kinase activity, leading to a decrease in fructose-2,6-bisphosphate (F-2,6-P2) levels. As a result, the FBPase2 activity (which is the phosphatase function of PFK-2) becomes more prominent, favoring gluconeogenesis and inhibiting glycolysis.
How does insulin influence PFK-2 activity?-119
Insulin promotes the dephosphorylation of PFK-2. When PFK-2 is dephosphorylated, its kinase activity is enhanced, leading to an increase in fructose-2,6-bisphosphate (F-2,6-P2) levels. This increase in F-2,6-P2 activates PFK-1, which stimulates glycolysis
Which molecules inhibit the link reaction, and which one stimulates it?-119
Inhibitors: ATP, NADH, and Acetyl CoA inhibit the link reaction.
Stimulator: ADP stimulates the link reaction.
What happens to pyruvate dehydrogenase (PDH) when it is in the dephosphorylated state compared to the phosphorylated state?-119
In the dephosphorylated state, PDH is active, meaning it can convert pyruvate to acetyl-CoA.
In the phosphorylated state, PDH is inactive, and it cannot perform this conversion
describe the enzyme regulation of the link reaction , using pyruvate dehydrogenase-119
PDH phosphatase removes the phosphate groups from the PDH complex, reactivating the enzyme.
-PDH kinase adds a phosphate , inactivating the complex so that pyruvate can no longer convert into Scetyl CoA
-ATP,NADH,Acetyl CoA will inhibit it (conversion of pyruvate to Acetyl CoA)
-ADP will stimulate it
-In the dephosphorylate state its active , in the phosphorylated state its not active
-PDH kinase (pyruvate dehydrogenase kinase ) switches it off
-PDH phosphatase switches it back on again
-The phosphorylation can also be controlled allosterically , ATP , NADH , Acetyl CoA stimulate the PDH Kinase
-CoA , ADP and NAD+ inhibit the PDH Kinase
-Pryuvate will also inhibits the PDH Kinase
-Calcium ions inhibit the PDH Kinase but stimulate the PDH phosphatase
-Dont need to learn every arrow in this diagram
what is the role of AMP-activated protein kinase (AMPK)
Links allosterism to phosphorylation
Energy sensor
AMP binds cooperatively and allosterically -> 1000-fold increase in activity of AMPK
Phosphorylates multiple targets (enzymes and transcription factors)
Activated by Metformin (diabetes drug)
how do hormones / transcription factors regulate enzymes
-trancsription factors bind genes and eother increase / decrease expression
-TF either activate / deactivate a gene
-Conc of enzymes in cell goes up or down , Vmax goes up or down , rate goes up or down
-Two explanations : some TFs are metabolite receptors , gene binding follows the binding on the metabolite
-Phosphorylation of Tfs , causes gene binding
what does CREB stand for
-CREB=cyclic AMP responsive element binding protein
What is CREB and what role does it play in cellular signaling?
CREB (cyclic AMP responsive element binding protein) is a transcription factor that regulates gene expression. It is activated by phosphorylation and can bind to the CREB binding element (a specific DNA sequence) to initiate transcription.
What happens to CREB when it is dephosphorylated?
When CREB is dephosphorylated, it is inactive and cannot bind to the CREB binding element, thus not promoting transcription.
How is CREB activated?
CREB is activated when protein kinase A (PKA) phosphorylates it. Once phosphorylated, CREB can bind to the CREB binding element, a specific stretch of DNA, to initiate transcription.
-CREB is inactive when its dephosphorylated , PKA then phosphorolyates it and can now bind to a region called the CREB binding element ,a binding element is a stretch of DNA that a transcription factor can bind too
-We have the same hormone but two different effects : phosphorylation and transcriptional regulation
what happens when someone has lots of lipoprotein kinase , in terms of the chylomicron and fatty acids
-Lipoprotein lipase cleaves off fatty acids , which enter cells
-Someone who exercises lots has lots of lipoprotein lipase , so the chylomicron can offload more FA
-By doing exercise we have lots of lipoprotein lipase on the cell , so more fatty acids are removed from chylomicron onto the lipoprotein lipase
list the three metabolic controls via enzyme regulation
Allosterism /inhibitors : very quick , graded but limited effect
Phosphorylation : quite quick , on/off effect
Gene expression : Slow but sustained effect Vmax can increase /decrease, mutations in the gene knock Vmax into 0
list the three types of enzyme regulation
Intrinsic control by metabolites : allosterism / inhibitors
Fast extrinsic control via hormones : covalent modification
Slow extrinsic control via hormones : gene expression
Mixtures of 1-3
caffiene inhibits cAMP phospodiesterase , explain this process-123
Dietary additions : Caffeine , its a purine , similar to adenine and guanine , it can sometimes take place of these molecules but doesnt do the function of the molecules , ie its an inhibitor , inhibitor of cAMP phosphodiesterase
-caffiene inhibits cAMP phosphodiesterase = more protein Kinase A
-cAMP phosphodiesterase switches of everything that Cyclic AMP stimulates
-cAMP phosphodiesterase breaks down the cyclic AMP , meaning it no longer activates protein Kinase A and you therefore dont get the rest of the cascade
-Caffeine inhibits the cAMP phosphodiesterase= more protein Kinase A
-Overall effect = more protein Kinase A in the cell
-caffeine also influences gene expression
-Boosting glycogenolysis and lipolysis , releasing energy molecules into the body for use
list the altered metabolic states( refers to a condition where normal processes of metabolism in the body are significantly changed or disrupted)
Fed state
High fructose
Alcoholism
Fasting state
Starvation
Exercise
Thermogenesis
Insulin resistance / diabetes
regulation of metabolism revision-125 diagrams
what does adipose tissue release
-fatty acids and glycerol
what is the preffered fuel for the heart
Heart:preferred fuel are ketone bodies (heart runs on ketone bodies)
what is the preferred fuel source for intestines
Intestines: preferred fuel source is glutamine
what is the preffered fuel source for immune cells and spermatozoa
Immune cells : preferred fuel source is glutamine
Spermatozoa : only fuel source is fructose
what two molecules can stimulate insulin release
-Blood glucose levels go up or rise in leucine = release insulin
what two molecules stimulate the release of glucagon
-Blood glucose levels drop or the levels of glucogenic AA increases = release of glucagon
in the anabolic state , what is glucose , amino acids and fatty acids used for
-50% of this glucose used in glycolysis , 10% used to convert into glycogen 30% used in triglycerides
-AA used to make proteins and some diverted into carbon skeletons
-FA used in triglycerides
describe the storage organs with regards to FA , glucose and AA
-FA absorbed by gut and go into Adipose tissue into TG
-FA taken up by muscle and turned into TG
Glucose taken up by liver turned into glycogen
-Glucose taken up by muscle , converted into glycogen in muscle
-The liver turns excess glucose into TG , same happens in adipose tissue
-AA turned into protein in muscles
-Liver turns AA into some sort of carbon skeleton if in excess
describe enzyme activity in the anobolic state in the pancreas , with regards to glucose-127
-Glycogen synthase switches on , phosphorylase switched off
-Pyruvate kinase turned on (more active)
-In the anabolic state theres a boost of glycogen synthase (due to increase in glycogenesis ), because we are trying to make glycogen and at the same time we switch of phosphorylase (decrease in glycogenolysis)
-We boost glycolysis , so pyruvate kinase boosted
-We cancel gluconeogenesis because at this stage we have lots of glucose , dont need to make it
describe enzyme activity in the anobolic state in the pancreas , with regards to FA-127
-Boost in Acetyl CoA carboxylase , this is used to make malonile CoA - the starting point for making FA
describe enzyme activity in the anobolic state in the adipose tissue , with regards to FA128
-boost in activity of pyruvate D ,makes more acetyl CoA to make more FA
describe enzyme activity in the anobolic state in the adipose tissue , with regards to tryglercides -128
-big inhibition of Hormone sensitive lipase , big drop in breakdown of triglycerides
-Tiny amount of insulin to stop the breakdown of fats
describe enzyme activity in the anobolic state in the liver , with regards to glucose -128
-Glucokinase levels are boosted - speeds up glycolysis
-Drop in the levels of gluconeogenesis enzymes
-in terms of glucose , theres a boost of glycolysis in adipose tissue
describe enzyme activity in the anobolic state in the liver , with regards to FA -128
-Malic enzyme + ATP citrate lyase used for boosting FA synthesis
Adipose tissue : (bottom half of diagram) in terms of glucose
-Have a boost of glycolysis , to make Acetyl CoA to make FA but also to make glycerol
describe enzyme activity in the anobolic state in the adipsoe tissue , with regards to glucose -128
-Have a boost of glycolysis , to make Acetyl CoA to make FA but also to make glycerol
describe enzyme activity in the anobolic state in the adipsoe tissue , with regards to triglycerides -128
-In terms of triglycerides theres a boost of lipoprotein lipase (boost in FA entry)
-boost in the enzyme glycerol3-P acyltransferase (as we need a source of glycerol)-boost in lipogensis
what is GLUT
glucose transporter
what type of hexokinase and glucose transporter will most tissues in the body have
-Most tissues in the body will have GLUT 1 + 3 = have a low Km , high affinity transporters for glucose and Hexokinase 1-3 , low Km , high affinity
what type of hexokinase and glucose transporter does the liver and beta cells in the pancreas have
-Liver has GLUT 2 which is a lower affinity transporter-high Km
-Liver has HK IV (its hexokinase 4 also known as glucokinase) - High Km - low affinity , not inhibited by G-6-P
what type of hexokinase and glucose transporter does muscle and adipsoe tissue have
-Muscle and adipose tissue (these are the two insulin responsive tissues )contain GLUT-4 , not present on membrane , medium Km , GLUT4 is inside the cell (induced by insulin )
-Muscle and adipose tissue contains HK (hexokinase ) 2 - low Km
why do fat swells store in terms of insulin breaking down fats
-Insulin turns glucose into fat = more fat made
-Insulin blocks fat breakdown thats already in adipose tissue = no fat used
-One way process of these cause the fat stores to swell
describe high fructose corn syrup with regards to the amount of fat , isulin and glucose
Derangement of metabolism : fructose
High fructose corn syrup (HFCS)
Sweetener in food
Less glucose than sugar
Less insulin release
Less fat storage
But: fructose is metabolised faster than glucose in the liver
describe the fructose metabolism pathway, particularly focusing on the fructose bypass of the regular glycolytic pathway in the liver :
-In the liver it has its own fructokinase
-Product split into DHA and glyceraldehyde
-Have triose kinase that sticks the phosphate onto the products
-We are short circuiting glycolysis here , skipped the two steps that are slowed down
-This runs faster than when we start with glucose
-Avoiding the regulating steps and is quicker process
-Fructose ends up as FA
describe the metabolism of ethanol in the liver
-Ethanol turned into Acetyl CoA
-Alcohol dehydrogenase is the first step and this generates NADH , this produces Acetaldehyde
- This then gets turned into Acetate by aldehyde dehydrogenase
- Acetyl-CoA synthetase turns it into Acetyl CoA
what is the consequences of drinking alcohol , in terms of ethanol and NAD+
-No regulation of ethanol metabolism
-Ethanol oxidised in preference to other nutrients (for example the TCA cycle is run entirely from ethanol)
-Results in high levels of NADH + H , high levels of NAD+
-If we dont have enough NAD+ the TCA cycle is inhibited and we then wont be able to turn lactate back into pyruvate
what is the first metabolic priority when maintaining blood glucose, how does the body maintain blood glucose level
-maintaining blood glucose
-adrenaline and glucagon cause increase in glycogenolysis , GNG (gluconeogensis), lipolysis , glycerol for GNG
-Cortisol causes protein degradation and increase in GNG
what happens when you dont eat for a couple of days
-Not eating for a couple of days = cortisol is released , protomotes protein degradation , to greatly increase gluconeogenesis
in the catabolic state (fasting) describe how the adrenal gland, pancreas , apidose tisue , liver and muscle respond to this ( what do they release and where )-134
-(1)blood glucose levels start to drop, detected by pancreas + release of glucagon to the liver , liver breaks down glycogen
-pancreas release glucagon , stimulates the liver to produce glycogen
-adrenaline release , by adrenal medulla, mimicking what the glucagon is doing
-adipose tissue release FA to rest of body , liver can make glucose from the glycerol
-cortisol now released from the adrenal cortex , muscle is forced to break itself down to release AA - alanine , alanine is a source of glucose
describe the enzyme activity due to adrenaline , in the muscle in respsonse to glucose in the catabolic state
-switch of glycogen synthase , switch on phosphorylase , boost PFK2
-switch off glucogenesis , switch on glycogenolysis and glycolysis
describe the enzyme activity due to adrenaline , in the muscle in response to triglycerides the catabolic state
-boost in lipoprotein lipase , increase in FA intake
describe the enzyme activity due to adrenaline , in the adipose tissue in respsonse to triglycerides in the catabolic state
Triglycerides in adipose tissue
-Increase in HS lipase , increase in lipolysis
describe the enzyme activity due to adrenaline , in the liver in respsonse to glucose, in the catabolic state
-stopping synthesis of glycogen , decrease in glycogen synthase , switch off glycogenesis
-increase phosphorylase
Decrease PFK2 , want to stop it doing glycolysis
-increase in F-1,6-bisphosphatase , switch on gluconeogenesis
describe the enzyme activity due to adrenaline , in the liver in respsonse to FA , in the catabolic state
-decrease in Acetyl CoA , decrease in FA synthesis
describe the enzyme levels , in the catabolic state (fasting state) in response to glucagon in the liver-134/135
-stop glycolysis from happening ( decrease in glucokinase)
- pyruvate kinase also stopped
Increase in PEP carboxykinase
-increase in F1,6 bisphosphatase
-increase in G-6-phosphatase , all about boosting gluconeogenesis
describe the enzyme levels , in the catabolic state (fasting state) in response to FA in the liver-135
-switch of Acetyl CoA
-boost in Carnitine , helps FA get into mitochondria
describe the enzyme levels , in the catabolic state (fasting state) in response to glucose due to cortisol in the liver-135
-cortisol only effects enzyme levels , slower longer term effect
-boosting PEP carboxylase , AA catabolizing enzymes , enzymes to do with gluconeogenesis
-Boost urea enzymes
-boost in glycogen synthase (boost on glycogenesis ) - this is the first contradiction , promotes creation of glycogen , so liver can fill up with glycogen to support the need for it
describe the enzyme levels , in the catabolic state (fasting state) in response to FA due to cortisol in the adipose tissue-136
-boost in HS lipase (increase in glycerol , FA)
describe the enzyme levels , in the catabolic state (fasting state) in the muscles
Muscle -protein degradation
-Transmaniation causes an increase in alanine , increase in GNG
what is the bodies adaptation to prolonged fasting or starvation , where the body shifts its metabolic strategy to preserve protein and reduce the reliance on glucose (second metabolic priority)
-we now need to preserve functional protein
-we have to drop the glucose requirements , body has to adapt to this
-brain converts to Ketone body use (70% of energy used from KB, 30% used from glucose )
-reduced need for GNG - gluconeogenesis
-Reduced need for protein catabolism
during starvation the brain changes to using something else , what is it
-ketone bodies
during short term , intense excerise what does the body rely on and make
-atp , creatine phopshate , glucose
during long duration , low intensity excerise what does the body rely on and make
-with longer durations , we produce lactate now
-lactate builds up , becomes a signal against exercise
-muscles have to switch between two states depending on the two types of exercise
during short term exercise how is ATp rapdily replenished (what two enzymes)
ADP+ creatine P = ATP + creatine ( creatine kinase)
ADP+ADP = ATP + AMP (adenylate kinase)
-this is the idea of the quick top up of ATP , using adenylate kinase and creatine kinase
in the supermouse there was an overxpression of PEP-carboxykinase in muscle , what did this lead to
-low lactate production
-increased FA use
-increased TG in muscles
-more mitochondria
what are the two ways we can generate heat from metabolc processes
1)shivering
2)uncoupled respiration
-thermogenin (UCP1)
-Fatty acyl amino acids
small hibernating animals have brown adipose tissue , what is this
Small hibernating animals have brown adipose tissue
-modified adipocytes which generate heat by wasting energy in store fats
what are the features of brown adipsoe tissue in small animals
-numerous small TG droplets
-more mitochondria
-sympathetic innervation (noradrenaline)
what does brown adipose tissue do
-activates the uncoupling of protein 1 (UCP1)
-leading to the uncoupling of the ETC and ATP synthesis energy is wasted as heat rather than captured at ATP
UCP1 intefers with the normal running of the ETC , explain how -140
-UCP1 allows electrons to come in through a different route , FA bind to UCP1 and allow proteins in , energy is now lost as heat
-thermogenin/UCP1 activated by FFA
-ETC speeds up
-UCP1 exerts into the membrane and allows the protons to come in through a different route
-FA get released and bind to the UCP1 and this opens the channel and lets protons in
-Energy not captured as ATP =now lost as heat , ETC speeds up , rate limiting step of ATP synthase has now gone
what are the features of brown adipose tissue
-numerous small TG droplets
-more mitochondria
-sympathetic innervation (noradrenaline)
what does brown adipose tissue do
-release into the blood of N-acyl amino acid synthase
-joining of fatty acid + amino acid to make an N-acyl amino acid
with brown adipsoe tissue , in the ETC there is the presence of N-acyl AA proton transport , how does this intefer with the electron transport chain-142
-it interferes with the ATP/ADP carrier (translocase)
-There is now an ATP/ADP carrier (translocase ) proton leak
- Acyl amino acid binds to this and alters its shape and allows protons through , creates a gap
-dont get ATP made due to short circuit , energy lot captured , lost as heart and ETC speeds up
DNP is a protonophore that works similarly to uncoupling proteins like UCP1 , explain how it works-142
-move protons across mitochondrial membrane without them going through the ATP synthase
-This is very easily lethal , as it hits every mitochondria so every mitohoncdria releases heat not makes ATP
compre a healthy situation ( the muscle and livers and adipose tissues resposne to insulin) to an insulin resistant situation-143
-In a healthy situation : the muscle liver and adipose tissue are the ones that respond to insulin , muscle will take up glucose , liver will turn it into glycogen and adipose tissue will turn glucose into FA
Insulin resistant situation :
-muscle stops taking up glucose
-liver still takes up glucose , but no limit on it releasing glucose , liver will release glucose even if levels are too high
-only tissue left is adipose tissue which soaks up all of the excess glucose , causes swelling
what are the two types of mutation (inborn errors of metabolism )-144
Types of mutation : point mutations (substitution - change sequence of gene)+ insertion/deletion mutations (can make DNA larger or shorter)
what are the causes of replication : explain normal replication and replication errors
Causes of mutations
-Replication errors-spontaneous:
Normal replication introduces the wrong base once every 10 to the power of 10 base pairs , theres a good chance it will get repaired
-some repetitive regions cause slippage of the polymerase and insertion of more repeats ,gene gets bigger and it cant be repaired
explain tautomeric shifts - spontaneous mutation
Spontaneous - tautomeric shifts
-naturally occurring
–spontaneously rearrange itself
-shifted form binds G instead of A (wrong base is put in on strand)
-not a permanent thing
-each base can change to imino / enol form
-Any mistake will be consolidated on next round of replication (A-C can be detected and repaired )
-MUtation will become a problem if theres another round of replication
-number of hydrogen bonds changed
-145
mutations can either be caused sponatenously or be induced , give examples of each
spontaneous:Replication errors
Tautomerization
Deamination
depurination
induced:
Intercalating agents
Base analogues
Deaminating agents
Alkylating agents
Oxidising agents
Radiation, U/V
explain deamination mutations - spontaneous type of mutation-146
Deamination
-loss of amino group
-changes the base
-number of hydrogen bonds changed
-100 of our C is changed to U per cell per day
C changed to uracil
A changed to inosine
G changed to Xanthine
-All of these should not be in DNA so are recognised and will be repaired
-5-Methyl-C turned to T which cant be repaired , as its a normal base to be present in DNA
explain depurination mutation - spontaneous type of mutation-147
Depurination
-losing the entire part of the nucleotide
-cleavage of base-sugar bond
-end up with an abasic site
-Loss of G from strand , ends up with a random mutation introduced (The A is introduced randomly as theres no base to gte the correct match so cant match with the G)
-10,000 purine in the cell a day are going to experience this
-Mutation consolidated on next replication
describe intercalating agents - mutagen (cause mutations)-147
Intercalating agents-Mutagens
-Insert themselves between bases
-Causes either insertion or deletion
-The insertion will cause a complementary base (G-C)
–Intercalated agent will insert itself and integer with replication process
-intercalated disc = diamond emoji in photo
describe base analogues - type of mutagens -148
-Base analogues
-chemicals that look like normal nucleotides
-do the same thing but arent the same thing
-incorporated into dna
Problem: when it is in DNA its more prone to tautomeric shifts
describe how alkylating agents cause mutations-type of mutagen - 148
Alkylating agents
-add alkyl groups to nucleobases
-chemicals that cause this for example are nitrosamines and Methyl bromide
-Add a methyl group to G and it now pairs to T , which it shouldnt
-Can now form only 2 hydrogen bonds , cant pair to C anymore , side affect is that it speeds up depurination , makes it more likely G will fall off all together
describe how deaminating agents cause mutations -148
-remove Amino acids
-all of the bases lose their amino groups
-far quicker than spontaneous deamination
-Example , nitrous acid made from nitrosamines , nitrite and nitrate
describe how oxidising agents cause mutation-149
Example-superoxide ion , H202
-cause of most mutations
-many possible nucleotide alterations
-base pairs to A instead of G
descrine how radiation , x rays and u/v can cause mutations
-break bonds and create free radicals
-bases on DNA chemically altered , linked or detached
-leading source of mutagens
-number of mutations directly proportional to radiation dose
describe the consequences of mutations
Protein deficiency / excess : because the mutation occurs in a regulatory region of gene ,end up with low/high enzyme activity
Protein dysfunction : because mutation occurs in intron/exon boundary , or mutation in coding region of gene (changes which amino acid it is ) , results in no / low or unregulated enzyme activity
describe the anabolic , catabolic and storage consequences of mutations -149
-Anabolic= cant make something , end up with a deficiency
-catabolic = lose ability to get rid of something , metabolite F builds up , excess of metabolite F
-Storage = cant breakdown stores ,cellular deposits of macromolecule X (build up ) but also have a deficiency of monomers but monomers arent made
alkaptonuria is an inborn error of metabolism , describe the colour of the urine and why
Inborn errors of metabolism (IEMS)
-First inborn error of metabolism : alkaptonuria
-Loss of an enzyme leads to a build-up of a metabolite which is excreted in the urine
-urine turns black on exposure to air
phenylketonuria is an inborn error of metabolism , describe this -150
PKU= excess / build up of phenyl-ketones in urine
-Enzyme affected Phenylalanine Hydroxylase
-normally phe converted to Tyr
-Phe builds up if not converted to Tyr
-Phe goes into blood , blood levels go up
-Liver will attempt to convert phe to phenyl pyruvate and then from that the other molecules (blue ) which can be lost in urine
-recessive disorder
-comes in various types , most due to point mutations
-40% in intron/exon splice sites
-20% of mutations found in coding regions
-Other PKU( types 4 and 5 ) are not due to PAH , theyre due to dihydropteridine reductase
IEMS:phenylketonuria (PKU)
-Disease progress
-PKU manifests after birth
-During pregnancy mother breaks down Phe
-Neonate develops hyperphenylalaninemia after a few days of eating protein
Consequences : mental retardation , organ damage , unusual posture
-Sufferer just be put on a low phenylalanine diet
glycogen storage disease is an example of an inborn error of metabolism , what is meant by this
-14 different types : autosomal recessive
-various enzymes known to be affected: phosphorylase , debranching enzyme , branching enzyme
-inability to convert glycogen to glucose (cant use glycogen stores)
Consequences : enlarged liver (glycogen builds up in liver ) and hypoglycemia
glycogen storage disease- GSD1 von gierke disease is an example of an inborn error of metabolism , what is meant by this
Absence of glucose-6-phosphate = no glucose released into the blood
Appears in early childhood
Sweating , poor growth , muscle weakness
Treatment: regular glucose drinks
Naso-gastric drip overnight
glycogen storage disease- GSD V McArdle disease is an example of an inborn error of metabolism , what is meant by this
Absence of phosphorylase in muscle = no glycogen usage by muscles
Basically normal , except when exercising
Pain in muscles due to damage in muscles ; urine looks like wine due to breakdown of muscle
list the order of cytochrome x oxidase, NADH-Q reductase , Q-cytochrome c oxidoreductase , cytochrome C and ubiquinone
NADH-Q reductase (Complex I): Electrons are first donated by NADH to NADH-Q reductase (Complex I). This complex transfers the electrons to ubiquinone (CoQ) and pumps protons across the inner mitochondrial membrane.
Ubiquinone (CoQ): Ubiquinone (CoQ) is a mobile electron carrier that picks up electrons from Complex I (or Complex II) and carries them to the next complex, Q-cytochrome c oxidoreductase (Complex III).
Q-cytochrome c oxidoreductase (Complex III): Q-cytochrome c oxidoreductase (Complex III) receives electrons from ubiquinone and passes them to cytochrome c while also pumping protons across the membrane.
Cytochrome C: Cytochrome C is a small, soluble protein that shuttles electrons from Complex III to cytochrome c oxidase (Complex IV).
Cytochrome C oxidase (Complex IV): Cytochrome c oxidase (Complex IV) receives electrons from cytochrome c and transfers them to molecular oxygen (O₂), reducing it to water (H₂O). This step also pumps protons across the membrane.
name the 3 irreversible steps in glycolysis
Hexokinase/Glucokinase (Step 1):
Reaction: Glucose → Glucose-6-phosphate (G6P)
This step is irreversible because it involves the phosphorylation of glucose, which traps it inside the cell and commits it to glycolysis. It consumes one ATP molecule.
Phosphofructokinase-1 (PFK-1) (Step 3):
Reaction: Fructose-6-phosphate → Fructose-1,6-bisphosphate
This is a key regulatory step in glycolysis. The enzyme phosphofructokinase-1 (PFK-1) is highly regulated and commits the intermediate to continue through glycolysis. This step also consumes one ATP molecule.
Pyruvate Kinase (Step 10):
Reaction: Phosphoenolpyruvate (PEP) → Pyruvate
This is the final step in glycolysis, where ATP is generated. The conversion of PEP to pyruvate is irreversible and is catalyzed by pyruvate kinase. This step produces one ATP and one pyruvate molecule.
ranks the lipoproteins , chylomicron, LDL,HDL,VLDL,IDL in order from smallest to largest
HDL (High-Density Lipoprotein) – Smallest and densest
LDL (Low-Density Lipoprotein)
IDL (Intermediate-Density Lipoprotein)
VLDL (Very Low-Density Lipoprotein)
Chylomicron – Largest and least dense
rank the following in terms of physical size , triglyceride , FA , glycerol , glycogen , glucose smallest to largest
Glucose – Smallest
Fatty Acid (FA)
Glycerol
Triglyceride
Glycogen – Largest
whic of the following can be converted to acetylc CoA to access energy within them : palmitic acid,glycerol,ornithine,ethanol,aspartate,acetooectate
palmitic acid,glycerol,ethanol,acetoaetate
match the lipase to the molecule it acts on MAG , TAG DAG to hormone sensitive lipase , adipose triglercide lipase and monoglyceride lipase
Hormone-Sensitive Lipase (HSL):
Acts on TAG (Triacylglycerol)
Hormone-sensitive lipase is primarily responsible for breaking down triacylglycerols (TAGs) into diacylglycerol (DAG) and free fatty acids (FFAs) in adipose tissue in response to hormonal signals, especially during periods of fasting or exercise.
Adipose Triglyceride Lipase (ATGL):
Acts on TAG (Triacylglycerol)
Adipose triglyceride lipase acts primarily on triacylglycerols (TAGs), breaking them down into diacylglycerol (DAG) and a free fatty acid. It’s a key enzyme in the initial step of lipolysis in adipocytes.
Monoglyceride Lipase (MGL):
Acts on DAG (Diacylglycerol) and MAG (Monoglyceride)
Monoglyceride lipase acts on diacylglycerol (DAG), converting it to monoglyceride (MAG), and then it can further break down monoglycerides (MAGs) into glycerol and free fatty acids (FFAs).
