Cell Metabolism Flashcards
What are the types of reactions? (6)
Oxidation reduction
Ligation requiring ATP cleavage
Isomerization
Group transfer
Hydrolytic
Addition or removal of functional groups
What is an oxidation reduction reaction?
electron transfer
What is a ligation requiring ATP cleavage reaction?
Formation of covalent bonds (e.g., C-C bonds)
What is an isomerization reaction?
Rearrangement of atoms to form isomers
Usually isomerase enzyme
What is a group transfer reaction?
Transfer of a functional group from one molecule to another
Usually a kinase enzyme e.g., hexokinase
What is a hydrolytic reaction?
Cleavage of bonds by the addition of water
What is an addition or removal of functional groups reaction?
Addition of functional groups to double bonds or their removal to form double bonds
What does glycolysis produce?
2 x Pyruvate
2 x NADH
2 x Net ATP (4 made 2 used)
What reaction is irreversible and commits the cell to glycolysis?
The conversion of glucose to glucose - 6 - phosphate
What is the complete reaction steps of glycolysis?
Glucose
Glucose - 6 - Phosphate
Fructose - 6 - Phosphate
Fructose - 1,6 - Bisphosphate –> dihydroxyacetone phosphate and
Glyceraldehyde - 3 - Phosphate
1,3 - Bisphosphoglycerate
3 - Phosphoglycerate
2 - Phosphoglycerate
Phosphenolpyruvate
Pyruvate
How does glucose to glucose-6-phosphate?
Group transfer
Hexokinase
ATP-> ADP
forms H+ asw
How does glucose-6-phosphate go to fructose-6-phosphate?
Isomerisation
phosphoglucose isomerase
What is special about fructose?
It can be split into equal halves when cleaved
How does fructose-6-phosphate go to fructose-1,6-bisphosphate?
Group transfer
phosphofructokinase
ATP-> ADP
How does phosphofructokinase use ATP?
uses it to attach phosphate to fructose-6-phosphate which makes biphosphate
Which step of glycolysis does phosphofructokinase control?
The conversion of fructose - 6 - phosphate into fructose - 1,6 - bisphosphate
How does fructose-1,6-bisphosphate fo to glyceraldehyde-3-phosphate and dihydroxyacetone phosphate?
Hydrolytic reaction
Aldolase
Glyceraldehyde-3-phosphate can progress through glycolysis
Dihydroxyacetone cannot
They are both high E compounds
How does dihydroxyacetone phosphate go to glyceraldehyde-3-phosphate?
Isomerisation
Triose phosphate isomerase (TPI)
Why is deficiency in Triose phosphate isomerase fatal?
RBCs in brain would suffer most because only half of your input of ATP would be there/ consumed ATP
How does glyceraldehyde-3-phosphate go to 1,3-bisphosphoglycerate?
Redox and group transfer
Glyceraldehyde 3-phosphate dehydrogenase
NAD+ +Pi –> NADH
How does 1,3-bisphosphoglycerate go to 3-phosphoglycerate?
Group transfer
Phosphoglycerate kinase
ADP–> ATP
(remember at this stage its x2 as its split)
How does 3-phosphoglycerate make 2-phosphoglycerate?
Isomerisation
Phosphoglycerate mutase
How does 2-phosphoglycerate make phosphoenolpyruvate?
Group removal/ dehydration
Enolase
How does phosphoenolpyruvate make pyruvate?
Group transfer
Pyruvate kinase
ADP-> ATP
transfer of high E phosphate to ADP
What is the only glycolytic enzymopathy which is fatal?
Deficiency in TPI
Which reactions produce ATP in glycolysis?
The conversion of 1,3-Bisphosphoglycerate into 3-phosphglycerate and phosphenolpyruvate into pyruvate
What do kinases do?
Transfer phosphate groups to molecules
Which step in glycolysis needs NAD+?
Glyceraldehyde - 3 - phosphate into 1,3 - bisphosphoglycerate
Which steps of glycolysis require ATP?
Glucose -> glucose - 6 - phosphate
Fructose - 6 - phosphate -> Fructose - 1,6 - bisphosphate
Does glycolysis need oxygen to occur?
No - it is anaerobic
Where does glycolysis occur?
In the cytoplasm
Why are high energy phosphate groups added to some of the substrates involved in glycolysis?
Adding the phosphate groups makes them easier to split as they are more reactive
What are the three fates of pyruvate?
- Lactate generation
- Acetyl CoA Production
- Alcohol fermentation
What enzyme is needed to generate Acetyl CoA from pyruvate?
Pyruvate dehydrogenase complex
What occurs during alcohol fermentation?
Pyruvate->acetaldehyde (via pyruvate decarboxylase H+-> CO2)
acetaldehyde-> ethanol (via alcohol dehydrogenase NADH + H+ -> NAD+)
This is a characteristic of yeasts and can occur under anaerobic conditions
What does pyruvate dehydrogenase complex needed as a cofactor?
Thiamine pyrophosphate
It readily loses a proton and resulting carbanion attacks pyruvate
What does a deficiency in thiamine result in?
Beri - Beri
This is a condition which leads to muscle weakness
impaired dehydrogenation of pyruvate
What are the symptoms of beri-beri syndrome?
damage to PNS, weakness of the musculature and decreased cardiac output
The brain is particularly vulnerable as it relies heavily on glucose metabolism
How is pyruvate converted into lactate?
Using lactate dehydrogenase complex
What is lactate generation?
Anaerobic and is a characteristic of mammalian muscle during intense activity when O2 is a limiting factor.
What does the fermentation of alcohol and lactate production both regenerate?
NAD+ - this is needed for glycolysis to continue occurring (by NADH + H+-> NAD+)
In condition of oxygen deprivation
How long does ATP work in muscles?
The amount of ATP needed during exercise is only enough to sustain contraction for around 1 second
What is the role of creatine phosphate?
It is a large reservoir of creatine phosphate and buffers the demands for phosphate (25mM creatine phosphate c.f. 4mM ATP in resting muscle)
Reservoir of phosphate groups to make ATP
creatine phosphate –> <– creatine + ATP (via creatine kinase)
buffers ATP concentrations
How pyruvate make acetyl CoA?
pyruvate + HS-CoA–> acetyl CoA + CO2
via pyruvate dehydrogenase complex
NAD+ –> NADH
This is a series of reactions in the mitochondria of the cell. The acetyl CoA thus formed is committed to entry into the TCA cycle.
What is special about Acetyl CoA?
Has a high E bond (ester linkage) between C-S
Acetyl CoA can enter TCA CYCLE
What happens to the Acetyl CoA that is produced?
It enters into the Krebs Cycle
What are the stages of the Krebs Cycle?
Acetyl CoA combines with oxaloacetate to make Citrate
Then Alpha - keto glutarate
Succinyl CoA
Succinate
Fumerate
Malate
What does one turn of the Krebs cycle produce?
2 x CO2
1 x GTP
3 x NADH
1 x FADH
Are the kreb’s cycle enzymes soluble?
Yes, except 1
they are located in the mitochondrial matrix space
When is the bulk of ATP generated?
when the reduced coenzymes are re-oxidised with the help of oxygen (aka oxidative phosphorylation)
What reaction in the Krebs cycle produces FADH2?
The conversion of succinate to fumerate
When is NADH + H+ formed in the Krebs cycle?
isocitrate -> alpha-ketoglutarate (also makes CO2)
alpha-ketoglutarate -> succinyl CoA (also makes CO2)
malate-> oxaloacetate
When is GTP formed in the krebs cycle?
succinyl CoA to succinate
Where does the krebs cycle occur?
The mitochondrial matrix
What is the order of the Krebs cycle? 8 steps…
Acetyl CoA (2C) enters the krebs cycle and reacts with oxaloacetate (4C) to from citrate (6C)
Citrate (6C)
Isocitrate (6C)
alpha-ketoglutarate (5C)
Succinyl CoA (4C)
Succinate (4C)
Fumerate (4C)
Malate (4C)
Oxaloacetate (4C)
What is a transamination reaction?
the process of removing an amine group from one amino acid and transferring it to a ketoacid, producing another ketoacid and amino acid
What are the seven things which can be produced from transamination reactions?/ What are the only 7 molecules that can be made by the degradation of all 20 AA?
Pyruvate
Succinyl CoA
Acetoacetyl CoA
Acetyl CoA
Oxaloacetate
Alpha Keto Glutarate
Fumerate
What is the general strategy of AA degradation?
remove the AA group (which is excreted as urea) whilst the carbon skeleton is either funnelled into the production of glucose or fed into the TCA cycle
Why is it essential that NAD+ is regenerated?
Needed for dehydrogenation of glyceraldehyde-3-phosphate to produce ATP
Allows glycolysis to occur anaerobically
What is the Warburg effect?
Mutations in TCA genes of Fumerase, Succinate Dehydrogenase, Isocitrate Dehydrogenase, decreases Kreb’s Cycle activity which enhances anaerobic glycolysis
- the preferential generation of lactate from glucose even under conditions of ample O2
What are glucogenic amino acids?
Ones whose carbon skeletons are used to make glucose
What are ketogenic amino acids?
Amino acids which when they are broken down, form ketone body precursors like Acetyl CoA
What are the glucogenic AA and what do they make?
Alanine, Cysteine, Glycine, Serine, Threonine, Tryptophan= pyruvate
Asparagine, Aspartate= oxaloacetate
Aspartate, Phenylalanine, Tyrosine= Fumarate
Isoleucine, Methionine, Threonine, Valine= succinyl CoA
Arginine, Glutamate, Glutamine, Histidine, Proline= alpha-ketoglutarate
How does alanine form pyruvate?
Alanine metabolism
Alanine undergoes transamination by the action of the enzyme alanine aminotransferase
alanine + alpha-ketoglutarate-> pyruvate + glutamate
How is glutamate re-converted to alpha-ketoglutarate?
via glutamate dehydrogenase
this generates NH4+ which is ultimately converted to urea
During fasting, which type of metabolism dominates?
fat metabolism, resulting in the production of ketone bodies
What happens when the levels of Acetyl CoA is not equal to Oxaloacetate?
The excess Acetyl CoA is used to make ketone bodies
What are the names of the three ketone bodies?
Acetone, Acetoacetate and 3 - Beta - Hydroxy Butyrate
Why can ketone bodies be utilised by the brain but fatty acids cannot?
Fatty acids can’t cross the blood brain barrier
What is the purpose of the Glycerol Phosphate Shuttle
To carry electrons from NADH across the matrix - this is because the mitochondrial matrix is impermeable to NADH
Where in the body is the Glycerol-Phosphate Shuttle used?
brain and skeletal muscle
Explain how the Glycerol-Phosphate Shuttle works
Cytosolic glycerol-3-phosphate dehydrogenase transfers electrons from NADH to DHAP to generate Glycerol-3-Phosphate
A membrane bound form of the same enzyme transfers the electrons to FAD
The FADH2 electrons are then passed onto coenzyme Q which is in the electron transport chain
Where in the body is the Malate-Aspartate Shuttle used?
Liver, kidney and the heart
Outline the processes in the Malate-Aspartate Shuttle
What reactions are happening in the malate-aspartate shuttle?
REDOX and transamination
What are the transamination reactions in the malate-aspartate shuttle?
glutamate + oxaloacetate–> alpha-ketoglutarate + aspartate
How many ATP do you get from NADH and FADH2?
3 ATP from NADH
2 ATP from FADH
From their re-oxidation of the reduced cofactors by the process of oxidative phosphorylation
What are the two main concepts of glycolysis?
The formation of a high energy compound, and the splitting of this compound
Why is the generation of NADH useful?
NADH is generated here which can be later used to generate yet more ATP within the mitochondria in a process known as oxidative phosphorylation
How is creatine used by athletes?
As a dietary supplement
How is Acetyl CoA able to donate the acetate group (2C) to other molecules?
The thioester linkage which it contains is a high energy linkage so is readily hydrolysed
Mutations in which TCA genes have been shown to decrease TCA activity and enhance aerobic glycolysis?
Isocitrate dehydrogenase
Succinate dehydrogenase
Fumerase
How many ATP does the TCA cycle give?
12= 3xNADH + 1xFADH + 1xGTP
What is the name of the process of fatty acid metabolism?
Beta oxidation
How much of your body’s energy needs come from? (including liver, not the brain)
fatty acid oxidation (enhanced over long periods of fasting)
where does beta oxidation occur?
In the mitochondria
What is the general formula of beta-oxidation of fatty acids?
How are fatty acids converted into an Acyl CoA Species?
Using Acyl CoA synthetase
Where does the generation of Acyl CoA occur?
In the outer mitochondrial membrane
What is the name of the shuttle used to transport Acyl CoA species into the matrix?
Carnitine shuttle
Describe how the carnitine shuttle works?
Acyl CoA is coupled to the molecule carnitine to form acyl carnitine - this is done using an enzyme carnitine acyltransferase 1
The acyl carnitine is then shuttle across the membrane via translocase
The acyl Carnitine is then converted back into carnitine and Acyl CoA via carnitine acyltransferase II
What is used as a supplement when you have primary carnitine deficiency?
Carnitor / levocarnitine
What type of deficiency is primary carnitine deficiency?
Autosomal recessive disorder
What are some symptoms of primary carnitine deficiency?
encephalopathies, cardiomyopathies, muscle weakness; and hypoglycaemia
symptoms appear during infancy or early childhood
Describe the mutations involved in primary carnitine deficiency?
Mutations in a gene known as SLC22A5 which encodes a carnitine transporter result in reduced ability of cells to take up carnitine, needed for the β-oxidation of fatty acids.
What are the four reactions in Beta-oxidation?
oxidation, hydration, oxidation and thiolysis
What does one cycle of beta oxidation result in?
The production of Acetyl CoA and an Acyl CoA species which is 2 carbons shorter than the original
Write the overall equation for the Beta-Oxidation of palmitoyl CoA?
palmitoyl CoA + 7 FAD + 7 NAD+ + 7 H2O + 7 CoA —-> 8 acetyl CoA + 7 FADH2 + 7 NADH
(the b oxidation reactions continue to consecutively remove 2C units from the acyl CoA thereby producing acetyl CoA)
On the final cycle (4C fatty acyl CoA intermediate), 2 acetyl CoA molecules are formed
From just 7 b-oxidation reactions, the 16 carbon palmitoyl CoA molecule produces 8 molecules of acetyl CoA
During each cycle one FADH2 and one NADH are produced
What happens to the acetyl CoA generated through beta-oxidation?
Enters the TCA cycle only if Beta oxidation and carbohydrate metabolism are balanced, as oxaloacetate is needed for entry. Hence the saying “fat burns in the flame of carbohydrate”
What does Acetyl CoA form during fasting/ when fat breakdown predominates?
D-3-hydroxybutyrate, Acetone and Acetoatcetate (collectively known as ketone bodies)
What is fatty acid biosynthesis known as?
Lipogenesis
What are the two enzymes involved in fatty acid biosynthesis/ lipogenesis?
Acetyl CoA Carboxylase and fatty acid synthase
Following each round of elongation, what occurs to the fatty acid in lipid biosynthesis?
undergoes reduction and dehydration by the sequential action of ketoreductase (KR), dehydratase (DH) and enol reductase (ER) activity
What are the key difference between fatty acid synthesis and degradation? (carriers, reducing power, locations)
Degradation: CoA is carrier, FAD/ NAD+ is reducing power, in mitochondrial matrix
Synthesis: Acyl carrier protein, NADPH, Cytoplasm
During lipogenesis, what is the growing fatty acid group linked to?
An Acyl carrier protein
What is the overall reaction of lipogenesis, to form Palmitate?
Acetyl CoA (C2) + 7 Malonyl CoA (C3) + 14 NADPH +14 H+
—-> Palmitate (C16) + 7 CO2+ 6 H2O + 8 CoA-SH + 14 NADP+
Elongation of the acyl group to make fatty acids longer than 16C occur where?
Occurs separately from palmitate synthesis in the mitochondria and endoplasmic reticulum (ER)
What does the desaturation of fatty acids required?
the action of fatty acyl-CoA desaturases
What is the enzyme that creates oleic acid and palmitoleic acid from stearate and palmitate, respectively called?
∆-9 desaturase
As it generates a double bond nine carbons from the terminal carboxyl group
In adults where is de novo Faty acid biosynthesis restricted to?
The liver, adipose tissue and lactating breasts
Can reactivation of fatty acid synthesis occur in certain cancer cells, and give an example of inhibition of this.
Yes, evidence suggests it can
Leads to Q of “can we selectively target FA synthetase in cancer?”
Inhibition of FASN by cerulenin shown to reduce tumour growth of ovarian cancer cells
What is meant by Acyl-CoA-dehydrogenase specificity?
Each acyl-CoA-dehydrogenase can bind a fatty acid chain of varying lengths
What are the families of acyl-CoA-dehydrogenases?
Short chain acyl-Co enzyme A dehydrogenase (<6C)
Medium chain acyl-Co enzyme A dehydrogenase (C6-C12)
Long chain acyl-Co enzyme A dehydrogenase (C13-C21)
Very long chain acyl-Co enzyme A dehydrogenase (>22C)
What is MCADD?
Medium chain Acyl CoA dehydrogenase deficiency
- disorder of fatty acid metabolism, can be treated with lifestyle
- if undiagnosed can be fatal
- autosomal recessive
What are the lifestyle adaptations of MCADD?
- A high carbohydrate diet
- Never go without food for longer than 10-12 hours (typical overnight fast)
What must patients with MCADD need it their illness manifests as apetite loss or severe vomiting?
i.v glucose to make sure their body is not dependant on fatty acids for energy
How are fats stored in the adipocytes?
As triglycerides
What are triglycerides broken down into?
glycerol and fatty acids using lipase
How many ATP does the generation of the Fatty Acyl CoA need?
2
What is the net gain of ATP per molecules of palmitoyl?
129 ATP
How much ATP is formed overall by glucose metabolism?
8 from glycolysis
6 from TCA/ krebs cycle
24 from oxidative phosphorylation
How many NADH and FADH2 does beta oxidation produce?
1 of each
