Metabolism Flashcards
What is the key purpose of glycolysis
- Employed by all tissues for glucose oxidation to provide energy (ATP)
With an adequate supply of oxygen (+mitocondria)…
- Pyruvate is the end product
- Aerobic glycolysis as O₂ required to reoxidise NADH
- Oxidative decarboxylication of pyruvate to acetyl-CoA (which is then used in the TCA cycle)
Without an adequate supply of oxygen (+mitocondria)…
- Anaerobic glycolysis
- Pyruvate is reduced to lactate as NADH reoxidised
How can glucose enter cells as it is two large to diffuse
There are two methods:
* Na⁺ - independent facilitated diffusion transport
* ATP-dependent Na⁺-monosaccharide transport
Describe the process of Na⁺-independent facilitated diffusion
- Glucose moves via concentration gradient
- Glucose bind to the GLUT transporter and is moved through the membrane
- These transporters exhibit tissue-specific expression (GLUT 1-14)
- This type of transport relies on there being a concentration gradient (e.g. not possible for cells with a large amount of glucose within them)
Describe the process of ATP-dependent Na⁺-monosaccaride transport system
- A co-transport system
- Transports glucose against a concentration gradient (coupled to Na⁺ gradient)
- Found in intestinal epithelial cells
Conversion of glucose to pyruvate occurs in two stages, what are they?
- The energy investment phase (first 5 reactions): phosphorylated forms created using ATP
- Energy generation phase
What is the first step of glycolysis and why does it occur
Phosphorylation of glucose
Phosphorylated sugar molecules don’t cross cell membranes easily
irreversible phosphorylation of glucose traps it in cytosol and commits it
What is the enzyme that catalyses the reaction of glucose phosphorylation?
What type of enzyme is it?
What it its Km and Vmax like?
Hexokinase (l-lll)
Allosterically regulated enzyme of glycolysis (can be inhibited by glucose-6-phosphate)
Low Km (high affinity for glucose)
Low Vmax (means no overabundance of glucose-6-phosphate)
What is Glucokinase and how does it relate to the consumption of different foods
- Glucokinase is a form of Hexokinase (iv)
- It has a high Km (low affinity) so only active following consumption of carb-rich meals
- High Vmax allowing glucose delivered to liver to be maximally absorbed
What is the second step of glycolysis
- Isomerisation of glucose-6-phosphate to fructose-6-phosphate
- Catalysed by phosphoglucose isomerise
- Readily reversible + not rate limiting
What is the 3rd step of glycolysis
- Another phosporylation
- Fructose-6-phosphate is phosphorylsed to form Fructose-1,6-bisphosphate
- Irreversible reaction
- Catalysed by phosphofructokinase-1
- Most important control point
In step no3 of glycolysis, where Fructose-6-phosphate is phosphorylate, why is this considered an important control step
Because the enzyme phosphofructokinase-1 (PFK-1) is controlled by ATP and allosterically through fructose-6-phosphate
* High amount of ATP will cause inhibition of step 3, as it indicates high amount of energy available
* High amount of AMP will cause activition as ATP has be dephosphorylated - energy deficition
Also inhibited by citrate from the TCA, as high amount of this indicate a lot of energy
What happens in steps 4 and 5 of glycolysis
- Aldolase cleaves fructose-1,6-bisphosphate to form Dihydroxyacetone phosphate (DHAP) and Glyceraldehyde-3-phosphate
- Reversible and unregulated
- Triose phosphate isomerise allows interconversion of DHAP to form Glyceraldehyde-3-phosphate
What other cellular process is Dihydroxyacetone phosphate (DHAP) involved in
Triacylgycerol synthesis
As only glyceraldehyde-3-phosphate (GAP) can be used in glycolysis)
What happens in step 6 in glycolysis
- Oxidation-reaction reaction: adds a phosphate group and removes two electrons forming NADH
- Two molecules of glyceraldehyde-3-phosphate are converted into 1,3-bisphosphoglycerate (1,3-BPG) using glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
- Drives the synthesis of ATP in the next reaction
What happens in step 7 of glycolysis
- Substrate-level phosphorylation
- Forms** two 3-phosphoglycerate** from two 1,3-bisphosphoglycerate and two molecules of ATP
- The ATP produced replaces the ATP consumed earlier
- Catalysed by physiologically reversible enzyme
What happens in step 8 of gylcolysis
- Forms 2-phosphoglycerate
- Phosphoglycerate mutase shifts the phosphate from carbon 3 to 2
- Reversible reaction
What happens in step 9 of glycolysis
- Forms Phosphoenolpyruvate
- Enolase redistributes the energy within the molecule by dehydration
- Reversible reaction
- Creates a high energy intermediate
What happens in step 10 of gylcolysis
- Forms pryuvate
- Catalysed by pryuvate kinase
- Irreversible reaction of glycolysis
- Substrate level phosphorylation forming two molecule of ATP
- Links with the Fructose-1,6-bisphosphate to regulate the speed of this reaction
What is TARU disease
Where phosphofructokinase-1 isn’t functioning optimally, so sufferers tend to utilise the build up of metabolites before phosphofructokinase-1 and they end-up creating a large amount of glycogen
Glycogen storage disease
How is Haemolytic anemia related to glycolytic enzyme deficiencies
- Deficiencies in pryuvate kinase, which impact RBC mortality
- RBC are biconcave, where the shape is dependent on the ability to maintain the activity of iron pumps
- Without this the RBC change shape, there is failure to generate ATP and phagocytosis of RBC will occur
- Suffers require regular transfusions
Pyruvate is the product of glycolysis
Without the presence of oxygen (+mitocondria) anerobic respiration occurs, how?
(This most likely occurs in RBC, testes and respiring muscle, cornea)
- Pyruvate is reduced to lactate by lacatate dehydrogenase
- Lactate dehydrogenase reaction direction depends on metabolite concentration + NADH/NAD⁺ ratio (low ratio casues latate to be oxidise e.g. in liver)
What are the 3 likely outcome for pyruvate
- Oxidiative decarboxylation into Acetyl CoA (Pyruvate dehydrogenase): major fuel for TCA cycle + fatty acid synthesis
- Carboxylated to oxaloacetate (Pyruvate carboxylase): Replenishes TCA cycle intermediates + substrate fpr gluconeogenesis
- Reduced to ethanol (yeast)
How can the regulation of those 3 outcomes be controlled in the short-term
Short-term regulation (mins/hrs) by allosteric activation/deactivation
phosphorylation/dephosphorylation of kinases
How can the regulation of those 3 outcomes of pryuvate be controlled in the long-term
Hormones can determine the amount of enzyme produced effecting the amount of pryuvate formed
e.g. if there is a sudden increase in carbs in a diet, increase transcription of glucose kinase/pryuvate kinase etc
The TCA cycle is the next stage
What does TCA stand for
Tricarboxlic Acid Cycle
Also know as ‘Critic Acid Cyle’ or ‘Krebs Cycle’
The TCA cycle is the next stage
What does TCA stand for
Tricarboxlic Acid Cycle
Also know as ‘Critic Acid Cyle’ or ‘Krebs Cycle’
What are the roles of the TCA cycle
- Where oxidative catabolism of carbohydrates, amino acids, and fatty acids converge
- Produces most of the ATP found in Humans
- Supplies intermediates for synthetic reactions (e.g. heme)
Where does the TCA cycle occur?
What is the main function of it for the production of energy?
What does it require?
Occurs in the Mitocondria (close to the ETC)
Allows oxidation of NADH and FADH₂
Requires Oxygen
Glycolysis occurs within the cytosol, then the product pyruvate must be transported into the mitocondria by a transporter
What happens next?
Pryuvate is then coverted to acetyl CoA by the pyruvate dehydrogenase complex
PDH complex is aggregate of 3 enzyme types
What are they
- Pyruvate carboxylase
- Dihydrolipoyl transacetylase
- Dihydrolipoyl dehydrogenase
What is Leigh syndrome
Mutations in the Pyruvate dehydrogenase complex (PDH)
Progressive neurological disorder
Defects in mitocondrial ATP production
What happens within the first step of the TCA cycle
- In the first reaction oxaloacetate is first condensed with an acetyl group from acetyl coenzyme A
- This forms Critrate
- Catalysed by Citrate synthase
- Reaction is regulated by product and substrate (allosteric regulation)
- Equilibrium favour the forwards reaction
What happens in the second step of the TAC cycle
- Citrate is isomerised to form Isocitrate
- Catalysed by Aconitase
What happens in the 3rd step of the TAC cycle
- Isocitrate is oxidised + decarboxylated to form α-Ketoglutarate
- Catalysed by Isocitrate dehydrogenase (encoraged by ADP)
- Irreversible = rate limiting
- Yeilds NADH
- Releases CO₂
What happens in step 4 of the TAC cycle
- α-ketoglutarate is oxidatively decarboxylared forming Succinyl-CoA
- Catalysed by α-ketoglutarate dehydrogenase complex
- Produces NADH + CO₂
- Equilibrium favours the forward reaction
What happens in step 5 of TAC cycle
- Succinyl Co-A is cleaved at the high-energy thioester bond forming Succinate
- Catalysed by Succinate Thiokinase
- Substrate level phosphorylation of GDP, which is then interconverted to ATP by nucleoside diphosphate kinase
What happens in Step 6 of the TCA cycle
- Succinate is oxidised to fumarate
- Catalysed by Succinate dehydrogenase
- FAD is reduced to FADH₂
What happens in Step 7 of the TCA cycle
- Fumarate is hydrated to Malate
- Catalysed by Fumerase
- Reversible reaction
What happens in Step 8 of the TCA cycle
- Malate is oxidised to oxaloacetate
- Catalysed by malate dehydrogenase
- Produces final NADH
- Needs an input of energy (endgergonic)
What is the overall output of the TCA cycle
2 carbon atom enter as Acetyl Co-A (and leave as CO₂)
3 NADH and 1 FADH₂ are formed
How is the TCA cycle controlled
It is controlled by serveral enzyme:
* Citrate synthase
* Isocitrate dehydrogenase
* α-ketoglutarate dehydrogenase complex
How many ATP are producer per molecule of NADH and molecule of FADH₂
- 3 ATP per NADH
- 2 ATP per FADH₂
What is Metabolism
- Is the process by which living systems acquire + use free energy in order to carry out their functions
What are the two tradition divisions of metabolism
Catabolic and Anabolic
What is the difference between catabolic and anabolic metabolism
- Catabolic: The degradation of nutrients to salvage componets + gain energy (using carbs, fats + proteins)
- Anabolic: The synthesis of biomolecules from simpler componets (forming biological molecules)
Metabolism involves many highly complicated reaction, what, however, are the two main principles that govern them all?
- Common evolutionary origin
- Laws of Thermodynamics
What are Autotrophs?
What are the two types of autotrophs?
Autrotrophs: Synthesise all cellular componets from simple molecules
Two types: Photoautotrophs and Chemolithotrophs
What is a Photoautotroph
Photoautotrophs: use light energy to produce carbohydrates which are oxidised giving free energy
What is a Chemolithotrophs
Obtain free energy from inorganic compound oxidation (NH₃, H₂S)
What are Heterotrophs
Oxidise carbohydrates, lipids and proteins (gained from other ‘trophs’)
Obligate aerobes use what for oxidation?
Oxygen
Anerobes use what as oxidising agents
Sulfate or nitrate
What two things bar oxygen are needed by obligate aerobic heterotrophs
- Macronutrients (lipids, carbs and proteins)
- Micronutrients to help with metabolism of breakdown products: including vitamins (organic molecules obtained from diet) and minerals (ions)
As well as polysaccharides, what else can enter into glycolysis or TAC cycle at different points
Proteins and Triglycerols
They are known as degradative pathways
What is a biosynthetic pathways
They carry out the opposite of a degradative pathway
What are the benefits of enyzmes in metabolism reactions
- Without enzymes metabolic reactions would occur far to slowly
- Specificity prevents useless or toxic product formation
- Couples endergonic reaction with energetically favourable reactions
What are the 4 types of reactions seen in metabolism reactions?
- Oxidation + Reduction
- Group transfer reactions
- Eliminations, isomerisations + rearrangements
- Carbon-Carbon bond breakage
Some reactions have a -ΔG
What does this mean
The reaction is spontaneous and favourable
Some reactions have a ΔG = 0
Meaning?
This reaction is at equilibrium
Some reactions have a ΔG = 0
Meaning?
This reaction is at equilibrium
Some metabolic reactions are highly spontaneous (-ΔG) some are not
What is the benefit of this
Enzymes can coupled these reactions together and the energy for one can provide the energy for another
Oxidative metbolism proceeds in a step-wise fashion
What is the benefit of this?
- Released energy can be recovered at each exergonic step
- This energy is conserved as ‘high-energy’ intermediates
Give some examples of cellular energy currency
- Thioester bond-containing compounds
- Reduced coenzymes
- ATP
What is a co-enzyme
As metabolic fuels are oxidised to CO₂, electrons are transferred to molecular carriers. Often in oxidation-reduction reactions
Which are the most common two co-enzyme (electron carriers)
- Nicotinamide Adenine Dinucleotide (NAD⁺)
- Flavin Adenine Dinucleotide (FAD)
Explain the reaction to convert NAD⁺ in its oxidised form into NADH in its reduced form
NAD⁺ + 2H⁺ + 2e⁻ → NADH + H⁺
Explain the reaction to convert FAD in its oxidised form into FADH₂ in its reduced form
FAD + + 2H⁺ + 2e⁻ → FADH₂
The energy in ATP comes from
ATP’s biological importance depends on the free energy change that accompanies cleavage of the phosphoanhydride
Where is the electron transport chain located
Inner mitocondrial membrane
In an overview, however is ATP synthesised in the electron transport chain
- Reduced co-enzyme can donate electrons pairs to electron carriers in the Electron transport chain located in the inner mitocondrial membrane
- As the electrons pass down the ETC, they loose free energy
- Used to move protons across the inner mitocondrial membrane
- Creates a proton gradient which drives ATP synthesis from ADP and Pi
The inner mitochondrial membrane contains how many protein complexes
5 separate protein complexes
Complexes l, ll, lll , lV, V
There are two mobile electron carrier
What are they called?
- Coenzyme Q
- Cytochrome C
What is the use of oxygen in the electron transport chain
Oxygen is the terminal electron acceptor, where they combine to form water
This accounts for the greatest porption of the body’s oxygen use
What happens at complex l
- NADH binds to the complex and electrons are transferred to CoQ
- Electrons energy is lost, as it is used to pump 4 protons across the inner membrane
What are the two used of complex ll
- Accepts electrons from FADH₂ and transfers them to CoQ via Fe-S proteins
- No energy is lost, hence no protons are pumped at complex ll
- Contains succinate dehydrogenase which catalyses succinate to fumarate in TCA cycle
What is the hindrance around cytochrome c
It only can recieve one electron at a time
Hence CoQ and complex lll transfer electrons between another to meet this requirement
What is Coenzyme Q
It is a small lipid soluble compound - hydrophobic quinone
Which diffuses rapidly with IMM
What is Coenzyme Q
It is a small lipid soluble compound - hydrophobic quinone
Which diffuses rapidly with IMM
Both Complex III and Cytochrome C are known as…
Why?
Cytochrome proteins
contain a heme group
Cytochrome C is a peripheral protein meaning?
membrane proteins that adhere only temporarily to the biological membrane with which they are associated
How does electron movement occur between Complex lll and Cyt C
Complex 3 transfers electrons to Cyt C which then transfers them to Complex lV
At Complex lll energy is lost which is used to pump 4 protons across the inner membrane
What happens at Complex lV
- This electron carrier has a co-ordination site for O₂ within the heme group
- Transfers a pair of electrons to 0.5O₂ which is reduced to form H₂O
- 2 electrons are pumped across inner mitocondrial membrane
The transfer of electrons down the ETC has a ΔG = -52.6 kcal mol⁻¹
Meaning?
- The transfer of electrons down the ETC is energetically favourable
- NADH is a strong electron donor (reducing agents)
- O₂ is a strong electron acceptor (oxidising agent)
What is the Chemiosmotic hypothesis
Proton pumping across the inner mitocondrial membrane creates a proton gradient (more +ve change on the outside than inside)
This drives ATP synthesis via ATP synthase (complex V)
How does ATP synthase (Complex V) operate
- Protons pumped to the cytosolic side of mitocondrial membrane re-enter the matrix by passing through F0 proton channel
- As protons pass down the channel they drive the rotation of the C ring of F0 which causes a conformational change in the β-subunit of the F1
- ADP and Pi bond and ATP is formed and released
For every pair of electrons from NADH and FADH₂, how many ATP are generated
NADH: 2.5 ATP
FADH₂: 1.5 ATP
From 1 glucose molecule, how many ATP can be generate
30 ATP generated by oxidative phosphorylation
(Compared to 2 from glycolysis)
Inhibitors of the electron transport chain, do what?
Prevent the passage of electrons down the ETC and so prevent protons being pumped across the inner mitocondrial membrane
Hence inhibiting ATP synthesis
What complex does cyanide, azide and CO effect
Complex lV
How do uncoupling proteins affect ATP synthesis
- Created a pore across the membrane and hence a dissipation of the proton gradient BUT the ETC will still be operational
- The free energy will be dissipated as heat
Why do some organisms not due O₂ as the terminal electron acceptor
Allow these organisms to live in anaerobic environments e.g. soil, hydrothermal vents, bottom of lakes
