Section 3: Energetics of Life Flashcards
3 key common features of life
Proton gradients
Reducing power (FAD/FADH, NAD+/NADH, Fe2+/Fe3+, FeS compounds)
ATP (energy currency)
Proton gradients
Essentially universal for metabolism by all living organisms
An energy-coupling mechanism that uses energy stored in the form of an H+ gradient across a membrane to drive cellular work
Proton gradients - mitochondria
Energy for gradient from: food
Proton gradient concentrated in: intermembrane space
Proton gradients - bacteria
Energy for gradient from: nutrients
Proton gradient concentrated in: intermembrane space
Proton gradients - chloroplasts
Energy for gradient from: light
Proton gradient concentrated in: thylakoid lumen
Electron donor AKA
Reducing agent
Electron acceptor AKA
Oxidising agent
Oxygen is an example of a(n) _____ agent
Oxidising
What is ferredoxin
An example of an FeS compound
What does nature use to produce cellular products
Both reducing power and ATP
What are NAD(P)H and ATP widely used in
Widely used in metabolism to reduce CO2
Structure of NAD+, NADP+ and FAD
Share structural similarities
NADP+ is NAD+ except with a phosphate group attached to the ribose sugar
FAD also structurally similar
(must be able to recognise the structures!)
Levels of NAD+ and NADH that indicate energy state of a cell
Low NADH compared to NAD+ = low energy
High NADH compared to NAD+ = high energy
What was present in LUCA
Proton gradients
Reducing power (ferredoxin)
ATP
What did LUCA’s metabolism rely on
Relied on using H2 as an energy source to reduce CO2
O2 was largely absent –> very reducing atmosphere
LUCA genes
Those of a strictly anaerobic H2-dependent thermophilic
Genetic data places LUCA in a ___ setting, rich in ____
Hydrothermal vent setting
H2, CO2, transition metals, sulfur
Lots of abundant Fe2+
LUCA might have evolved at…
Alkaline hydrothermal vents
White smokers
Chimneys characterised by barium, calcium and silicon deposit which are white
What did the alkaline vent provide
Provided a natural proton gradient
Ocean had pH 6 and vent had pH 9
pH = ?
-log10 [H+]
Each pH unit represents a 10-fold change in H+ conc
Hadean ocean - H+ conc
Contained 1000x more H+ than the alkaline vent
What led to the reduction of CO2 by hydrogen
A combination of proton gradients and reducing power (FeS clusters)
Vents: Reduction of CO2 by H - steps
H2 within vent transfers its e- to FeS clusters at vent interface
FeS clusters transfer these e- to CO2 to reduce it to formic acid (HCOOH) and more reduced compounds (CH2O)
Vents: Reduction of CO2 by H - reducing power is generated where?
Within the FeS clusters which mediate the reduction of CO2 by H
Reduction of CO2 by H ultimately led to..
The development of the building blocks needed for LUCA to evolve
LUCA now had an established genetic code and ability to produce proteins
Protocel membrane
Leaky –> provides some protection
LUCA - ATP synthase
After reduction of CO2, ATP was produced through ATP synthase utilising proton gradient provided by vent
LUCA: ECh
Energy converting hydrogenase
Harnessed power of natural proton gradient by vent to generate reducing power (e- from H2) in the form of ferredoxin
Ancestor of complex I
LUCA: Reduced ferrodoxin and ATP can then be used to…
Reduce CO2 directly to provide the building blocks LUCA needed to function Forms C(x)H(y)O(z)
Archaea bacteria producing methane
Known as methanogens
Still use H2 as an energy source to reduce CO2
Has similarities in process to LUCA
Methanogens - FeS clusters
Methanogens still use FeS clusters within proteins to catalyse reactions (preserved within active sites of proteins)
What could methane indicate
Existence of methane on other planets (Mars) could indicate presence of life by microbes
Problem with genetic analysis of LUCA
Things like bacteria can transfer its DNA which then becomes incorporated into the genome
Reducing power of FeS complexes
Accept e- then donate them to something else
Where is the alkaline vent located
Along the mid-Atlantic ridge - the point in the earth’s crust where 2 tectonic plates are moving away from each other
Mid-Atlantic ridge
Responsible for breaking up the potent Pangea
Comes to surface in Iceland
Vents form
LUCA: Ocean was rich in..
CO2
LUCA: Where were FeS clusters located
In wall of the vent itself
What is free energy
A quantity used to determine the spontaneity of a process, i.e. what direction a reaction will occur
Refers to change of enthalpy and change of entropy, the combination of which determines whether a process occurs
ΔH
Enthalpy change
Describes heat of a reaction
Describes first law of thermodynamics
ΔS
Entropy
Change in order to disorder
The entropy (disorder) of any closed system not in thermal equilibrium almost always increases (2nd law of thermodynamics)
Gibbs free energy (G)
The energy that can be converted into work at a uniform temp and pressure throughout a system
Free energy - -ve, +ve and 0 values
If ΔG -ve (E° +ve), reaction proceeds in direction indicated
If ΔG zero, reaction is in equilibrium
If ΔG +ve (E° -ve), reaction proceeds in opposite direction, i.e. becomes a strong reducing agent
A reaction towards ‘more organised’ can only proceed if…
The enthalpy change (ΔH) overrides the decrease in entropy (ΔS)
ATP to ADP - entropy
Entropy increases as one ATP molecule is split into one ADP and one Pi (i.e. one molecule to 2 molecules)
First step of glycolysis
Reaction is regarded as essentially irreversible as it proceeds with a large -ve free energy change
However, the driving force comes from the free energy change that occurs during the conversion of ATP to ADP
Attaching a phosphate group to glucose doesn’t proceed spontaneously under standard conditions, so couple to ATP hydrolysis to make it spontaneous
Rust - what is oxidised and reduced
Iron is oxidised
Oxygen is reduced
Reduction potential
A measure of the tendency of a chemical species to acquire from or lose e- to an electrode and thus be reduced or oxidised
i.e. measures free energy changes for REDOX reactions
What reduction potential measured in
Volts (V)
Reduction potential - a higher E° value means…
It has a higher ‘pulling’ power to accept electrons (i.e. takes e- from other compound reaction)
Standard reduction potential is defined relative to…
A standard H reference electrode, given a potential of 0V
Standard reduction potential - concentrations
Each compound is at a conc of 1M (pH 0) and H2 is 1 atm
Reduction potential - the half reaction with the more -ve E° value is…
Reversed
Reactions - pH
Changing the pH (H+ conc) can alter the direction of the reaction
E°’
The reduction potential under physiological conc; a H+ conc of 10^-7 mol/litre (i.e. pH 7)
A very large -ve change in free energy essentially means…
The reaction is irreversible (steep waterfall)
ATP conversion to ADP and Pi - enthalpy and entropy change
Enthalpy change is -ve
Entropy change is +ve (1 –> 2 molecules)
Overall ΔG is -ve
Half reactions have a _____ associated with it
Standard reduction potential (E°)
Calculating standard reduction potential - agar bridge
Links two solutions for charge neutrality
If calculating reduction of compound x by H2..
Reverse the H2 reaction
Chiral molecule
Non-superimposable on its mirror image
4 diff groups attached
Glucose - numbering of Cs
Numbering of Cs starts from aldehyde group
In what forms do glucose and ribose exist in
Both exist in equilibrium as open and ring structurse
Glucose and ribose - chiral or non-chiral?
Both have chiral Cs and non-chiral Cs
What does the D/L notation tell us
Which of the two chiral isomers we are referring to
Glucose and ribose: Determining D/L notation
If -OH on highest numbered chiral C points to the right, isomer is D-isomer
If -OH on highest numbered chiral C points to the left, isomer is L
Which D/L form is usually found in nature
D form
Fischer projection - right vs left
Straight line
Right = below plane of ring
Left = above plane of ring
Haworth projection
Ring structure
Cyclic form - aldehyde
In cyclic form, the aldehyde group is lost because it’s used to complete the cyclic structure
Equilibrium - cyclic vs straight chains
Equilibrium heavily favours cyclic structures, so only a small amount of straight chain form of carbohydrate is present
Cyclic form - forms of glucose
2 distinct forms of glucose
C1 can have its attached -OH group either below the plane of the ring (α-glucose) or above the ring (β-glucose)
In aqueous solution, are in equilibrium
How do α and β forms interchange
Molecules pass through the straight-chain form to get from one structure to the other
Difference between α and β ring structures
Position of hydroxyl group attached to C1
In α form, it’s below plane of ring
In β form, it’s above plane of ring
Anomeric C and anomers
Since there can be 2 diff orientations around C1, it’s referred to as the anomeric C, and the two forms of glucose (α and β) are called anomers
Enantiomers
Compounds that are mirror images of each other
Diastereomers
Other compounds that aren’t enantiomers
Epimers
Compounds that differ only in the orientation of ONE hydroxyl group attached to a chiral C
i.e. hydroxyl group can occur on left or right-hand side
Cellulose - α or β?
Cellulose is a polymer of glucose monomers, using β-1,4-glycosidic linkages - allows cellulose to form very long and straight chains - tend to be very strong
Cellulose - how do hydroxy groups on glucose molecules align
Side-by-side (straight road)
Cellulose - branching
Cellulose doesn’t contain a branchpoint
Cellulose makes up ___% of organic matter in the biosphere
~50%
Most of the carbohydrate found in nature occurs as…
Polysaccharides
How do polysaccharides differ from each other
Recurring monosaccharide unit
Length of chains
Types of bonds linking units
Degree of branching of chains
Most abundant polysaccharides
Cellulose and starch - both made by plants and consist of recurring units of D-glucose, but differ in type of linkage between glucose molecules
Examples of α-glucose polymers
Glycogen (muscle) and starch (plants)
Form helical-like structures - not straight –> accessible?
Glycogen
Humans and other vertebrates store glycogen in liver and muscles
During intense exercise, glycogen is degraded in skeletal muscle through glycolysis to produce ATP
Glycogen and starch - OH groups
Hydroxy groups point outwards
Shaped a bit like a corkscrew
Types of α bonds
α-1,4,-glycosidic bonds: linear chains of glucose molecules
α-1,6-glycosidic bonds: branch points, form at every ~10 glucose units
Glycogen - branching
Glycogen is a highly branched molecule
Glycolysis: “Rome of metabolism”?
All catabolic routes lead to glycolysis
Fundamental pathway where many things link in and link out
Ways glycolysis produces energy (as ATP)
- Directly via substrate level phosphorylation
- Indirectly through production of reducing power in form of NADH
Glycolysis: Substrate level phosphorylation
Where a substrate donates a phosphate to ADP to form ATP
Glycolysis: ‘Energy’ in released e- is captured by..
NAD+ to produce NADH
Le Chatelier’s principle
The effect of a change in conditions (e.g. substrates or products) will result in a change in equilibrium of the system
Glycolysis: High vs low NAD+/NADH ratio
High NAD+/NADH ratio (glycolysis) drives reaction forward
Low NAD+/NADH ratio (gluconeogenesis) drives reaction in reverse
Hexokinase
Inhibited by its product G6P
Has a rather braod specificity - able to phosphorylate to a number of hexode and pentose sugars - enables them to release energy via glycolysis
Hexokinase - K(M) for glucose
10-20 µm
Phosphofructokinase (PFK)
Composed of 4 monomeric protein units that are tightly controlled so feeding-in of substrates into pathway can be switched on/off
What is PFK activated/inhibited by
Activated by several compounds, e.g. ADP, AMP and fructose-2,6-bisphosphate –> stimulates glycolysis
Inhibited by ATP and citrate
What is pyruate kinase inhibited by
High levels of ATP
Acetyl-CoA
What is pyruvate kinase activated by
Fructose-1,6-bisphosphate
ATP from glycolysis vs from mitochondria
Amount of ATP you can generate through glycolysis is more than through the mitochondria
Free energy for glucose to pyruvate is…
-ve
Used to drive energy production; one in form of ATP and the other in form of reduced co-factors
Why are e- transported by a chain
Couples the energy in a form of co-factors so you don’t get an ‘explosion’
When is glucose completely oxidised
When pyruvate is formed, still not completely oxidised
Only when it enters the mitochondria it is completely oxidised to CO2 and H2O
ATP yield for 1 molecule of NADH
2.5
ATP yield for 1 molecule of FADH2
1.5
Number of protons pumped across membrane by complexes I-IV
C I: 4 H+
C III: 4 H+
C IV: 2 H+
How mitochondria evolved
Archaea engulfed a protobacterium to form a proto-eukaryotic cell
Protobacterium is what evolved into the mitochondrion
What is chemiosmosis
The diffusion of ions across a selectively permeable membrane
Relates to generation of ATP by movement of H+ ions across a membrane during cellular respiration
Cellular respiration generates ____ ATPs per second in one cell
10 million
Chemiosmotic hypothesis
Electron transfer through the respiratory chain leads to pumping of protons from matrix to cytoplasmic side of inner mitochondrial membrane
pH gradient and MP constitute a proton-motive force used to drive ATP synthesis
Chemiosmotic coupling
Pumping of protons across inner mitochondrial membrane produces a H+ gradient
Membrane is impermeable to protons, so uses channels to allow protons to diffuse back
However, to get back into the matrix, protons are forced to do some work - chemiosmosis
ATP synthase - protein complexes
Composed of 2 complexes
F(0) and F(1) protein complexes
ATP synthase - F(0) complex
Incorporated into the membrane
Comprises 3 diff polypeptide chains
Forms the channel through which protons can diffuse from intermembrane space into matrix
ATP synthase - F(1) complex
Buds into matrix side of membrane
Catalytic known - shaped like a sphere, composed of 5 protein chains, and is the site where ATP synthesis occurs
ATP synthase - stator
Connects F(0) and F(1) complexes Consists of an 'a' subunit, 'b' subunits and the δ subunit
Oxidative phosphorylation: For every 2 e- carriers…
One O2 molecule is reduced to 2 water molecules
Does ETC generate ATP
Not directly, but flow of e- through complexes is used to pump H+ from matrix into intermembrane space
ETC - free energy
ETC breaks the large free energy drop from food to oxygen into a series of smaller steps that release energy in manageable amounts
Electronegativity
The tendency of an atom to attract e- to itself
Direction of e- flow in electron transport chain
O2 > IV > C > III > Q > I and II > NADH and FADH2
ETC: NADH electrons
E- carried by NADH lose very little of their potential energy in this process
This energy is tapped to synthesise ATP as e- ‘fall’ from NADH to O2
Where are copies of ETC found
In extensive surface of cristae (inner membrane of mitochondrion)
ETC: Are proteins fixed?
Most components are proteins that are bound with prosthetic groups that can alternate between reduced and oxidised states as they accept and donate e-
ETC: Free energy change from ‘top’ to ‘bottom’
-53 k.cal/mol of NADH
Complex I - what does it contain
An FMN prosthetic group and an Fe-S cluster
Complex I - process
NADH –> NAD+ and the e- are passed onto an Fe-S protein where Fe3+ is reduced to Fe2+
E- make their way via additional Fe-S centres to UQ / coenzyme Q
Fe within Fe-S clusters alternate between Fe2+ and Fe3+
Complex Q ultimately becomes reduced to CoQH2
Complex II - what does it contain
Succinate dehydrogenase (from CAC)
Complex II - process
H+ ions obtained from conversion of succinate to fumerate are transferred to CoQ along with 2e-
FADH2 is re-oxidised and e- are transferred to an FeS-containing protein where Fe3+ is reduced to Fe2+
FeS containing protein donates e- to coenzyme Q –> CoQH2
Fe2+ of FeS containing protein is re-oxidised to Fe3+
Complex II - FADH2
FADH2 produced by succinate DH is very tightly bound
FAD is covalently bound to enzyme so the FADH2 produced can’t be released into the medium
Complex III - what does it contain
Heme groups and Fe-S containing proteins
Complex III - process
E- from reduced CoQH2 are passed through FeS proteins and eventually to cyt C
Q cycle takes place
E- from either NADH or FADH2 end up on a cytochrome c enzyme, which is attached to intermembrane space side of membrane
Complex III - Q cycle
Indicates the flow of e- from CoQH2 doesn’t take a simple direct path
Complex IV - what does it contain
Fe-S containing proteins
2 copper ions - participate in flow of e- and lie between cyt a and cyt a3
Complex IV - process
Transfers e- from cyt c to oxygen through Fe-S containing proteins, producing water
Brown fat cell
Converts chemical energy to heat to protect against cold weather
Beige fat cell
Immature cell in white fat tissue matures to burn fat
White fat cell
Most common fat cell
Used to store fat
Found beneath skin and abdomen
Stores triglycerides
Uncoupling protein (UCP)
Process that simply lets protons back in without having to drive ATP synthase - generates heat
Brown fat in adults
Humans do have brown fat stores, but are only activated in cold temperatures
Brown fat in adults
Humans do have brown fat stores, but are only activated in cold temperatures
ETS: Q and C
Soluble mediators
Shuttle e- from complexes to each other
ATP synthase: Where does catalysis occur
At interface between dimers
Brown and beige fat cell vs white fat cell
Brown and beige fat cells have more mitochondria
Glycolysis: Net equation
Glucose + 2NAD+ + 2ADP + 2Pi –> 2 pyruvate + 2NADH + 2ATP
Glucogeneogenesis - pyruvate
Pyruvate (generated in muscle and other tissues) is converted/transanimated to alanine, which is then returned to the liver for gluconeogenesis
Known as transamination reaction
Glucose-alanine cycle
An indirect way for muscle to get rid of nitrogen while replenishing its energy supply
Allows non-hepatic tissues to deliver the amino portion of catabolised amino acids to liver for excretion as urea by kidneys
Transamination reaction
Glucose-alanine cycle
Requires transfer of an amino group
Glucose-alanine cycle - liver
Alanine is converted back to pyruvate and used to make glucose or be oxidised further through CAC
In the liver, what is the first step of gluconeogenesis
Conversion of pyruvate to oxaloacetate
Conversion of pyruvate to oxaloacetate
Anabolic reaction
Catalysed by pyruvate carboxylase which uses CO2 and ATP as the free energy source –> enters Krebs cycle
Carboxylation
Addition of CO2
Conversion of pyruvate to oxaloacetate is stimulated by…
Acetyl CoA
Pyruvate - if O2 is present…
Pyruvate can enter the mitochondria and be completely oxidised to CO2 and H2O
Pyruvate - if O2 isn’t present…
Pyruvate can’t be completely oxidised
Cell needs other ways to regenerate NAD+ for glycolysis to proceed
To do this, pyruvate can be reduced to alcohol/ethanol (fermentation) or lactate
Without mitochondria or oxygen…
NADH builds up and exhausts the NAD+ pool, causing glycolysis to shut down
Thus, cells must have a way of reconverting NADH to NAD+ - fermentation
Alcohol fermentation
Occurs under anaerobic conditions
Allows generation of ATP by glycolysis and regenerates NAD+ by transferring e- from NADH to acetaldehyde
Alcohol fermentation: How is pyruvate converted to ethanol
- Pyruvate is converted to acetaldehyde by removal of CO2
2. Acetaldehyde is reduced by NADH to ethanol
Alcohol - acetaldehyde
Quite toxic
Lactic acid fermentation
Pyruvate is directly reduced by NADH to form lactate
Allows a way for NAD+ to be regenerated
Lactate
Ionised form of lactic acid
Lactic acid fermentation in humans
Strenous exercise –> anaerobic conditions
O2 in muscles is depleted
Lactate builds up as glycolysis continues
Muscles tire and become painful
Breathing rate increases
In animals under anaerobic conditions, where is lactate produced
In muscles
Lactate dehydrogenase
Catalyses reduction of pyruvate
Transport of lactate
In human muscles, lactate can be readily transported across cell membrane via bloodstream to liver where there is good oxygen supply
Cori cycle
Transfer of lactate from muscle to liver, and transfer of glucose from liver to muscle
i.e. lactate –> pyruvate –> glucose –> resupplied to muscle by bloodstream
In the liver, lactate can be converted to glucose by…
Gluconeogenesis
Operation of glycolysis and gluconeogenesis
Possible to have both operating simultaneously in body, i.e. diff tissues can operate in diff ways
Aerobic respiration: Conversion of pyruvate to acetyl CoA - enzyme
Pyruvate dehydrogenase converts pyruvate to acetyl CoA
Occurs in mitochondria, so requires transport of pyruvate into mitochondrial matrix
Pyruvate dehydrogenase
Converts pyruvate to acetyl CoA
Regulates entry of pyruvate into CAC
How much of the original energy in glucose is still present in two molecules of pyruvate
More than 3/4
Aerobic respiration - NADH
e- of NADH are ultimately passed to O2, generating ATP by oxidative phosphorylation
Pyruvate dehydrogenase catalyses these sequence of reactions
A CO2 is removed from pyruvate - 3C –> 2C in form of an acetyl group
NAD+ is reduced to NADH
CoA is coupled to acetyl group molecule to form acetyl CoA, which is ready to be completely oxidised through CAC
Total yield from one glucose
4 ATP (2 from glycolysis, 2 from CAC) 10 NADH (2 from glycolysis, 8 from CAC) 2 FADH2 (from CAC)
CAC aka
Krebs cycle
TCA cycle
Breakdown of glucose to CO2 and H2O is coupled to…
ATP production and generation of reducing power (NADH and FADH2)
Pyruvate dehydrogenase - switch
Acts as a switch
If switched off, pyruvate can’t be converted to acetyl CoA, so instead is made into lactate
What is pyruvate dehydrogenase regulated by
Metabolic conditions within the cell
Net ATP yield from diff stages of cellular respiration
Glycolysis: 2 ATP
CAC: 2 ATP
ETS: 26-28
Cellular respiration is very efficient in…
Energy conversion
A single 6C glucose molecule is oxidised to..
6 CO2 molecules
Gluconeogenesis
The generation of glucose from other organic molecules (e.g. pyruvate and lactate)
Where does gluconeogenesis take place
Mostly in liver, and to a smaller extent in the kidney
What does gluconeogenesis require
An investment of energy in the form of ATP and NADH
How are glycolysis and gluconeogenesis regulated
Reciprocally regulated
Both pathways don’t operate at the same time
Occurs through:
- local allosteric control (Determined by cell’s energy status)
- global control (circulating hormones which can activate cellular signalling cascades that override local metabolic conditions)
Can skeletal muscle make glucose
No - it traps glucose from bloodstream and stores it as glycogen or metabolises it
Gluconeogenesis: How does oxaloacetate leave the mitochondria
By a specific transport system in the form of malate, which is re-oxidised to oxaloacetate in the cytoplasm
Gluconeogenesis: Bypass I
First step:
Involves carboxylation of pyruvate to produce oxaloacetate
Adds a CO2
Second step:
Catalyses phosphorylation and decarboxylation of oxaloacetate to yield phosphoenol pyruvate
Phosphate group is derived form GTP or ATP
Hexokinase vs glucokinase
Glucokinase has a much lower affinity for glucose, so glycolysis is less prone to proceed in the liver - the main site for gluconeogenesis
Gluconeogenesis: Bypass III
Removal of phosphate from G6P to give glucose, which can then pass through the cell membrane into the blood
Gluconeogenesis: Increased conc of acetyl CoA leads to…
Inhibition of pyruvate kinase –> helps prevent futile cycle
Inhibition of pyruvate DH –> pyruvate doesn’t enter oxidative route to acetyl CoA
Stimulation of pyruvate carboxylase
Glycolysis equation
Glucose + 2NAD+ + 2ADP + 2Pi –> 2 pyruvate + 2NADH + 2ATP
Gluconeogenesis equation
2 pyruvate + 2 NADH + 4ATP + 2GTP –> glucose + 2NAD+ + 4ADP + 2GDP + 6Pi
Gluconeogenesis expends how many ATP/GTP?
6
A futile cycle of both pathways (glycolysis and gluconeogenesis) would waste how many ATP/GTP per cycle?
4
Regulation of bypass I, II and III
Bypass III isn’t as regulated compared to I and II
Hexokinase and glucokinase - G6P
Glucokinase is NOT inhibited by G6P
What can be used as a carbon source
Alanine
Lactate (from muscle)
Glycerol
Is glucokinase required for glycogen degradation
No
Glucokinase is a(n) _____ of hexokianse
Isoform
What can be used as a carbon source for gluconeogenesis
Alanine
Lactate
Glycerol
Not fatty acids
