Week 4 Flashcards
Bioenergetics
- How organisms manage energy resources via metabolic pathways
- Catabolic pathways (catabolism) release energy – breaking complex molecules into simpler ones
- Anabolic pathways (anabolism) consume energy - build complex molecules from simpler ones
- Energy = capacity to do work or cause change
- Forms of energy (can be interconverted):
• Potential energy = stored energy (includes chemical energy in molecules)
• Kinetic energy = currently causing change Involves some type of motion
Thermodynamics
The study of energy change
- two fundamental laws govern thermodynamics
First law of Thermodynamics
- Energy cannot be created or destroyed
- Energy can be transferred and transformed
- Conversion of: a) Electrical to mechanical energy, b) chemical to mechanical & thermal energy, c) chemical to light energy
Second law of Thermodynamics
- Disorder (entropy) in universe increasing
- Energy transformations proceed spontaneously
• convert matter from more ordered, less stable to less ordered, more stable - Spontaneous changes that do not require outside energy, increase entropy (disorder)…
For a process to occur without energy input, it must increase the entropy of the system. - During each conversion, some energy dissipates as heat.
- During energy transfer or transformation, some energy is unusable, often lost as heat
- Heat = measure of random motion of molecules
- Cells convert organised forms of energy to heat
- According to the second law of thermodynamics:
Every energy transfer or transformation increases entropy (disorder) of the universe
Gibbs’ Free Energy
- In test tube, some reactions release heat (exothermic), others absorb heat (endothermic).
- In cells, molecules - certain amount of free energy (G)
- Chemical reactions - change in free energy (∆G)
- The free energy associated with a reaction = energy available for doing work.
- Gibbs’ free energy (G) – energy contained in molecule’s chemical bonds (Temp & Press constant).
- ΔG can be positive or negative.
- Not all this energy available for chemical reactions - some transferred as heat, as entropy increases
Life requires a lack of Entropy (Disorder)
- Less energy needed for disorder, than for ordered systems.
- Living systems
• Increase the entropy of the universe
• Use energy to maintain order
• Have free energy to do work in cellular conditions
• Organisms live at the expense of “free energy”
Exergonic
- Reaction releases free energy
- ΔG is -ve
- substrates have more free energy than products
- Net release of energy &/or increase in entropy
- occur spontaneously (without net input of energy)
Endergonic reactions
- Reaction requires energy input
- ΔG is +ve
- substrates have less free energy than products
- net input of energy &/or decrease in entropy
- do not occur spontaneously
Energetics of reactions
- When molecules (substrates) are altered to form new
molecules (products), the energy change is given by: - ∆G = Gproducts - Gsubstrates
S → P - ∆G = -10 kJ/mole, S has more energy than P
-ve ∆G, so reaction releases energy - ATP = principal molecule providing energy for endergonic cellular reactions
So how much ATP do we have?
- Estimated to be around 100 g in a healthy adults, some estimates up to 250 g… that’s not a lot.
- We use around 70 kg ATP/day. So, we have to generate ATP, recycle & reuse the core components.
- Cells need 1 – 10 mM ATP to function.
Energy charge
- A way to describe the energy status of a cell.
- Value can range from 0 (all AMP) to 1 (all ATP) in cell. Important in regulating some key metabolic enzymes
Energy metabolism - generating ATP
- ATP levels bust be maintained or the cell runs down & dies, very quickly - this is what happens when we are deprived of oxygen
- ATP is made by burning fuels
Reduced Bonds
- main fuels = carbohydrates, fats, proteins (alcohol)
- contain lots of reduced binds
- electrons NOT shared with oxygen
Oxidation and Reduction
- during catabolism, electron are removed to become part of a bond with O
- this is oxidative metabolism - we need O2 to make enough ATP in our cells
Redox
Can involve simply electron transfer or can involve transfer of H (as in NADH)
Energy storage in cells
- oxidation of foods releases energy, which is stored in other molecules that are used to perform work
- energy can also be stored as ion gradients & in other high energy phosphate bonds
Activated carrier and its High energy component
- ATP → phosphate
- NAD(P) H,FADH2 → electrons & hydrogens
- Acetyl CoA → acetyl group
ATP
- ATP = Adenosine Triphosphate
- terminal phosphate bonds of ATP = high energy bond
- ATP hydrolysis (-ve ∆G) yields 29.3 kJ/mol energy
- this energy can be used to drive other reactions, such as formation of new bonds & molecules
NADH
- NADH = Nicotinamide adenine dinucleotide
- electron carrier
- cellular currency of reductive potential energy produced during respiration
FADH2
- FADH2 = Flavin adenine dinucleotide
- Another important electron carrier
Acetyl Coenzyme A
- AKA Acetyl CoA
- used to add 2C units to other molecules
- has high energy thioester bond that facilitates this
Oxidation of Fuels
- Major stores are
• carbohydrate
• glycogen/glucose in animals
• starch/sucrose in plants
• fats (trigycerides)
• alcohol (not!) - Hydrogens are stripped out of the fuels
- Multi-step process
- As H are removed, the fuels gradually broken
down to CO2 (have oxidised the reduced bonds)
Phosphagens
High energy compounds for bursts of activity in muscles
Phosphocreatine (PCr)
Buffers the TAP pool during bursts of activity
- synthesised by creatine kinase (CK)
cCK (cytosolic CK)
Has 2 functions:
1. Passes phosphoryl group from PCr to ADP, to form ATP. This prevents ADP from building up to levels that could inhibit ATP- dependent enzymes.
2. Uses ATP produced by glycolysis to synthesise PCr.
mCK (mitochondrial CK)
Synthesises PCr in mitochondria. PCr diffuses to sites of ATP use. During rest, ATP & PCr pools are replenished in preparation for next period of intense ATP demand.
Reaction Rates
- molecules do not have enough kinetic energy to reach transition state when they collide, so most collisions are non-productive & reaction proceeds very slowly, if at all
How to speed upon reaction?
• Add energy (heat) - molecules move faster, collide more frequently & with greater force
• Add a catalyst - reduces energy needed to reach transition state, without being changed itself
• Enzymes - protein catalysts
Cellular reactions
- they have an energy barrier which must be overcome (activation energy = Ea) before reaction proceeds, even if that reaction is exergonic
- Even if there is a net release of energy, some energy is required to start reaction
- transition state is at higher free energy level than substrates
Activation Energy (Ea)
- Reactions require input of energy to get started, Ea
= initial amount energy needed to start chemical rxn - Needed to bring reactants close together & weaken existing bonds – initiate chemical reaction.
- Often supplied by heat, but body temperature does not get substrates to transition state
- Enzyme active site binding lowers energy needed to reach transition state.
- Ea: kilojoule / mole (kJ/mol)
Reaction can be catalysed by
- chemical catalyst
- colloidal catalyst
- biological catalyst
- catalase
Catalysts
- catalysts reduce Ea, do not affect ∆G, can’t make a thermodynamically unfavourable reaction occur, but speed up reactions that are reversible by the same degrees in BOTH directions
- Enzymes are protein catalysts - usually much more efficient than chemical catalysts
- enzymes enhance the rate at which a reaction occurs by lowering the activation energy
- Activation energy (Ea) is always positive.
- It relates to the entropy (S - disorder/randomness) & enthalpy (H - heat content)
- in transition state there is loss of molecular motion & disorder (DS is negative), while DH is positive (due to partial covalent bond breaking), thus Ea must be positive, & that’s all we’ll say about that
Enzymes
- protein catalysts
- catalytic activity - very effective at body temperature
- highly specific
- many are regulated, activity is controlled
- increase reaction rate - no change themselves
Cells have thousands of enzymes to perform thousands of cellular functions - Metabolic pathways: chains, cycles, spirals, or chains & cycles…
- unlike heat, enzymes are highly specific for reactions they catalyse & substrates they choose
- polypeptide chain of enzyme folded to form a pocket where substrate/s bind (ES complex) & reactions occur = the active site
- active site structure very specific - binds limited substrates
- typically speed up only one or very few reactions, many fold
- not changed or consumed in the reaction, only a small amount is needed, & can then be reused
- so, by regulating which enzymes are expressed, cells can control which reactions occur
- substrate has to reach unstable, high-energy “transition state” = bonds destabilised
- once substrate reaches transition state, product can form.
- enzymes lower activation energy, so get quicker conversion of S to P
- much of the catalytic power of enzymes comes from bringing substrates together in favourable chemical orientation
- unique 3-D shape of active site allows temporary association with substrates, stressing existing bonds & reducing energy needed to attain transition state.
Enzyme structure and functional process
- AA side chains in active site arranged in 3-D space so as to interact with specific parts of substrate molecules e.g. hydrophobic parts (h) of substrate bind to hydrophobic parts of active site, -vely charged parts of
substrate bind to +vely charged active site AA, hydrogen bonds also form between substrate & active site AA. - As a result:
(i) gives the enzyme its substrate specificity (can only catalyse a specific reaction)
(ii) substrates are bound in a specific orientation in active site (correctly orientated to react) - When enzyme binds its substrate they do not fit into active site like a key into a lock, but is induced to fit. - Binding positions in active site are arranged such that, on binding S, molecules are distorted to have a conformation that approaches that of the transition state.
- Often, additional bonds are formed between the enzyme & substrates in the transition state, stabilising it.
Enzyme Catalytic Cycle
- Substrates enter active site; E changes shape so active site embraces S (induced fit).
- S held in active site by weak interactions, such as hydrogen bonds.
- Active site (& R groups of its AA) can lower Ea & speed up reaction by:
- Substrates converted into products (EP).
- Products released
- Active site available for new substrate
Factors affecting Enzyme Activity
Protein shape determined by 1° structure, AA sequence
• Covalent modification - can change enzyme shape, e.g., phosphorylation/dephosphorylation.
• Synthesis & degradation – protein availability.
• Temperature - rate of an enzyme-catalysed reaction increases with temperature, up to optimum. Heat denatures proteins.
• pH - ionic interactions influence protein charge & shape. pH extremes denature proteins.
• Substrate availability (concentration [S])
• Compartmentalisation allows incompatible reactions to take place simultaneously in cells.
• Activators – regulatory molecules that bind enzyme & keep in active configuration – increased activity.
• Cofactors - chemical components that facilitate enzyme activity (e.g., metal ions, Mg++ for DNA pol)
• Coenzymes - organic molecules that function as cofactors (e.g., vitamins)
Enzyme Activity is affected by: Temperature (up to ~40°C)
- Rate of reaction increases with increasing temperature, but after temperature reaches a certain point, protein structure unfolds & enzyme inactivated.
- structure → function
Enzyme Activity is affected by: pH
- Most enzymes have max activity between pH 6-8
- Some AA side chains need to be protonated/deprotonated for substrate binding &/or catalysis (pH must be below/above pKa).
- Some substrates need to be correctly protonated for binding &/or catalysis.
- Extremes of pH disrupt hydrogen bonding destabilising protein structure, unfold, lose catalytic activity.
Enzyme Activity is affected by: Substrate concentration
Enzyme catalysed activities show saturation kinetics which reflect the saturation of active sites on enzyme as substrate concentration increases.
Enzyme Regulation Controls Metabolism
- Chaos if cell’s metabolic pathways were not tightly regulated.
- So, cells switch on & off genes that encode specific enzymes.
- Allosteric regulation describes any case where protein function at one site is affected by binding of regulatory molecule at another site, e.g., cofactor binds at an allosteric site & causes change in protein shape that influences S binding at active site.
Factors Affecting Enzyme Activity: Allosteric Enzymes
- Most allosterically regulated enzymes have active & inactive forms.
- Allosteric sites are specific binding sites acting as on/off switches
- Activator binding stabilises active form
- Inhibitor binding stabilises inactive form
- Inhibitor - substance that binds to an enzyme & decreases its activity:
• Competitive inhibitors - compete with substrate for active site
• Noncompetitive inhibitors - bind at another location than the active site
• Uncompetitive inhibitors - bind only ES complex
Allosteric Enzymes
Can inhibit or stimulate an enzyme’s activity
Feedback Inhibition
- End product of metabolic pathway shuts down the pathway by inhibiting activity of earlier enzyme
- Advantageous for cell to temporarily shut down biochemical pathways when their products are not needed
Competitive Inhibition
Competitive inhibitor mimics substrate, competing for active site binding
- Many prescription drugs are competitive inhibitors e.g. viagra
Noncompetitive Inhibition
Noncompetitive inhibitor bonds to different site, changing conformation
- many toxins are non-competitive inhibitors e.g. mercury & lead
