Week 4 Flashcards
(45 cards)
1
Q
Bioenergetics
A
- 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
2
Q
Thermodynamics
A
The study of energy change
- two fundamental laws govern thermodynamics
3
Q
First law of Thermodynamics
A
- 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
4
Q
Second law of Thermodynamics
A
- 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
5
Q
Gibbs’ Free Energy
A
- 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
6
Q
Life requires a lack of Entropy (Disorder)
A
- 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”
7
Q
Exergonic
A
- 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)
8
Q
Endergonic reactions
A
- 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
9
Q
Energetics of reactions
A
- 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
10
Q
So how much ATP do we have?
A
- 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.
11
Q
Energy charge
A
- 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
12
Q
Energy metabolism - generating ATP
A
- 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
13
Q
Reduced Bonds
A
- main fuels = carbohydrates, fats, proteins (alcohol)
- contain lots of reduced binds
- electrons NOT shared with oxygen
14
Q
Oxidation and Reduction
A
- 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
15
Q
Redox
A
Can involve simply electron transfer or can involve transfer of H (as in NADH)
16
Q
Energy storage in cells
A
- 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
17
Q
Activated carrier and its High energy component
A
- ATP → phosphate
- NAD(P) H,FADH2 → electrons & hydrogens
- Acetyl CoA → acetyl group
18
Q
ATP
A
- 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
19
Q
NADH
A
- NADH = Nicotinamide adenine dinucleotide
- electron carrier
- cellular currency of reductive potential energy produced during respiration
20
Q
FADH2
A
- FADH2 = Flavin adenine dinucleotide
- Another important electron carrier
21
Q
Acetyl Coenzyme A
A
- AKA Acetyl CoA
- used to add 2C units to other molecules
- has high energy thioester bond that facilitates this
22
Q
Oxidation of Fuels
A
- 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)
23
Q
Phosphagens
A
High energy compounds for bursts of activity in muscles
24
Q
Phosphocreatine (PCr)
A
Buffers the TAP pool during bursts of activity
- synthesised by creatine kinase (CK)
25
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.
26
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.
27
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
28
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
29
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
30
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)
31
Reaction can be catalysed by
- chemical catalyst
- colloidal catalyst
- biological catalyst
- catalase
32
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
33
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.
34
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.
35
Enzyme Catalytic Cycle
1. Substrates enter active site; E changes shape so active site embraces S (induced fit).
2. S held in active site by weak interactions, such as hydrogen bonds.
3. Active site (& R groups of its AA) can lower Ea & speed up reaction by:
4. Substrates converted into products (EP).
5. Products released
6. Active site available for new substrate
36
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)
37
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
38
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.
39
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.
40
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.
41
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
42
Allosteric Enzymes
Can inhibit or stimulate an enzyme’s activity
43
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
44
Competitive Inhibition
Competitive inhibitor mimics substrate, competing for active site binding
- Many prescription drugs are competitive inhibitors e.g. viagra
45
Noncompetitive Inhibition
Noncompetitive inhibitor bonds to different site, changing conformation
- many toxins are non-competitive inhibitors e.g. mercury & lead
