Chapter 8 - Introduction to Metabolism Flashcards
Metabolism
the totality of an organisms chemical reactions in cells
- Increased metabolism increases the energy output by breaking down carbs
Metabolic Pathway
a serious of chemical reactions which either build a complex molecule(anabolic) or break down a complex molecule(catabolic) catalyzed by a specific enzyme at each step
Types of Metabolic Pathways
- Catabolic reactions are degradative; release energy
○ E.g. cellular respiration- Anabolic reactions consume energy to build complicated molecules
○ e.g. photosynthesis
- Anabolic reactions consume energy to build complicated molecules
Bioenergetics
the study of how energy flows through living organisms
Energy and types:
the capacity to cause change and the rearrangement of a collection of matter
Types:
- Thermal
- Kinetic
- Potential
- Chemical: the potential energy available for release in chemical reactions
Thermodynamics
the study of energy transformations in a collection of matter
- System is the matter under study while surroundings is everything outside the system
Laws of Thermodynamics:
1st Law: the principle of conservation of energy
The Energy of the universe is constant, energy can only be transferred and transformed
2nd Law:
- Every energy transfer increases the entropy(molecular disorder) of the universe
- Only a small amount of energy(chemical) is extracted from sources (food), meaning that there is more and more usable energy lost as heat to the surroundings
Spontaneous Process
a process occurring without an overall input of energy because it leads itself to an increase in entropy
- Process is energetically favorable
- Can occur fast(explosion) or slow(rusting of a car)
- If Delta G < 0, then spontaneous because it doesn’t require energy
Nonspontaneous Process
a process, on its own, leading to a decrease in entropy because energy is supplied however it leads to overall increase in entropy in the universe.
- Water flowing downhill is spontaneous but in order for it to go uphill it is nonspontaneous because it requires a pump to push it up, from which some energy is lost as heat, increasing entropy
- If Delta G > 0, then nonspontaneous because it requires energy
Entropy
the transformation of energy creating disorder in the surroundings(everything)
- living systems increase entropy(disorder)
- However they can still create ordered structures by taking in organized matter and energy and replacing them with less ordered forms
Free Energy(G):
- Free energy is a measure of a systems instability - the tendency to change to a more stable state
Free energy is the difference between the end state and the initial state
- For a reaction to have a -ve G, the system must lose free energy during the change - Due to it losing free energy, the system in its final state is less likely to change and therefore more stable
Change in Free Energy Equation(Delta D)
H -T x S
-Delta H
- Is the change in the systems enthalpy(equivalent to total energy)
- delta S
- Is the change in the systems entropy
T- The absolute temperature in Kelvin(K) units(degrees + 273)
Equilibrium
Equilibrium: the forward and reverse rate of equations occur at the same rate and there is no net change in the relative concentrations of products and reactants.
- For a system at equilibrium, G is at its lowest
- Free energy will increase when a reaction is pushed away from equilibrium(e.g. removing some products)
- Systems never spontaneously move away from equilibrium due to it not being able to spontaneously change
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Exergonic Reactions
a spontaneous chemical reaction where there is a net release of free energy
- Due to it losing free energy(G decreasing) the Change in Free Energy is negative
○ The greater the decrease in free energy, the greater the amount of work that can be done as more energy is released
Endergonic Reaction
a non-spontaneous reaction which absorbs free energy from its surroundings
- Because it stores free energy in molecules(G increases), the change in free energy is positive
○ The magnitude of change in free energy is the amount of energy needed to drive the reaction
Importance of regulating Equilibrium
○ If a cell reached a metabolic equilibrium, it would be dead because G would be at the minimum, meaning no work can be done
- In order to prevent equilibrium being reached, some reversible reactions are constantly ‘pulled in one direction and waste products are expelled
○ Cellular Respiration is an example as some of the products are used straight away in other reactions
Types of ‘Work’ Done by Cells
- Chemical work: the pushing of endergonic reactions that would not occur spontaneously such as the process of synthesizing polymers from monomers
- Transport Work: the pumping of substances across the membranes against the direction of spontaneous movement
- Mechanical Work: e.g. the beating of cilia, the contraction of muscle cells
Energy Coupling
it’s the use of energy released from exergonic reactions to drive an endergonic reaction
- A key way to manage energy resources
Mediated by ATP and can actually act as the immediate source of energy
Structure and Hydrolysis of ATP
- Bonds between phosphate groups can be broken down by hydrolysis creating Pi and ADP
- is an exergonic reaction which releases energy
- release of energy is due to all three phosphates negative charges keeping them together ‘coiled’ with potential energy
- cells then harness this released energy
Ways which Cells Harness Energy Released from ATP
- enzymes help the cell use the high free energy of ATP to drive endergonic chemical reactions
- If the change in free energy of an endergonic reaction is less than the amount of energy released by ATP hydrolysis, the two reactions can be coupled and therefore exergonic
- Transport and mechanical work can be powered by hydrolysis which leads to a change in a proteins shape and its ability to bind with certain molecules;
- Phosphorylation and dephosphorylation promote crucial protein conformation changes during many other important cellular processes
ATP Cycle
- ATP is a renewable energy source by ADP being combined back with a phosphate group
○ Is an catabolic endergonic reaction as energy is required- the ATP cycle couples the cells exergonic process and endergonic processes in order to recycle ATP
Activation Energy Barrier
The initial energy required to start a reaction, the energy required to contort the molecules in order for bonds to break
- Helps regulate so that reactions don’t just happen all the time
Transition State
when molecules have absorbed enough energy for the bonds to break leaving the reactants in an unstable state
How Enzymes catalyze Reactions
lowering the Energy Activation barrier through enabling the reactants to absorb enerough energy to reach transition state
- however they cannot change the change in free energy for a reaction(making exergonic endergonic)
Enzyme Substrate Complex
a temporary complex molecule formed when an enzyme binds to its substrate molecule
- Enzymes only react with their specific substrates and this specificity is a result of their shape - Must be complementary fit between active site on enzyme and shape of substrate
Active Site
a specific region on an enzyme which binds with the substrate in order for catalysis to occur
Induced Fit
the active site is also not rigid but changes shape slightly due to interactions with the substrates chemical group
This leads to an even tighter fit
How Active Site can Lower Eactivation Barrier
- Orienting substrates correctly
- Straining substrate bonds towards transition state
- Provides a favorable microenvironment conducive to the reaction
- Covalently bond to the substrate to directly participate in the reaction
Enzyme Saturation
when the rate of reaction is determined by the speed of the active site converting reactant to product
Temperature effect on Enzyme Activity
- Up to a point enzyme activity increases as temperature increases due to collisions occurring more frequently
- Enzymes all have an optimal temperature and Above a certain temperature, the heat disrupts the bonds in the enzyme(protein) denaturing its shape and preventing substrates from binding to the active site
pH effect on Enzymatic Activity
- Enzymes also have optimal pH levels normally between 6-8
- Environments too high or low in pH denature enzymes and reduce the rate of reactions
Cofactors
a non protein molecule or ion required for the proper functioning of an enzyme
- either permanently bound to the active site or bind loosely and reversely with the substrate during catalysis
- If organic molecule it’s a coenzyme
- Most are inorganic such as zinc, iron, vitamins and copper
Irreversible Inhibitors
inhibitors that attach through covalent bonds which are irreversible inhibitors
- E.g. poisons and toxins
Competitive Inhibitors
a substance which weakly binds to enzymes in order to reduce activity by entering the active site in place of the substrate through mimicking its structure
- Can be overcome by increasing substrate concentration and increasing the likelihood of the substrate binding to the enzyme
Noncompetitive Inhibition
a substance which reduces activity of enzymes by binding to a different site on an enzyme, changing its shape of the active site and making it less effective for substrates to bind to
How Cells Regulate Metabolic Pathways
Allosteric Regulation: the binding of a regulatory molecule to a protein at one site which affects the protein at another site
- Helps regulate the shape of the enzyme in order to have an effect on the intended substrate
Feedback inhibition: a metabolic pathway is halted by the inhibitory binding of its end product to an enzyme in the earlier stages of the pathway
- Prevents the cell from making more of a product than necessary
Process of Allosteric Regulation
- Enzymes that are allosterically regulated are composed of two polypeptide subunits, each with their own active site
- The complex oscillates between two different shapes; catalytically active and the other inactive, with regulatory molecules binding to a separate(allosteric) site
The binding of an activator to an allosteric site stabilizes the shape and functional active sites whereas an inhibitor binds to the allosteric site and stabilizes the inactive form
- The complex oscillates between two different shapes; catalytically active and the other inactive, with regulatory molecules binding to a separate(allosteric) site
Cooperativity
a form of allosteric regulation where a shape change in one subunit of a protein caused by substrate binding is transmitted to all other subunits, facilitating binding of additional substrate molecules to those subunits.
- Primes enzymes as one substrate molecule primes an enzyme to act more readily on other substrates
- Considered allosteric as even though a substance binds to an active site, it affects catalysis in other active sites
Example of Hemoglobin in Cooperativity
- Hemoglobin is an example of this as its made up of 4 subunits and when oxygen binds to one, it increases the affinity of the other sites for oxygen
○ When Oxygen level is high it increases the affinity for more oxygen- Similarly in oxygen deprived tissues the release of Oxygen decreases the affinity of oxygen at other binding sites
