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Chapter 8-9 (Concept 8.3 (Hydrolysis of ATP Function (Cells are able to…
Chapter 8-9
Concept 8.3
ATP
Cells do three kinds of work:
- Chemical Work - pushes endergonic reactions that would not occur spontaneously, such as synthesis of polymers from monomers
- Transport Work - the pumping of substances across membranes against the direction of spontaneous movement
- Mechanical Work - such as beating of cilia, the contraction of muscle cells, and the movement of chromosomes during cellular reproduction
Energy coupling - use of exergonic process to drive an endergonic one. ATP is responsible for mediating most energy coupling in cells
Structure and Hydrolysis
ATP (adenosine triphosphate) - contains sugar ribose, one nitrogenous base adenine, and a chain of three phosphate groups. ATP is also used to make RNA.
Hydrolysis - the breaking of compounds; therefore, bonds between phosphate groups in ATP are broken by this process. ATP and H2O yield to ADP + inorganic phosphate to produce and release energy
ADP (adenosine diphosphate) - formed when a phosphate bond is broken by adding a water molecule and an inorganic molecule leaves the ATP;
ATP + H2O YIELDS ADP + Pi; ΔG = -7.3 kcal/mol (-30.5kJ/mol)
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Regeneration
Any organism doing work is constantly using ATP, but ATP is renewable and can be regenerated by adding phosphate to ADP.
Free energy required for phosphorylate ADP comes from exergonic breakdown (catabolism).
ATP cycle - shuttles inorganic phosphate and energy, and it couples energy yielding (exergonic) processes to energy consuming (endergonic). This cycle also resembles the transfer of catabolic pathways to anabolic.
The process is irreversible, thus:
ADP + Pi YIELDS ATP + H2O; ΔG = +7.3 kcal/mol (+30.5 kJ/mol)
Concept 8.2
Free-Energy
(Gibbs) Free Energy - portion of a system's energy that performs work when the temperature and the pressure are uniform, or equal, throughout the system
Chemical Reaction Equation:
ΔG = ΔH -TΔS
change in free energy = change in enthalpy - the absolute temperature (K) change in the entropy
ΔG can also be represented as: ΔG = G (final state) - G (initial state). It can only be represented as negative when energy loss is detected
Systems want to reach stability, until they are disrupted. Equilibrium is seen as the maximum stability that can be reached.
Chemical reactions are reversible and eventually reach the same rate, which will balance out to chemical equilibrium.
Reaching equilibrium, free energy decreases. However, free energy increases when a reaction is moved away from equilibrium, causing a break in products.
"A process is spontaneous and can perform work only when it is moving toward equilibrium."
Sunlight provides a daily source of free energy for plants and other photosynthetic organisms. So, animals and other nonphotosynthetic organisms must gain a source of free energy.
Metabolism and FE
Exergonic reaction - occur spontaneously; energy going outward, net release of free energy and because it loses free energy, ΔG becomes negative. Also, the greater decrease in free energy, the greater amount of work done. downhill
(Breaking bonds doesn't mean that energy is released)
Endergonic reaction - occur nonspontaneously; absorbs free energy from its surroundings; because energy is "stored", it becomes positive. The magnitude of ΔG is needed to drive this reaction. uphill
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Concept 8.1
Metabolism
Forms of Energy
Energy exists in many forms and can be used to do work, which can move and rearrange matter against resisting forces, such as gravity and friction
- Kinetic Energy - motion of objects; moving objects that also perform work
- Thermal Energy - kinetic energy associated with random movement of atoms or molecules; this energy transfer from one object to another is heat
- Potential Energy - possesses still energy from location of object
- Chemical Energy - potential energy available for release in a reaction
- Energy is important because it is fundamental to all metabolic processes of cell and is necessary to know how a living cell works with energy.
- Bioenergetics - study of how energy flows through living organisms
Metabolism - emergent property of life that arises from orderly interactions between molecules. A "road map" of chemical reaction throughout a cell, arranged in pathways.It also manages material and energy in the cell.
Metabolic Pathway - has a starting molecule, then it is changed through different steps, and a certain product is produced. Each step is catalyzed by an enzyme.
Corresponds well with supply and demand and this process works very closely to traffic lights that control automobile traffic.
Metabolic Pathways
Catabolic pathways (breakdown) - pathway that releases energy to break down complex molecules to simple compounds; "downhill"
Cellular respiration - major catabolism pathway, when glucose and organic fuels break down when O2, CO2, and H2O are present
Biochemical pathway - carries out the cellular structures, which allows cells to release chemical energy from molecules and use the energy
Anabolic pathways (biosynthetic) - the total opposite, consume energy to build complex molecules from simple compounds; "uphill"
Anabolism Examples:
Synthesis of an amino acid from simple compounds
Synthesis of a protein from amino acids
Thermodynamics
Thermodynamics - study of energy transformation that occurs in collection of matter
Isolated systems are unable to exchange energy or matter with its surroundings, or everything outside of it. However, in an open system, both energy and matter can transferred between the system and surroundings. Organisms are open.
First Law
The First Law - known as the principle of conservation of energy, energy of the universe is constant. "Energy can be transferred or transformed, but it can't be created nor destroyed."
Energy can be shifted from one object to the next but that doesn't make the originating form of energy the producer of the energy. It is simply carried to and from and possessed throughout the organism.
Second Law
The Second Law - "Every energy transfer" or transformation increases the entropy, a quantity as a measure of molecular disorder, of the universe."
There is order when it comes to energy. However, there is also a drastic shift toward randomization of universal energy
Spontaneous process (energetically favorable) - process given, entropy increases, allowing the process to proceed without any input of energy
Nonspontaneous process - entropy decreases, and only occurs if energy is supplied to it; example: water can easily flow downhill but energy needed to push water uphill
Concept 9.1
Catabolic Pathways
- Fermentation - catabolic process that is partial degradation of sugars or other organic fuel that occur without the use of oxygen.
- Aerobic respiration - when oxygen is consumed as a reactant; involves prokaryotic and eukaryotic cells to carry out this process
- Anaerobic respiration - prokaryotic cells that don't use oxygen to harvest chemical energy
- Cellular respiration - considered both aerobic and anaerobic; set a metabolic reactions to convert nutrients to energy to produce ATP and then release waste products afterwards
Carbohydrates, fats, and proteins from food can be consumed as fuel for organisms. Starch is a major source of carbohydrates for animals to break down into glucose.
Cellular respiration:
C6H12O6 + 6O2 YIELDS 6H2O + Energy (ATP + heat) - exergonic
Catabolism is chemically linked only. Mainly through ATP.
Redox Reactions
Oxidation-reduction (redox) reaction - loss of electrons from one substance is oxidation; gain of electrons to one substance is reduction (reduction does add. it adds negative charges so the positive charge decreases)
- Reducing agent - electron donor
- Oxidizing agent - electron acceptor
Energy must be added in order for electrons to be pulled away from atoms. Electrons can also loss potential energy based on electronegativity
Concept 8.4
Enzymes
- Enzymes are macromolecules that act as catalysts - chemical agent that speeds up a reaction without being consumed by the reaction.
- Enzymes also help with the chemical flow of metabolism
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Speed Up Reactions
Heat can increase the rate of a reaction.
However:
1) High temperature denatures proteins and kill the cell
2) Heat would speed up all reactions, not just needed ones
For this matter, organisms should carry out catalysis - a process used y a catalyst to selectively speed up a reaction
Enzymes are specific as they catalyze reactions by lowering the EA barrier, which allows reactants to absorb energy to proceed to transition state. "An enzyme cannot change the ΔG for a reaction: it cannot make an endergonic reaction exergonic."
Substrate Specificity
- Substrate - reactant an enzyme acts on
- Enzyme-substrate complex - enzyme binding to its substrate(s) to create this
Active site - restricted region where enzymes bind the their corresponding substrate; this pocket is also where catalysis occurs.
The structure isn't set as a flat shape. It can alternate based on what best fits the substrate.
- Induced fit - tight binding after substrate contacts the enzyme; clasps
Catalysis in Active Site
Catalytic Cycle
- Two or more reactants present, allows active site to form accordingly
- Substrates enter the active site of the enzyme and clasp together
- Substrates are taken through multiple chemical reactions to reach transition state
- It is then taken down to the products, and when one substrate exits, another enters
- After this whole process is complete, enzymes can become saturated
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- Cofactors - bound tightly to the enzyme as permanent residents or they bind loosely and are reversibly along with substrates; cofactors of enzymes are inorganic like metals, iron, zinc
- Coenzyme - organic molecule where vitamins are important in nutrition because they act as raw material
Many enzyme inhibitors bind to enzymes with weaker interactions.
- Competitive inhibitors - reduced the productivity of enzymes by blocking substrates from entering active sites
- Noncompetitive inhibitors - do not directly compete with the substrate to bind to the enzyme active site; they will impede enzymatic reactions to bind to another part
It is common for natural molecules in the cell to act as inhibitors.
Concept 8.5
Controlling Metabolism
Tight regulation for cells metabolic pathways is crucial for organism to survive. If they ran the enzymes rabid throughout, issues would occurs.
Allosteric Regulation
- Allosteric regulation - describes a protein's function at one site is affected by binding to regular molecule at a separate site. Activate or inhibit regular molecules bind to regulatory site
- Enzymes naturally regulate throughout the cells and will regularly change shape and size to function accordingly in their active sites.
- Activators stabilize active forms and Inhibitors stabilize inactive forms
- Cooperativity has one binding substrate from inactive and stabilizes by locking the subunits in active confrontation.
Most enzymes are constructed from subunits, and are composed of polypeptide chains.
- Cooperativity - when catalytic activity is increased at other active sites; amplifies response of enzymes to substrates
- Feedback inhibition - metabolic control where metabolic pathways are halted by the binding of end products to an enzyme in the early stage
Concept 9.2
Glycolysis
Glycolysis - "sugar splitting" process; glucose is split from 6 carbons to 3 carbons; small sugars are oxidized and rearranged to form two pyruvate molecules
- This process occurs whether O2 is present or not.
Divided into two phases:
- Energy Investment Phase: cell "spends ATP"
- Energy Payoff Phase: "investment is paid off" when ATP is produced by substrate-level phosphorylation and NAD+ is reduced to NADH by electrons released from oxidation of glucose
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