Please enable JavaScript.
Coggle requires JavaScript to display documents.
Metabolism and Cellular Respiration (Enzymes (Regulation of Enzyme…
Metabolism and Cellular Respiration
Metabolism
Definitions
Def
. Anabolic Pathways: Consumption of energy to build complex molecules from simpler compounds.
Def
. Metabolic Pathway: A series of chemical reactions, catalyzed by enzymes, that start with a molecule and ends with the product(s).
Def
. Bioenergetics: The study of how energy flows through organisms.
Def
. Metabolism: The chemical processes that occur within a living organism in order to maintain life.
An emergent property of life that arises from orderly interactions between molecules.
Def
. Catabolic Pathway: The breakdown of complex molecules into simpler compounds to release energy.
Ex. Cellular Respiration: the break down of glucose in the presence of oxygen.
Reactions in Metabolism
Def
. Exergonic Reaction: Proceeds with a net release of free energy and is spontaneous.
Def
. Endergonic Reaction: Absorbs free energy from it's surroundings and is non-spontaneous.
Equilibrium and Metabolism
Reactions in a closed system eventually reach equilibrium and can do no work.
Cells are not in equilibrium; they're open systems experiencing a constant flow of materials.
Metabolism is never at equilibrium.
Catabolic pathways in a cell releases free energy in a series of reactions.
Energy and Energy Transformation
Def
. Energy: The capacity to cause change, existing in various forms; some of which can do work.
Forms
Kinetic Energy: Energy associated with motion.
Thermal Energy: Kinetic energy associated with random movement of atoms or molecules.
Chemical Energy: Potential energy available for release in a chemical reaction.
Potential Energy: Energy matter possesses because of it's location or structure.
Energy can be converted from one form to another.
Laws of Energy Transformation
Def
. Thermodynamics: The study of energy transformations.
In an isolated system the system is unable to exchange energy or matter with it's surroundings.
In an open system the system is able to exchange energy and matter with it's surroundings.
Organisms are open systems.
Second Law of Thermodynamics
Every energy transfer or transformation increases the entropy of the universe.
Entropy is a measure of molecular disorder, or "randomness".
First Law of Thermodynamics
Energy can be transferred and transformed, but it cannot be created or destroyed.
The energy of the universe is constant.
Spontaneous processes occur without energy input; They can be quick or slow.
Living cells convert organized forms of energy into heat, a disordered form of energy.
For a process to happen spontaneously, it must increase the entropy of the universe.
Processes that decrease entropy are non-spontaneous; only occurring if energy is provided.
Biological Order and Disorder
Organisms create ordered structure from less organized forms of energy and matter.
Organisms also replace ordered forms of matter and energy in their surroundings with less ordered forms.
Evolution of complex organisms doesn't violate the second law of thermodynamics.
Entropy (disorder) may decrease in a particular system as long as the total entropy of the system and surroundings increases.
Free Energy, Stability, and Equilibrium
Def
. Free Energy: Energy that can do work when temperature and pressure are uniform.
Free energy is the measure of a system's instability, and it's tendency to change to a more stable state.
During a spontaneous change, free energy decreases and the stability of the system increases.
A process is spontaneous and can perform work only when it's moving towards equilibrium.
The change in free energy (ΔG) during a process is related to the change in entropy (ΔS) and temperature in Kelvin units (T).
ΔG = ΔH-TΔS
ΔG is negative for all spontaneous processes.
Processes with zero or positive ΔG are never spontaneous.
Equilibrium is the state of maximum stability.
Cellular Work
Cells do three main kinds of work.
Transport Work - Ex. Pumping substances against the direction of spontaneous movement
Mechanical work - Ex. such as contraction of muscle cells.
Chemical Work - Ex. pushing endergonic reactions.
Cells manage resources by energy coupling, the use of an exergonic process to drive an endergonic one, to do work.
Most energy coupling in cells in mediated by ATP.
ATP (Adenosine Triphosphate) is the cell's energy shuttle.
ATP is composed of a Ribose (sugar), adenine (nitrogenous base), and three phosphate groups.
The bonds between the phosphate groups of ATP's tail can be broken by hydrolysis.
Energy is released from ATP when the terminal phosphate bond is broken.
Energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds.
ATP drives endergonic reactions by phosphorylation transferring a phosphate group to some other molecule, such as a reactant.
Reactions
Glutamic Acid + Ammonia :arrow_right: Glutamine (Glutamic acid conversion to Glutamine)
Glutamic Acid + ATP :arrow_right: Phosphorylated intermediate + ATP [in the presence of ammonia] :arrow_right: Glutamine + ADP + Pi (Conversion Reaction coupled with ATP Hydrolysis)
ATP hydrolysis leads to a change in protein shape and binding ability.
ATP Regeneration
ATP is a renewable source that is recognized by the addition of a phosphate group to adenosine diphosphate (ADP).
The energy to phosphorylate ADP comes from catabolic reactions in the cell.
The ATP cycle is a revolving door through which energy passes during it's transfer from catabolic to anabolic pathways.
Enzymes
Catalysis
Def
. Catalysis: Enzymes or other catalysts speed up specific reactions by lowering the Ea barrier.
Enzymes do not effect the change in free energy (ΔG); instead, they hasten reactions that would occur eventually.
Is an Enzymatic reaction, the substrate binds to the active site of the enzyme.
Enzymes are extremely fast acting and emerge from reactions in their original form.
Very small amounts of enzyme can have huge metabolic effects because they are used repeatedly in catalytic cycles.
The Active Site Can Lower The Ea Barrier By
Straining substrate bonds
Providing a favorable micro-environment
Orienting substrates correctly
Covalently bonding the substrate
Substrate Specificity
The reactant that an enzyme acts on is called the enzyme substrate.
The enzyme binds to its substrate forming an enzyme-substrate complex.
While bound, the activity of the enzyme converts the substrate to product.
The activation site is the region on the enzyme where the substrate binds.
Induced fit of a substrate brings chemical groups of the activation site into positions that enhance their ability to catalyze the reaction.
The reaction catalyzed by each enzyme is very specific.
The Rates of an Enzyme-Catalyzed Reaction Can be Sped up by Increasing Substrate Concentration
When all enzyme molecules have their active sites engaged, the enzyme is saturated.
If the enzyme is saturated, the reaction rate can only be sped up by adding more enzyme.
Activation Energy Barrier
Every chemical reaction between molecules involves bond breaking and forming.
The initial energy required to start a chemical reaction is called the free energy activation, or activation energy (Ea).
Activation energy is often supplied in the form of thermal energy that the reactant molecules absorb from their surroundings.
Effects of Local Conditions on Enzyme Activity
Enzyme activity can be affected by
Environmental Factors; pH and Temperature
Chemicals
Effects of Temperature and pH
Each Enzyme has an optimal temperature in which it can function.
Each enzyme has an optimal pH in which it can function.
Optimal conditions favor the most active shape for the enzyme molecule.
Cofactor
Cofactor are non-protein enzyme helpers
May be inorganic, such as metals in ion form, or organic.
An organic cofactor are called coenzymes
Coenzymes include vitamins
Enzyme Inhibitors
Def
. Noncompetitive Inhibitors: Bind to another part of the enzyme, causing the enzyme to change shape and making the active site less effective.
Some examples of inhibitors are toxins, poisons, and antibiotics.
Def
. Competitive Inhibitors: Bind to the active site of an enzyme, competing with the substrate.
Enzymes are catalytic proteins.
Catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction.
Evolution of Enzymes
Altered amino acid, particularly at the activation site, can result in novel enzyme activity or altered substrate specificity.
Under environmental conditions where the new function is beneficial, natural selection would favor the mutated allele.
Enzymes are proteins encoded by genes.
Changes (mutations) in genes lead to changes in amino acid composition of an enzyme
Regulation of Enzyme Activity & Metabolism
Cells switch on and off genes that encode specific enzymes, and regulate the activity of these enzymes.
Allosteric Regulation
Either inhibits or stimulates enzyme activity.
Occurs when a regulatory molecule binds to a protein at one side and effects the proteins function and another site.
Allocentric Activation and Inhibition
Allosterically regulated enzymes are made from polypeptide sub-units, each with it's own active site.
The enzyme complex has active and inactive forms
The binding of an inhibitor stabilizes the inactive from of the enzyme.
The binding of an activator stabilizes the inactive form of the enzyme.
Cooperativity is a form of allosteric regulation that can amplify enzyme activity
One substrate molecule primes an enzyme action additional molecules more readily.
Cooperativity is allosteric because binding by a substance to one active site affects catalysis in a different active site.
Feedback Inhibition
Feedback inhibition, the end product of a metabolic pathway shuts down the pathway.
Feedback Inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed.
Cellular Respiration
Breathing vs. Respiration
Def
. Breathing: The alteration of inhalation and exhalation.
Def
. Respiration: Gas exchange between organisms and it's environment.
Groups
Aerobic - with oxygen
anaerobic - without oxygen
Steps of Cell Respiration
Transition Reaction
Occurs from the cytoplasm tot he mitochondria; doesn't require oxygen
Reaction
Pyruvate + Coenzyme A + NAD
:arrow_right:
Acetyl CoA
CO2
NADH
Reactants and Products
Reactants
2 Pyruvic Acid
2 NAD
2 Coenzyme A
Products
2 CO2
2 NADH
2 Acetyl CoA
Krebs Cycle
Occurs within mitochondrial matrix; doesn't require oxygen
Reaction (occurs x2 per glucose)
Acetyl CoA + 2C
:arrow_right:
Citric Acid + NAD
:arrow_right:
Alpha-Ketoglutaric Acid + NAD + ADP + P
1 more item...
CO2
CoA
Reactants and Products
Reactants
2 Acetyl CoA
6 NAD
2 ADP + 2P
2 FAD
Products
4CO2
6NADH
2FADH2
2ATP
Glycolysis
occurs in cytoplasm of cell near the mitochondria; Doesn't require oxygen.
Reactions
Glucose + ATP
:arrow_right:
Glucose-6-Phosphate
:arrow_right:
Fructose-6-Diphosphate + ADP
1 more item...
ADP
Reactants and Products
Reactants
Glucose
2NAD
2 ADP +2P
Products
2 ATP
2 Pyruvic acid
2 NADH
2H
Phosphorylation
Enzymes transfer a phosphate group from a substrate molecule directly to ADP to make ATP
Electron Transport System
Occurs with in inner mitochondrial membrane; Aerobic
Reaction
NADH + Electron carrier
:arrow_right:
Electrons passed down the chain of carriers
:arrow_right:
4 Electrons + O2 + 8H
1 more item...
H+ pumping
Hydrogen Ion gradient creates potential energy which is used by the synthase to bond P to ADP to form ATP.
Reactants and Products
Reactants
10 NADH
2FADH2
O2
H+
ADP & P
Products
H2O
32-34 ATP
NAD
FAD
Oxidative Phosphorylation
Occurs in cristea of mitochondrion
Responsible for greatest ATP preoduction
Term Oxidative comes from the use of oxygen as terminal electron acceptor.
Term Phosphorylation comes from the molecule of ADP being phosphorylated to ATP
As electrons are transported down the chain, energy is released
Energy is used to make ATP from ADP and P
Final acceptor of the electrons is oxygen
Aerobic
Oxygen removes the hydrogen and electrons making water
Electron carriers bring electrons to a groups of coenzymes
How Various Nutrients Yield Energy
Fatty Acids
:left_right_arrow:
Fats
:left_right_arrow:
Glycerol
:left_right_arrow:
Glycolysis
1 more item...
Fermentation
Anaerobic Reaction
Break down of glucose into two pyruvic acid
Pyruvic acid is converted into carbon dioxide and either ethyl alcohol or lactic acid.
Ethyl Alcohol Fermentation
Yeast :arrow_right: Wine or Bread
Pyruvic acid is converted into CO2 and Ethyl alcohol; and NAD is recycled
Glucose + 2ADP +2P
(Glycolysis) :arrow_left:
2 Pyruvic Acid + 2NADH + 2H
:arrow_left:
3 more items...
2ATP
2NADH
Lactic Acid Fermentation
Bacteria :arrow_right: Cheese or Yogurt
Pyruvic Acid is converted into Lactic acid and NAD is recycled.
Glucose + 2 ADP +2P + 2NAD
:arrow_left:
Pyruvic Acid + 2NADH + 2H
:arrow_left:
2 more items...
2ATP
2NADH
