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Metabolism/Cellular Respiration (Enzymes in metabolic reactions (Cofactors…
Metabolism/Cellular Respiration
Metabolism transforms matter and energy
Metabolism is the totality of an organism's chemical reactions
Metabolism is an emergent property of life
Arises from orderly interactions between molecules
Pathways
Metabolic Pathway
begins with a specific molecule and ends with a product
each step is catalyzed by a specific enzyme
Catabolic Pathways
release energy by breaking down complex molecules into simpler compounds
Cellular respiration is an example of a pathway of catabolism
releases free energy in a series of reactions
Anabolic Pathways
Consume energy to build complex molecules from simpler ones
the synthesis of protein from amino acids is an example
Bioenergetics is the study of how energy flows through living organisms
Energy
Forms of Energy
Kinetic energy is associated with motion
Thermal energy is the kinetic energy associated with random movements
Potential energy is the energy that matter possesses due to location/structure
Chemical energy is potential energy available for release in a chemical reaction
Energy is the capacity to cause change
Can be converted from one form to another
Laws of energy transformation
Thermodynamics is the study of energy transformations
Isolated system
unable to exchange energy or matter with its surroundings
Open system
energy and matter can be transferred between system and its surroundings
Organisms are open systems
Laws of thermodynamics
Energy can be transferred and transformed, but it cannot be created or destroyed (principle of conservation of energy)
Every energy transfer or transformation increases the entropy of the universe
Entropy is a measure of molecular disorder, or randomness
Living cells unavoidably convert organized forms of energy to heat (more disordered form of energy)
Spontaneous processes occur without energy input; they can happen quickly or slowly
for a process to occur spontaneously, it must increase the entropy of the Earth
Processes that decrease entropy are non-spontaneous: only occur is energy is provided
Free-energy showing if reactions are spontaneous or not
Free Energy, stability, and equilibrium
Free energy is energy that can do work when temp and pressure are uniform, as in a living cell
the change in free energy is negative for all spontaneous processes; processes with zero/positive Delta Gs are never spontaneous
During spontaneous changes, free energy decreases and the stability of a system increases
Equilibrium is a state of maximum stability
processes can only be spontaneous when moving towards equilibrium
Reactions/Equilibrium in metabolism
Exergonic reactions proceed with a net release of free energy and is spontaneous
Endergonic reactions absorb free energy from its surroundings and is non-spontaneous
Reactions in a closed system eventually reach equilibrium and can then do no work
Cells are not in equilibrium; they're open systems with constant flow of materials
A defining feature of life is that metabolism is never at equilirbium
ATP in cell
Three kinds of work a cell does
Transport Work
Pumping substances against the direction of spontaneous movement
Chemical work
Pushing endergonic reactions
Mechanical Work
contraction of muscle cells
Energy coupling
use of an exergonic process to drive an endergonic one
mostly mediated by ATP
ATP structure/hydrolysis
ATP is the cell's energy shuttle
composed of a sugar (ribose), adenine (nitrogenous base), and three phosphate groups
Hydrolysis
The bonds between the phosphate groups of ATP's tail can be broken down by hydrolysis
Coupled reactions are exergonic
when the terminal phosphate is broken, energy is released
this comes from the chemical change to a state of lower free energy
all three types of cellular work are powered by the hydrolysis of ATP
the energy from the exergonic reaction can be used to drive an endergonic reaction
ATP drives endergonic reactions by phosphorylation (transfer of a phosphate groups to another molecule)
the recipient molecule is then called a
phosphorylated intermediate
ATP is regenerated by addition of a phosphate group to
adenosine diphosphate
(ADP + P)
the energy to phosphorylate ADP comes from catabolic reactions in the cell
ATP cycle is a revolving door through which energy passes during transfer from catabolic to anabolic pathways
Enzymes in metabolic reactions
Enzymes are catalytic proteins (speeds up reactions without being consumed by reaction)
Activation energy barrier
The initial energy needed to start a chemical reaction is called the
activation energy
Activation energy is often suppled through thermal energy that reactant molecules absorb from surroundings
Catalysis
enzymes or other catalysts speed up specific reactions by lowering the activation energy barrier
enzymes do not affect the change in free energy; they actually quicken reactions that would naturally occur
In an enzymatic reaction, the substrate binds to the active site of the enzyme
Enzymes emerge from their reactions in their original form
Catalysis in the active site
The rate of an enzyme-catalyzed reaction can be sped up by increasing substrate concentration
The active site can lower can lower the E(A) barrier by
orienting substrates correctly
straining substrate bonds
providing a favorable microenviornment
covalently bonding to the substrate
when all enzyme molecules have active sites engaged, the enzyme is
saturated
If an enzyme is saturated, the reaction can only be sped up by adding more enzyme
Substrate Specificity
an
enzyme substrate
is the reactant that an enzyme acts on
the enzyme binds to its substrate, forming an enzyme-substrate complex
the
active site
is the region on the enzyme where the substrate binds
induced fit
of a substrate brings chemical groups from the active site into advantageous positions for catalyzation
while bound, the enzyme converts the substrate to a product
Effects of Temperature and pH
Each enzyme has an optimal temp/pH that it can function in
Optimal conditions favor the most active shape for the enzyme molecule
Cofactors
nonprotein enzyme helpers
cofactors may be inorganic (like metal in ionic form) or organic
an organic cofactor is called a
coenzyme
Coenzymes include vitamins
Enzyme Inhibitors
Competitive inhibitors
bind to the active site of an enzyme, competing with the substrate
noncompetitive inhibitors
bind to another part of an enzyme, causing the enzyme to change shape--making the active site less effective
Some examples of inhibitors are toxins, poisons, pesticides, and antibiotics
Regulation of enzyme activity
Allosteric regulation of enzymes
occurs when a regulatory molecule binds to a proteins at one site and affects the protein's function to another site
may either inhibit or stimulate an enzyme's activity
Allosteric activation/inhibition
most allosterically regulated enzymes are made from polypeptide subunits, each with it's own active site
the enzyme complex has active and inactive forms
The binding of an activator stabilizes the active form of the enzyme
The binding of an inhibitor stabilizes the inactive form of the enzyme
cooperativity
is a form of allosteric regulation that can amplify enzyme activity
One substrate molecule primes an enzymes to act on additional substrate molecules more readily
Cooperativity is allosteric because binding by a substrate to one active site affects catalysts in a different active site
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 needed
Localization of enzymes
Some enzymes act as structural components of membranes
In eukaryotic, some enzymes reside in specific organelles (i.e. enzymes for cellular respiration are located in the mitochondria)
Cellular respiration
Respiration
is a gas exchange between organism and its environment
Aerobic respiration occurs with oxygen
Anaerobic occurs without ;
Breathing
is the alternation of inhalation and exhalation
Steps in Cell Respiration
Glycolysis (Transition Reaction)
Anaerobic reaction that occurs in cytoplasm of cell near mitochondria
Reactants
1 gkucose
2NAD+ from ETS
2ADP +2P
Products
2 ATP
2 pyruvic acid
2 NADH go to ETS
2H +
Transition Reaction
Anaerobic reaction that occurs from cytoplasm through the mitochondria
Reactants
2 Pyruvic acid
2 NAD+ from ETS
2 coenzyme A
Products
2CO2
2NADH-go to ETS
2 Acetyl CoA
Krebs Cycle
Anaerobic reaction that occurs in the mitochondrial matrix
Reactants
2 Acetyl CoA
6 NAD+ from ETS
2 ADP + 2P
2 FAD from ETS
Products
4 CO2
6 NADH go to ETS
2 FADH2 go to ETS
2 ATP
Electron Transport System
Aerobic reaction that occurs in the inner mitochondrial membrane
Reactants
10 NADH
2 FADH2
O2
H+
ADP, P
Products
H20
32 or 34 ATP
NAD+
FAD
Oxidative Phosphorylation
occurs in cristae of mitochondrian
responsible for greatest production of ATP
oxidative comes from use of oxygen as terminal electron acceptor
term phosphorylation comes from molecule of ATP being phosphorylated to ATP
Aerobic
electron carriers bring the electrons to a group of coenzymes (the electron transport chain)
energy is released as electrons are transported down the unit
the energy is used to make ATP from ADP and P
Final Acceptor of the electrons is oxygen
Oxygen removes the hydrogen and electrons, making water