Chapter 8 - An Introduction to Metabolism Flashcards
1
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A
Bioluminescence: When organisms convert energy into light.
2
Q
Metabolism
A
- The totality of an organism’s chemical reactions, consisting of catabolic and anabolic pathways, which manage the material and energy resources of the organism.
- An emergent property of life that arises from interactions between molecules within the cell
3
Q
Metabolic Pathway
A
- A series of chemical reactions that either builds a complex molecule (anabolic pathway) or breaks down a complex molecule to simpler molecules (catabolic pathway)
- Begins with a specific molecule and ends with a product
- Each step is catalyzed by a specific enzyme
- Structures within the cell help bring order to metabolic pathways
4
Q
Catabolic Pathways
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- A metabolic pathway that releases energy by breaking down complex molecules to simpler molecules
- Cellular respiration, the breakdown of glucose in the presence of oxygen, is an example of a pathway or catabolism
5
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Anabolic Pathways
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- A metabolic pathway that consumes energy to synthesize a complex molecule from simpler molecules
- The synthesis of protein from amino acids is an example of anabolism
6
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Bioenergetics
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- The study of how energy flows through organisms
- The overall flow and transformation of energy in an organism
7
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Energy
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- The capacity to cause change, especially to do work (to move matter against an opposing force)
- Energy can be converted from one form to another
- Forms of energy
- Kinetic energy
- Potential Energy
8
Q
Kinetic Energy
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- The energy associated with the relative motion of objects
- Moving matter can perform work by imparting motion to other matter
9
Q
Potential Energy
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- The energy that matter possesses as a result of its location or spatial arrangement (structure)
10
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Chemical Energy
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- Energy available in molecules for release in a chemical reaction
- A form of potential energy
11
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Heat (Thermal Energy)
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- The total amount of kinetic energy due to the random motion of atoms or molecules in a body of matter
- Heat is energy in its most random form
12
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Thermodynamics
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- The study of energy transformations that occur in a collection of matter
- Has 2 laws
- Energy flows into an ecosystem in the form of light and exits in the form of heat
13
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Isolated System
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- An energy system isolated from its surroundings
- Example is the liquid in a thermos
- Reactions in a closed system eventually reach equilibrium and then do no work
14
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Open System
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- An energy system where energy and matter can be transferred between the system and its surroundings
- Organisms are open systems
- Energy flows into an ecosystem in the form of light and exits in the form of heat
- Not in equilibrium; they are open systems experiencing a constant flow of materials
15
Q
The First Law of Thermodynamics
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- The principle of concervation of energy: Energy can be transferred and transformed, but it cannot be created or destroyed
- The energy of the universe is constant
16
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The Second Law of Thermodynamics
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- The principle stating that every energy transfer or transformation increases the entropy of the universe.
- During every energy transfer or transformation, some energy is often lost as heat
- Living cells unavoidably convert organized forms of energy to heat
17
Q
Entropy
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A measure of disorder, or randomness
18
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Spontaneous Process
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- A process that occurs without an overall input of energy
- For a process to occur without energy input, it must increase the entropy of the universe
- A process that is energetically favorable
- Can happen quickly or slowly
19
Q
Biological Order and Disorder
A
- Cells create ordered structures from less ordered materials
- Simpler molecules are ordered into the more complex structure of an amino acid, and amino acids are ordered into polypeptide chains.
- At the organismal level, complex and ordered structures result from biological processes that use simpler starting materials. (As in the picture)
- Organisms also replace ordered froms of metter and energy with less ordered forms
- An animal obtains starch, proteins, and other complex molecules from the food it eats. As catabolic pathways break these molecules down, the animal releases carbon dioxide and water (smaller molecules that possess less chemical energy than the food did.
- Energy flows into ecosystems in the form of light and exits in the form of heat.
20
Q
How does the evolution of more complex organisms not violate the second law of thermodynamics?
A
Entropy may decrease in an organism, but the universe’s total entropy increases.
21
Q
Free Energy (ΔG or δG)
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- The portion of a biological system’s energy that can perform work when temperature and pressure are uniform throughout the system.
- A measure of a system’s instability, its tendency to change to a more stable state
- Equilibrium is a state of maximum stability
- Spontaneous processes can be harnessed to perform work
- Only Processes with a negative ΔG are spontaneous
- During a spontaneous change, free energy decreases and the stability of a system increases
- A process is spontaneous andn can perform work only when it is moving toward equilibrium
- The change in free energy of a system (ΔG) during a process is related to the change in enthalpy, or change in total energy (ΔH), change in entropy (ΔS), and temperature in kelvin (T)
- ΔG = ΔH - TΔS
22
Q
Exergonic Reaction
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A spontaneous chemical reaction, in which there is a net release of free energy
23
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Endergonic Reaction
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A nonspontaneous chemical reaction, in which free energy is absorbed from the surroundings
24
Q
A defining feature of life is that metabolism is _____ at equilibrium.
A
Never
25
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Catabolic Pathway
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- A metabolic pathway that releases energy by breaking down complex molecules into simpler molecules.
- Releases free energy in a series of reactions
26
Q
The three main kinds of work done by the cell:
A
- Chemical
- Transport
- Mechanical
27
Q
Energy Coupling
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- In cellular metabolism, the use of energy released from an exergonic reaction to drive an endergonic reaction
- To do work, cell manage energy resources by energy coupling
- Most energy coupling in cells is mediated by ATP
28
Q
ATP (Adenosine Triphosphate)
A
- An adenine-ccontaining nucleoside triphosphate that releases free energy when its phosphate bonds are hydrolyzed.
- The release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves
- This energy is used to drive endergonic reactions in cells
- The cell’s “energy shuttle”
- Composed of a ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups
29
Q
How does the hydrolysis of ATP perform work?
A
- The three types of cellular work (mechanical, transport, and chemical) are powered by the hydrolysis of ATP
- In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction
- Overall, the coupled reactions are exergonic
- ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule
- The recipient molecule is now called a phosphorylated intermediate
30
Q
Phosphorylated Intermediate
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A molecule (often a reactant) with a phosphate group covalently bound to it, making it more reactive (less stable) than the unphosphorylated molecule
31
Q
How does ATP drive chemical work?
A
32
Q
How does ATP drive transport work?
A
33
Q
How does ATP drive mechanical work?
A
34
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The ATP Cycle
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- ATP is a renewable resource that is regenerated by 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 its transfer from catabolic to anabolic pathways
35
Q
Enzyme
A
- A macromolecule serving as a catalyst, a chemical agent that increases the rate of a reaction without being consumed by the reaction.
- Enzymes catalyze reactions by lowering the EA barrier
- Enzymes do not affect the change in free energy (ΔG); instead, they hasten reactions that would occur eventually
- The reactant than an enzyme acts on is called the enzyme’s substrate
- Enzymes have active and inactive forms
- Most enzymes are proteins encoded by genes
- Some enzymes act as structural components of membranes
- In eukaryotic cells, some enzymes reside in specific organelles
- Enzymes for cellular respiration are located in mitochondria
- Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction
36
Q
Activation Energy (EA)
A
- The amount of energy that reactants must absorb before a chemical reaction will start.
- Also called free energy of activation
- Activation energy is often supplied in the form of thermal energy that the reactant molecules absorb from their surroundings
37
Q
What is the effect of enzymes on the EA barrier?
A
- Enzymes catalyze reactions by lowering the EA barrier
- Enzymes do not affect the change in free energy (ΔG); instead, they hasten reactions that would occur eventually
38
Q
Substrate
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- The reactant on which an enzyme works
- In an enzymatic reaction, the substrate binds to the active site of the enzyme
39
Q
Enzyme-Substrate Complex
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- Formed when an enzyme binds to a substrate
40
Q
Active Site
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The specific region of an enzyme that binds the substrate and that forms the pocket in which catalysis occurs
41
Q
Induced Fit
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- Caused by entry of the substrate, the change in shape of the active site of an enzyme so that it binds more snugly to the substrate
- Induced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction
42
Q
The four ways the active site can lower an EA barrier:
A
- Orienting substrates correctly
- Straining substrate bonds
- Providing a favorable microenvironment
- Covalently bonding to the substrate
43
Q
What ca an enzyme’s activity can be affected by?
A
- General environmental factors, such as temperature and pH
- Each enzyme has an optimal an optimal temperature and pH in which it can function
- Optimal conditions favor the most active shape for the enzyme molecule
- Chemicals that specifically influence the enzyme
44
Q
Cofactors
A
- Any nonprotein molecule or ion that is required for the proper functioning of an enzyme.
- Cofactors can be permanently bound to the active site or may bind loosely and reversibly, along with the substrate, during catalysis
- May be inorganic (such as a metal in ionic form) or organic (coenzyme)
45
Q
Conenzyme
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- An organic molecule serving as a cofactor
- Most vitamins function as coenzymes in metabolic reactions
46
Q
Competitive Inhibitor
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- A substance that reduces the activity of an enzyme by entering the active site in place of the substrate, whose structure it mimics
- Compete with the substrate
- Examples of inhibitors include toxins, poisons, pesticides, and antibiotics
47
Q
Noncompetitive Inhibitor
A
- A substance that reduces the activity of an enzyme by binding to a location remote from the active site, changing the enzyme’s shape so that the active site no longer effectively catalyzes the conversion of substrate to product
- Examples of inhibitors include toxins, poisons, pesticides, and antibiotics
48
Q
The Evolution of Enzymes:
A
- Enzymes are proteins encoded by genes
- Changes (mutations) in genes lead to changes in amino acid composition of an enzyme
- Altered amino acids in enzymes may alter their substrate specificity
- Under new environmental conditions a novel form of an enzyme might be favored
49
Q
Allosteric Regulation
A
- The binding of a regulatory molecule to a protein at one site that affects the function of the protein at a different site
- May inhibit or stimulate an enzyme’s activity
- The binding of an activator stabilizes the active form of an enzyme
Inactive form - The binding of an inhibitor stabilizes the inactive form of the enzyme
- The binding of an activator stabilizes the active form of an enzyme
- Most allosterically regulated enzymes are made from polypeptide subunits
50
Q
Activator
A
- A protein that binds to DNA and stimulates gene transciption
- In eukaryotes, activators generally bind to control elements in enhancers
- In prokaryotes, activators bind in or near the promoter
51
Q
Cooperativity
A
- A kind of allosteric regulation whereby a shape change in one subunit of a protein caused by substrate binding is transmitted to all the other subunits, facilitating binding of additional substrate molecules to those subunits.
- Amplifies enzyme activity
- One substrate molecule primes an enzyme to act on additional substrate molecules more readily
- Cooperativity is allosteric because binding by a substrate to one active site affects catalysis in a different active site
52
Q
Why are allosteric regulators attractive drug candidates for enzyme regulation?
A
- Allosteric regulators are attractive drug candidates for enzyme regulation because of their specificity
- Inhibition of proteolytic enzymes called caspases may help management of inappropriate inflammatory responses
53
Q
Feedback Inhibition
A
- A method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway
- Prevents a cell from wasting chemical resources by synthesizing more product than is needed
