BIOL 1406 FLASHCARDS: Exam #3

Metabolism

Metabolism

The totality of an organism's chemical reactions; an emergent property of life that arises from orderly interactions between molecules

Metabolic Pathway

Begins with specific reactants and ends with specific products; each step is catalyzed by a particular enzyme

Catabolic Pathway

Releases energy by breaking down complex molecules into simpler compounds; cellular respiration is an example of this

Anabolic Pathway

Consumes energy in order to construct complex molecules from simpler ones; photosynthesis is an example of this

Bioenergetics

The study of how energy flows through living organisms

Energy

The capacity to cause change; can be converted from one form to another

Kinetic Energy

Energy associated with motion

Heat (Thermal Energy)

Kinetic energy associated with the random movement of atoms or molecules

Potential Energy

Energy that matter possesses because of its location or structure

Chemical Energy

Potential energy available for release in a chemical reaction

Isolated System

A system that is unable to exchange energy or matter with its surroundings

Open System

A system that has the ability to exchange energy and matter with its surroundings

Thermodynamics

The study of energy transformations

First Law of Thermodynamics

Also referred to as the principle of conservation of energy; states that energy can be transferred or transformed, but cannot be created nor destroyed

Second Law of Thermodynamics

States that every energy transfer or transformation increases the entropy of the universe

Spontaneous Process

A process that can occur without energy input; can happen quickly or slowly; must increase the entropy of the universe

Entropy (S)

The measure of the total amount of disorder caused by a thermodynamic system

Enthalpy (H)

The measure of the total amount of energy present in a thermodynamic system; represented by the equation H = G + TS

Free Energy (G)

The measure of the total amount of energy that is available to do work in a thermodynamic system; represented by the equation G = H - TS

Change in Free Energy (ΔG)

A measure of a thermodynamic system's instability; takes into account the system's "desire" to achieve a more stable state; represented by the equation ΔG = ΔH – TΔS

Positive ΔG

Means that free energy is required by a thermodynamic system

Negative ΔG

Means that free energy is released by a thermodynamic system

Equilibrium

A state of maximum stability that can be achieved in a reaction

Exergonic Reaction

A reaction that proceeds with a net release of free energy and is spontaneous (-ΔG); catabolic pathways are an example of this, as they generate disorder by decreasing complexity

Endergonic Reaction

A reaction that absorbs free energy from its surroundings and is not spontaneous (+ΔG); anabolic pathways are an example of this, as they create order by increasing complexity

Energy Coupling

The use of exergonic processes to drive endergonic processes

ATP (Adenosine Triphosphate)

The cell's main source of energy - captures and transfers free energy; composed of ribose, adenine, and three phosphate groups

Cellular Activities

Powered by ATP hydrolysis; includes mechanical work, chemical work, and the cell's transport of other molecules

ATP Hydrolysis

A chemical reaction where a phosphate bond on ATP is broken by water, thereby releasing a lot of energy - ATP is converted to ADP in this process

Phosphorylation

The process by which ATP drives endergonic reactions by transferring a phosphate group to another molecule

Phosphorylated Intermediate

The molecule that receives the phosphate group from ATP in phosphorylation

Catalyst

A chemical agent that speeds up a chemical reaction without being consumed by the reaction

Enzyme

A catalytic protein; increases the rate of a chemical reaction by decreasing the reaction's activation energy

Activation Energy

The initial energy required to start a chemical reaction; often supplied in the form of thermal energy that the reactants of the chemical reaction can absorb from their surroundings

Transition State

An intermediate state during a chemical reaction that has a higher energy than the reactants or the products; highly reactive and unstable

Substrate

The reactant that an enzyme acts on; the rate of a catalyzed reaction depends on the overall concentration of this

Enzyme-Substrate Complex

Created when an enzyme binds to its substrate

Active Site

Region of an enzyme where the substrate binds; catalyzes the reaction resulting in the production of particular products

Allosteric Site

Region of an enzyme where activators or inhibitors can bind in order to stimulate or hinder enzyme activity

Induced Fit

A continuous change in the conformation and shape of an enzyme in response to substrate binding

Saturation Point

A point at which all of the enzymes are bound to substrates, and no free enzymes exist in a particular chemical reaction; the enzyme is operating at maximum rate in this situation

Maximum Rate

Used to calculate enzyme efficiency

Factors Impacting Enzyme Activity

Can include temperature, pH, the presence of activators or inhibitors, and the overall substrate concentration and enzyme concentration within a particular reaction

Cofactors

The inorganic substances that are needed by certain enzymes in order to carry out catalysis of particular chemical reactions

Prosthetic Groups

Non-amino acid groups bound to enzymes

Inorganic Cofactors

Ions which are permanently bound to enzymes

Coenzymes

Small, carbon-containing molecules; not permanently bound to enzymes; vitamins are example of these

Allosteric Regulation

Can either stimulate or hinder an enzyme's activity in a reaction; occurs when a regulatory molecule binds to an enzyme's allosteric site, thereby affecting the functionality of the enzyme's active site

Active Form of an Enzyme

The binding of an activator to an enzyme's allosteric site stabilizes this form of the enzyme

Inactive Form of an Enzyme

The binding of an inhibitor to an enzyme's allosteric site stabilizes this form of the enzyme

Competitive Inhibitors

Bind to an enzyme's active site, thereby competing with the substrate in a particular reaction

Noncompetitive Inhibitors

Bind to a different part of an enzyme, thereby causing the enzyme to change shape and making the enzyme's active site less effective

Cooperativity

A form of allosteric regulation that can amplify enzyme activity

Feedback Inhibition

A cellular control mechanism in which the final product produced by a particular reaction acts as a noncompetitive inhibitor of the enzyme that created it, thereby shutting down the pathway; keeps a cell from wasting chemical resources by synthesizing more product than it actually needs

Aerobic

Describes respiration or other catabolic process that require oxygen; the citric acid cycle and oxidative phosphorylation are examples of this type of process

Anaerobic

Describes respiration or other catabolic process that do not require oxygen; glycolysis and fermentation are examples of this type of process

Fermentation

An anaerobic process that uses glycolysis and the reduction of pyruvate or acetaldehyde in order to generate ATP; produces 2 ATP molecules per glucose molecule

Alcohol Fermentation

Converts pyruvate to ethanol; releases carbon dioxide in order to form acetaldehyde, then reduces acetaldehyde in order to make ethanol; this process is used by yeast in brewing, winemaking, and baking

Lactic Acid Fermentation

Reduces pyruvate by using NADH and forms lactate as an end product with no release of carbon dioxide; used by some fungi and bacteria in order to make dairy products and human muscle cells use this process in order to generate ATP when oxygen is scarce

Obligate Anaerobes

Carry out fermentation and anaerobic respiration; cannot survive in the presence of oxygen

Facultative Anaerobes

Can survive by using either fermentation or cellular respiration; yeast and many bacteria are examples of these

Redox/Oxidation-Reduction Reactions

Chemical reactions that transfer electrons between reactants

Oxidation

A process in which an electron is removed from a molecule during a chemical reaction; the molecule's overall positive charge is increased by this process

Reduction

A process in which an electron is added to a molecule during a chemical reaction; the molecule's overall positive charge is decreased by this process

Oxidizing Agent

An electron acceptor

Reducing Agent

An electron donor

Cellular Respiration

A process that occurs in the mitochondria of eukaryotic cells and in the cytosol of prokaryotic cells; broken down into the subprocesses of glycolysis, pyruvate oxidation, the citric acid/Krebs cycle, and oxidative phosphorylation; uses glucose and oxygen in order to produce carbon dioxide, water, and energy (in the forms of ATP and heat); produces approximately 30-32 ATP molecules per glucose molecule

NAD+

A coenzyme and electron acceptor that functions as an oxidizing agent during cellular respiration

NADH

The reduced form of NAD+; represents stored energy that is tapped to synthesize ATP

Substrate Level Phosphorylation

A process in which a phosphate group from another carrier is added to ADP in order to form ATP; occurs in both glycolysis and the citric acid cycle

Electron Transport Chain (ETC)

A series of proteins and organic molecules found in the inner membrane of mitochondria; does not directly generate any ATP; works to create a proton concentration gradient across the inner mitochondrial membrane that plays a large role in chemiosmosis

Glycolysis

The first step in all forms of cellular energy harvesting; an anaerobic process that uses a glucose molecule and 2 ATP in order to produce 2 pyruvic acid molecules, 4 ATP, and 2 NADH; occurs inside the cytoplasm of both eukaryotic and prokaryotic cells

Pyruvate Oxidation

The intermediate step which links glycolysis to the citric acid cycle; occurs inside the mitochondrial matrix; the 2 pyruvic acid molecules produced by glycolysis are oxidized and converted to make 2 molecules of acetyl CoA in this step

Citric Acid Cycle/Krebs Cycle

The cyclical conversion of acetyl CoA into various other substances inside the mitochondrial matrix using recycled oxaloacetate; an aerobic process that generates 1 ATP, 3 NADH, and 1 FADH2 per rotation; produces 2 ATP, 6 NADH, and 2 FADH2 total

Oxidative Phosphorylation

The final step of cellular respiration; involves the use of the ETC and the process of chemiosmosis; uses oxygen in order to phosphorylate ADP molecules, producing approximately 26-28 ATP and a lot of water and heat

Chemiosmosis

The process by which ATP is produced during oxidative phosphorylation; the proton-motive force generated by the electrons moving down the ETC powers ATP synthase, which acts as a mill; H+ powers the phosphorylation of ADP, forming ATP

Cytochromes

Redox-active proteins containing a heme, with a central iron atom at its core, that function as electron carriers in the electron transport chain

ATP Synthase

A multi-subunit protein complex that uses an electrochemical proton motive force across a membrane to make the cell's supply of ATP from ADP and inorganic phosphate (Pi)

Proton Motive Force

Energy that is generated by the transfer of protons or electrons across an energy-transducing membrane

Beta Oxidation

A metabolic process involving multiple steps by which fatty acid molecules are broken down to produce energy and acetyl CoA

Gluconeogenesis

The process of making glucose from its own breakdown products, or from the breakdown products of lipids or proteins; often uses glycolysis and citric acid cycle intermediates

Photosynthesis

An autotrophic process that converts solar energy into chemical energy; occurs in plants, algae, other unicellular eukaryotes, and some prokaryotes

Autotrophs

Organisms that can produce their own food using materials from inorganic sources

Photoautotrophs

Organisms that carry out photosynthesis

Heterotrophs

Organisms that cannot produce their own food and must obtain their energy by consuming other organisms

Chloroplasts

A cell organelle that produces energy through photosynthesis

Stomata

Microscopic pores in the shoot epidermis of plants; allow for carbon dioxide to enter and for oxygen the mesophyll layer of leaves

Stroma

The fluid-filled internal space of the chloroplasts which encircle the grana and the thylakoids

Lumen

The space inside of thylakoid discs

Thylakoids

The internal membranes of chloroplasts that provide the platform for the light-dependent reactions of photosynthesis

Grana

Stacks of thylakoid discs

Chlorophyll

The pigment that gives plants their green color and allows them to absorb sunlight; resides in the thylakoid membranes; absorbs red and blue light and reflects green light

Chlorophyll A

The main photosynthetic pigment; has a hydrocarbon "tail" which anchors it into a photosystem in the thylakoid membrane

Chlorophyll B

Accessory pigments that broaden the spectrum used for photosynthesis

Anoxygenic Photosynthesis

The phototrophic process where light energy is captured and converted to ATP, without the production of oxygen; often used by bacteria

Light-Dependent Reactions

The first half of photosynthesis; captures light energy and uses it to create a concentration gradient that is used to produce NADPH and ATP; occurs in the thylakoids of chloroplasts

Photophosphorylation

A process in which light energy is converted to ATP once the transfer of electrons from chlorophyll pass through a system of carrier molecules

Calvin Cycle

The second half of photosynthesis; for the net synthesis of 1 G3P, the cycle must turn 3 times, fixing 3 molecules of carbon dioxide; it takes 6 carbon dioxide molecules, 18 ATP, and 9 NADPH to produce one molecule of glucose (or 2 G3P), meaning that the cycle must turn 6 times per the production of one molecule of glucose

Rubisco

Catalyzes the first step of carbon fixation; functions as a carbon dioxide acceptor

Carbon Fixation

The first phase of the Calvin cycle wherein photosynthetic organisms turn inorganic carbon into organic compounds, primarily carbohydrates