Biology Test 2 Terms

Oxidation-reduction (redox) reactions

Chemical reactions that involve electron transfers

Oxidizing agent

The electron acceptor in a redox reaction; it is reduced

Reduced

Gains a share of electrons

Reducing agent

The electron donor in a redox reaction; it is oxidized

Oxidized

Loses a share of electrons

Energy

Capacity for change or to do work; released as heat and light

Chemical equilibrium

When the forward and reverse reactions occur at the same rate

Metabolism

All of an organism’s chemical reactions

Catabolic pathways

Release energy by breaking down molecules into smaller components; exergonic

Exergonic

A reaction that releases energy; has a negative ΔG

Spontaneous

Happens without energy input

Anabolic pathways

Require or consume energy to build complex molecules from smaller building blocks; endergonic

Endergonic

A reaction that requires energy input; has a positive ΔG

Nonspontaneous

requires E input

ADP

Adenosine diphosphate

Pi

Inorganic phosphate

ATP

Adenosine triphosphate; the energy currency/source of energy of the cell

Potential energy

Stored energy; energy of state or position

Kinetic energy

Energy of movement

1st Law of Thermodynamics

Energy can change forms but cannot be created or destroyed

Entropy (S)

Disorder; higher when molecules have more space to move around

Unusable energy

Energy that is lost during energy transformations as entropy increases

Gibbs’ Free Energy (G)

Energy available to do work

Enthalpy (H)

Total energy

S × absolute temperature (T in K)

Unusable energy

Equilibrium

A state in which there is no net change; at equilibrium, ΔG = 0

Catalysts

Increase the speed of reactions by lowering activation energy; are not altered by the reaction and can be reused; do not change ΔG

Activation energy

Energy required to achieve the transition state of a reaction

Enzymes

Biological catalysts, often proteins and sometimes RNA molecules, that are highly specific for reactants and reactions

Enzyme substrate (ES) complex

The substrate and enzyme approach one another

Functional groups align so that the substrate can non-covalently bind to the active site (conformational change)

Substrate binds to enzyme’s active site, forming an enzyme-substrate complex

Substrate is converted into product(s); enzyme is released

The products are released (conformational change allows this to happen)

High-energy transition state

unstable arrangement of atoms at the peak of a reaction's E barrier where old bonds break and new bonds form (height of EA)

Path determines speed

Living cells can’t use this strategy because of non-specificity and denaturation of proteins

Oxidoreductases

Enzymes that catalyze electron transfer/oxidation

Transferases

Enzymes that catalyze movement of functional groups between molecules

Hydrolases

Enzymes that use water to break covalent bonds

Lyases

Enzymes that break covalent bonds without water, often forming new bonds

Isomerases

Enzymes that change covalent bonding patterns within the same molecule

Ligase

Enzyme that joins two molecules together

Orientation

Enzyme mechanism in which substrates are lined up in the correct orientation to react

Physical strain

Enzyme mechanism in which the enzyme puts pressure on bonds that will be broken and strains the substrate

Chemical charge

Enzyme mechanism in which R groups lining the active site directly make substrates more reactive

Acid-base catalysis

acidic or basic side chains can transfer H+ or accept H+ from substrate

Covalent catalysis

A temporary covalent bond forms between the enzyme and substrate and is resolved during the reaction cycle

Metal ion catalysis

Metal ion cofactors bound to R groups can lose or gain electrons and are important for redox reactions

Prosthetic groups

permanently bound to their enzymes, non-amino acid

Inorganic cofactors

Metal ions that are permanently bound to their enzyme

Coenzymes

Organic molecules that are not permanently bound; bind to an active site, change chemically, then separate and participate in other reactions

Induced fit

Conformational change that occurs upon substrate binding

Michaelis-Menten enzyme kinetics

When not much enzyme is present, can get a representation of enzyme activity – “How good is an enzyme at high concentration vs. low concentration?”

Michaelis-Menten equation developed by lining up tubes with the same amounts of enzymes and different amounts of substrates

Ended up being very useful in the development of pharmaceuticals (Leonor Michaelis & Maud Menten)

Enzyme kinetics

Measuring the rate of reactions under varying conditions

Vmax

Saturation point for a particular amount of enzyme; maximal reaction rate when substrate is not limiting

KM

Substrate concentration at which reaction velocity is half maximal

Enzyme affinity

How often an enzyme sticks to substrates while collisions are occurring

Post translational modifications

regulates enzymes; Covalent addition of a functional group (i.e., phosphate), causing a conformational change in the protein to regulate its activity; includes phosphorylation

Phosphorylation

Addition of a phosphate group onto a protein

Irreversible enzyme inhibitors

Inhibitors that bind covalently to the active site of enzymes and change their activity

Reversible enzyme inhibitors

nnon-covalently; normal enzyme-substrate binding to active site

• INCLUDES ALL COMPETITION

Competitive inhibition

Inhibitor binds to the active site, preventing substrate binding; resembles the substrate but does not act the same

Uncompetitive inhibition

inhibitor bnds to the ES complex, preventing release of products; only happens when correct substrate is already bound

Noncompetitive inhibition

Inhibitor binds at a site other than the active site, changing enzyme structure so normal substrate binding cannot occur

Allosteric site

A site other than the enzyme’s active site where a molecule can bind and change enzyme structure

Glycolysis

The process of breaking apart/splitting glucose; converts one 6

Kinase

Enzyme that transfers a phosphate group from one molecule to another

Isomerase

Enzyme that converts a molecule into an isomeric form

Glyceraldehyde 3-phosphate (G3P)

oxidized to give 1 NADH & 2 ATP in Energy Payoff phase of glycolysis

Dehydrogenase

Enzyme that catalyzes a redox reaction

Mutase

Enzyme that moves a functional group within a molecule; a type of isomerase

NADH (adenine dinucleotide)

carrier of “high-energy” electrons

NAD+

Oxidized form of NADH; accepts electrons and is reduced to NADH

Substrate level phosphorylation

transfer phosphate to make ATP; glycolysis

Fermentation

Anaerobic process that re-oxidizes NADH back to NAD+

in cytosol

Lactic Acid Fermentation

Pyruvate is directly reduced to lactate by lactate dehydrogenase while NADH is oxidized to NAD+

Alcoholic Fermentation

A two-step process: pyruvate is decarboxylated into acetaldehyde (releasing CO2), which is then reduced to ethanol, oxidizing NADH to NAD+; occurs in yeast

Pyruvate Oxidation

Process that converts each 3-Cpyruvate into acetyl-CoA to connect glycolysis with the citric acid cycle in cellular respiration

Pyruvate

a three-carbon molecule that serves as a central intersection point for cellular energy metabolism

Citric Acid Cycle (CAC)

Acetyl-CoA (2C) condenses with oxaloacetate (4C; regenerates Acetyl-CoA) to form citrate (6C)

Through sequential steps, oxaloacetate is regenerated, fully oxidizing the carbon skeletons of glucose into CO2

Acetyl-CoA

a crucial molecule in metabolism that delivers acetyl groups to the citric acid cycle to produce cellular energy (citric acid cycle)

Oxaloacetate

4-C molecule that regenerates Acetyl-CoA

Citrate

6-C; rearranged and reproduced, setting up the subsequent carbon-loss and energy-yielding steps in CAC

Citrate synthase

Enzyme involved in the citric acid cycle that catalyzes formation of citrate

Isocitrate dehydrogenase

Enzyme in the citric acid cycle that catalyzes a reaction involving NAD+ → NADH + H+

a-ketoglutarate dehydrogenase

a key multi-enzyme complex in the mitochondria in the CAC

Electron Transport Chain (ETC)

a series of protein complexes and organic molecules in the inner mitochondrial membrane that transfer electrons to generate a proton gradient, which powers ATP synthesis

Cristae

Folds of the inner mitochondrial membrane where the electron transport chain is embedded

Complex I (NADH Q reductase)

Accepts electrons from NADH

Complex II (Succinate dehydrogenase)

ETC complex that accepts electrons from FADH2

Ubiquinone (Coenzyme Q)

Mobile electron carrier that shuttles electrons from Complexes I and II to Complex III

Chemiosmosis

Process in which protons flow down their electrochemical gradient through ATP synthase to drive ATP production

F0

Rotor subunit of ATP synthase that rotates as protons flow through it

Cellular respiration

Aerobic process involving complete oxidation of glucose; produces CO2 and H2O and captures energy as ATP

Photosynthesis

Process that is essentially respiration in reverse; oxidizes H2O and reduces CO2 to produce glucose and O2

Stomata

Openings that allow gas exchange; CO2 enters while O2 and H2O exit

Grana

Stacks of thylakoids

Thylakoid lumen

One continuous inner aqueous space enclosed by the thylakoid membrane

Thylakoid membrane

Specialized internal membrane system that hosts the light

Light-dependent reactions

Occur in thylakoid membrane

Split H2O (releasing O2)

Reduce NADP+ to NADPH (stroma)

Generate ATP from ADP + Pi (stroma)

NADP+

Electron acceptor that is reduced to NADPH during the light reactions

NADPH

Reduced electron carrier produced during the light reactions; provides reducing power for the Calvin cycle

Photons

Discrete particles of light whose absorption can increase the energy level of an electron

Pigment molecules

Molecules that absorb light energy at different wavelengths

Chlorophyll a

Chlorophyll containing a CH3 group