BIO 101

activation energy

energy necessary for reactions to occur

active site

enzyme's specific region to which the substrate binds

allosteric inhibition

inhibition by a binding event at a site different from the active site, which induces a conformational change and reduces the affinity of the enzyme for its substrate

anabolic

pathways that require an input of energy to synthesize complex molecules from simpler ones. Endergonic

Bioenergetics

the study of how energy flows through living organisms

catabolic

pathways in which complex molecules are broken down into simpler ones. Exergonic

chemical energy

potential energy stored in chemical bonds that releases when bonds are broken

coenzyme

a small organic molecule, such as a vitamin, required to enhance an enzyme's activity

cofactor

inorganic ion, such as iron and magnesium ions, required for optimal regulation of enzyme activity

competitive inhibition

type of inhibition in which the inhibitor competes with the substrate molecule by binding to the active site of the enzyme

denature

process that changes the natural properties of a substance

endergonic

describes chemical reactions that require energy input

energy coupling

process during which energy released by one reaction is used to drive another reaction

enthalpy

a system's total energy

entropy

A measure of disorder or randomness within a system

exergonic

describes chemical reactions that release free energy

feedback inhibition

a product's effect of a reaction sequence to decrease its further production by inhibiting the first enzyme's activity in the pathway that produces it

Free energy

Gibbs free energy is the usable energy, or energy that is available to do work

heat

energy transferred from one system to another that is not work (energy of the molecules' motion or particles)

heat energy

total bond energy of reactants or products in a chemical reaction

induced fit

dynamic fit between the enzyme and its substrate, in which both components modify their structures to allow for ideal binding

kinetic energy

energy type that takes place with objects or particles in motion

Metabolism

All of the chemical reactions that occur within an organism

potential energy

energy type that has the potential to do work; stored energy

substrate

a molecule on which the enzyme acts

Thermodynamics

study of energy and energy transfer involving physical matter

transition state

high-energy, unstable state (an intermediate form between the substrate and the product) occurring during a chemical reaction

Acetyl CoA

the combination of an acetyl group derived from pyruvic acid and coenzyme A which is made from pantothenic acid (a B-group vitamin)

aerobic respiration

process in which organisms convert energy for their use in the presence of oxygen

anaerobic respiration

Process where organisms convert energy for their use that does not require oxygen

ATP synthase

(also F1F0 ATP synthase) membrane-embedded protein complex that adds a phosphate to ADP with energy from protons diffusing through it

Chemiosmosis

process in which there is a production of ATP in cellular metabolism by the involvement of a proton gradient across a membrane

citric acid cycle

(also Krebs cycle) series of enzyme-catalyzed chemical reactions of central importance in all living cells for extraction of energy from carbohydrates (Hans Kreb)

dephosphorylation

removal of a phosphate group from a molecule

fermentation

process of regenerating NAD+ with either an inorganic or organic compound serving as the final electron acceptor; occurs in the absence of oxygen

GLUT protein

integral membrane protein that transports glucose

Glycolysis

the process of breaking glucose into two three-carbon molecules with the production of ATP and NADH. First part of respiration; occurs in cytoplasm;

isomerase

enzyme that converts a molecule into its isomer

oxidative phosphorylation

production of ATP using the process of chemiosmosis in the presence of oxygen. (ATP synthase + an electrochemical gradient draws protons near the ATP synthase. Spinning of ATP synthase phosphorylates many ADP simultaneously (efficient)

Phosphorylation

addition of a high-energy phosphate to a compound, usually a metabolic intermediate, a protein, or ADP (transfer of 3rd phosphate group of ATP to another molecule)

pyruvate

three-carbon sugar that can be decarboxylated and oxidized to make acetyl CoA, which enters the citric acid cycle under aerobic conditions; the end product of glycolysis

substrate-level phosphorylation

production of ATP from ADP using the excess energy from a chemical reaction and a phosphate group from a reactant. (Uses enzyme)

ubiquinone

soluble electron transporter in the electron transport chain that connects the first or second complex to the third

absorption spectrum

range of wavelengths of electromagnetic radiation absorbed by a given substance

antenna protein

pigment molecule that directly absorbs light and transfers the energy absorbed to other pigment molecules

calvin cycle

light-independent reactions of photosynthesis that convert carbon dioxide from the atmosphere into carbohydrates using the energy reducing power of ATP and NADPH

carbon fixation

process of converting inorganic CO2 gas into organic compounds

carotenoid

photosynthetic pigment (yellow-orange-red) that functions to dispose of excess energy

Chemoautotrophs

organism that can build organic molecules using energy derived from inorganic chemicals instead of sunlight

chlorophyll a

form of chlorophyll that absorbs violet-blue and red light and consequently has a bluish-green color; the only pigment molecule that performs the photochemistry by getting excited and losing an electron to the electron transport chain

chlorophyll b

accessory pigment that absorbs blue and red-orange light and consequently has a yellowish-green tint

Chloroplast

organelle where photosynthesis takes place

cytochrome complex

group of reversibly oxidizable and reducible proteins that forms part of the electron transport chain between photosystem II and photosystem I

electromagnetic spectrum

range of all possible frequencies of radiation

Electron Trasnport Chain (ETC)

group of proteins between the PSII and PSI that pass energized electrons and use the energy released by the electrons to move hydrogen ions against their concentration gradient into the thylakoid lumen

granum

A stack of thylakoids in a chloroplast

Heterotroph

organism that consumes organic substances or other organisms for food

light-harvesting complex

complex that passes energy from sunlight to the reaction center in each photosystem; it consists of multiple antenna proteins that contain a mixture of 300-400 chlorophyll a and b molecules as well as other pigments like carotenoids

light-dependent reaction

first stage of photosynthesis where certain wavelengths of the visible light are absorbed to form two energy-carrying molecules (ATP and NADPH)

Light Independent Reactions (Calvin Cycle)

second stage of photosynthesis, through which carbon dioxide is used to build carbohydrate molecules using energy from ATP and NADPH

mesophyll

middle layer of chlorophyll-rich cells in a leaf

P680

reaction center of PSII

P700

reaction center of photosystem I

Photoautotrophs

organism capable of producing its own organic compounds from sunlight

photon

a distinct quantity or "packet" of light energy

Photosystem

a group of proteins, chlorophyll, and other pigments that are used in the light-dependent reactions of photosynthesis to absorb light energy and convert it into chemical energy

PSI

integral pigment and protein complex in the thylakoid membranes that uses light energy to transport electrons from plastocyanin to NADP+ (which is reduced to NADPH in the process)

PSII

integral protein and pigment complex in the thylakoid membranes that transports electrons from water to the electron transport chain; Oxygen is a product of PSII

pigment

molecule that is capable of absorbing certain wavelengths of light and reflecting others (which accounts for its color)

primary electron acceptor

pigment or other organic molecule in the reaction center that accepts an energized electron from the reaction center

reaction center

complex of chlorophyll molecules and other organic molecules that is assembled around a special pair of chlorophyll molecules and a primary electron acceptor; capable of undergoing oxidation and reduction

spectrophotometer

instrument that can measure transmitted light and compute the absorption

stoma

opening that regulates gas exchange and water evaporation between leaves and the environment, typically situated on the underside of leaves

stroma

fluid-filled space outside the grana in which light-independent reactions take place

thylakoid

disc-shaped, membrane-bound structure inside a chloroplast where the light-dependent reactions of photosynthesis take place; stacks of thylakoids are called grana

thylakoid lumen

aqueous space bound by a thylakoid membrane where protons accumulate during light-driven electron transport

Wavelength

the distance between two consecutive peaks or troughs in a wave

Photosynthesis equation

(light) + 6CO2 + 6H2O ------> C6H12O6 + 6O2

Short term storage carbohydrates

Starch (plants); glycogen (animals)

quick energy carbohydrates

glucose and fructose

structural carbohydrates

cellulose and chitin

Cellulose

alternating orientation of carbon side chains makes it difficult to break down

Starch

repeating orientation of carbon side chains makes it easier to break down

ATP

when interacting with another molecule, it transfers a phosphate group to the other molecule. This destabilizes the other molecule, allowing work to be done. (chemical work--phosphorylating reactants; mechanical work--phosphorylates motor proteins)

Phosphorylation of ADP

ATP-->ADP + Pi

reactants and products of light dependent reaction

Location=thylakoid membrane; reactants=ADP, NADP+, light, water; Products=ATP, NADPH, O2; purpose=generate ATP and NADPH to later combine with O2 in Calvin Cycle to reconfigure atoms of molecules into simple carbs

reactants and products of light independent reaction (calvin cycle)

Location=stroma

Reactants=ATP, NADPH, CO2

Products=ADP, NADP+, Pi, monosaccharides

Purpose=combine CO2 with carbon compounds already in the cycle, through phosphorylation by ATP and addition of hydrogens from NADPH to make G3P. two G3P make a monosaccharide

Photolysis

resupplies protons and electrons.

photorespiration

Most plants, initial fixation of CO2, via rubisco, forms a 3-carbon compound. Rubisco adds O2 instead of CO2 in the calvin cycle. Photoresp. consumes O2 and organic fuel and releases CO2 without producing ATP or sugar.

-Limits damaging products of light reactions that build up in absence of Calvin Cycle

Photorespiration reduces plant productivity

C4 plants

minimize cost of photorespiration by incorporating CO2 into 4-carbon compound in mesophyll cells.

PEP carboxylase has a higher affinity for CO2 than rubisco, so it can fix CO2 even when concentrations are low

CAM plants

includes succulents; open stomata at night, incorporating CO2 into organic acids. Close during day and CO2 is released from organic acids and used in the calvin cycle

Respiration equation

C6H12O6 + 6O2 --→ 6CO2 + 6H20 + Energy

respiration=energy released from glucose helps make ATP

example of phosphorylation

Phosphorylation couples an endergonic reaction with the breakdown of ATP (exergonic). the change in free energy can be driven to a negative value resulting in an exergonic reaction. (Glutamic acid and Ammonia)

reactants and products of glycolysis

Reactants=glucose and 2 ATP; Products=2 pyruvate 2NADH, 2 ATP (net). purpose: convert glucose into a pyruvate, which can be transported into the mitochondria

Oxidation of Pyruvate

conversion of pyruvate to Acetyl CoA. In matrix solution of mitochondria. Reactants=2 pyruvates 2 CoA

Products=2 Acetyl CoA, 2 NADH, 2CO2

Purpose-convert pyruvate into a molecule which is reactive in Krebs Cycle

reactants and products of Krebs Cycle

Reactants=2 acetyl CoA

Products (each Acetyl CoA)=2CO2, 3 NADH, 1 FADH2, 1 ATP

Purpose=thru conversion of mlcls in the cycle, hydrogens are released which are transported to the inner membrane to create an electrochemical gradient

ETC and Chemiosmosis

mitochondria membrane

Reactants=3 NADH, 1FADH2, and O2

Products=6H2O, 32 ATP

Purpose=enzymatically splitting hydrogen into protons and electrons then actively transporting protons into the intermembrane space creates an electrochemical gradient which can drive spinning of ATP synthase

Alcohol fermentation

anaerobic; nonreversible, net 2 ATP and ethanol

Lactic acid fermentation

anaerobic; reversible; net 2 ATP and lactic acid

oxixdation

reactant loses electrons