Biology 1.2

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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 enzyme's affinity for its substrate

anabolic (also, anabolism)

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

ATP

adenosine triphosphate, the cell’s energy currency

bioenergetics

study of energy flowing through living systems

catabolic (also, catabolism)

pathways in which complex molecules break down into simpler ones

chemical energy

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

coenzyme

small organic molecule, such as a vitamin or its derivative, which is required to enhance an enzyme's activity

cofactor

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

competitive inhibition

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

denature

process that changes a subtance's natural properties

endergonic

describes chemical reactions that require energy input

enthalpy

a system's total energy

entropy (S)

measure of randomness or disorder 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 the chemical reactions that take place inside cells, including anabolism and catabolism

phosphoanhydride bond

bond that connects phosphates in an ATP molecule

potential energy

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

substrate

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

active transport

method of transporting material that requires energy

amphiphilic

molecule possessing a polar or charged area and a nonpolar or uncharged area capable of interacting with both hydrophilic and hydrophobic environments

antiporter

transporter that carries two ions or small molecules in different directions

aquaporin

channel protein that allows water through the membrane at a very high rate

carrier protein

membrane protein that moves a substance across the plasma membrane by changing its own shape

channel protein

membrane protein that allows a substance to pass through its hollow core across the plasma membrane

concentration gradient

area of high concentration adjacent to an area of low concentration

diffusion passive

transport process of low-molecular weight material according to its concentration gradient

electrogenic pump

pump that creates a charge imbalance

facilitated transport

process by which material moves down a concentration gradient (from high to low concentration) using integral membrane proteins

fluid mosaic mode

describes the plasma membrane's structure as a mosaic of components including phospholipids, cholesterol, proteins, glycoproteins, and glycolipids (sugar chains attached to proteins or lipids, respectively), resulting in a fluid character (fluidity)

glycoiplid

combination of carbohydrates and lipids

glycoprotein

combination of carbohydrates and proteins

hypertonic

situation in which extracellular fluid has a higher osmolarity than the fluid inside the cell, resulting in water moving out of the cell

hypotonic

situation in which extracellular fluid has a lower osmolarity than the fluid inside the cell, resulting in water moving into the cell

integral protein

protein integrated into the membrane structure that interacts extensively with the membrane lipids' hydrocarbon chains and often spans the membrane

isotonic

situation in which the extracellular fluid has the same osmolarity as the fluid inside the cell, resu

osmosis

transport of water through a semipermeable membrane according to the water's concentration gradient across the membrane that results from the presence of solute that cannot pass through the membrane

passive transport

method of transporting material through a membrane that does not require energy

primary active transport

active transport that moves ions or small molecules across a membrane and may create a difference in charge across that membrane

pump

active transport mechanism that works against electrochemical gradients

secondary active transport

movement of material that results from primary active transport to the electrochemical gradient

acetyl CoA

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 in the presence of oxygen

anaerobic

process that does not use oxygen

anaerobic cellular respiration

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

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 adenosine triphosphate (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

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

process of breaking glucose into two three-carbon molecules with the production of ATP and NADH

oxidative phosphorylation

production of ATP using the process of chemiosmosis in the presence of oxygen

phosphorylation

addition of a high-energy phosphate to a compound, usually a metabolic intermediate, a protein, or ADP

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

redox reaction

chemical reaction that consists of the coupling of an oxidation reaction and a reduction reaction

substrate-level phosphorylation

production of ATP from ADP using the excess energy from a chemical reaction and a phosphate group from a reactant

absorption spectrum

range of wavelengths of electromagnetic radiation absorbed by a given substance

Calvin cycle

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

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 redorange light and consequently has a yellowish-green tint

chloroplast

organelle in which photosynthesis takes place

electron transport chain

group of proteins between 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

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 to 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 reaction

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

photosystem

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

photosystem I

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

photosystem II

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

primary electron acceptor

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

stroma

fluid-filled space surrounding the grana inside a chloroplast where the light-independent reactions of photosynthesis 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 lightdriven electron transport

stoma

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

anaphase

stage of mitosis during which sister chromatids are separated from each other

binary fission

prokaryotic cell division process

cell cycle

ordered series of events involving cell growth and cell division that produces two new daughter cells

cell plate

structure formed during plant cell cytokinesis by Golgi vesicles, forming a temporary structure (phragmoplast) and fusing at the metaphase plate; ultimately leads to the formation of cell walls that separate the two daughter cells

centriole

rod-like structure constructed of microtubules at the center of each animal cell centrosome

chromatid

single DNA molecule of two strands of duplicated DNA and associated proteins held together at the centromere

condensin

proteins that help sister chromatids coil during prophase

cytokinesis

division of the cytoplasm following mitosis that forms two daughter cells.

G0

phase distinct from the G1 phase of interphase; a cell in G0 is not preparing to divide

G1 phase

(also, first gap) first phase of interphase centered on cell growth during mitosis

G2 phase

(also, second gap) third phase of interphase during which the cell undergoes final preparations for mitosis

gene

physical and functional unit of heredity, a sequence of DNA that codes for a protein.

genome

total genetic information of a cell or organism

interphase

period of the cell cycle leading up to mitosis; includes G1 , S, and G2 phases (the interim period between two consecutive cell divisions)

metaphase

stage of mitosis during which chromosomes are aligned at the metaphase plate