Atom smallest complete unit of an element
Proton positively charged particles
Neutron particles carrying no charge
Electron negatively charged particles
Element substance that cannot be broken down into other substances
Atomic number number of protons; usually protons = electrons
Atomic mass protons + neutrons
Isotope atoms of an element that possess different numbers of neutrons; unstable, give off energy, can be used for tracking
PET scan Positron Emission Tomography; glucose C-11
Polar a molecule with an uneven distribution of charges in different regions of the molecule
Nonpolar charges are distributed equally throughout the molecule
Covalent bond strong, stable bond of shared electrons
Valence shell outermost electron shell
Ionic bond when a more electronegative atom steals the electrons from another; forms due to opposites attracting
Hydrogen bond weak bonds between atoms in 2 different molecules; formed when hydrogen atom (that is covalently bonded to a more electronegative atom) is attracted to an electronegative atom of another molecule
Van de Waals interactions "hot spots" of +/- charges that allow temporary interactions
Cohesion hydrogen bonding holds water together; includes adhesion and surface tension
Adhesion attraction between different substances
Surface tension a measure of how hard it is to break the surface of a liquid
High specific heat the amount of heat that must be absorbed or lost for 1g of substance to change its temperature by 1 degree C
High heat of vaporization the quantity of heat a liquid must absorb for 1g of it to be converted from the liquid to the gaseous state
Solvent the dissolving agent of a solution; water is the most versatile solvent known
Colloid a mixture made up of a liquid and particles that remain suspended rather than dissolved in the liquid
Lysozyme an enzyme that destroys bacterial cell walls; in mammals found in sweat, tears, and saliva
pH a measure of the H+ in solution; pH = -log [H+]
Buffer substances that minimize changes of [H+] or [OH-] in a solution
Hydrophobic substance that does not have an affinity for water
Hydrophilic substance that has an affinity for water
Organic compounds chemical compounds that contain carbon
Functional groups a specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and involved in chemical reactions
Dehydration removes water to synthesize polymers
Hyrdolysis adds water to break down polymers
Carbohydrate serve the dual purpose of energy storage and structural support
Monosaccharide simple sugars with C:H:O ration 1:2:1
Disaccharide two monosaccharides joined by a glycosidic linkage; are less readily metabolized; used for transport
Polysaccharide long polymers of monosaccharides; used for storage or structural support
Lipid any of a group of large biological molecules, including fats, phospholipids, and steroids that mix poorly, if at all, with water
Protein a biologically functional molecule consisting of one or more polypeptides folded and coiled into a specific three dimensional structure
Amino acid The structural subunit of proteins
Primary structure of proteins the specific amino acid sequence
Secondary structure of proteins folding of amino acid chain into structures such as alpha helices and beta pleated sheets
Tertiary structure of proteins final folded globular protein, shaped by hydrophobic interactions with water
Quaternary structure of proteins association of two or more polypeptide chains to form a functional protein
Nucleic acids Information storage devices of cells
DNA deoxyribonucleic acid
RNA ribonucleic acid
Purines large, double ring (A and G)
Pyrimidines small, single ring (C, T, and U)
Fluid mosaic a membrane is a fluid structure with a "mosaic" of various proteins embedded in it
Phospholipid forms a bilayer which is a cell membrane; composed of glycerol, fatty acids, and phosphorylated alcohol; has a polar head and 2 nonpolar tails
Carbohydrate stuck onto some membrane proteins (glycoproteins) and lipids (glycolipids); used in cell-cell recognition
Membrane proteins 6 types: transporters, enzymes, cell surface receptors, cell surface identity markers, cell adhesion proteins, cytoskeletal attachment proteins
Peripheral proteins bound to the surface of the membrane
Integral proteins nonpolar amino acids in hydrophobic interior, polar/ionic amino acids protrude
Membrane transport membranes are selectively permeable: regulates the cell's molecular traffic
Passive transport: simple diffusion spontaneous; diffusion is the tendency for molecules to spread out evenly into the available space; may be directional
Osmosis the movement of water from an area of higher free water concentration to an area of lower free water concentration
Passive transport: facilitated diffusion transport proteins speed the passive movement of molecules across the plasma membrane; channel proteins and carrier proteins
Active transport molecules move across membrane from lower to higher regions of concentration against gradient; requires pumps or other special cells machinery; requires energy (ATP)
Cotransport occurs when active transport of a solute indirectly drive transport of other solutes
Endocytosis regions of plasma membrane pinch in and bring the particles into the cell via vesicle
Phagocytosis a type of endocytosis in which large particulate substances or small organisms are taken up by a cell
Pinocytosis a type of endocytosis in which the cell ingests extracellular fluid and its dissolved solutes
Receptor mediated endocytosis the movement of specific molecules into a cell by the inward budding of vesicles containing proteins with receptor sites specific to the molecules being taken in; enables a cell to acquire bulk quantities of specific quantities
Potential energy stored energy
Chemical energy exists in bonds, potential energy stored in molcules due to the arrangement of atoms; can be transformed into chemical/potential energy in another mc or into kinetic energy
Kinetic energy the energy of motion
Free energy energy in a system available to do work
ΔG change in free energy; difference in bond energies between reactants and products
Exergonic spontaneous reactions; ΔG < 0; net free energy is released
Endergonic non spontaneous reacitons; ΔG > 0; net energy must be added to make a reaction go
Feedback inhibition the end product of a metabolic pathway shuts down the pathway
Activation energy energy required to destabilize existing chemical bonds and start the chemical reaction
Enzyme a catalytic protein
Catalyst a chemical agent that speeds up a rxn without being consumed by the rxn by reducing activation energy
Substrate the reactant on which the enzyme works
Active site the specific region of an enzyme that binds the substrate and that forms the pocket in which catalysis occurs
Competitive inhibitor inhibitor binds to the same place as substrate (active site)
Noncompetitive inhibitor inhibitor binds enzyme at some location other than active site, changes shape of enzyme
Cofactors additional non-protein components that assist enzyme activity
Coenzymes an organic molecule serving as a cofactor
Oxidation the complete or partial loss of electrons from a substance involved in a redox reaction
Reduction the complete or partial addition of electrons to a substance involved in a redox reaction
Glycolysis a series of reactions that ultimately splits glucose into two pyruvate mcs
NADH and NAD+ nicotinamide adenine dinucleotide, a coenzyme that cycles easily between oxidized and reduced states, thus acting as an electron carrier
FADH2 another electron carrier
Electron transport chain a sequence of electron carrier molecules (membrane proteins) that shuttle electrons down a series of redox reactions that release energy used to make ATP
Chemiosmosis an energy coupling mechanism that uses energy stored in the form of a hydrogen ion gradient across a membrane to drive cellular work, such as the synthesis of ATP
Pyruvate the products of glycolysis; goes into the citric acid cycle
ATP Adenosine triphosphate; the cell's energy shuttle; composed of a ribose, adenine, and three phosphate groups; bonds between phosphate groups are unstable
Oxidative phosphorylation the production of ATP using energy derived from the redox reactions of an electron transport chain
ATP synthase a complex of several membrane proteins that functions in chemiosmosis with adjacent electron transport chains using the energy of a proton concentration gradient to make ATP
Citric acid cycle a chemical cycle that completes the metabolic breakdown of glucose mcs begun in glycolysis by oxidizing acetyl CoA to carbon dioxide
Oxaloacetic acid acetyl CoA combines with this to form citric acid
Mitochondria an organelle in eukaryote cells that serves as the site of cellular respiration; uses oxygen to break down organic molecules and synthesize ATP
Cytoplasm the contents of the cell bounded by the plasma membrane
Fermentation a catabolic process that makes a limited amount of ATP from glucose (or other organic molecules) without an electron transport 'chain and that produces an end product such as ethyl alcohol or lactic acid
Deamination proteases break down protein into amino acids; aa's converted to pathway components by this
Sucrase breaks sucrose down into fructose and glucose
Lactase breaks lactose down into glucose and galactose
Beta-oxidation breaks fatty acid down into 2 carbon units
Oxaloacetic acid aspartic acid is converted into this through deamination
Alanine is deaminated into pyruvate and glutamate
Aspartic acid is deaminated into oxaloacetic acid
Phosphofructokinase an allosteric enzyme that responds to feedback inhibition
Citrate this and ATP inhibit phosphofructokinase
Catabolism this type of metabolic pathway releases energy by breaking down complex molecules to simpler molecules
Feedback inhibition a method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway
Photosynthesis the process that converts solar energy into chemical energy; converts light energy into the chemical energy of food
Anabolic synthesis of chemical compounds
Chlorophyll a main photosynthetic pigope atoms of an element acts directly to convert light E to chemical E; absorb violet, blue, and red light
Chlorophyll b accessory pigment; broadens the spectrum used for photosynthesis; absorb violet, blue, and red light
Caratenoid accessory pigment for capturing energy from wavelengths not efficiently absorbed by either chlorophyll; absorb mostly blue and green light
Chloroplast organelle that carries out photosynthesis; contained within a layer of cells called the mesophyll
Grana column of stacked thylakoid sacs
Thylakoid flattened sacs, membranes contain pigments which absorb light energy
Reaction center complex a complex of proteins associated with a special pair of chlorophyll a mcs and a primary e- acceptor; triggers the light reactions of photosynthesis
Photosystem I a light capturing unit in a chloroplast's thylakoid membrane; has two mcs of P700 as its reaction center
Photosystem II one of two light-capturing units in a chloroplast's thylakoid membrane; has two mcs of P680 at its reaction center
Light-harvesting complex a complex of proteins associated with pigmentmcs that captures light energy and transfers it to reaction center pigments in a photosystem
Primary electron acceptor a specialized mc that shares the reaction-center complex with a pair of chlorophyll a mcs and accepts an e- from them
Linear electron flow a route of electron flow during the light reactions of photosynthesis that involve PSI and PSII and produces ATP, NADPH, and oxygen
Photon units of energy from light
Plastoquinone & Plastocyanin Ps and Pc; these plus the cytochrome complex form the ETC between PSII and PSI
Cyclic electron flow a route of electron flow during the light reactions that involves only PSI and produces ATP only
Chemiosmosis used to generate ATP using a proton gradient and ATP synthase
Calvin cycle uses the chemical energy of ATP and NADPH to reduce CO2 to sugar
Rubisco ribulose biphosphate carboxylase; catalyzes carbon fixation
RuBP ribulose biphosphate; combines with CO2 to form an unstable 6C intermediate which splits into 3-phosphoglycerate in the Calvin cycle
G3P glyceraldehyde 3-phosphate; the product of the Calvin cycle
Carbon fixation the initial incorporation of carbon from CO2 into an organic compound
CAM crassulacean acid metabolism; an adapdation for photosynthesis; stomata are open during the night and closed during the day; organic acids formed @ night, release CO2 for Calvin cycle during the day
C4 pathway Calvin cycle preceded by reactions that incorporate CO2 in a 4 carbon organic material, forming a 3-carbon compound as the first stable intermediate
Stomata a microscopic pore surrounded by guard cells in the epidermis of leave and stems that allows gas exchange between the environment and the interior of the plant
Photorespiration a metabolic pathway that consumes oxygen and ATP, releases CO2 and decreases photosynthetic output; occurs on hot, dry, bright days
Mesophyll cell where carbon fixation occurs during the C4 pathway
Bundle-sheath cell where the Calvin cycle occurs during the C4 pathway
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Chemistry Vocab
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