Cell Bio FINAL - Terms and Definitions

Archaeon

• microscopic organism that is a member of one of the two divisions of prokaryotes

• often found in hostile environments such as hot springs or concentrated brine

Bacterium

• microscopic organism that is a member of one of the two divisions of prokaryotes

• some species cause disease

• the term is sometimes used to refer to any prokaryotic microorganism, although they are only distantly related to archaea

Cell

• the basic unit from which a living organism is made

• an aqueous solution of chemicals, enclosed by a membrane, that has an ability to self-replicate

Chloroplast

specialized organelle in algae and plants that contains chlorophyll and serves as the site for photosynthesis

Chromosome

• long, threadlike structure composed of DNA and proteins that carries the genetic information of an organism

• becomes visible as a distinct entity when a plant or animal cell prepares to divide

Cytoplasm

contents of a cell that are contained within its plasma membrane but, in the case of eukaryotic cells, outside the nucleus

Cytoskeleton

• system of protein filaments in the cytoplasm of a eukaryotic cell that gives the cell shape and the capacity for directed movement

• its most abundant components are actin filaments, microtubules, and intermediate filaments

Cytosol

• contents of the main compartment of the cytoplasm, excluding membrane-enclosed organelles

• also used to refer to the cell fraction remaining after membranes, cytoskeletal components, and other organelles have been removed

DNA (deoxyribonucleic acid)

• double-stranded polynucleotide formed from two separate chains of covalently linked deoxyribonucleotides

• it serves as the cell’s store of genetic information that is transmitted from generation to generation

Electron microscope

instrument that passes a beam of electrons through the specimen to reveal and magnify the structures of very small objects, such as organelles and large molecules

Endoplasmic reticulum (ER)

• labyrinthine, membrane-enclosed compartment in the cytoplasm of eukaryotic cells where lipids and proteins are made

  • includes the Rough ER and the Smooth ER

Eukaryote

an organism whose cells have a distinct nucleus and cytoplasm

Evolution

process of gradual modification and adaptation that occurs in living organisms over generations

Fluorescence microscope

• instrument used to visualize a specimen that has been labeled with a fluorescent dye

• samples are illuminated with a wavelength of light that excites the dye, causing it to fluoresce

Genome

• the total genetic information carried by all the chromosomes of a cell or organism

• in humans, the total number of nucleotide pairs in the 22 autosomes, plus the X and Y chromosomes

Golgi apparatus

membrane-enclosed organelle in eukaryotic cells that modifies the proteins and lipids made in the endoplasmic reticulum and sorts them out for transport to other sites

Homologous

• describes genes, chromosomes, or any structures that are similar because of their common evolutionary origin

• can also refer to similarities between protein sequences or nucleic acid sequences

Microscope

• instrument for viewing extremely small objects

  • some use a focused beam of visible light and are used to examine cells and organelles

  • others use a beam of electrons and can be used to examine objects as small as individual molecules

Mitochondrion

membrane-enclosed organelle, about the size of a bacterium, the carries out oxidative phosphorylation and produces most of the ATP in eukaryotic cells

Model organism

a living thing selected for intensive study as a representative of a large group of species

Nucleus

the prominent, rounded structure that contains the DNA of a eukaryotic cell

Organelle

a discrete structure or sub-compartment of a eukaryotic cell that is specialized to carry out a particular function (examples include mitochondria and the Golgi apparatus)

Photosynthesis

the process by which plants, algae, and some bacteria use the energy of sunlight to drive the synthesis of organic molecules from carbon dioxide and water

Plasma membrane

the protein-containing lipid bilayer that surrounds a living cell

Prokaryote

• major category of living cells distinguished by the absence of a nucleus

  • includes the archaea and the eubacteria (commonly called bacteria)

Protein

macromolecule built from amino acids that provides cells with their shape and structure and performs most of their activities

Protozoan

a free-living, nonphotosynthetic, single-celled, motile eukaryote

Ribosome

large macromolecular complex, composed of RNAs and proteins, that translates a messenger RNA into a polypeptide chain

RNA (ribonucleic acid)

• molecule produced by the transcription of DNA

• usually single-stranded, it is a polypeptide composed of covalently linked ribonucleotide subunits

• serves a variety of informational, structural, catalytic, and regulatory functions in cells

Acid

• a molecule that releases a proton when dissolved in water

  • this dissociation generates hydronium (H3O+) ions, thereby lowering the pH level

Amino acid

small organic molecule containing both an amino group and a carboxyl group; serves as the building block of proteins

Atom

• the smallest particle of an element that still retains its distinctive chemical properties

• consists of a positively-charged nucleus surrounded by a cloud of negatively-charged electrons

ATP

• activated carrier particle - serves as the principal carrier of energy in cells

• a nucleoside triphosphate composed of adenine, ribose, and three phosphate groups

Avogadro’s number

• the number of molecules in a mole - the quantity of a substance equal to its molecular weight in grams

  • approximately 6 × 10^23

Base

• molecule that accepts a proton when dissolved in water

• also used to refer to the nitrogen-containing purines or pyrimidines in DNA and RNA

Buffer

mixture of weak acids and bases that maintains the pH of a solution by releasing and taking up protons

Chemical bond

an attraction that holds two atoms together

Chemical group

a combination of atoms, such as a hydroxyl group (OH-) or an amino group (-NH2), with distinct chemical and physical properties that influence the behavior of the molecule in which it resides

Condensation reaction

• chemical reaction in which a covalent bond is formed between two molecules as water is expelled

• used to build polymers, such as proteins, polysaccharides, and nucleic acids

Conformation

precise, three-dimensional shapes of a protein or other macromolecule, based on the spatial location of its atoms in relation to one another

Covalent bond

stable chemical link between two atoms produced by sharing one or more pairs of electrons

Electron

negatively-charged subatomic particle that occupies space around an atomic nucleus (e-)

Electronegativity

• the tendency of an atom to attract electrons

  • increases left-to-right across the periodic table

Electrostatic attraction

• force that draws together oppositely-charged atoms

  • examples include ionic bonds and the attractions between molecules containing polar covalent bonds

Fatty acid

• molecule that consists of a carboxylic acid attached to a long hydrocarbon chain

• used as a major source of energy during metabolism and as a starting point for the synthesis of phospholipids

Hydrogen bond

• a weak, noncovalent interaction between a positively-charged hydrogen atom in one molecule and a negatively-charged atom, such as nitrogen or oxygen, in another

  • these bonds are key to the structure and properties of water

Hydrolysis

• chemical reaction that involves cleavage of a covalent bond with the accompanying consumption of water

  • -H is added to one product of the cleavage and -OH is added to the other

  • the reverse of a condensation reaction

Hydronium ion

the form taken by a proton (H+) in aqueous solution (H3O+)

Hydrophilic

“water-loving” - molecule or part of a molecule that readily forms hydrogen bonds with water, allowing it to readily dissolve

Hydrophobic

“water-fearing” - nonpolar, uncharged molecule or part of a molecule that forms no hydrogen bonds with water molecules and therefore does not dissolve

Hydrophobic force

• a noncovalent interaction that forces together the hydrophobic portions of dissolved molecules to minimize their disruption of the hydrogen-bonded network of water

• causes membrane phospholipids to self-assemble into a bilayer and helps to fold proteins into a compact, globular shape

Inorganic

not composed of carbon atoms

Ion

an atom carrying an electrical charge, either positive or negative

Ionic bond

interaction formed when one atom donates electrons to another —> transfer of electrons causes both atoms to become electrically charged

Lipid

• an organic molecule that is insoluble in water but dissolves readily in nonpolar organic solvents

  • typically contains a long hydrocarbon chain or multiple rings

  • one class, the phospholipids, forms the structural basis for biological membranes

Lipid bilayer

thin pair of closely juxtaposed sheets, composed mainly of phospholipid molecules, that forms the structural basis for all cell membranes

Macromolecule

polymer built from covalently-linked subunits - includes proteins, nucleic acids, and polysaccharides

Molecule

group of atoms joined together by covalent bonds

Monomer

small molecule that can be linked to others of a similar type to form a larger molecule (polymer)

Noncovalent bond

• chemical association that does not involve sharing of electrons

  • they are relatively weak on their own, but can sum together to produce strong, highly specific interactions between molecules

  • examples are hydrogen bonds and van der Waals attractions

Nucleotide

• the basic building block of the nucleic acids, DNA and RNA

• comprised of a nucleoside linked to a phosphate

Organic molecule

chemical compound that contains carbon and hydrogen

pH scale

concentration of hydrogen ions in a solution, expressed as a logarithm

Polar

a molecule or bond in which electrons are distributed unevenly

polymer

long molecule made by covalently linking multiple identical or smaller subunits (monomers)

Proton

• positively-charged particle found in the nucleus of every atom

• another name from a hydrogen ion, H+

Sequence

• the linear order of monomers in a large molecule

  • for example, amino acids in a protein or nucleotides in DNA —> encodes information that specifies a macromolecule’s precise biological function

Subunit

• a monomer that forms part of a larger molecule, such as an amino acid in a protein or a nucleotide in a nucleic acid

• can also refer to a complete molecule that forms part of a larger molecule

Sugar

• a substance made of carbon, hydrogen, and oxygen - general formula (CH2O)

  • a carbohydrate or a saccharide

van der Waals attractions

weak, noncovalent interactions, due to fluctuating electrical charges, that come into play between atoms located very close to one another

Acetyl CoA

• activated carrier that donates the carbon atoms in its readily transferable acetyl group to many metabolic reactions, including the citric acid cycle and fatty acid biosynthesis

• the acetyl group is linked to coenzyme A by a thioester bond that releases a large amount of energy when hydrolyzed

Activated carrier

small molecule that stores energy or chemical groups in a form that can be donated to many different metabolic reactions; (examples include ATP, acetyl CoA, and NADH)

Activation energy

the energy that must be acquired by a molecule to undergo a chemical reaction

ADP

nucleoside diphosphate produced by hydrolysis of the terminal phosphate of ATP

Anabolism

set of metabolic pathways by which large molecules are made from smaller ones

Biosynthesis

an enzyme-catalyzed process, also called anabolism, by which complex molecules are formed from simpler substances by living cells

Catabolism

• set of enzyme-catalyzed reactions by which complex molecules are degraded to simpler ones with release of energy

• intermediates in these reactions are sometimes called catabolites

Catalyst

• substance that accelerates a chemical reaction by lowering its activation energy

• enzymes perform this role in cells

Cell respiration

process by which cells harvest the energy stored in food molecules; usually accompanied by the uptake of O2 and the release of CO2

Coupled reaction

linked pair of chemical reactions in which free energy released by one reaction serves to drive the other reaction

Diffusion

process by which molecules and small particles move from one location to another by random, thermally driven motion

Entropy

thermodynamic quantity that measures the degree of disorder in a system

Enzyme

a protein that catalyzes a specific chemical reaction

Equilibrium

state in which the forward and reverse rates of a chemical reaction are equal so that no net chemical change occurs

Equilibrium constant, K

for a reversible chemical reaction - the ratio of substrate to product when the rates of the forward and reverse reactions are equal

Free energy, G

energy that can be harnessed to do work, such as driving a chemical reaction

Free-energy change, “Delta G”

• in a chemical reaction, the difference in free energy between reactant and product molecules

• a large negative value of free energy difference indicates that the reaction has a strong tendency to occur (spontaneous)

Metabolism

the sum total of the chemical reactions that take place in the cells of a living organism

NAD+

a molecule that accepts a hydride ion (H-) from a donor molecule (reduction), thereby producing the activated carrier NADH

NADH

activated carrier of electrons that is widely used in the energy-producing breakdown of sugar molecules; oxidized to NAD+

NADP+

molecule that accepts a hydride ion (H-) from a donor molecule (reduction), thereby producing the activated carrier NADPH

NADPH

activated carrier closely related to NADH and used as an electron donor in biosynthetic pathways; in the process, it is oxidized to NADP+

Oxidation

• removal of electrons from an atom, as occurs during the addition of oxygen to a carbon atom or when a hydrogen is removed from a carbon atom

• it can also refer to a partial shift of electrons between atoms linked by a covalent bond

Reduction

• addition of electrons to an atom, as occurs during the addition of hydrogen to a carbon atom or the removal of oxygens from it

• can also refer to a partial shift of electrons between atoms linked by a covalent bond

Substrate

a molecule on which an enzyme acts to catalyze a chemical reaction

Thermodynamics

the branch of science that studies the relationship between work, heat, and other forms of energy

Active site

region on the surface of an enzyme that binds to a substrate molecule and catalyzes its chemical transformation

Allosteric

• describes a protein that can exist in multiple conformations, depending on the binding of a molecule (ligand) at the site other than the catalytic site

  • such changes from one conformation to another often alter the protein’s activity or ligand affinity

alpha-helix

folding pattern, common in many proteins, in which a single polypeptide chain twists around itself to form a rigid cylinder stabilized by hydrogen bonds between every fourth amino acid

Amino acid sequence

the order of the amino acid subunits in a protein chain; sometimes called the primary structure of a protein