Oregon State BI 212
Terms
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- Atoms
- Basic unit of matter surrounded by negatively charged electrons
- Orbitals
- Electron cloud having an energy state described by given values of the n, l, and m
- Valence Electrons
- ⬢In chemistry, valence electrons are the outermost electrons of an atom, which are important in determining how the atom reacts chemically with other atoms
- Covalent bond
-
⬢a chemical bond that involves sharing a pair of electrons between atoms in a molecule
- ionic bond
-
⬢a chemical bond in which one atom loses an electron to form a positive ion and the other atom gains an electron to form a negative ion
- Hydrogen bond
-
⬢a chemical bond consisting of a hydrogen atom between two electronegative atoms (e.g., oxygen or nitrogen) with one side be a covalent bond and the other being an ionic bond
- Isomer
-
⬢a compound that exists in forms having different arrangements of atoms but the same molecular weight
- macromolecule
-
⬢any very large complex molecule; found only in plants and animals
- condensation reaction
- a chemical reaction in which two molecules or moieties (functional groups) combine to form one single molecule, together with the loss of a small molecule
- ddehydration reaction
- defined as a chemical reaction that involves the loss of water from the reacting molecule
- Hydrolysis
-
⬢a chemical reaction in which water reacts with a compound to produce other compounds; involves the splitting of a bond and the addition of the hydrogen cation and the hydroxide anion from the water
- polymer
- a large molecule (macromolecule) composed of repeating structural units typically connected by covalent chemical bonds
- monomer
-
⬢a simple compound whose molecules can join together to form polymers
- carbohydrate
- ⬢an essential structural component of living cells and source of energy for animals; includes simple sugars with small molecules as well as macromolecular substances
- monosaccharide
-
⬢a sugar (like sucrose or fructose) that does not hydrolyse to give other sugars; the simplest group of carbohydrates
- glycosidic linkage
-
a glycosidic bond is a type of functional group that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate.
- polysaccharide
-
⬢any of a class of carbohydrates whose molecules contain chains of monosaccharide molecules
- starch
- ⬢a complex carbohydrate found chiefly in seeds, fruits, tubers, roots and stem pith of plants, notably in corn, potatoes, wheat, and rice
- glycogen
-
⬢A polysaccharide that is the main form of carbohydrate storage in animals; converted to glucose as needed
- cellulose
- ⬢A complex carbohydrate that forms the main constituent of the cell wall in most plants and
- lipid
-
⬢an oily organic compound insoluble in water but soluble in organic solvents; essential structural component of living cells (along with proteins and carbohydrates)
- fatty acid
- a carboxylic acid with a long unbranched aliphatic tail (chain), which is either saturated or unsaturated
- saturation
- based on reaching a maximum capacity
- phospholipid
-
⬢any of various compounds composed of fatty acids and phosphoric acid and a nitrogenous base; an important constituent of membranes
- amino acid
- ⬢Small organic molecule containing both a carboxyl group and an amino group bonded to the same carbon atom
- polypepetide
-
⬢A chain of linked amino acids. When folded in a particular three-dimensional configuration, it becomes a protein.
- peptide bond
- a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amine group of the other molecule, thereby releasing a molecule of water (H2O).
- Disulfide bridge
- a covalent bond, usually derived by the coupling of two thiol groups
- polynucleotide
-
Long chains of nucleotides formed by chemical links between the sugar and phosphate groups.
- nucleotide
- molecules that, when joined together, make up the structural units of RNA and DNA
- DNA
- a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses
- RNA
- mainly in the cytoplasm of a cell where it is associated with microsomes; it transmits genetic information from DNA to the cytoplasm and controls certain chemical processes in the cell
- purine
-
⬢a colorless crystalline organic base containing nitrogen; the parent compound of various biologically important substances
- Pyrimidine
-
⬢A nitrogen-containing, double-ring, basic compound that occurs in nucleotides of DNA and RNA. The pyrimidines in DNA are cytosine and thymine. Those in RNA, are cytosine and uracil.
- adenine
-
pairs with thymine in DNA and with uracil in RNA
- cytosine
-
⬢a base found in DNA and RNA and derived from pyrimidine; pairs with guanine
- phosphodiester linkage
- ⬢A phosphodiester bond is a group of strong covalent bonds between a phosphate group and two 5-carbon ring carbohydrates (pentoses) over two ester bonds. Phosphodiester bonds are central to all life on Earth, as they make up the backbone of the strands of DNA
- Complementary
-
⬢The preferential binding of bases A to T (or U) in DNA or RNA. For example, if there is a GTC on the DNA strand, the complementary RNA or DNA sequence will be CAG. ...
www.yourgenome.org/glossary/ - plasma membrane
- a thin membrane (a double layer of lipids) enclosing the cytoplasm of a cell; proteins in the membrane control passage of ions (like sodium or potassium or calcium) in and out of the cell
- cytoplasm
-
⬢The contents of a cell except for the nucleus. It includes cytosol, organelles, vesicles, and the cytoskeleton
- cytosol
-
⬢the aqueous part of the cytoplasm within which various particles and organelles are suspended
- organelle
-
an organelle is a specialized subunit within a cell that has a specific function, and is usually separately enclosed within its own lipid bilayer.
- nucleus
- the nucleus (pl. nuclei; from Latin nucleus or nuculeus, meaning kernel), also sometimes referred to as the "control center", is a membrane-enclosed organelle found in eukaryotic cells
- nuclear envelope
-
⬢Double membrane forming the surface boundary of a eukaryotic nucleus; consists of outer and inner membranes perforated by nuclear pores.
- nuclear lamina
- nuclear lamina is a dense (~30 to 100 nm thick) fibrillar network inside the nucleus of an eukaryotic cell
- nuclear pores
- ⬢Nuclear pores are large protein complexes that cross the nuclear envelope, which is the double membrane surrounding the eukaryotic cell nucleus
- chromosome
-
⬢a threadlike strand of DNA in the cell nucleus that carries the genes in a linear order; "humans have 22 chromosome pairs plus two sex chromosomes"
- chromatin
-
⬢Chromatin is the complex combination of DNA and proteins that makes up chromosomes. It is found inside the nuclei of eukaryotic cells. It is divided between heterochromatin (condensed) and euchromatin (extended) forms.
- Ribosome
-
⬢ribosome - an organelle in the cytoplasm of a living cell; they attach to mRNA and move down it one codon at a time and then stop until tRNA brings the required amino acid; when it reaches a stop codon it falls apart and releases the completed protein molecule for use by the cell; "the ribosome is the site - endomembrane cell
- ⬢The endomembrane system is composed of the different membranes that are suspended in the cytoplasm within a eukaryotic cell.
- endoplasmic reticulum
-
⬢A network of membranes within the cytoplasm of cells, where proteins and lipids are synthesized
- Cisternae of ER
-
a sac or cavity containing fluid especially lymph or cerebrospinal fluid
- transport vesicle
- vesicle is a bubble of liquid within a cell. More technically, a vesicle is a small, intracellular, membrane-enclosed sac that stores or transports substances within a cell.
- glycoprotein
-
⬢A protein coated with sugars. For example, cytokines - golgi apparatus
- ⬢A series (stack) of flattened, membrane-bound sacs (saccules) involved in the storage, modification and secretion of proteins and lipids destined to leave the cell (extracellular) and for use within the cell (intracellular
- lysosome
-
⬢an organelle found in the cytoplasm of most cells (especially in leukocytes and liver and kidney cells)
- phagocytosis
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⬢process in which phagocytes engulf and digest microorganisms and cellular debris; an important defense against infection
- vacuole
-
⬢a tiny cavity filled with fluid in the cytoplasm of a cell
- mitochondria
- a mitochondrion (plural mitochondria) is a membrane-enclosed organelle found in most eukaryotic cells, produces energy
- matrix
- matrix (plural: matrices) is the material (or tissue) between animal or plant cells, in which more specialized structures are embedded, and a specific part of the mitochondrion that is the site of oxidation of organic molecules
- Cristae
- ⬢Cristae (singular crista) are the internal compartments formed by the inner membrane of a mitochondrion. They are studded with proteins, including ATP synthase and a variety of cytochromes
- peroxisome
-
⬢An intracellular organelle found in all eukaryotes (except Archezoa) which is the source of the enzymes that catalyze the production and breakdown hydrogen peroxide, and are responsible for the oxidation of long-chain fatty acids
- cytoskeleton
-
⬢The cytoskeleton (also CSK) is a cellular "scaffolding" or "skeleton" contained within the cytoplasm and is made out of protein. - motor protein
-
⬢Motor proteins are a class of molecular motors that are able to move along the surface of a suitable substrate. They are powered by the hydrolysis of ATP and convert chemical energy into mechanical work.
- microtubules
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⬢small tubes made of protein and found in cells and is part of the cytoskeleton
- microfilament
-
⬢long thin fiber that functions in the movement and support of the cell
- intermediate filament
- ⬢Intermediate filaments (IFs) are a family of related proteins that share common structural and sequence features
- tubulin
-
⬢A protein found in the membrane of the star cells of the connective tissues and nerve cells to strengthen skin elasticity.
- actin
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⬢A contractile protein found in muscle cells. Together with myosin, actin provides the mechanism for muscle contraction.
- keratin
-
⬢The protein that makes up nails, hair, hooves, and horns and other such vertebrate structures - centrosome
- ⬢The microtubule organizing centre that forms the mitotic spindle in dividing cells
- centrioles
-
one of a pair of small cylindrical cell organelles near the nucleus in animal cells; composed of nine triplet microtubules and form the asters during mitosis
- cilia
-
a hairlike projection from the surface of a cell; provides locomotion in free-swimming unicellular organisms
- flagella
- a tail-like projection that protrudes from the cell body of certain prokaryotic and eukaryotic cells, and functions in locomotion
- basal body
-
⬢A basal body (also called a basal granule or kinetosome) is an organelle formed from a centriole, and a short cylindrical array of microtubules - dynein
- ⬢Dynein is a motor protein (also called molecular motor or motor molecule) in cells which converts the chemical energy contained in ATP into the mechanical energy of movement
- extracellular matrix
- the extracellular matrix (ECM) is the extracellular part of animal tissue that usually provides structural support to the animal cells in addition to performing various other important functions.
- collagen
- ⬢Collagen is a group of naturally occurring proteins. In nature, it is found exclusively in animals. It is the main protein of connective tissue. It is the most abundant protein in mammals
- elastin
- ⬢Elastin is a protein in connective tissue that is elastic and allows many tissues in the body to resume their shape after stretching or contracting.
- proteoglycans
-
⬢A class of proteins with a high polysaccharide content.
- tight junctions
- ⬢are regions where there is no space in between cells
- desmosomes
- is a cell structure specialized for cell-to-cell adhesion
- gap junction
-
⬢A gap junction or nexus is a specialized intercellular connection between a multitude of animal cell-types. It directly connects the cytoplasm of two cells, which allows various molecules and ions to pass freely between cells.
- amphipathic
- ⬢describing a molecule, such as a detergent, which has both hydrophobic and hydrophilic groups; often refers to the surface(s) on a protein, particularly an alpha helix, where one surface of the alpha helix has hydrophilic amino acids and the opposite face has hydrophobic
- Fluid Mosaic Model
-
⬢The cell membrane (also called the plasma membrane or plasmalemma) is one biological membrane separating the interior of a cell from the outside environment.
- phospholipid bilayer
-
⬢A double layer of phospholipids that makes up plasma and organelle membranes.
- Cholesterol
- ⬢Cholesterol is a waxy steroid metabolite found in the cell membranes and transported in the blood plasma of all animals. It is an essential structural component of mammalian cell membranes, where it is required to establish proper membrane permeability and fluidity
- Integral membrane protein
- is a protein molecule (or assembly of proteins) that is permanently attached to the biological membrane. Such proteins can be separated from the biological membranes only using detergents, nonpolar solvents, or sometimes denaturing agents
- transmembrane proteins
-
Transmembrane proteins aggregate and precipitate in water. They require detergents or nonpolar solvents for extraction, although some of them (beta-barrels) can be also extracted using denaturing agents.
- Peripheral membrane proteins
- ⬢Peripheral membrane proteins are proteins that adhere only temporarily to the biological membrane with which they are associated. These molecules attach to integral membrane proteins, or penetrate the peripheral regions of the lipid bilayer
- diffusion
-
the process in which there is movement of a substance from an area of high concentration of that substance to an area of lower concentration
- dynamic equilibrium
-
any equilibrium in which opposite changes occur simultaneously; an equilibrium in which two reversible reactions occur at the same rate
- passive transport
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⬢transport of a substance across a cell membrane by diffusion; expenditure of energy is not required
- facilitated diffusion
-
⬢movement of specific molecules across cell membranes through protein channels
- active transport
- active transport involves the transportation of things from a region of lower concentration to a higher concentration. If the process uses chemical energy, such as from adenosine triphosphate (ATP), it is termed primary active transport
- Channel Protein
-
Protein forming an aqueous pore spanning the lipid bilayer of the cell membrane.
- Carrier Proteins
- proteins involved in the movement of ions, small molecules, or macromolecules, such as another protein, across a biological membrane
- membrane potential
- ⬢Membrane potential (or transmembrane potential) is the voltage difference (or electrical potential difference) between the interior and exterior of a cell.
- Electrochemical gradient
- ⬢An electrochemical gradient is a spatial variation of both electrical potential and chemical concentration across a membrane. Both components are often due to ion gradients, particularly proton gradients, and the result can be a type of potential energy available for work in a cell
- Na/K Pump
-
⬢Na+/K+-ATPase (also known as the Na+/K+ pump, sodium-potassium pump, or simply sodium pump, for short) is an enzyme located in the plasma membrane (specifically an electrogenic transmembrane ATPase) in all animals.
- proton pump
-
⬢A structure in the body that produces and pumps acid into the stomach.
- osmosis
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⬢(biology, chemistry) diffusion of molecules through a semipermeable membrane from a place of higher concentration to a place of lower concentration until the concentration on both sides is equal
- Tonicity
- ⬢Tonicity is a measure of the osmotic pressure (as defined by the water potential of the two solutions) of two solutions separated by a semipermeable membrane.