Biology 107 Midterm terms

Polymer

A long molecule consisting of many similar or identical monomers linked together by covalent bonds.

Macromolecules

A giant molecule formed by the joining of smaller molecules, usually by a dehydration reaction. Polysaccharides, proteins, and nucleic acids are macromolecules.

Monomer

The subunit that serves as the building block of a polymer.

Enzyme

A macromolecule serving as a catalyst, a chemical reagent that increases the rate of reaction without being consumed by the reaction. Most are proteins. A typical one can perform 1000 reactions/second (sucrose ~ 1000 rx/sec, catalase ~ 300000 rx/sec, rubisco ~ 3 rx/sec). Most are named substrate + ase. Most cellular processes require several of them. Are optimized for their environment (e.g. temp, pH). Can be regulated (e.g. regulatory site which requires regulatory molecules). Can be permanently inhibited by several toxins which mimic enzyme substrates.

Dehydration reaction

A chemical reaction in which two molecules become covalently bonded to each other with the removal of a water molecule.

Hydrolysis

A chemical reaction that breaks bonds between two molecules by the addition of water; functions in disassembly of polymers to monomers.

Carbohydrate

A sugar (monosaccharide) or one of its dimers (disaccharides) or polymers (polysaccharides).

Monosaccharide

The simplest carbohydrate, active alone or serving as a monomer for disaccharides and polysaccharides. Also known as simple sugars, monosaccharides have molecular formulas that are generally some multiple of CH2O. Glucose (C6H12O6) is the most common monosaccharide.

Oligosaccharide

3 to 10 monosaccharides joined together.

Disaccharide

A double sugar, consisting of two monosaccharides joined by a glycosidic linkage formed by a dehydration reaction. Functions as an energy source and carbon source.

Polysaccharide

A polymer of many monosaccharides, formed by dehydration reactions. Made of 100s to 1000s of glucoses joined together. Glycogen and starch are used for energy storage, and are easy to make, however they are heavy, which makes fats and oils preferable.

Glucose (C6H12O6)

Most common monosaccharide. Has two ring structures (α and β). There are also modified ones such as NAG and NAM.

Glycogen

An extensively branched glucose storage polysaccharide found in he liver and muscle of animals; the animal equivalent of starch. Polymer of α-glucose.

Starch

A storage polysaccharide in plants, consisting entirely of glucose monomers joined α-glycosidic linkages. Polymer of α-glucose.

Cellulose

A structural polysaccharide of plant cell walls, consisting of glucose monomers joined by β glycosidic linkages. Polymer of β-glucose.

Chitin

A structural polysaccharide, consisting of amino sugar monomers, found in many fungal (yeast) cell walls and in the exoskeletons of all arthropods. Polymer of NAG.

Protein

A biologically functional molecule consisting of one or more polypeptides folded and coiled into a specific three-dimensional structure.

Polypeptide

A polymer of many amino acids linked together by peptide bonds.

Amino acids

An organic molecule possessing both a carboxyl and an amino group. Amino acids serve as the monomers of polypeptides.

Primary structure

A linked series of amino acids with a unique sequence.

Secondary structure

Segments of the polypeptide chains in most proteins that are repeatedly coiled or folded in patterns that contribute to the protein's overall shape. Are the result of hydrogen bonds between the repeating constituents of the polypeptide backbone (not the amino acid side chains)

α helix

One of the main types of secondary structures, a delicate coil held together by hydrogen bonding between every fourth amino acid.

β pleated sheet

One of the main types of secondary structures. In this structure, two or more strands of the polypeptide chain lying side by side are connected by hydrogen bonds between parts of the two parallel polypeptide backbones.

Tertiary structure

The overall 3D shape of a polypeptide resulting from interactions between side chains (R groups) of the various amino acids. One type of interaction is hydrophobic interaction.

Hydrophobic interaction

One type of interaction that contributes to the tertiary structure. As a polypeptide folds into its functional shape, amino acids with hydrophobic (nonpolar) side chains usually end up in clusters in the core of a protein, out of contact with water. Thus, is actually caused by the exclusion of nonpolar substances by water molecules.

Quaternary structure

The overall protein structure that results from the aggregation of two or more polypeptide chains aggregated into one functional macromolecule. The 3D shape of proteins made with 2 or more

polypeptides stabilized by side chain interactions.

Hemoglobin

The oxygen-binding protein of red blood cells. An example of a globular protein with quaternary structure. Consists of four polypeptide subunits, two of one kind (α) and two of another kind (β). Both α and β subunits consist primarily of α-helical secondary structure. Each subunit has a nonpolypeptide component, called heme, with an iron atom that binds to oxygen.

Phosphate group

A chemical group consisting of a phosphorous atom bonded to four oxygen atoms; important in energy transfer.

Transport protein

A transmembrane protein that helps a certain substance or class of closely related substances cross the membrane.

Defensive protein

A protein on the outer cell membrane that protects against disease (e.g. antibodies inactivate and help destroy viruses and bacteria).

Storage proteins

Proteins that function as storage of amino acids. E.g. Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants have these proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo.

Hormonal proteins

Proteins that function in coordination of an organism's activities. E.g. Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration.

Receptor proteins

Proteins that function in the response of the cell to chemical stimuli. E.g. receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells.

Contractile and motor proteins

Proteins that function in movement. E.g. Are responsible for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contraction of muscles.

Structural proteins

Proteins that function in support. E.g. Keratin is the protein of hair, horns, feathers, and other skin appendages. Insects and spiders use silk fibers to make their cocoons and webs, respectively. Collagen and elastin proteins provide a fibrous framework in animal connective tissues.

Nucleic acid

A polymer (polynucleotide) consisting of many nucleotide monomers; serves as a blueprint for proteins and, through the actions of proteins, for all cellular activities. The two types are DNA and RNA.

DNA (deoxyribonucleic acid)

A double-stranded, helical nucleic acid molecule, consisting of nucleotide monomers with a deoxyribose sugar and the nitrogenous bases adenine (A), cytosine (C), guanine (G), and thymine (T); capable of being replicated and determining the inherited structure of a cell's proteins. Stores information for cells. Because most molecules are double stranded (ds) their length is measured in base pairs (bp). Because many molecules are long their length is often measured in kilobases (kb) or Megabases (Mb).

RNA (ribonucleic acid)

A type of nucleic acid consisting of a polynucleotide made up of nucleotide monomers with a ribose sugar and the nitrogenous bases adenine (A), cytosine (C), guanine (G), and uracil (U); usually single-stranded; functions in protein synthesis, gene regulation, and as the genome of some viruses. Allows the information stored in the DNA to control the cell. Because most molecules are single stranded (ss) their length is measured in nucleotides (nt).

Nucleotide

The building block (monomer) of a nucleic acid, consisting of a five-carbon sugar covalently bonded to a nitrogenous base and one or more phosphate groups. Hydrogen bonds between certain bases give DNA and RNA molecules their shapes.

Purine

One of two types of nitrogenous bases found in nucleotides, characterized by a six-membered ring fused to a five-membered ring. Includes adenine (A) and guanine (G).

Pyrimidine

One of two types of nitrogenous bases found in nucleotides, characterized by a six-membered ring. Includes cytosine (C), thymine (T), and uracil (T).

ATP (adenosine triphosphate)

An adenine-containing nucleoside triphosphate that releases free energy when its phosphate bonds are hydrolyzed. This energy is used to drive endergonic reactions in cells.

GTP (guanosine triphosphate)

A molecule similar to ATP in its structure and cellular function. Used to regulate the activity of a few proteins.

Lipid

Any of a group of large biological molecules, including fats, phospholipids, and steroids, that mix poorly, if at all, with water. Are not polymers. Hydrophobic (partially or completely). Fats and oils are used for energy storage.

Fat

A lipid consisting of three fatty acids linked to one glycerol molecule; also called a triacylglycerol or triglyceride. Contain saturated fatty acids. E.g. butter is made from these lipids in cow milk. Easier to make than oils.

Oil

A lipid that refers to plant and fish fats that are usually liquid at room temperature. The kinks where the cis double bonds are located prevent the molecules from packing together closely enough to solidify at room temperature. Used because they don't freeze (however they are more difficult to make due to the carbon-carbon double bond).

Amphipathic

Molecule has both a hydrophilic region and a hydrophobic region.

Phospholipid

A lipid made up of glycerol joined to two fatty acids and a phosphate group. The hydrocarbon chains of the fatty acids act as nonpolar, hydrophobic tails, while the rest of the molecule acts as a polar, hydrophilic head. Phospholipids form bilayers that function as biological membranes. Are amphipathic.

Glycerol

An alcohol; each of its three carbons bears a hydroxyl group. In making a fat, three fatty acid molecules are joined to glycerol by an ester linkage, a bond between a hydroxyl group and a carboxyl group. Spontaneously form bilayers in water.

Glycolipids

A lipid with one or more covalently attached carbohydrates. Similar in composition and identical in shape with phospholipids, but has 1 or more monosaccharides as its head, rather than 1 phosphate group.

Steroid

A type of lipid characterized by a carbon skeleton consisting of four fused rings with various chemical groups attached. E.g. Cholesterol (membranes in animal cells precursor). Hormones signaling molecules used in animals (e.g. human sex hormones, or ecdysone; insect molting hormone).

Cholesterol

A steroid that forms an essential component of animal cell membranes and acts as a precursor molecule for the synthesis of other biologically important steroids, such as many hormones. Prevents plasma membrane from leaking at high temperatures and from solidifying at low temperatures. With exposure to sunlight, produces Vitamin D.

Waxes

A type of lipid. A soft and waterproof material used by bees and tropical plants.

Lipopolysaccharide

Carbohydrates bonded to lipids. A mixed macromolecule used in the outer membrane of Gram negative Bacteria.

Peptidoglycan

Used in the cell walls of most Bacteria. A type of polymer in bacterial cell walls consisting of modified sugars cross-linked by short polypeptides. Made by transpeptidase.

Cofactor

Any nonprotein molecule or ion that is required for the proper functioning of an enzyme. Can be permanently bound to the active site or may bind loosely and reversibly, along with the substrate, during catalysis. E.g. Heme and Fe++.

Properties of all living organisms

Organized (made of one or more cells), metabolize (consume energy for maintanence, growth, and reproduction), interact with environment (find food, time to make flowers, etc.), reproduce (because don't live forever), evolve (change over many generations).

Scientific theory

An important and well supported explanation.

Cell theory

States that living organisms are made of cells.

Theory of evolution

States that living organisms change over many generations.

Germ theory

States that some diseases are caused by microorganisms.

Scientific law

An important and well supported statement.

Fauna (animals)

Ancient term for things that move around and eat.

Flora (plants)

Ancient term for things that don't move around to eat.

Archaea

One of two prokaryotic domains, the other being bacteria. Live in extreme environments.

Antigens

Distinctive molecules on the surface of a cell that could be the target of antibody proteins.

Human pathogens

Microorganisms, viruses, or cell products that harm us when they reproduce. Can be Fungi, Protista, Bacteria, Archaea (possibly), virus, or prions.

Prions

An infectious agent that is a misfolded version of a normal cellular protein. Appear to increase in number by converting correctly folded versions of the protein to more of the misfolded proteins.

Desmosomes

Protein discs on human cells that function in adhesion.

Spot desmosomes

Protein discs on human cells that function specifically in adhesion to other cells.

Hemidesmosomes

Protein discs on human cells that function specifically in adhesion to ECM.

Tight junctions

Chains of integral membrane proteins that function in occlusion.

Gap junctions

Tubes made of integral membrane proteins that function in communication with other cells.

Evolution

Descent with modification; the idea that living species are descendants of ancestral species that were different from the present-day ones; also defined more narrowly as the change in the genetic composition from generation to generation.

Sex Pilus

In bacteria, structure that links one structure to another at the start of conjugation.

Diffusion

The movement of molecules from regions of high concentration to low concentration.

Osmosis

The movement of water molecules from a region of low solute concentration to high solute concentration.

Isotonic

Solute concentration outside the cell = inside the cell. Normal for animal cells.

Hypotonic

Solute concentration outside cell < inside cell. Normal for cells with cell walls (e.g. plants, most unicellular organisms) or contractile vacuoles (freshwater protists).

Hypertonic

Solute concentration outside cell > inside cell. Kills most cells.

Nucleus

The organelle of a eukaryotic cell that contains the genetic material in the form of chromosomes, made up of chromatin. The defining feature of Eukaryotic cells. ~6% of cell's volume.

Chromatin

The complex of DNA and proteins that makes up eukaryotic chromosomes. When the cell is not dividing, chromatin exists in its dispersed form, as a mass of vey long, thin fibers that are not visible with a light microscope. Functions in RNA synthesis and Ribosome assembly. Humans have 46 chromosomes, total length = 6400 Mb. Different types are distinguishable in TEM cross sections.

Euchromatin

The less condensed form of eukaryotic chromatin that is available for transcription. Functions in mRNA and tRNA synthesis.

Heterochromatin

Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed. Centromere DNA (moves chromosomes during cell division)

Nucleolus

A specialized structure in the nucleus, consisting of chromosomal regions containing ribosomal RNA (rRNA) genes along with ribosomal proteins imported from the cytoplasm; site of rRNA synthesis and ribosomal subunit assembly.

Ribosome

A complex of rRNA and protein molecules that function as a site for protein synthesis in the cytoplasm; consists of a large and a small subunit. In eukaryotic cells, each subunit is assembled in the nucleolus.

Nuclear envelope

In a eukaryotic cell, the double membrane that surrounds the nucleus, perforated with pores that regulate traffic with the cytoplasm. The outer membrane is continuous with the endoplasmic reticulum. Separates nucleoplasm from cytoplasm. Contains two phospholipid bilayers fluid filled space, nuclear lamina, and nuclear pores.

Nuclear lamina

A netlike array of protein filaments that lines the inner surface of the nuclear envelope and helps maintain the shape of the nucleus.

Endoplasmic reticulum

An extensive membranous network in eukaryotic cells, continuous with the outer nuclear membrane and composed of ribosome-studded (rough) and ribosome-free (smooth) regions. Consists of ER membrane (50-90% of cell's total membrane) and ER lumen (15% of cell's volume).

Rough ER

That portion of the endoplasmic reticulum with ribosomes attached. Functions in synthesis of membrane proteins and export proteins and synthesis of membrane lipids.

Smooth ER

Functions in drug metabolism in liver cells (but not alcohol). Enzymes (membrane proteins) add -OH groups to toxic molecules to make them more soluble. Also stores calcium ions in muscle cells. A sudden rise in cytosolic Ca++ triggers cell contraction.

Endomembrane system

The collection of membranes inside and surrounding a eukaryotic cell, related either through direct physical contact or by the transfer of membranous vesicles; includes the plasma membrane, the nuclear envelope, the smooth and rough endoplasmic reticulum, the Golgi apparatus, lysosomes, vesicles, and vacuoles.

Golgi apparatus

An organelle in eukaryotic cells consisting of stacks of flat membranous sacs that modify, store, and route products of the endoplasmic reticulum and synthesize some products, notably noncellulose carbohydrates. Animal cells have a single large stack, plant cells have many little stacks. Modify and distribute proteins and lipids made in ER.

Lysosome

A membrane-enclosed sac of hydrolytic enzymes (M6P tagged) found in the cytoplasm of animal cells and some protists. Functions in intracellular digestion. Are pH 5 because of the active import of H+. Digest macromolecules from outside the cell and inside the cell.

Peroxisome

An organelle containing enzymes that transfer hydrogen atoms form various substrates to oxygen (O2), producing and then degrading hydrogen peroxide (H2O2). Structure is vesicles filled with oxidative enzymes. Perform dangerous reactions.

Vacuole

A membrane-bounded vesicle whose specialized function varies in different kinds of cells.

Vesicle

A membranous sac in the cytoplasm of a eukaryotic cell.

Contractile vacuoles

Used by freshwater protists to expel water.

Central vacuole

Used in plant cells for storage and expansion. Store waste, nutrients, red and blue pigments, and toxins (to poison whatever eats it).

Plastid

One of a family of closely related organelles that includes chloroplasts, chromoplasts, and amyloplasts. Are found in cells of photosynthetic eukaryotes. small organelles with two membranes.