Matter

Anything that takes up space and has mass.

Elements

Substances that cannot be broken down into substances with different properties; composed of only one type of atom.

Atom

Smallest particle of an element that displays the properties of the element.

Proton

Positive subatomic particle located in the nucleus and assigned one atomic mass unit.

Neutron

Neutral subatomic particle, located in the nucleus and assigned one atomic mass unit.

Electron

Negative subatomic particle, moving about in an energy level around the nucleus of an atom.

Electron shell / orbital

The average location, or energy level, of an electron in an atom. Often drawn as concentric circles around the nucleus.

Atomic number

Number of protons within the nucleus of an atom.

Mass number

Mass of an atom equal to the number of protons plus the number of neutrons within the nucleus.

Isotopes

Atoms of the same element having the same atomic number but a different mass number due to a variation in the number of neutrons.

Atomic mass

Average of atom mass units for all the isotopes of an atom.

Mass versus weight

Mass is constant, while weight changes according the gravitational force of a body. For example, substances weight less on the moon, even though their mass has not changed.

Periodic table

Organizes elements, and therefore atoms, according to chemical and physical characteristics. Elements are arranged according to increasing atomic numbers, with groups listed in vertical columns, and periods in horizontal rows.

Radioactivity

Release of energy from the decay of the nuclei of certain kinds of atoms.

Radioactive isotopes

Critical to modern society, with uses in medicine, chemistry, energy, environmental sciences, manufacturing, and national security.

Tracer

Radioactive isotope that serves as a chemical tag that can be used to detect molecular changes. For example, positron emission tomography (PET) uses radioactively-labeled glucose (which emits a subatomic particle known as a positron), to track the uptake of glucose by metabolically active cells in the brain.

Valence shell

The outer electron shell of an atom. Contains the valence electrons, which determine the chemical reactivity of the atom.

Octet rule

The observation that an atom is most stable when its outer shell is complete and contains eight electrons; an exception is hydrogen, which requires only two electrons in its outer shell to have a completed shell.

Molecule

Union of two or more atoms of the same element; also, the smallest part of a compound that retains the properties of the compound.

Compound

Substance having two or more different elements in a fixed ratio.

Ion

Charged particle that carries a negative or positive change. Ions form when electrons are transferred from one atom to another. For example, sodium (Na), with only one electron in its valence shell, tends to be an electron donor. Chlorine (Cl), with seven electrons in its valence shell, tends to be an electron acceptor. This electron transfer causes a charge imbalance in each atom. The sodium atom has one more proton then it has electrons and therefore has a net charge of +1 (symbolized by Na+). The chlorine atom has one more electron than it has protons and therefore has a net charge of -1 (symbolized by Cl-). Such charge particles are called ions.

Ionic bond

Chemical bond in which ions are attracted to one another by opposite charges. When sodium (Na+) reacts with chlorine (Cl-), an ionic compound forms called sodium chloride (NaCl).

Covalent bond

Chemical bond in which atoms share one pair of electrons, allowing each atom to have a completed valence shell. A double covalent bond occurs when two atoms share two pairs of electrons. Similarly, a triple covalent bond can also form between atoms that share electrons. Single covalent bonds are strong, but double and triple covalent bonds are even stronger.

Nonpolar covalent bond

Bond in which the sharing of electrons between atoms is fairly equal.

Polar covalent bond

Bond in which the sharing of electrons between atoms is unequal.

Electronegativity

The ability of an atom to attract electrons toward itself in a chemical bond.

Hydrogen bond

Weak bond that arises between a slightly positive hydrogen atom of one molecule and a slightly negative atom of another molecule, or between parts of the same molecule. Because a hydrogen bond is easily broken, it is often represented by a dotted line. Although a hydrogen bond is more easily broken than a covalent bond, many hydrogen bonds taken together are quite strong. Hydrogen bonds between cellular molecules help maintain their proper structure and function. For example, hydrogen bonds hold the two strands of DNA together.

Chemistry of Water

Water is a polar molecule, and water molecules are hydrogen-bonded to one another. 1. Water has a high heat capacity. The many hydrogen bonds what link water molecules help water absorb heat without a great change in temperature. Because the temperature of water rises and falls slowly, organisms are better able to maintain their normal internal temperatures and are protected from rapid temperature changes. 2. Water has a high heat of vaporization. Hydrogen bonds must be broken before the water boils and changes to a vaporized state. This gives animals in a hot environment an efficient way to release excess body heat, i.e. when we sweat or get water splashed on us, our body is used to vaporize the water, thus cooling us down. 3. Water is a solvent. Due to its polarity, water facilities chemical reactions and it dissolved a great number of substances. 4. Water molecules are cohesive and adhesive. They cling to each other (cohesion) and cling to other polar surfaces (adhesion). 5. Frozen water is less dense than liquid water. This allows ice to float on the surface of bodies of water and acts as an insulator to prevent the water below it from freezing, thus protecting aquatic organisms during the winter. As ice melts in the spring, it draws heat from the environment, helping to prevent a sudden change in temperature that might be harmful to life.

Calorie

Amount of heat energy required to raise the temperature of one gram of water 1 degree Celsius.

Solution

Fluid (the solvent) that contains a dissolved solid (the solute).

Solute

Substance that is dissolved in a solvent, forming a solution.

Hydrophilic

Type of molecule, often polar, that interacts with and attracts water by dissolving in water and/or by forming hydrogen bonds with water molecules.

Hydrophobic

Type of molecule that is typically nonpolar and therefore does not attract or interact easily with water.

Cohesion

The ability of water molecules to cling to each other due to the process of hydrogen bonding.

Adhesion

The ability of water molecules to cling to, or be attracted to, a surface, such as a transport vessel in a plant or animal.

Surface tension

Force that holds moist membranes together due to the attraction of water molecules through hydrogen bonds.

Acid

Molecules tending to raise the hydrogen ion concentration in a solution and thus to lower its pH numerically. For example, hydrogen peroxide is strong acid that dissociates to H+ and Cl-, thus increasing hydrogen ions (H+) in a solution.

Acidic solutions

High H+ concentrations. Lemon juice, vinegar, tomatoes, and coffee are all acidic solutions.

Base

Molecules tending to lower the hydrogen ion concentration in a solution and thus raise the pH numerically. Bases either take up hydrogen ions (H+) or release hydroxide ions (OH-). For example, sodium hydroxide (NaOH) is a strong base that dissociates to Na+ and OH-, this increasing hydroxide ions (OH-) in a solution.

Basic solutions

Low H+ concentrations. Baking soda and antacids are common basic solutions.

pH scale

Measurement scale for hydrogen ion concentration. Based on the formula −log[H+]. pH reflects the acidity or basicity (alkalinity) of solutions. The pH scale ranges from 0 to 14, with a pH of 7 being neutral where the hydrogen ion and hydroxide ion concentrations are equal. A pH below 7 is acidic due to a greater H+ concentration, whereas a pH above 7 is basic due to a greater OH- concentration.

Buffer

Substance or group of substances that tend to resist pH changes of a solution, thus stabilizing its relative acidity and basicity. They resist pH changes by taking up excess hydrogen ions (H+) or hydroxide ions (OH-).

Acidosis

Occurs when the blood pH drops to about 7 (healthy blood pH is about 7.4).

Alkalosis

Occurs when the blood pH rises to about 7.8 (healthy blood pH is about 7.4).

Organic

Molecule that always contains carbon and hydrogen, and often contains oxygen as well; these molecules are associated with living ¬organisms. Examples are carbohydrates, lipids, proteins, and nucleic acids.

Inorganic

Molecules that do not contain carbon and hydrogen molecules together. Examples are water, carbon dioxide, and salts.

Isomers

Molecules with the same molecular formula but a different structure, and therefore a different shape.

Functional group

Specific cluster of atoms attached to the carbon skeleton of organic molecules that enters into reactions and behaves in a predictable way. Common functional groups include: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, and phosphate.

Polymer

Macromolecule consisting of covalently bonded monomers; for example, a polypeptide is a polymer of monomers called amino acids.

Monomer

Small molecule that is a subunit of a polymer (e.g., glucose is a monomer of starch).

Macromolecules / Biomolecules

Smaller subunits joined together to build organic molecules such as carbohydrates, lipids, proteins, and nucleic acids.

Dehydration reaction

Chemical reaction in which a water molecule is released during the formation of a covalent bond. This reaction is a common way to join organic monomers to build polymers.

Hydrolysis reaction

Splitting of a chemical bond by the addition of water, with the H+ going to one molecule and the OH− going to the other. This reaction is a common way to degrade organic polymers.

Carbohydrate

Class of organic compounds that typically contain carbon, hydrogen, and oxygen in a 1:2:1 ratio; includes the monosaccharides, disaccharides, and polysaccharides. Carbohydrates are almost universally used as an energy source for living organisms, they play structure roles in a variety of organisms, and they are found on cell surfaces and are involved in cell-to-cell recognition.

Monosaccharide

Simple sugar; a carbohydrate that cannot be broken down by hydrolysis (e.g., glucose); also, any monomer of the polysaccharides. Examples include the isomers glucose, fructose, and galactose.

Pentose

Five-carbon monosaccharide. Examples are deoxyribose found in DNA and ribose found in RNA.

Hexose

Any monosaccharide that contains six carbons; examples are glucose and galactose.

Glucose

Six-carbon monosaccharide; used as an energy source during cellular respiration and as a monomer of the structural polysaccharides. Life all organisms, our bodies use glucose as an immediate source of energy.

Disaccharide

Sugar that contains two monosaccharide units. Maltose forms when two glucose monomers join during a dehydration reaction. Similarly, sucrose forms when glucose combines with fructose, and lactose forms when glucose joins with galactose.

Lactose intolerance

Occurs in individuals who lack lactase, which is the enzyme that breaks down the disaccharide lactose to form glucose and galactose in a hydrolysis reaction.

Polysaccharide

Polymer made from carbohydrate monomers; the polysaccharides starch and glycogen are polymers of glucose monomers. Polysaccharides serve as storage molecules because they are not as soluble in water, they are much larger than simple sugar, and they cannot easily move in or out of cells.

Starch

Storage polysaccharide found in plants that is composed of glucose molecules joined in a linear fashion with few side chains.

Glycogen

Storage polysaccharide found in animals; composed of glucose molecules joined in a linear fashion but having numerous branches. After we eat, the release of the hormone insulin from the pancreas promotes the storage of glucose as glycogen in the liver.

Cellulose

Polysaccharide that is the major complex carbohydrate in plant cell walls. The glucose units in cellulose are joined differently than starch or glycogen. This prevents us from digesting foods containing this type of bonding pattern, and it largely passes through our digestive tract as fiber.

Chitin

A structural polysaccharide that is found in the exoskeleton on (shell) of crabs and related animals.

Lipid

Class of organic compounds that tends to be soluble in nonpolar solvents; includes fats and oils.

Triglyceride

Neutral fat composed of glycerol and three fatty acids; typically involved in energy storage.

Fat

Organic molecule that contains glycerol and three fatty acids; energy storage molecule. Fats are the primary lipid used by animals for insulation and long-term energy storage.

Oil

Triglyceride, usually of plant origin, that is composed of glycerol and three fatty acids and is liquid in consistency due to many unsaturated bonds in the hydrocarbon chains of the fatty ¬acids.

Emulsifier

Allows fats and oils (which are hydrophobic molecules) to mix with water.

Emulsification

The mechanism that fat or oil is dispersed in water by emulsifiers, which position its nonpolar ends inward towards an oil droplet and its polar ends outward towards water.

Fatty acid

Molecule that contains a hydrocarbon chain and ends with an acid group (--COOH).

Saturated fatty acid

Fatty acid molecule that lacks double bonds between the carbons of its hydrocarbon chain. The chain bears the maximum number of hydrogens possible. Solid at room temperature, these include lard and butter.

Unsaturated fatty acid

Fatty acid molecule that contains double bonds between some carbons of its hydrocarbon chain; thus contains fewer hydrogens than a saturated hydrocarbon chain. Liquid at room temperature, these include vegetable oils.

Trans fats

Unsaturated fatty acid chains in which the configuration of the carbon-carbon double bonds is such that the hydrogen atoms are across from each other, as opposed to being on the same side (cis). An unintended consequence of hydrogenation is the formation of trans fats.

Phospholipid

Molecule that forms the bilayer of the cell's membranes; has a polar, hydrophilic head bonded to two nonpolar, hydrophobic tails.

Steroid

Type of lipid molecule having a complex of four carbon rings (e.g., cholesterol, estrogen, progesterone, and testosterone).

Cholesterol

A steroid formed by the body and ingested; it is a component of an animal cell's plasma membrane and it the precursor of several other steroids, such as bile salts and the sex hormone testosterone and estrogen.

Protein

Polymer of amino acids; often consisting of one or more polypeptides and having a complex three-dimensional shape. As much as 50% of the dry weight of most cells consists of proteins.

Protein functions

1. Metabolism: Enzyme proteins bring reactants together, increasing the rate of chemical reactions in cells. 2. Support: Some structures such as hair, nails, skin, and ligaments are primarily composted on structural proteins. 3. Transport: Channel and carrier proteins in the plasma membrane regulate which substances enter and exit cells. Additionally, special proteins transport molecules in blood. 4. Defense: Complement proteins and antibodies assist the immune system in defending the body against pathogens. 5. Regulation: Some hormones are proteins that influence cellular behavior; others serve as intercellular messengers that influence cell metabolism, such as using nutrients for energy. 6. Motion: The contractile proteins of the muscular system allow muscles to contract. All cells contain proteins that move cell components to different internal locations.

Amino acid

Organic molecule composed of an amino group (--NH2) and an acid group (--COOH); covalently bonds to produce peptide molecules. The third group is an R group that determines the uniqueness of each amino acid. Amino acids are linked by dehydration reactions that connect the carboxyl group of one amino acid to the amino group of another amino acid.

R group

The third group that comprises an amino acid, it impacts the structure and chemical reactivity of amino acids. Some R groups are polar and associate with water, whereas others are nonpolar and do not interact with water. The amino acid cysteine has an R group that ends with a -SH (sulfide) group, which often covalently connections of chain of amino acids to another by a disulfide bone.

Peptide bond

Type of covalent bond that joins two amino acids. Peptide bonds are formed during dehydration reactions, and broken during a hydrolysis reaction.

Polypeptide

Polymer of many amino acids linked by peptide bonds.

Levels of Protein Organization

1. Primary structure: Linear sequence of amino acids joined by peptide bonds. 2. Secondary structure: Occurs when a polypeptide takes on a certain orientation in space (alpha helices, beta pleated sheets). 3. Tertiary structure: Three-dimensional shape of a polypeptide. 4. Quaternary structure: Multiple polypeptides arrange to form higher-order protein structures.

Denatured

Loss of a protein's normal shape so that it no longer functions; usually caused by a less than optimal pH and temperature. Denaturation occurs because the normal bonding between the R groups has been disturbed.

Prions

Proteinaceous infectious particles. Infectious protein agents that cause transmissible spongiform encephalopathies. The prion protein binds to the normal protein and induces it to misfold to form additional prion proteins. With time, the prion proteins aggregate to form clumps and can interfere with brain function.

Nucleic acid

Polymer of nucleotides; both DNA and RNA are nucleic acids.

DNA (deoxyribonucleic acid)

Nucleic acid polymer produced from covalent bonding of nucleotide monomers that contain the sugar deoxyribose; the genetic material of living organisms.

RNA (ribonucleic acid)

Nucleic acid produced from covalent bonding of nucleotide monomers that contain the sugar ribose; occurs in many forms, including messenger RNA, ribosomal RNA, and transfer RNA.

Nucleotide

Monomer of DNA and RNA consisting of a 5-carbon sugar bonded to a nitrogenous base and a phosphate group.

Adenine (A)

One of four nitrogen-containing bases in nucleotides composing the structure of DNA and RNA. Pairs with uracil (U) and thymine (T).

Thymine (T)

One of four nitrogen-containing bases in nucleotides composing the structure of DNA; pairs with adenine.

Guanine (G)

One of four nitrogen-containing bases in nucleotides composing the structure of DNA and RNA; pairs with cytosine.

Cytosine (C)

One of four nitrogen-containing bases in nucleotides composing the structure of DNA and RNA; pairs with guanine.

Uracil (U)

Pyrimidine base that occurs in RNA, replacing thymine.

Double helix

Double spiral; describes the three-dimensional shape of DNA.

DNA structure

DNA is double-stranded, with the two strands twisted to form a double helix. The two DNA strands are held together by hydrogen bonds between the bases. When unwound, DNA resembles a ladder. The sides of the ladder are made entirely of alternating phosphate and sugar molecules, and the rungs of the ladder are made of complementary paired bases. T pairs with A, and G pairs with C. Complementary base pairing allows DNA to copy itself during replication. The base sequence of specific DNA sections or genes specifics the sequence of RNA and ultimately amino acids in proteins.

Structure of DNA versus RNA

1. Sugar: Deoxyribose (DNA) vs. Ribose (RNA) 2. Bases: A, G, T, C (DNA) vs. A, G, U, C (RNA) 3. Strands: Double-stranded with base pairing (DNA) vs. Single-stranded (RNA) 4. Helix: Yes (DNA) vs. No (RNA)

Adenosine triphosphate (ATP)

Nucleotide with three phosphate groups. The breakdown of ATP into ADP + phosphate makes energy available for energy-requiring processes in cells. ATP is the "energy currency" of cells.