Biomolecules and the Chemistry of Life Terms
Get down with the lingo
Amino AcidThe single unit building block (or, technically speaking, monomer) of proteins. Every amino acid has these three things: a central carbon atom bound to a hydrogen atom, a carboxyl group (COOH), an amino group (NH2), and a variable "R" group. The R group is a placeholder for another chemical structure that gives the amino acid its unique identity and affects its properties. The chemical structures that link amino acids together to form proteins are called peptide bonds. Twenty to thirty amino acids strung together make a peptide, and many more amino acids form a polypeptide. Polypeptides are also sometimes called proteins if they have lots and lots of amino acids (in the hundreds to thousands). Amino acids you may have heard of include tryptophan—the molecule often blamed for post-Thanksgiving drowsiness—and glutamic acid, which, when combined with an ion (Na+), gives us MSG, a common flavor enhancer. Random fact: Titin is the largest known "polypeptide," or protein, and has 34,350 amino acids. Yowza.
AtomThe structural unit of an element. In other words, an atom is the smallest "piece" of an element that has all the properties of that element. A gold (Au) atom hanging out with lots of other gold atoms makes, well, gold.
Atomic NumberThe number of protons in each atom of a given element. If you change the atomic number, you get a different element.
BaseA substance with lots of hydroxide ions (OH-) that combine with hydrogen ions (H+). This combining effectively occupies them for the moment and increases the pH of a solution. A base has a pH above 7 on a scale of 1 to 14. Tums® and Drano® both have bases in them. (All your base are belong to us.)
BufferA substance, usually a salt, that helps to maintain constant pH conditions by giving or accepting hydrogen (H+) ions. The purpose of a buffer is to prevent the pH of a solution from wildly fluctuating when an acid or a base enters the situation. If your blood were not buffered, its pH would fly all over the place depending on what you ate. Amazingly, the buffer keeps your blood at a steady pH of 7.41.
CarbohydrateA biological molecule that has the elements carbon (C), hydrogen (H), and oxygen (O) in a ratio of 1:2:1. Carbs provide energy to cells, can be used for energy storage, and provide structural support. Gatorade, anyone?
CelluloseA structural polysaccharide (a type of sugar, aka a carbohydrate) in which alternating glucose (C6H12O6) molecules are upside down and right side up in terms of orientation. Animals cannot digest cellulose so it usually passes through the digestive tract. Some animals have helpful gut microbes that break the cellulose down, and those lucky souls get energy from cellulose. Cellulose is the most abundant organic compound on Earth. Take that.
ChitinA structural polysaccharide (a type of sugar, aka a carbohydrate) found in some animals and fungi. Chitin is made from glucose (C6H12O6) molecules that have nitrogen-containing functional groups attached. If you have ever tried eating a roasted cricket or grasshopper—they are delicacies in some places—chitin is what made it crispy. Mmmm.
CompoundA substance that is formed from more than one kind of atom chemically bound together. For example, carbon dioxide (CO2) and sodium chloride (NaCl) are compounds because each one has two kinds of atoms that are bound by covalent or ionic bonds. Oxygen (O2) is not a compound, however, because it has one single kind of atom (O). Oxygen is referred to a diatomic molecule.
Covalent BondThe bond between atoms that share some of their electrons. If one pair of electrons is shared, it is called a single covalent bond. If two pairs are being shared, it is a double covalent bond. And if three pairs are being shared, it is a—wait for it—triple covalent bond.
Dehydration SynthesisThe process of removing a water molecule (H2O) and simultaneously joining together monomers, or individual units. One monomer coughs up a hydrogen (H), and the other coughs up a hydroxyl group (OH). Those two things bind to form a water molecule, which is removed, and the monomers bind to each other where they were originally bound to their H and OH groups.
DNAThe official nickname for deoxyribonucleic acid, a nucleic acid whose sugar is deoxyribose. DNA is double-stranded in its naturally occurring form and contains information that is used to synthesize proteins, solve crimes, and settle paternity disputes. It is the molecule of heredity.
ElectronA teeny, tiny, negatively charged subatomic particle that orbits the nucleus of an atom. It weighs 9.109389 x 10-28 g and is so small that its mass is ignored in most circumstances. Poor little electrons.
ElementA pure chemical substance that cannot be broken down and still identified as a substance. The periodic table of elements is a good place to view all the information about known elements.
EnzymeA protein that catalyzes a chemical reaction (makes it go faster).
Fatty AcidA long chain of hydrocarbons (only consisting of carbons and hydrogens) with a carboxyl group (COOH) at the end. Fatty acids join with a molecule of glycerol (C3H8O3), and through dehydration synthesis (see definition), make a triglyceride. If all the carbons have single covalent bonds to either other carbons or hydrogens, the fatty acid is saturated. But, if a hydrogen sneaks off and causes two of the carbons to double bond, the fatty acid is unsaturated, and finds itself with a bend in the chain. Kinky. Saturated fat is made of saturated fatty acids (mmm, cheese); unsaturated fats contain unsaturated fatty acids (mmm, avocados).
GlucoseC6H12O6. Glucose is a monosaccharide, or sugar, produced in the process of photosynthesis, and it is also the building block for many disaccharides and polysaccharides (other sugars).
GlycogenA storage polysaccharide (sugar, or carbohydrate) in animals. Glycogen is extensively branched and is stored in liver and muscle cells. It can be broken down into glucose as needed, but in most animals, there is not enough glycogen to last very long.
Hydrogen BondThe electrical attraction between the positive side of one polar molecule (a hydrogen, as the name suggests) and the negative side of another polar molecule.
HydrophilicHydrophilic molecules <3 water. They are attracted to either the positive or negative side of the polar water molecule, which means that they are either charged (ions) or they are polar molecules themselves.
HydrophobicHydrophobic molecules do NOT <3 water. They are electrically neutral and are therefore not polar. They also will not dissolve in a water solution, a property known as insolubility, because there is nothing for the highly polar water to be attracted to. Note that hydrophobic substances do not hate water, per se; they just aren’t attracted to it. They have a bit of a "phobia," if you will.
InorganicA characteristic that is defined as a lack of any combination of carbon (C) and hydrogen (H). An inorganic compound can have either carbon (like CO2) or hydrogen (like H2O). If the compound has both, it is organic (see definition).
IonAn atom that has either gained or lost at least one electron, throwing off that perfect balance between positive and negative charges. An ion is either positively charged or negatively charged.
Ionic BondThe electrical attraction that holds ions together. Opposites attract! Electrons are stolen rather than shared during ionic bonds. For instance, Cl steals the electron from Na to form NaCl, or Na+ + Cl-. (Shared bonding is covalent bonding.)
IsotopeA different version of an element. Isotopes have the same number of protons as the original element so their chemical properties are the same. However, since they have different numbers of neutrons, the atomic masses of isotopes are different from the original element. Due to this imbalance, many isotopes are radioactive.
LipidA kind of biomolecule that has a long, nonpolar stretch of hydrocarbons (carbons and hydrogens), and due to this hydrocarbon chain, is not soluble in water. Lipids can be fats, oils, waxes, phospholipids, or steroids.
MoleculeTwo or more atoms bound together by covalent bonds. The atoms can be two or more of the same thing, as in O3 and N2, or they can be different, as in CO2 and H2O. NaCl is not a molecule; it is an ionic compound. No sharing electrons = no molecule status.
MonomerA relatively small molecule or unit that serves as a building block for bigger molecules. Monomers bind together to form polymers. An example of a monomer is an amino acid, and an example of a polymer is a peptide.
NeutronAs its name suggests, a neutron is a neutral subatomic particle. It resides in an atom’s nucleus, and weighs 1.6749286 x 10-24 g, which is slightly more than the proton. Together, neutrons and protons constitute most of the mass of an atom. Sorry, electrons.
Nucleic AcidA chain of nucleotides. Nucleic acids—DNA and RNA—are involved in protein synthesis, storing genetic information, and passing that information from generation to generation. Are they actually acids? Yes, they are.
NucleotideA nucleotide consists of a sugar (a carbohydrate), a phosphate group (–H2PO4R, where R is a functional group), and a nitrogen-containing base (usually ring structures with a few carbons and nitrogens). Nucleotides are the monomers of nucleic acids, and also play many other roles in cells, including the roles of cellular messengers, energy transporters, or coenzymes.
OrganicThe characteristic of having a carbon backbone and some hydrogen atoms to boot. Other elements can be present, too. Glucose (C6H12O6) is a good example of an organic compound.
Peptide BondThe covalent bond between two amino acids that forms in nature as a product of dehydration synthesis. When many amino acids are bound together, they form a peptide, polypeptide, or protein.
PHA measure of how acidic a solution is, on a scale of 1 to 14. As the concentration of free hydrogen ions (H+) increases, pH decreases. That’s right…more acidic means a lower pH. In pure water, the number of H+ ions exactly matches the number of OH- ions, and the pH is 7.0. Anything with a pH less than 7 is acidic, and anything with a pH higher than 7 is basic. Each step on the pH scale represents a tenfold difference in acidity.
PhospholipidA glycerol (C3H8O3) backbone that is bound to two fatty acid chains (see definition) and a phosphate group (–H2PO4R). The phosphate group makes the polar "head," and the fatty acids make the nonpolar "tails." Cell membranes largely consist of a phospholipid bilayer.
PolarWe’re not referring to white bears or an ice cap. Polar covalent bonds form when atoms share electrons, but one (or more) of the atoms hogs more than its fair share. More like a pig than a bear, if you ask us. The result of a polar covalent bond is a polar molecule—one with an unequal distribution of electrical charges. Polarity is one of the properties that makes water important for life. Like really, really important.
PolymerA relatively large molecule that is composed of smaller subunits, or monomers. DNA is a polymer, or more specifically, a polynucleotide. Peptides and proteins are also polymers.
ProteinAn organic molecule comprises amino acids. Proteins have four levels of structure: Primary structure is the sequence of amino acids that form the unfolded polypeptide chain. Secondary and tertiary protein structures are the result of bonds between different parts of the polypeptide chain, and yield a 3D shape. (Think of a curly fry.) Quaternary structure, when present, is the overall shape of an aggregation of polypeptide chains. (Think of multiple curly fries stuck together.) Proteins do lots of important things: they act as enzymes, support structures, facilitate movement, communication, and transport, and are also used in storage and defense. Each protein has a specific function, and its structure is critical for allowing it to fulfill its duty.
ProtonA positively charged subatomic particle that makes its happy home in the nucleus of an atom. It weighs 1.672623 × 10-24 g, or slightly less than the neutron, and together, these subatomic particles constitute most of the mass of an atom. The electrons get shafted again.
RNAThe official nickname for ribonucleic acid. RNA is a nucleic acid (see definition) whose sugar is ribose. RNA is single-stranded and is involved in protein synthesis.
SaturatedWhen all carbons in a fatty acid have as many hydrogens bound to them as possible. This means there are no double bonds between carbons.
SolventA solid, liquid, or gas that causes another substance to dissolve. Water is a top-notch solvent.
Specific HeatThe amount of energy needed to heat 1 gram of a substance by 1 °C. Water absorbs a lot of energy before it actually changes temperature, which means it has a high specific heat capacity. This is the reason that water is still cool in early summer even though the weather is hot, but is still warm in the late summer when temperatures have started to drop.
StarchA storage polysaccharide (a sugar, or carbohydrate) in plants. Starch is formed when glucose monomers (C6H12O6) join together. Enzymes can break down starch and release glucose as needed.
SteroidA class of lipids composed of four carbon rings. Well-known steroids include sex hormones and cholesterol. Baseball players have gotten into some serious trouble messing around with these things.
TriglycerideA glycerol (C3H8O3) molecule that has blissfully united with not one, not two, but three fatty acids.
UnsaturatedWhen two or more carbons in a fatty acid form double bonds, and do not have the maximum number of hydrogens possible. Unsaturation causes kinks in the fatty acid chain, which makes it harder for triglycerides to pack closely together. Unsaturated fats are usually liquids at room temperature, like olive oil, rather than closely packed saturated fats, like a solid brick of butter.
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