Glossary -- Chemistry and molecular biology


Introduction

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This Glossary was started because one textbook I was using did not have one. The Index can help, but sometimes a glossary is easier. So I started this, as a supplement. I'll add things to this as they come up; your suggestions welcomed! Although it was started for a specific context, I am happy to add things to it for any subject matter relevant to this site.

This is a developing page. All feedback encouraged.

I don't intend this to be a complete glossary. Instead, it is a place for us to record any terms that need supplemental discussion, or where additional examples or comparisons would help.

Please e-mail me any comments/corrections/suggestions: Contact information.

Terms

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Addition (organic chemistry reaction type). Some chemical of the form A-B is added across a double bond. A and B are now attached to the two atoms that had been double-bonded.

Allele. A form of a gene. It is a very general term. As an example, sickle cell is caused by a mutation in the beta gene of hemoglobin. Hb-S is an allele of the Hb-β gene. Importantly, the normal (wild type) form of the gene is also called an allele; it might be called the wild type allele.

Alpha (α, Α). See Greek letters.

Alternative splicing. A process that allows an organism to make more than one protein from the same gene. The simple view of gene function is that the DNA copy of the gene is copied into an mRNA (messenger RNA), and then the mRNA is translated into a protein. However, it can be more complex. In some cases, part of the mRNA is removed before the mRNA is translated into protein. This process is called splicing, and is extremely common with higher organisms. Further, there may be more than one way to splice the same mRNA. This is called alternative splicing. There may be regulatory factors that determine which splicing pathway is followed. As a result of alternative splicing, it is possible to make more than one protein from a single gene; further, regulation of splicing regulates the production of a protein even after the mRNA is made.

In one case, a single gene has been shown to yield 38,016 different proteins, by the alternative splicing of 95 exons. This is the Dscam gene of the fruit fly Drosophila melanogaster; similarly complex genes are found in other insects. The multiple proteins serve as markers of individuality for developing neurons.

Benzene. The terms phenyl and phenol, along with benzene and benzyl, are explained and compared on the page The phenyl group -- and related terms.

Benzyl. The terms phenyl and phenol, along with benzene and benzyl, are explained and compared on the page The phenyl group -- and related terms.

Chemical change. A process in which the basic chemical identity of the substances is changed. That is, new chemical substances are made. The atoms of the "old" chemicals (the reactants) rearrange to form new chemicals (the products). A good example is the decomposition of water to its elements, which can be done by electrolysis: H2O(l) --> H2(g) + O2(g). In this reaction, the reactant is the chemical substance H2O (water); the products are new chemical substances H2(g) and O2(g) (hydrogen gas and oxygen gas).

See Physical change for more; it is best to consider these two terms together, to focus on the distinction between them. Also see Nuclear change; this third type of change is also mentioned briefly at the end of this entry.

The distinction between chemical changes and physical changes is often presented at the beginning of a chemistry course. It is a useful distinction to help students who are beginning to learn about atoms vs molecules, and the idea of distinct chemical substances. However, there are some cautions about this issue.

There are cases where the distinction between chemical and physical changes is not entirely clear. This isn't the place to go into them, and it shouldn't be a problem at the beginning of a chem course. However, occasionally an example will come up. In such a case, the best approach is to focus on the underlying issue: what chemical substances are involved, and are new chemical substances made? If the ambiguity holds at this level, so be it. Sometimes, there is more than one way to look at a process. That is, the chemical-physical distinction is not rigid.

Some textbooks will try to provide some guidelines as to how you can tell the difference between a chemical change and a physical change simply by observation. I find this a rather futile exercise -- and one that is unnecessary. Although some observations may provide clues about whether a change is chemical or physical, they are not likely to be foolproof. Further, this really misses the point, which is that the difference involves whether or not new substances are formed. I encourage students to put little effort into the macroscopic correlates, but rather to think about the chemical substances that are involved.

There is a third type of change, besides chemical and physical, and that is a nuclear change. In a nuclear change, the atoms themselves are changed. The fusion of two hydrogen atoms to form a helium atom, as in the sun, is one example. The fission of a uranium atoms into two smaller atoms (such as barium and krypton), in an atomic bomb, is another. Nuclear reactions may or may not be introduced early in a chem class.

Coenzyme. See Cofactor

Cofactor. For enzyme-catalyzed reactions, a cofactor is something other than the enzyme itself that is required. Cofactor is a general term. A cofactor may be organic or inorganic (e.g., metal ions), and may be loosely or tightly (even covalently) bound to the enzyme. An organic cofactor is called a coenzyme; NADH and heme are common examples. NADH is loosely bound to the enzyme. Heme is covalently bound; a tightly bound cofactor such as this is called a prosthetic group. These terms have developed over time, and are not always used precisely. Note that heme is a coenzyme that is also a prosthetic group -- and it also has an inorganic part. The top-level idea is that enzymes may require one or another cofactor.

Conformation. A particular shape of a molecule; a particular orientation of the atoms of a molecule. Conformations of a molecule are rapidly interconverted, and are not distinct chemicals.

It is particularly important to distinguish conformations and isomers. Conformations are shapes of a particular molecule; isomers are different molecules. If you think in terms of the ball-and-stick models, you can convert from one conformation to another by rotating around a single bond; converting from one isomer to another requires breaking bonds and reassembling the model.

Some people use the term "conformational isomers" for conformations. In fact, there are some special cases where rotation around a single bond is restricted, and conformations may be only slowly interconvertible and therefore may appear as distinct compounds. But this is a complication we do not need in an introductory course.

Also see Isomers.

Dehydration. A reaction in which water, H-OH, is removed (eliminated). See hydration.

Dehydrogenation. A reaction in which hydrogen H-H is removed (eliminated). See hydrogenation.

Diatomic. Containing two atoms.

A common usage of this term is with the "seven common diatomic elements": seven elements that are normally found as diatomic molecules (hydrogen H2, nitrogen N2, oxygen O2, and the four common halogens). Caution. Do not over-interpret this "rule". It refers to the common form of the free element. Consider oxygen as an example. Common oxygen gas, in the air, is diatomic, O2. O3 (ozone) is also a real and important chemical; it is rather unstable, compared to ordinary oxygen, but that is part of why it can be interesting. Ozone is a key part of "smog", and is a key part of the upper atmosphere, where it absorbs ultraviolet radiation from the sun; in both cases, the amount of ozone is small. Under special conditions, oxygen atoms, O, may even be important. But when someone refers to ordinary oxygen, to oxygen gas, it means O2. And when oxygen occurs in molecules with other atoms -- not as a free substance -- there may be any number of O atoms or ions, as appropriate to the particular substance. Examples include H2O, Fe2O3, and C12H22O11 (sucrose).

Enthalpy.

The enthalpy, denoted by H, is one way to account for the energy of a system.

Enthalpy is commonly first encountered as ΔH, the enthalpy change for a reaction or process. For example, we talk about the ΔH for burning gasoline or the ΔH for boiling water. Although ΔH is the enthalpy change, it is often referred to as "heat" -- especially in introductory courses. That is, we may speak of ΔH as the heat of reaction for burning gasoline, or the ΔH for boiling water as the heat of vaporization. Why? Partly because it is easier, especially for beginners. However, it is also true that ΔH = q (heat) for a process at constant pressure, i.e., in an open container.

Formally, H = U + PV, where U = energy, P = pressure, V = volume. The energy U is the sum of heat + work (U = q + w).

Also see Heat.

Exome. The portion of the genome that codes for proteins. The word derives from exon, a coding region of a gene (without the introns). The exome is the collection of all exons. The word is most commonly encountered in the context of genome sequencing. Only about 2% of the human genome codes for protein; sequencing that exome is an approach to getting the most information for the effort.

Greek letters. Greek letters, usually lower case, are used for various purposes. In general, they are used as a way of "numbering" a list, but the specifics vary.

It is probably good to know that the first five letters are α (alpha), β (beta), γ (gamma), δ (delta) and ε (epsilon).

Showing Greek letters on web pages is tricky. Older browsers may not show them correctly; fortunately, most newer ones do it fine. If you have any trouble with Greek letters not appearing properly on any of my web pages, please let me know (and be sure to tell me which browser -- including version -- you are using). If you would like a chart of the Greek letters, many are available on the web (as well as in many printed resources). An example is http://www.ibiblio.org/koine/greek/lessons/alphabet.html. (Useful tables such as this are graphic images, which display properly regardless of your browser.)

Greek letters are sometimes used as locants. In IUPAC nomenclature, the C atoms of the main chain are numbered, from 1 onwards. But the common names of some compounds, especially carboxylic acids, use Greek letters for the "numbering". What is special is that the designation starts not at C#1 but at C#2 -- the first C that is "available". Example: 2-hydroxypropanoic acid would be α-hydroxypropanoic acid. (This has the common name lactic acid.)

The numbering may be "relative", rather than absolute. For example, the carbon next to a carbonyl group is called the α-carbon and its hydrogens are α-hydrogens. In 4-heptanone, the 3 and 5 positions are α positions -- understood to mean α to (next to) the carbonyl.

The last C of a chain is sometimes called the ω (omega) position, reflecting that ω is the last letter of the Greek alphabet.

The use of α and β with the two major types of protein secondary structures (α helix and β sheet) has no special meaning. That is, they simply refer to "structure #1" and "structure #2."

The letters σ (sigma) and π (pi) are used to refer to two types of bond. These terms are not used as numbering, but relate to s and p atomic orbitals.

The letter delta, both upper and lower case, is used in contexts such as (upper case) ΔH to indicate a change in enthalpy, and (lower case) δ+ to indicate a partial positive charge at one end of a polar bond. These are general usages of delta in chemistry, and are not specific to organic chemistry.

Heat. The term "heat" can cause confusion, because it is used in different ways. "Heat" has a technical meaning in physics (and hence in chemistry), to describe one type of energy. It is also loosely used to describe another type of energy. And of course, "heat" is also a word familiar in ordinary speech.

Heat is the energy that flows from an object of high temperature to one of low temperature. It is denoted by the symbol q. The common use of the word heat more or less corresponds to this formal meaning.

However, the term heat is sometimes used when what is really meant is enthalpy (H). In particular, in introductory chemistry classes, it is common to use the familiar term heat rather than the new term enthalpy. Heat and enthalpy are distinct, but are often very close. In casual conversation, even chemists may use the two terms almost interchangeably. For example, it is common to refer to ΔH as the heat of reaction, even though it is properly the enthalpy of reaction.

If you are taking a chem class and find these terms confusing, check your book and ask your instructor; follow whatever convention your instructor prefers for now -- and realize that others may do it differently.

Other than being confusing, the distinction between heat and enthalpy is not likely to be a problem unless you are doing some serious thermodynamic calculations where it is important to keep a clear distinction between the different forms of energy.

Also see Enthalpy.

Hydration. An addition reaction in which water, H-OH, is added. The reverse reaction is called dehydration.

Hydrogenation. An addition reaction in which hydrogen, H-H, is added. The reverse reaction is called dehydrogenation.

Isomers. Compounds with the same molecular formula but different structural formulas. Butane and isobutane are simple examples of isomers. Isomers are distinct compounds with distinct chemical and physical properties.

It is particularly important to distinguish conformations and isomers. Also see Conformation, where the distinction is discussed further.

Kinase. A kinase is an enzyme that transfers a phosphate group to some molecule. Most commonly, ATP is the phosphate donor. For example, glucokinase phosphorylates glucose, using ATP. Hexokinase phosphorylates hexoses, using ATP. A protein kinase phosphorylates a protein, using ATP; this is an important type of reaction in biochemistry, as the phosphorylation modulates the shape -- and hence the activity -- of proteins.

Locant. A locant in a name is a prefix specifying the location of a substituent. For example, in the name 2-methylpentane, the 2 is a locant. The common locants we learn are numbers. However, locants may also be element symbols, such as N for nitrogen, or Greek letters. N-methyl aniline and α-hydroxybutanoic acid are examples of those types. These locants are discussed in the glossary entries for N- and n- and Greek letters. That is, the term locant is general. The term is not widely used.

The page Omitting numbers discusses some special cases where it is ok to omit the locants.

N- and n-. These are both used as prefixes in names, but are quite distinct. The capital N prefix is a locant for a group that is attached to a nitrogen. The small n prefix means "normal", and indicates that the C chain is a "straight chain". The n- is not part of formal IUPAC nomenclature, but is sometimes used to make explicit which isomer is intended.

Examples:
n-butane and isobutane are two isomers of C4H10.
N-methyl aniline means that the methyl group is attached to the N atom of aniline.

Neutral and related terms (neutrality, neutralize, neutralization). This term has multiple meanings, even in introductory chemistry. The big message is to stop and think about which meaning is relevant to the issue at hand.

When referring to chemical compounds (and their formulas), neutral refers to the lack of an electrical charge. For example, the sodium ion, Na+, has a single positive charge, but the compound sodium chloride, NaCl, is "neutral" -- has no charge. In general, atoms and molecules are neutral, but ions are not.

When referring to solutions, neutral refers to the lack of acidity or basicity. That is, the concentrations of hydrogen and hydroxide ions, H+ and OH-, are equal. At 25° C, an aqueous solution at pH 7 is "neutral".

The word neutrality refers to the state of being neutral.

A term that is closely related to neutral is neutralize (or neutralization). A reaction between an acid and base is a neutralization reaction. At some point, one has added the same amount of acid and base. However, the resulting solution may well not be neutral; if the acid strength is greater than the base strength, the neutralized solution will be acidic. That is, the term neutralization here refers to the equal amounts of acid and base, not to the acidity (pH). In a titration, one neutralizes the acid and base, but does not necessarily reach neutrality.

Nuclear change. A process in which the elemental identity of the atoms is changed. A good example is the fusion of two hydrogen atoms to form a helium atom, as occurs in the sun: new atoms are made. See Chemical change for more; considering these two terms together, along with Physical change, helps to focus on the distinction between them.

Phenol. The terms phenyl and phenol, along with benzene and benzyl, are explained and compared on the page The phenyl group -- and related terms.

Phenyl. The terms phenyl and phenol, along with benzene and benzyl, are explained and compared on the page The phenyl group -- and related terms.

Physical change. A process in which the basic chemical identity of the substances in unchanged. A good example is heating water to its boiling point. The water changes from liquid to gas, but is still water. H2O(l) --> H2O(g). See Chemical change for more; considering these two terms together, along with Nuclear change, helps to focus on the distinction between them.

Primary. The terms primary, secondary, tertiary, and quaternary have several meanings in organic and biochemistry. Those relevant to our course are summarized on the page Terms: Primary, Secondary, Tertiary, Quaternary.

Prosthetic group. See Cofactor.

Quaternary. See Primary.

Saturated (and unsaturated). The general meaning of the word saturated is "full", in some sense. In discussing solutions, chemists refer to a saturated solution: one having the maximum possible amount of solute dissolved. In organic chemistry, the term is used to refer to the count of hydrogens. There is a common "rule" that an alkane of n carbon atoms contains 2n+2 hydrogen atoms; this reflects the maximum number of H possible for a given number of C. Such an alkane is said to be saturated. An unsaturated compound, of course, has fewer H.

For simplicity here, we will consider compounds with only C and H atoms, and we will ignore triple bonds. All the ideas can be easily extended to include other cases.

Unfortunately, there is an inconsistency is how the terms are used, This comes from the fact that there are two different ways that a chemical can "lose" 2H. One is by forming a ring (cycloalkane), and the other is by forming a double bond (alkene). To use specific examples: pentane, C5H12, is an alkane; it is saturated. Cyclopentane and 1-pentene are both C5H10; one is a cycloalkane and one is an alkene. Are they both unsaturated? Some people would say so, since they are both short 2 H of the maximum. However, there is a chemical test for alkenes (such as adding bromine, and watching for a color change). The alkene reacts but the cycloalkane does not. Some people say that this is a test for unsaturation; by that criterion, they would say that cyclopentane is not unsaturated (i.e., it tests as saturated).

Most important is that you learn the chemistry. There is a maximum possible number of H for a given number of C. If a compound has fewer H than that, each loss of two H corresponds to the presence of either a ring or a double bond. The alkane, with 2n+2 H for n C, is clearly saturated, but different people will use the term unsaturated differently for the ones with fewer H. Usually, context makes it clear. Make sure that terminology does not get in the way of following the chemistry.

I need to emphasize that the main purpose here is to make people aware of the ambiguity in the terms saturated vs unsaturated, with some idea why the ambiguity occurs. I am not trying to endorse any particular use of the terms, but to make you aware that you need to be careful when you encounter them. I think many would argue that organic chemists, when being careful, would prefer to use the term "unsaturated" to refer to the chemical behavior rather than to the H-count per se. But then, is benzene unsaturated? It certainly is short of H, but it also does not have the chemical behavior commonly considered characteristic of unsaturated compounds. Some finesse this point by saying that saturated compounds use only sp3 hybrid orbitals (for C). No matter what rules one establishes, the point is that in the real world the terms are used with a range of (related) meanings. So, again, the main purpose here is to caution you to be sure of the chemistry and not get hung up on a term.

Scale. This term has at least two distinct meanings.

Scale is a common term for a "balance" -- an instrument used for weighing things.

Scale refers to a series of graduated marks, such as the markings on a ruler. Many measuring instruments have a scale; the scale is the part of the instrument from which we read the result.

The first meaning is common in the real world, but the second is more common in a chem lab. As a result, beginning students may be confused when the idea comes up of reading the scale -- of a graduated cylinder. Although one might speak of the scale on a scale, chemists are more likely to refer to the instrument used for weighing as a balance.

The two meanings of scale discussed above are etymologically independent of each other. Further, the word has many more meanings, as those who know about fish, music, or corroded metals are probably quite aware. Exploring all the entries for "scale" in your dictionary may be fun, but it will take a while.

Secondary. See Primary.

Splicing. See Alternative splicing.

Substrate. In the context of enzymes... The molecule(s) on which an enzyme acts. The substrate for the enzyme is the reactant of the enzyme-catalyzed reaction.

Tertiary. See Primary.

Unsaturated. See Saturated.

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