Elements of life

##Introduction

What is your body made of? Your first thought might be that it is made up of different organs—such as your heart, lungs, and stomach—that work together to keep your body going. Or you might zoom in a level and say that your body is made up of many different types of cells. However, at the most basic level, your body—and, in fact, all of life, as well as the nonliving world—is made up of atoms, often organized into larger structures called molecules.

Atoms and molecules follow the rules of chemistry and physics, even when they're part of a complex, living, breathing being. If you learned in chemistry that some atoms tend to gain or lose electrons or form bonds with each other, those facts remain true even when the atoms or molecules are part of a living thing. In fact, simple interactions between atoms—played out many times and in many different combinations, in a single cell or a larger organism—are what make life possible. One could argue that everything you are, including your consciousness, is the byproduct of chemical and electrical interactions between a very, very large number of nonliving atoms!

So as an incredibly complex being made up of roughly 7,000,000,000,000,000,000,000,000,000 atoms, you'll probably want to know some basic chemistry as you begin to explore the world of biology, and the world in general.

##Matter and elements

The term **matter** refers to anything that occupies space and has mass—in other words, the “stuff” that the universe is made of. All matter is made up of substances called elements, which have specific chemical and physical properties and cannot be broken down into other substances through ordinary chemical reactions. Gold, for instance, is an element, and so is carbon. There are 118 elements, but only 92 occur naturally. The remaining elements have only been made in laboratories and are unstable.

Each element is designated by its chemical symbol, which is a single capital letter or, when the first letter is already “taken” by another element, a combination of two letters. Some elements follow the English term for the element, such as C for carbon and Ca for calcium. Other elements’ chemical symbols come from their Latin names; for example, the symbol for sodium is Na, which is a short form of *natrium*, the Latin word for sodium.

The four elements common to all living organisms are oxygen (O), carbon (C), hydrogen (H), and nitrogen (N), which together make up about 96% of the human body. In the nonliving world, elements are found in different proportions, and some elements common to living organisms are relatively rare on the earth as a whole. All elements and the chemical reactions between them obey the same chemical and physical laws, regardless of whether they are a part of the living or nonliving world.

##The structure of the atom

An **atom** is the smallest unit of matter that retains all of the chemical properties of an element. For example, a gold coin is simply a very large number of gold atoms molded into the shape of a coin, with small amounts of other, contaminating elements. Gold atoms cannot be broken down into anything smaller while still retaining the properties of gold. A gold atom gets its properties from the tiny subatomic particles it's made up of.

An atom consists of two regions. The first is the tiny **atomic nucleus**, which is in the center of the atom and contains positively charged particles called **protons** and neutral, uncharged, particles called **neutrons**. The second, much larger, region of the atom is a “cloud” of **electrons**, negatively charged particles that orbit around the nucleus. The attraction between the positively charged protons and negatively charged electrons holds the atom together. Most atoms contain all three of these types of **subatomic particles**—protons, electrons, and neutrons. Hydrogen (H) is an exception because it typically has one proton and one electron, but no neutrons. The number of protons in the nucleus determines which element an atom is, while the number of electrons surrounding the nucleus determines which kind of reactions the atom will undergo. The three types of subatomic particles are illustrated below for an atom of helium—which, by definition, contains two protons.

[[☃ image 1]]

Protons and neutrons do not have the same charge, but they do have approximately the same mass, about $1.67 × 10^{-24}$ grams. Since grams are not a very convenient unit for measuring masses that tiny, scientists chose to define an alternative measure, the **dalton** or **atomic mass unit** (amu). A single neutron or proton has a weight very close to 1 amu. Electrons are much smaller in mass than protons, only about 1/1800 of an atomic mass unit, so they do not contribute much to an element’s overall atomic mass. On the other hand, electrons do greatly affect an atom’s charge, as each electron has a negative charge equal to the positive charge of a proton. In uncharged, neutral atoms, the number of electrons orbiting the nucleus is equal to the number of protons inside the nucleus. The positive and negative charges cancel out, leading to an atom with no net charge.

Protons, neutrons, and electrons are very small, and most of the volume of an atom—greater than 99 percent—is actually empty space. With all this empty space, you might ask why so-called solid objects don’t just pass through one another. The answer is that the negatively charged electron clouds of the atoms will repel each other if they get too close together, resulting in our perception of solidity.

[[☃ explanation 1]]

##Introduction

Carbon isn’t a difficult element to spot in your daily life. For instance, if you’ve used a pencil, you’ve seen carbon in its graphite form. Similarly, the charcoal briquettes on your barbeque are made out of carbon, and even the diamonds in a ring or necklace are a form of carbon (in this case, one that has been exposed to high temperature and pressure). What you may not realize, though, is that about 18% of your body (by weight) is also made of carbon. In fact, carbon atoms make up the backbone of many important molecules in your body, including proteins, DNA, RNA, sugars, and fats.

These complex biological molecules are often called macromolecules; they’re also classified as organic molecules, which simply means that they contain carbon atoms. (Notably, there are a few exceptions to this rule. For example, carbon dioxide and carbon monoxide contain carbon, but generally aren't considered to be organic.)

##The bonding properties of carbon

Why is carbon so popular for making molecular backbones? Why don’t we instead use, say, oxygen for the same purpose? For one thing, carbon-carbon bonds are unusually strong, so carbon can form a stable, sturdy backbone for a large molecule. Perhaps more important, however, is carbon’s capacity for covalent bonding. Because a C atom can form covalent bonds to as many as four other atoms, it’s well suited to form the basic skeleton, or “backbone,” of a macromolecule.

As an analogy, imagine that you’re playing with a Tinker Toy® set and have connector wheels with either two or four holes. If you choose the connector wheel with four holes, you’ll be able to make more connections and build a complex structure more easily than if you choose the wheel with two holes. A carbon atom can bond with four other atoms and is like the four-hole wheel, while an oxygen atom, which can bond only to two, is like the two-hole wheel.

Carbon’s ability to form bonds with four other atoms goes back to its number and configuration of electrons. Carbon has an atomic number of six (meaning six protons, and six electrons as well in a neutral atom), so the first two electrons fill the inner shell and the remaining four are left in the second shell, which is the valence (outermost) shell. To achieve stability, carbon must find four more electrons to fill its outer shell, giving a total of eight and satisfying the octet rule. Carbon atoms may thus form bonds to as many as four other atoms. For example, in methane (CH$_4$), carbon forms covalent bonds with four hydrogen atoms. Each bond corresponds to a pair of shared electrons (one from carbon and one from hydrogen), giving carbon the eight electrons it needs for a full outer shell.

Hydrocarbons

Hydrocarbons are organic molecules consisting entirely of carbon and hydrogen. We often use hydrocarbons in our daily lives: for instance, the propane in a gas grill and the butane in a lighter are both hydrocarbons. They make good fuels because their covalent bonds store a large amount of energy, which is released when the molecules are burned (i.e., when they react with oxygen to form carbon dioxide and water).

[[☃ image 1]]

Methane (CH$_4$), the simplest hydrocarbon molecule, consists of a central carbon atom bonded to four hydrogen atoms. The carbon and the four hydrogen atoms form the vertices of a three-dimensional shape known as a tetrahedron, which has four triangular faces; because of this, methane is said to have a tetrahedral geometry. More generally, when a carbon atom is bonded to four other atoms, the molecule (or part of a molecule) will take on a tetrahedral shape similar to that of methane. This happens because the electron pairs that make up the bonds repel each other, and the shape that maximizes their distance from each other is a tetrahedron.

Most macromolecules are not classified as hydrocarbons, because they contain other atoms in addition to carbon and hydrogen, such as nitrogen, oxygen, and phosphorus. However, carbon chains with attached hydrogens are a key structural component of most macromolecules (even if they are interspersed with other atoms), so understanding the properties of hydrocarbons is important to understanding the behavior of macromolecules.

[[☃ explanation 1]]

##Introduction

Hydrocarbons, made up entirely of carbon and hydrogen atoms, make wonderful combustion fuels (such fuels include propane, butane, and the bulk of commercial gasoline). But can you build a living organism out of only combustion fuels? Probably not. Most large biological molecules in fact contain many types of atoms beyond just carbon and hydrogen. These additional atoms allow for functionality not typically seen in hydrocarbons.

##Functional groups

Large biological molecules are generally composed of a carbon skeleton (made up of carbon and hydrogen atoms) and some other atoms, including oxygen, nitrogen, or sulfur. Often, these additional atoms appear in the context of functional groups. Functional groups are chemical motifs, or patterns of atoms, that display consistent “function” (properties and reactivity) regardless of the exact molecule they are found in. Biological molecules can contain many different types and combinations of functional groups, and a biomolecule’s particular set of groups will affect many of its properties, including its structure, solubility, and reactivity.

A few of the most important functional groups in biological molecules are shown in the table below. Functional groups can be classified as hydrophobic or hydrophilic based on their charge and polarity characteristics. The only hydrophobic group below is the methyl (CH$_3$) group, which is nonpolar. The remaining six functional groups in the table all have varying degrees of hydrophilic character.

One example of a strongly hydrophilic group is the carboxyl group (COOH), which can act as an acid and lose a proton to form a negatively-charged carboxylate ion (COO$^-$). Carboxyl groups are commonly found in amino acids, fatty acids, and other biomolecules. An example of a less hydrophilic group is the carbonyl group (C=O), an uncharged but polar (contains partial positive and partial negative charges) functional group. Carbonyls are found in many different biological molecules, including proteins, peptides, and carbohydrates.

Common functional groups in biology

Functional Group | Structure | Properties

• | - | -
  Hydroxyl | [[☃ image 1]] | Polar
  Methyl | [[☃ image 2]] | Nonpolar
  Carbonyl | [[☃ image 3]] | Polar
  Carboxyl | [[☃ image 4]] | Charged (forms R-COO$^-$) at the pH of most biological systems. Since carboxyl groups can release H$^+$ into solution, they are considered acidic.
  Amino | [[☃ image 5]] | Charged (forms R-NH$_3^+$) at the pH of most biological systems. Since amino groups can remove H$^+$ from solution, they are considered basic.
  Phosphate | [[☃ image 6]] | Charged (forms R-OPO$_3^2$$^-$) at the pH of most biological systems. Since phosphate groups can release H$^+$ into solution, they are considered acidic.
  Sulfhydryl | [[☃ image 7]] | Polar

Table modified from: OpenStax Biology.

In the table above, the letter R is used to represent the rest of the molecule that a functional group is attached to. For instance, R might be an ethyl (CH$_2$CH$_3$) group, in which case the first entry in the table would correspond to ethanol. But R could also represent the bulk of a much larger molecule, such as a protein. The letter R is used throughout biology and chemistry to simplify chemical structures and highlight the most important parts (often the functional groups!) of a molecule.

[[☃ explanation 1]]