Intro to Anatomy 2: Life, The World’s Biggest Chemistry Experiment

[The Lone Ranger]

An Introduction to Human Anatomy and Physiology
Chapter Two: Life: The World’s Biggest Chemistry Experiment

Introduction:
As you recall, the organization of living things goes, in order from least-complex to most-complex units, something like this:
Atoms → Molecules → Macromolecules → Organelles → Cells → Tissues → Organs → Organ Systems → Organisms

Since atoms are the fundamental subunits of which organisms are composed, if we wish to understand the structure and the functions of living organisms, we must gain a basic understanding of what atoms are and how they interact to form more complex structures.

The ways that atoms interact with each other determines what organisms can and cannot do. For example, the strength of the chemical bonds that hold atoms together in molecules sets an upper limit on how strong and how durable organisms can be. No creature can be stronger than the chemical bonds that hold it together. Sorry, Superman, but in the real world you simply couldn’t exist.

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Another sad victim of the pitiless laws of physics.


Energy and Matter:Energy, as noted in the first chapter, is the capacity to do mechanical work – that is, to move matter. Of course, matter and energy are closely related, as Einstein’s famous equation, E=mc2 shows. Matter is, in a sense, “frozen” energy. That’s why matter can be converted to energy and vice versa, under the proper conditions.

We’ll discuss energy, its importance to living organisms, and how organisms generate and control energy in the next chapter. For now, let’s discuss matter. Chemistry is the study of the atoms that make up matter, how they interact to form molecules, and how molecules interact with each other. So, in order to understand living organisms, one needs a basic understanding of chemistry.


What is Matter?:
Matter is the physical material of the Universe. Specifically, matter is anything that has mass and that occupies space – that is, it has volume.

When we say that matter has “mass,” we mean that it has three distinct properties. First, it has inertia, which means that it resists any change in motion when a force is applied to it. The more mass an object has, the more inertia it has, and so the more force is required to alter its motion.

The second property of mass is that it is affected by the force of gravity. In a gravitational field, anything with mass has weight. The more mass an object has, the greater its weight. Note that though many people use the terms interchangeably, “mass” and “weight” are not the same thing! In a zero-gravity environment, an object has no weight, but its mass remains unchanged.

The third property of mass is that it generates a force called gravity. Unsurprisingly, the more mass an object has, the more gravity it generates. The gravity generated by a human-sized object is infinitesimal, but something with the mass of, say, the Moon, generates a quite-noticeable gravitational field. The Earth, being more than 80 times the mass of the Moon, generates an even stronger gravitational field. The Sun, being more than 300,000 times the mass of the Earth, generates a gravitational field that’s stronger still.


Phases of Matter:
Matter can exist in several different phases, but the three phases of matter that most of us are familiar with and that are directly relevant to living organisms are: solid, liquid, and gas. When matter goes from one phase to another, it undergoes what’s known as a phase transition.

Heat is a form of energy, and when heat (thermal energy) is added to a substance, it causes the atoms and molecules that make up the substance to move faster. In a solid, the atoms or molecules are moving slowly, and can only vibrate back-and-forth because they’re closely-packed and locked together into a more or less rigid framework by the attractive forces between them. Because the molecules of a solid are held together in a (more or less) rigid framework, a solid has a definite shape and volume.

As you add thermal energy to a solid, its molecules vibrate more rapidly and the substance’s temperature rises. Its temperature is a measure of the average molecular motion of a substance. That is, since adding heat to a substance causes its molecules to move faster, what you’re actually measuring when you measure something’s temperature is the average motion of the molecules that make it up.

Keep adding heat to a solid and it will eventually reach a temperature where the average molecule of the substance has so much thermal energy that adding any more heat will cause it to vibrate with enough force to break the bonds that hold it rigidly in place. At this temperature (the substance’s melting point), the addition of any more heat will cause a phase transition from solid to liquid to occur.

When a substance is at its melting point, addition of heat will not cause its temperature to rise at first, because the heat goes not into making the molecules of the substance move faster, but into breaking the bonds that hold the molecules rigidly in place. Of course, once the substance has completely melted, adding more heat will cause the temperature of the now-liquid substance to rise.

A liquid is a substance in which the molecules that make it up are moving fast-enough to have broken free from their rigid lattice, but they’re still moving slowly-enough that attractive forces cause them to stick together. Since they’re not locked into a rigid lattice, the molecules of a liquid can move about relative to each other. Because the molecules of a liquid can move about, a liquid has no definite shape and will assume the shape of its container. A liquid does have a definite volume, however, since the molecules are clinging to each other instead of moving independently. Substance in which the molecules are free to move don’t resist deformation, and so will flow. That’s why liquids and gases are known as fluids.

If you keep adding heat to a liquid, it will eventually reach its boiling point. At that temperature, the average molecule has so much energy that addition of any more will cause it to break away from its fellows and begin to move independently. Adding energy to a liquid that’s at its boiling point will not cause the liquid’s temperature to rise, but will instead cause a phase transition from liquid to gas. Of course, once all of the liquid has made the transition to the gas phase, addition of yet more heat will cause the temperature of the gas to rise. Because the molecules that make up a gas are moving independently of each other, a gas has no definite volume, and it will expand to fill its container.


The differences between a solid, a liquid and a gas may seem somewhat abstract. How best to illustrate the differences between them in a way that might be fairly intuitive? Maybe the following mental picture will help. Imagine a bunch of steel balls that are magnetized, but not too strongly. Now weld them together. This is a solid.

Because the welded-together steel balls are held together in a tight, rigid matrix, they make up a structure that has a definite shape and volume. If you put that structure on an inclined surface, it would probably stay put.

Adding enough heat to a solid to melt it would be like breaking the welded bonds that hold the magnetized balls together. At that point, the balls would be free to move about, but their magnetism would still make them stick together. This would be a liquid.

If you tried to pile the steel balls on top of each other, they’d be pulled down by gravity, and if you put the mass of them on an inclined surface, they would “flow” downward. Because the balls were sticking together and not moving independently, the mass as a whole would have a definite volume (that is, it would take up a certain amount of space), but the ability of the balls to move would mean that the mass would have no definite shape.

Adding enough heat to a liquid to boil it would be like making the steel balls move so fast that their magnetism couldn’t hold them together. They’d fly all over the place, ricocheting off of anything they hit, including each other. Any given ball would move in a straight line until it hit another ball and bounced off in a new direction – or until it hit a wall and bounced off in a new direction. If you consider the group of steel balls as a whole, they would have no definite volume. Instead, the mass of balls would “expand” until it filled its “container.” This is how the molecules of a gas behave.

[BREAK=Atoms and Molecules]
[B]Atoms and Molecules:The smallest unit of matter that has a distinct chemical identity is an atom. Any substance that contains only one kind of atom is an element. Oxygen (O), carbon (C), sodium (Na), and nitrogen (N) are examples of elements.

Atoms can combine chemically to form molecules, and any substance that consists of molecules made of two or more different kinds of atoms is a compound. Water (H2O), table salt (NaCl), and table sugar (C12H22O11) are familiar examples of chemical compounds.

A chemical mixture contains two or different kinds of elements and/or compounds that are mixed together but that are not chemically bonded, so the molecules of the different elements/compounds in the mixture retain their individual properties. Ice cream, pizzas and humans are familiar examples of chemical mixtures – there’s no such thing as an “ice cream molecule” or a “pizza molecule.”


[B]Atomic Structure:Each atom contains a central nucleus containing at least one positively-charged proton. The symbol p represents a proton, as does the symbol H+. The reason H+ is used to represent a proton is that the nucleus of a hydrogen atom consists simply of a single proton. Each atomic nucleus (except that of a hydrogen atom) contains one or more uncharged neutrons as well. The symbol for a neutron is n or n0. The neutrons and protons are packed together very tightly in the nucleus of the atom.


One or more shells or orbitals surround the atomic nucleus, and these orbitals contain negatively-charged electrons (e-). Electrons “orbit” the nucleus in somewhat the same way that the planets of our solar system orbit the Sun.


By definition, an atom has the same number of positively-charged protons and negatively-charged electrons, and so it has no net electrical charge. The number of protons determines an atom’s identity, and the number of protons in an atom’s nucleus is its atomic number. For instance, carbon is atomic number 6, and every atom with six protons in its nucleus is a carbon at, regardless of how many neutrons are present. The number of protons plus the number of neutrons is an atom’s mass number. Carbon-12, for instance, has six neutrons. Carbon-13 has seven neutrons. Carbon-14 has eight neutrons. Atoms with the same number of protons but different numbers of neutrons are isotopes. Chemically, different isotopes of the same element will behave the same, but they may have slightly different physical properties, since they have different masses.

One interesting thing about the structure of atomic nuclei is that if there are “too many” or “too few” neutrons in an atom’s nucleus, it may be unstable. The nuclei of such unstable atoms are prone to disintegrate, releasing particles and radiation as they do. These unstable atoms are said to be radioactive.

The number and configuration of electrons in the orbitals (especially the outermost orbital) determine an atom’s chemical properties. Since the electrons are the only part of an atom that ever interact with other atoms, most of chemistry boils down to the behavior of electrons.

Just below, you can see a representation of a carbon atom. It’s worth keeping in mind that the representation is not to scale – if you enlarged an atom so that its nucleus was as large as the one in the illustration, the electrons in the first orbital would probably be somewhere out around the planet Neptune.

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An Atom of Carbon


[B]Atomic Numbers and Atomic Masses:
A proton or a neutron has more than 1,800 times the mass of an electron. So, for practical purposes, electrons don’t contribute to the mass of an atom. For that reason, we identify atoms by the number of protons and neutrons, not the number of electrons.

As mentioned earlier, the number of protons in the nucleus of an atom is the atomic number. This is the atom’s identity. For example, an atom of the element hydrogen contains just one proton in its nucleus and hydrogen therefore has the atomic number of “1.” A hydrogen atom may have one or more neutrons in its nucleus (most don’t), but no matter how many neutrons are present, it’s still a hydrogen atom with an atomic number of 1. An atom of helium has two protons in its nucleus, and so helium is atomic number 2. Carbon has six protons and so is atomic number 6; nitrogen has seven protons and is atomic number 7; oxygen has eight protons and is atomic number 8; iron has 26 protons and is atomic number 26; gold has 79 protons and is atomic number 79; and so forth.

Every chemical element is identified by a unique one- or two-letter combination. For example, the chemical symbol for hydrogen is “H,” the chemical symbol for oxygen is “O,” and the chemical symbol for sodium is “Na.” Sometimes, the atomic number is included as a subscript to the left of the symbol, though there’s really not a lot of point, since, by definition, every atom of a given element has the same atomic number. Still, you’ll sometimes see oxygen identified as 8O, for example.


The number of protons plus the number of neutrons in an atom’s nucleus is its atomic weight. For example, a typical helium atom (atomic number 2) has two neutrons in its nucleus, and so it has an atomic weight of 4.

As mentioned earlier, atoms with the same number of protons but different numbers of neutrons are isotopes. For example, a typical hydrogen atom has no neutrons, but the occasional hydrogen atom has a single neutron in its nucleus. Hydrogen with a single neutron per nucleus is sometimes referred to as deuterium. A hydrogen atom with two neutrons in its nucleus is known as tritium. Regardless of how many neutrons are present though, it’s the number of protons that determines an atom’s identity, so deuterium and tritium are both forms of hydrogen, and the chemical properties of all three hydrogen isotopes are virtually identical.

The atomic weight of an atom is often given as a superscript to the left of the atomic symbol. In this way, different isotopes can be represented simply and easily. For example, “normal” hydrogen is 1H, deuterium is 2H, and tritium is 3H.

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Different Isotopes of Carbon.


Though different isotopes of a given element don’t have different chemical properties, the number of neutrons in an atom’s nucleus is not completely irrelevant. For that reason, it’s sometimes important to know what isotope you’re dealing with.

For example, if an atom’s nucleus has “too many” or “too few” neutrons, it may be unstable or radioactive. The nuclei of radioactive atoms tend to break apart over time (decay), and so a radioactive atom will eventually change to an atom of a different element. For example, atoms of uranium-238 (238U) are unstable, and they ultimately decay to form lead-206 (206Pb), which is stable.


Another reason why it sometimes matters what isotope(s) you’re dealing with is that every “extra” neutron adds to the mass of an atom. So an atom of 12C weighs a bit less than does an atom of 14C, for example. The more massive something is, the more energy it takes to move it at a given speed, so atoms of a heavier isotope will tend to move more slowly at a given temperature than will atoms of a lighter isotope.


Consider the difference between oxygen-16 and oxygen-18. At any given temperature, a water molecule containing an 16O atom will be traveling (slightly) faster than will a heavier water molecule containing 18O, and so is more likely to have enough energy to escape the bonds that tie it to its fellow water molecules. In other words, the lighter water molecule is more likely to evaporate into the atmosphere. Conversely, “heavy” water molecules containing 18O are more likely to condense out of the atmosphere and fall to Earth as rain than are lighter molecules with 16O.


The practical effect of this is that as the Earth’s mean temperature rises, the amount of 18O in rain- and snowfall increases relative to the amount of 16O. By taking samples from glaciers (which, after all, are simply many years’ worth of compressed snow), and noting the ratio of 16O to 18O in the different layers, we can chart changes in the Earth’s mean temperature over time.


This works on a smaller scale as well. For example, the warmer an animal’s tissues are, the more readily they’ll absorb lighter 16O compared to heavier 18O. Examinations of bones from several dinosaur species have shown 16O/18O ratios indicative of animals that maintained high body temperatures – implying that they were “warm-blooded.”

[break=Electron Configurations and Chemical Properties of Atoms]
[b]Electron Configuration and Chemical Properties of Atoms:
Well, that’s all very interesting, but it’s the electrons that determine an atom’s chemical properties, not the protons. As mentioned earlier, an atom has the same number of electrons and protons, by definition. So an atom is electrically neutral by definition, since the positive charges of the protons in the nucleus exactly balance the negative charges of the electrons in the orbitals.

It is possible for an atom to either gain or lose electrons, however, and so an atom can become electrically charged. An atom that loses an electron becomes positively charged, since it now has more protons than electrons. An atom that gains an electron, becomes negatively charged, since it now has more electrons than protons.

An electrically-charged atom (or molecule) is known as an ion. The chemical properties of an ion will naturally be quite different from those of the original atom, since the number and arrangement of electrons has changed. Positively-charged ions are known as cations and negatively-charged ions are anions.


Each electron orbital (shell) can hold only so many electrons, and the orbitals typically fill up in order. The first orbital can contain a maximum of only two electrons. So helium, with its two electrons, has its single orbital filled. Heavier elements must therefore have additional orbitals. The second orbital can contain up to eight electrons before it is filled, which means that neon (atomic number 10) has its second orbital filled. Any element heavier than neon must have a third orbital. For elements up to atomic number 18 (argon), the third orbital can contain up to 8 electrons before it is filled, but larger and more complex atoms can have up to 18 electrons in the third orbital.

Under the proper circumstances, an electron can absorb energy (in the form of a photon of light) and in so doing, “jump” to a higher orbital. In this way, atoms can temporarily store energy. An atom that has absorbed photons and therefore has one or more electrons in higher orbitals is said to be excited. Sooner or later, an excited atom will re-emit the captured energy when the electron drops back to its “proper” place in a lower orbital. When this happens, the atom is said to return to its ground state.

The significance of this phenomenon is that living organisms can use certain molecules to temporarily store energy absorbed from light. It is an important component of photosynthesis in plants, for instance.

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Excitation of an Atom by Absorption of Energy

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Return of the Atom to Ground State by Release of Energy

[BREAK=Molecules and Chemical Bonds]
[B]Molecules and Chemical Bonds:Molecules:
A molecule, as we noted earlier, is the smallest chemically-distinct subunit of a compound. For instance, if you break a water molecule (H2O) into its component atoms, you no longer have water – you have hydrogen and oxygen.


Atoms, as you recall, are represented by one- or two-letter combinations – e.g. “H” represents “Hydrogen,” “He” represents “Helium,” and so forth. In the same way, combinations of atoms – molecules – can be represented by atomic symbols plus subscripted numbers to indicate the number of atoms of each type in the molecule. A water molecule, for instance, consists of two hydrogen atoms and a single oxygen atom, so its chemical formula is H2O.


An atom in which the outermost orbital is not full is chemically unstable. Such an atom will attempt to fill its outermost orbital, either by gaining extra electrons to fill that orbital or by getting rid of “excess” electrons to empty the outermost orbital. Since an orbital doesn’t exist if there are no electrons in it, if an atom can empty its outermost orbital of electrons, that will make the next-lower orbital (which should be filled with electrons) the new outermost orbital.

Naturally, those atoms whose outermost orbitals are already filled tend to be extremely non-reactive, and therefore seldom combine with other atoms to form molecules. These elements are known as the “noble gases.” For example, helium (atomic number 2) has two electrons, and so its single orbital is full. Helium is so non-reactive that helium atoms won’t bond to other atoms under anything but the most extreme of conditions. You have to remove almost all of the thermal energy (heat) from helium before the atoms are moving slowly-enough that they’ll even stick together and form a liquid. Helium won’t solidify even at temperatures less than one degree above Absolute Zero, and it’s virtally impossible to get helium atoms to form chemical bonds with other atoms.

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Because its outermost orbital is already filled,
a helium atom is almost totally nonreactive.

[break]
Atoms in which the outermost orbitals are not full are far more willing to join with other atoms in order to fill their outermost orbitals, and in so doing form chemical bonds. Atoms form chemical bonds and fill their outermost orbitals by either exchanging electrons or sharing electrons. When two or more atoms are joined together by chemical bonds, they form a molecule. There are two basic types of chemical bonds, ionic bonds and covalent bonds. A third, much weaker type of chemical bonding is known as a hydrogen bond.

[break=Ionic Bonds]
[B]Ionic Bonds:
Ionic bonds are formed when atoms physically exchange electrons to fill their outermost orbitals, forming ions in the process. For example, an atom of sodium (atomic number 11) has only one electron in its outermost orbital, and so can’t hang onto it very tightly. By contrast, chlorine (atomic number 17) has 7 electrons in its outermost orbital, and will readily “steal” electrons from other atoms. (This is one reason why chlorine is so dangerous to living things – it can rip apart organic molecules in its eagerness to get electrons.)

Bring a sodium atom and a chlorine atom close-enough, and the chlorine will pull the single electron out of the sodium’s outermost orbital and into its own outermost orbital. This makes the sodium atom into a positively-charged ion (Na+) and the chlorine atom into a negatively-charged ion (Cl-). (The chlorine ion is known as “chloride.”) Because the positively-charged sodium ion and the negatively-charged chloride attract each other, they tend to stick together, and so they form the compound sodium chloride (NaCl).

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Ionic Bonding to form a Molecule of Sodium Chloride

The ions in an ionic compound tend to arrange themselves into very evenly-spaced and regular arrangements, and so form crystals. Ionic compounds will readily dissolve in water, and because of their charged subunits, ionic compounds in water conduct electricity very well. Because of their very regular molecular structure, ionic compounds tend to be very hard and very brittle. Because the cations and anions hang onto each other so strongly, ionic compounds generally have extremely high melting points.

Common examples of ionic compounds include various kinds of salts. Sodium chloride (“table salt”), for example, is a common ionic compound.

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The ions of an ionic compound are usually very regularly-spaced.


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The regular spacing of ions in an ionic compound means that it forms crystals.


[B]Covalent Bonds:
If ionic bonding occurs when one atom “steals” one or more electrons from another, covalent bonding occurs when atoms come together and “share” electrons. Covalent bonds are chemical bonds that form when two or more atoms effectively merge their outermost orbitals and so share pairs of electrons.

Consider a hydrogen atom. It has only one electron in its single orbital. Therefore, it “wants” another electron, so that it can fill its orbital. Now consider an oxygen atom. Oxygen has six electrons in its outermost orbital, so it “wants” two electrons, in order to fill its outermost orbital. How can the atoms be satisfied?

If the hydrogen atom merges its orbital with the outermost orbital of the oxygen atom, the hydrogen can share its single electron with the oxygen atom, and it can share one of the oxygen’s electrons. In effect, the hydrogen atom will now have two electrons in its orbital, so its orbital will now be full and it can bond with no more atoms. The oxygen will now have seven electrons in its outermost orbital, so it still needs one more electron to fill its outermost orbital. If the oxygen bonds to another hydrogen atom, then each atom will now be satisfied, and a stable molecule results, consisting of two hydrogen atoms bound to a single oxygen atom. The molecule is stable because each atom making up the molecule has filled its outermost orbital by sharing electrons. Each hydrogen atom shares its single electron with the oxygen, so the oxygen will effectively have eight electrons in its outermost orbital, filling it. And each hydrogen atom shares one of the oxygen’s electrons, and so each hydrogen atom, in effect, has two electrons in its orbital.


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A Water Molecule
Note that each hydrogen fills its outermost orbital by sharing a pair
of electrons with the oxygen, and the oxygen fills its outermost orbital
by sharing a pair of electrons with each of the 2 hydrogen atoms.


A single covalent bond is formed when a pair of atoms shares a pair of electrons between them. It is also possible for two atoms to share two pairs of electrons. This is known as a double bond and as you might imagine, a double bond is rather stronger than is a single bond.


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A molecule of carbon dioxide consists of a carbon atom
double-bonded to two oxygen atoms. The carbon fills its
outermost orbital by sharing two pairs of electrons with each oxygen.


Some atoms can even form triple bonds by sharing three pairs of electrons with another atom. For example, a nitrogen atom can triple-bond with another nitrogen atom to form the molecule N2, or diatomic nitrogen. N2 makes up about 78% of the Earth’s atmosphere. You’d think this would be quite convenient, since nitrogen is an absolutely vital element for living things. Yet plants often suffer from lack of nitrogen. Why? Because the triple-bonds of N2 are dang-near unbreakable, and therefore few living organisms can convert N2 into usable substances. Fortunately, high-energy ultraviolet radiation can occasionally break the triple bonds of N2 and allow the nitrogen atoms to recombine with oxygen to form molecules that can be absorbed and used by living creatures. The energy released by lightning can also break the triple bonds of N2, allowing nitrogen-oxygen compounds to form. Many biologists believe that life would never has arisen on Earth were it not for ultraviolet radiation and lightning causing the formation of nitrogen-oxygen compounds.


[b]Covalent Bonds as Energy-Storage:It takes energy to form covalent bonds, and that energy is stored in the bonds themselves. This means that whenever covalent bonds are broken, energy is released. (In some cases, however, it requires more energy to break the bonds than is released when they are broken.)

An important result of this fact is that covalently-bound molecules can be used to store energy. That energy can be released when needed by breaking those bonds. This is how living creatures survive. Living organisms absorb energy – either directly from the sun or other energy sources, or by eating other organisms. The absorbed energy is stored in the molecular bonds of the sugar glucose (C6H12O6). When glucose molecules are combined with oxygen and broken down into carbon dioxide (CO2) and water (H2O), the breaking of the glucose molecules’ chemical bonds releases energy. That energy can then be used to do work.


[b]Polar and Nonpolar Covalent Bonds:Whether the atoms in a covalently-bound molecule share their electrons equally or not depends on a number of factors, including the size of the atoms relative to each other and the shape of their arrangement.

Some atoms, (notably oxygen), are notoriously “greedy,” and tend to “hoard” electrons. For instance, when an oxygen atom bonds to two hydrogen atoms to form a water molecule, the oxygen tends to “hoard” the electrons, and they tend to spend more time in the vicinity of the oxygen atom than in the vicinity of either of the hydrogen atoms. This means that the oxygen acquires a partial negative charge, since the electrons spend proportionately more time in the vicinity of the oxygen atom than in the vicinity of the hydrogen atoms. Of course, since the electrons spend more time in the vicinity of the oxygen atom, they aren’t fully balancing the positive charges of the hydrogen atoms’ protons, and so the two hydrogen atoms acquire partial positive charges.

A molecule in which the electrons are distributed unequally, so that portions of the molecule have slight positive charges and portions have slight negative charges is said to be a polar molecule. Naturally, molecules without such partial electric charges are non-polar. Polar molecules are particularly important because they will dissolve other polar molecules. Polar molecules are also particularly good at dissolving ionic substances, since ionic compounds consist of charged subunits.

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Water is a polar molecule because the oxygen atom and the two hydrogen atoms do not share their electrons equally. The “б” symbol indicates a partial charge.


[B]Hydrogen Bonds:Because of their weak partial charges, polar molecules tend to be attracted to each other, and will stick together. The partial positive charge on one molecule attracts the partial negative charge on another polar molecule. These weak bonds that form between polar molecules are known as hydrogen bonds. Individually, hydrogen bonds are very much weaker than ionic or covalent bonds, but the cumulative force of the hydrogen bonds between large numbers of polar molecules can be quite impressive.

If a polar molecule is large-enough, positively-charged portions of the molecule can attract negatively-charged portions of the same molecule, causing it to “fold” into a distinctive shape. As such, hydrogen bonding is an important factor in why large molecules such as proteins and DNA fold into distinct shapes.

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Hydrogen Bonding Between Water Molecules



[B]Water and Life:The importance of water to life simply cannot be overstated. In fact, life as we know it surely wouldn’t be possible were it not for water’s unusual properties.


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A Water Molecule

As you can see, a water molecule is not symmetrical. Because of its asymmetrical nature – and because of the “greediness” of oxygen for electrons – water is a polar molecule.

Because partial positive charges on the hydrogen atoms of one water molecule are attracted to the partial negative charges on the oxygen atoms of other water molecules, water molecules tend to form hydrogen bonds and so stick together. This “stickiness” of water molecules is why water is a liquid over such an extraordinarily wide temperature range. Most molecules the size of water are gases at the temperatures and pressures we normally encounter on Earth – think of carbon dioxide (CO2), nitrous oxide (N2O), or hydrogen sulfide (H2S), for example. Water is a liquid at these temperatures and pressures because of its “stickiness.”


Because of its polar nature and because its small molecules can move quite rapidly, water can dissolve a tremendous variety of ionic and polar substances. In fact, water is just-about the closest thing to a universal solvent known.

If two substances are at the same temperature, but one has more massive molecules than does the other, then the molecules of the higher-mass substance will be moving more slowly than the molecules of the lower-mass substance, other factors being equal. This is true for the same reason that if you apply “X” amount of energy to a baseball and the same amount to a bowling ball, the baseball will move much faster.


[b]Solutions:

A solution consists of one substance dissolved into – and equally distributed throughout – another. The substance that dissolves is known as the solute and the substance it dissolves into is the solvent. Ionic substances and other polar substances dissolve into water so readily because the small, rapidly-moving water molecules can easily slip in between charged molecules or ions and surround them, causing them to separate from their fellows.

The illustration below shows how water molecules surround the ions in sodium chloride and cause it to dissolve. The partial negative charges of the oxygen atoms are attracted to the positively-charged sodium ion and form a “shell” around it, canceling out its charge. This breaks the sodium ion’s bond with the negatively-charged chloride ion. At the same time, the partial positive charges of hydrogen atoms are attracted to the negatively-charged chloride ion and form a shell around it, canceling out its charge and breaking the bond between it and the sodium ion.

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Sodium Chloride Dissolved in Water


Substances that readily dissolve in water are said to be hydrophilic (“water-loving”). Non-polar, non-ionic substances that will not readily dissolve in water are described as hydrophobic (“water-fearing”).

For example, most lipids (fats) are very low in oxygen and, therefore, are nonpolar. Consequently, lipids are among the few organic molecules that will not readily dissolve into water. Nonpolar molecules don’t readily dissolve in water because the polar water molecules can neither hydrogen-bond to the uncharged molecules nor attract them away from each other with their partial charges. Since water molecules can neither hydrogen-bond with nonpolar molecules nor form shells around them, nonpolar molecules tend to cluster together in water, instead of dissolving into it. Think of the way oil molecules clump together in water to form droplets that won’t dissolve into the water.

Living cells consist almost entirely of various substances dissolved into water. No substance other than water is so common, is a liquid over such a wide range of the temperatures normally experienced on Earth, and is such an excellent solvent. For this reason, life as we know it simply couldn’t exist without water.

As if all of this weren’t enough, water has an extremely high specific heat. This means that it can absorb lots of heat energy without its temperature changing very much. The reason for this is that much of the energy absorbed by water goes into breaking its hydrogen bonds, rather than causing the molecules to move faster. This makes water an excellent insulator against temperature changes, and also helps explain why water is a liquid over such a tremendous range of temperatures.

Again because of its hydrogen bonds, water has a very high heat of vaporization. This means that it takes a tremendous amount of heat to vaporize (boil) water and convert it to steam. Consequently, water absorbs lots of heat when it evaporates. This is why sweating is such an effective way to cool the body – as the water in perspiration evaporates, it absorbs body heat and helps prevent overheating.

Marvelous stuff, that dihydrogen monoxide.


[B]Chemical Reactions:Chemical reactions occur when reactants recombine molecularly to form products. If the energy in the bonds of the reactants is greater than is the energy in the bonds of the products, then the chemical reaction releases energy as it progresses, and is said to be exothermic (or exergonic). Combustion is a familiar example of an exothermic chemical reaction.

If the energy in the bonds of the reactants is less than the energy in the bonds of the products, the chemical reaction can only progress by absorbing energy from its surroundings, and is known as an endothermic (or endergonic) reaction. Some of the “cooling packs” that are commercially available work because two different chemicals are allowed to mix when a vial that separates them is broken. The endothermic reaction between these chemicals draws energy (in the form of heat) from its surroundings as it proceeds.

As a rule, the warmer the temperature, the faster the rate at which chemical reactions occur. This is because higher temperatures mean that atoms and molecules are moving faster. Faster-moving atoms and molecules are more likely to encounter each other and react than are slower-moving atoms and molecules.

Broadly speaking, three kinds of chemical reactions are important to living organisms: synthesis reactions, decomposition reactions, and exchange reactions. Collectively, the sum of all the chemical reactions occurring in your body is your metabolism.


[b]Synthesis Reactions:
Synthesis reactions are chemical reactions in which large molecules are formed by combining smaller molecules. Most large organic molecules are polymers formed by combining smaller subunits known as monomers. For instance, proteins are formed by combining monomers known as amino acids. Polysaccharides such as starch are formed by combining monomers known as monosaccharides (simple sugars). Nucleic acids are formed by combining monomers known as nucleotides. The portion of your metabolism that consists of synthesis reactions is known as anabolism.

A great many of the synthesis reactions in living things occur through the process known as dehydration synthesis. This occurs when smaller molecules are combined by removing an oxygen and a hydrogen from one, and a hydrogen from the other. The oxygen and the two hydrogens combine to form water, while the smaller molecules combine with each other to make a larger molecule.

Consider amino acids. Every amino acid contains a carboxyl group (COOH) at one end, and an amine (NH2) group at the other end. Two amino acids can be combined by splitting off an oxygen and a hydrogen from the carboxyl group, and a hydrogen from the amine group. This leaves the nitrogen in the (former) amine group free to bond to the carbon in the (former) carboxyl group, which is what happens. And so the two amino acids are joined together. Meanwhile, the freed oxygen and hydrogen atoms bond to form water.


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[b]Decomposition Reactions:
Decomposition reactions are chemical reactions in which large molecules are broken down into smaller molecules. Usually, this is done in order to allow the molecular subunits to be rearranged into more useful molecules, or to harvest energy from the breaking of chemical bonds.

The portion of your metabolism that consists of decomposition reactions is known as catabolism, and a great many of the decomposition reactions in living things occur through the process of hydrolysis, which is the exact opposite of dehydration synthesis. In hydrolysis, a water molecule is added to a larger molecule, breaking it into two smaller subunits.


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Hydrolysis is the splitting of a polymer by adding water to a covalent bond.


[b]Exchange Reactions:
Exchange reactions are chemical reactions in which molecules are rearranged by “swapping partners.” Big molecules aren’t broken down into smaller ones, nor are small molecules combined into bigger ones.

Ionic substances are often involved in exchange reactions. For example, when they’re dissolved in water, the base sodium hydroxide can react with the acid hydrogen chloride (hydrochloric acid) to form water and sodium chloride. The reaction involves the chemical agents “swapping partners,” and looks like this: NaOH + HCl → H2O + NaCl


[B]Catalysts and Enzymes:
A certain amount of energy must be supplied before a chemical reaction can occur. This is known as the activation energy for that reaction. A catalyst is a substance that lowers the activation energy of a reaction, and so speeds up the rate at which it occurs.

A catalyst is neither a reactant nor a product in a chemical reaction, merely a facilitator. So catalysts are not consumed in reactions. For an example of how a catalyst works, think of the catalytic converter in an automobile’s exhaust system. Your car’s catalytic converter contains platinum, which acts as a catalyst to speed the conversion of deadly carbon monoxide to less-harmful carbon dioxide in your car’s exhaust system. This means that your car produces much less carbon monoxide when it burns fuel than it would otherwise.

Catalysts don’t cause chemical reactions to occur, so adding a catalyst won’t cause a reaction to occur that wouldn’t occur on its own. What catalysts do is make it easier for chemical reactions to occur, and so they speed up the rates at which chemical reactions progress.

An enzyme is a protein that functions as a catalyst and so speeds up the rate at which chemical reactions occur in the body. Often, enzymes work by bringing molecules close together, and thereby making it easier for them to react with each other. The chemical reactions necessary to support modern organisms would not occur at anywhere near the rates necessary to support life if it weren’t for the numerous enzymes present in every cell.


[B]Electrolytes, Acids, and Bases:
An electrolyte is any substance that, when dissolved in water, dissociates into electrically-charged subunits – that is, ions. For instance, when dissolved in water, the salt NaCl dissociates into sodium ions (Na+) and chloride ions (Cl-).


Because they dissociate into electrically-charged subunits in water, electrolytic solutions generally conduct electricity very well. Salts and other ionically-bound substances are often electrolytes. Acids and bases (alkalines) are also electrolytes.


An acid is a substance that, when dissolved into water, dissociates and releases positively-charged hydrogen ions (H+) – that is, protons. These hydrogen ions can be dangerous to living organisms, because they can tear apart organic molecules in their eagerness to acquire electrons with which to neutralize their positive charges.


A base or alkaline is a substance that, when dissolved in water, either releases negatively-charged hydroxide ions (OH-) or that absorbs H+ ions. Like acids, bases tend to attack and destroy organic molecules. When acids and bases react with each other, they chemically react to neutralize each other – typically, the reaction forms water and some sort of salt as a product.


The acidity/alkalinity of a solution is measured as its pH. The pH scale is logarithmic, meaning that a change of one unit on the scale represents a 10-fold change in acidity/alkalinity. The scale ranges from 0 – 14. Substances that are precisely neutral and release neither protons nor hydroxide ions in solution with water have a pH of 7.0. (More precisely, the numbers of H+ and OH- ions are balanced.) Pure water has a pH of 7.0.


Any substance with a pH less than 7 is an acid, because it has more H+ ions in solution than OH- ions. Rainwater normally contains small amounts of carbon dioxide, and when dissolved in water, CO2 forms carbonic acid. Thus, rainwater is normally slightly acidic, and has a pH of about 6, making it roughly ten times more acidic than pure water. (Other substances dissolved into the rainwater can make it significantly more acidic, of course, which is where “acid rain” comes from.) Black coffee has a pH of about 5, making it 100 times more acidic than pure water. Soda generally has a pH of about 4, and is roughly 1,000 times more acidic than pure water. Vinegar has a pH of about 3. Lemon juice has a pH of about 2. Battery acid has a pH of about 1. A very strong hydrochloric acid solution can have a pH approaching 0.


Any substance with a pH greater than 7 is a base (alkaline), because it releases more OH- ions into solution than H+ ions. Your blood is normally slightly alkaline, with a pH of about 7.4. Egg whites have a pH of about 8. Baking soda has a pH of about 9. Ammonia has a pH of 10 – 11. Drano has a pH of about 12 – that’s about 100,000 times more alkaline than pure water. This is why Drano is so caustic and so good at removing organic matter from your pipes. A strong sodium hydroxide (NaOH) solution can have a pH approaching 14.


A substance that causes a solution to resist any change in pH is known as a buffer. Baking soda is an excellent example of a buffer. A buffer works because it can release either H+ or OH- ions into solution. If an acid is added to a buffered solution, the buffer releases OH- ions, which neutralize the H+ ions of the acid. (H+ + OH- → H2O.) Similarly, addition of a base to a buffered solution causes the buffer to release H+ ions, neutralizing the OH- ions released by the base.


The blood of humans and most other vertebrates contains buffers which keep its pH at about 7.4. This is very important, because even a slight change in the pH of the blood is life-threatening.


When mixed, acids and bases neutralize each other. That’s because the H+ ions of the acid combine with the OH- ions of the hydroxide, forming water (H2O). Usually, the remaining reactants combine to make some sort of salt. As an example, consider what happens when you combine hydrochloric acid and the base sodium hydroxide; the result is water and sodium chloride (table salt):
HCl + NaOH → (H+ + Cl-) + (Na+ + OH-) → H2O + NaCl


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The pH scale




[B]Redox Reactions:
Redox reactions (oxidation-reduction reactions) are quite similar to acid-base reactions in some ways, insofar as they typically involve electrically-charged subunits. Basically, redox reactions are chemical reactions that involve the transfer of electrons between atoms/molecules. Metals easily lose their electrons to other substances, so redox reactions (like acid-base reactions) often involve metals.

Like acid-base reactions, redox reactions are always paired. When one substance is oxidized through loss of electrons, another substance is reduced by gaining those electrons.


A substance is reduced when it gains electrons. Since an electron has a negative charge, the net charge of a substance goes down (becomes more negative) when it gains electrons. This is why it is said to be reduced.

Below is an example of a reduction reaction. It shows two positively-charged silver cations being reduced. Each of them gains an electron, producing electrically-neutral silver atoms.
2Ag+ + 2e- → 2Ag


A substance is oxidized when it loses electrons. Since it loses electrons, the net charge of a substance goes up when it is oxidized. Oxygen, you recall, has a strong affinity for electrons and can take them from other atoms or molecules. So when oxygen is added to a substance, the oxygen is likely to oxidize it by taking electrons from it. This does not mean that oxygen is necessarily involved in an oxidation reaction, though; any chemical reaction in which a substance loses electrons is an oxidation reaction.

Below is an example of an oxidation reaction. It shows an electrically-neutral copper atom being oxidized through loss of two electrons. This results in a positively-charged copper(II) cation and two free electrons. (A copper atom that loses two electrons and thereby acquires a charge of 2+ is sometimes referred to as a cupric ion.)
Cu → Cu2+ + 2e-


If we combine the two reactions above, we have a complete oxidation-reduction reaction:
Cu + 2Ag+ + 2e- → Cu2+ + 2Ag + 2e-





[B]The Molecules of Life:In an episode of Star Trek: The Next Generation, humans were referred to as “ugly bags of mostly water,” which is quite accurate. (Well, “ugly” is rather subjective.) A living cell consists mostly of water, with inorganic salts plus various organic and inorganic molecules dissolved or suspended within it. Well over 90% of the molecules in your body are water molecules, and a human being is more than 50% water by weight.

Inorganic salts include ions such as Na+, Cl-, and K+ (potassium). These ions are vital in the proper functioning of nerves and muscles, and also in the makeup of bone tissue.

Organic molecules are simply those which contain the elements carbon and hydrogen. Most organic molecules contain oxygen as well. Lots of people are under the impression that “organic molecules” are necessarily formed by or found within living organisms, but this is not the case. Any molecule that contains both carbon and hydrogen is an organic molecule, regardless of its origins, and a molecule that does not contain both hydrogen and oxygen is an inorganic molecule, even if it was synthesized by a living organism.

What is the significance of the element carbon? A carbon atom can covalently bond with up to four other atoms. This means that carbon can form the “skeleton” of extraordinarily large and complex molecules. When aliens in science-fiction movies refer to humans as “carbon-based lifeforms,” they aren’t kidding – were it not for the extraordinary chemical versatility of carbon, we wouldn’t be here.

For all their complexity, there are only four principle types of organic molecules found in living organisms – carbohydrates, lipids, proteins, and nucleic acids. Most large organic molecules are made by chemically linking small monomers into large polymers via dehydration synthesis.

Organic molecules are often ring-shaped, especially when dissolved in water. When chemists depict a ring-shaped organic molecule, they often leave out some things, in order to simplify. For instance, it’s standard practice to not show the carbon atoms in the ring. Wherever you see a “bend” in a ring-shaped organic molecule indicating two (or more) bonds, it’s assumed that you understand that there’s a carbon atom sitting there. If there’s something other than a carbon atom in that bend (a nitrogen atom, for example), it will be indicated.

Similarly, in order to simplify chemical diagrams, you’ll sometimes see a single line extending off a ring and indicating a bond, with no atom shown at the end of that line. It’s assumed that you know that the atom at the end of such a line is a hydrogen atom.


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A glucose molecule. Each of the angles in the ring has a carbon
atom in its center, except for the one in the top right. That one
has an oxygen in it, so the oxygen atom is shown.


[B]Carbohydrates:
Carbohydrates are organic molecules that contain carbon, hydrogen, and oxygen, usually in the approximate formula (CH2O)n. For example, glucose is C6H12O6, as is fructose. (Molecules with the same chemical formula but different arrangements of their atoms are isomers.) Sucrose is C12H22O11. You may have noticed that sucrose has the chemical formula you’d expect if you combined a glucose molecule and a fructose molecule and removed a water molecule in the process. That’s not coincidental – dehydration synthesis of sucrose from glucose and fructose occurs in precisely that manner.

In living organisms, carbohydrate molecules are generally used as sources of energy. Using oxygen to break the covalent bonds of carbohydrates (especially glucose) in the process known as aerobic respiration is the chief way that living things generate the energy they need to power their metabolic processes. Carbohydrates can also be used to store energy for later use. For instance, humans store large carbohydrate molecules known as glycogen in their muscle and liver tissues. When energy reserves are low, some of the stored glycogen can be converted back into glucose and used for energy. Plants also store energy in the form of large carbohydrate molecules – namely, starch.

Because they contain lots of electron-greedy oxygen atoms, carbohydrate molecules are usually polar, and so dissolve quite well in water. The basic subunits of carbohydrates are known as monosaccharides or “simple sugars.” Most monosaccharides have the formula C6H12O6. In water, monosaccharides typically adopt ring-shaped structures, as you can see from the illustration of a glucose molecule, below.

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Glucose, A Monosaccharide


Two monosaccharides can be combined through dehydration synthesis to form a disaccharide or “complex sugar.” Sucrose (table sugar) is a common example of a disaccharide. Maltose is a disaccharide found in beer. Lactose is a disaccharide found in milk. Trisaccharides are also complex sugars, and include raffinose, which is found in molasses.

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Larger carbohydrate molecules (polysaccharides) can be formed by linking many monosaccharides together. These “complex carbohydrates” are generally much less soluble in water than are sugars, and are often used as structural materials by living organisms. For example, chitin is a complex carbohydrate that forms strong yet flexible structures. It forms the cell walls surrounding the cells of fungi, and is the main component in the exoskeletons of insects and some other animals. Cellulose is another complex carbohydrate that provides structural support; it is the primary component of the cell walls that surround plant cells.

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Glycogen is a polysaccharide that can be stored in the cells
of animals. When energy stores run low, glycogen can be
decomposed back into glucose, which can be broken down for energy.


Any organic molecule in which a hydroxyl group (OH) is bound to a carbon atom is known as an alcohol. Hydroxyl groups can be bound to monosaccharides or disaccharides to form sugar alcohols or polyols. Polyols, like sugars, taste sweet, and they’re often used as food additives because they aren’t as easily absorbed or digested as are sugars. Because the bacteria in your mouth can’t metabolize polyols, polyols don’t contribute to tooth decay like sugars do, which is another reason why they’re sometimes used to replace sugars in foods. A common example of a polyol that’s used as an artificial sweetener is sorbitol, which is made by converting glucose to an alcohol.


[B]Lipids:
Lipids are a diverse assortment of organic molecules, but they all have in common the fact that they contain large regions composed almost entirely of carbon and hydrogen atoms with few or no oxygen atoms. The lack of oxygen makes those regions nonpolar, and these hydrophobic regions mean that most lipids are more or less insoluble in water. Instead, lipids tend to clump together in water to form droplets.

Lipids are often used as long-term energy-storage molecules in the body. Lipids are sometimes used as waterproofing agents. Lipids are the primary components of the cellular membranes that surround and hold together cells. Many of your hormones are lipids.

Common lipids include oils, fats, waxes, phospholipids, and steroids.


[b]Oils, Fats, and Waxes:
A fatty acid chain is a long chain of carbon atoms bound to each other and to hydrogen atoms, with a carboxyl group (COOH) at one end. Since the carboxyl group is the only part of the fatty acid chain with any oxygen, a fatty acid chain is hydrophobic and will not dissolve in water.

If all the bonds are single bonds, the fatty acid chain is said to be saturated, because each carbon at is bound to as many other atoms as is possible – namely four. Saturated fatty acid chains, because they’re straight, can be packed together quite compactly, so they make excellent energy-storage molecules. Since the single bonds in saturated fatty acid chains are relatively easy to break, saturated fats are easy to digest.

If some of the carbons in the fatty acid chain are double bonded to each other, then the fatty acid chain is unsaturated (because the carbon atoms aren’t bound to as other atoms as they could be). The double bonds in unsaturated fatty acid chains cause the chains to be bent, so unsaturated fatty acid chains aren’t as useful as energy-storage molecules, since they can’t be packed together as compactly. On the other hand, since the double bonds are more difficult to break, unsaturated fatty acid chains aren’t as easily digested as are saturated fatty acid chains.

If the fatty acid chain in question has many double bonds, it is said to be polyunsaturated.

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Saturated and unsaturated fatty acid chains.


Three fatty acid chains bound to a molecule of glycerol form a triglyceride, also known as a fat or oil. Fats are solids at room temperature, and their fatty acid chains are usually saturated. Oils are liquids at room temperature, and typically contain unsaturated fatty acid chains. Fats and oils make excellent energy-storage molecules.

Waxes are similar in structure to fats and oils, except that they’re bound to alcohol groups. Lots of organisms use waxes as waterproofing materials.


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A Triglyceride Contains Three Fatty Acid Chains



[b]Phospholipids:
Phospholipids are a unique group of lipids. In a phospholipid, two fatty acid chains are bound to a phosphate group. The phosphate group contains lots of oxygen and is highly polar, and so it is hydrophilic. But the fatty acid chains are nonpolar and so hydrophobic. This gives phospholipids a sort of “split personality,” because the phosphate-containing “heads” are strongly attracted to water, whereas the fatty-acid “tails” are not. Molecules such as phospholipids that contain both polar and nonpolar portions are said to be amphipathic.


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The structure of a phospholipid molecule


Because the hydrophilic heads of phospholipids are attracted to water and the hydrophobic tails repelled by it, phospholipids will spontaneously arrange themselves into bilayers in water. A phospholipid bilayer consists of two layers of phospholipid molecules arranged so that the water-loving heads point outward and toward the surrounding water, and the tails point inward, away from the water.

Phospholipids are the primary components of the cellular membranes that surround and hold together all cells.


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[b]Steroids:
Steroids are lipids that consist of four fused rings of carbon atoms. Cholesterol is a common steroid, and it’s a major component of cellular membranes. However, because it is nonpolar and won’t dissolve in water, and because blood is mostly water, cholesterol has very low solubility in the blood. If there’s too much cholesterol in your diet, it tends to accumulate on the inside linings of your major blood vessels, contributing to the condition known as atherosclerosis.

Cholesterol is the “base” steroid, because most other steroid molecules are manufactured from it. Many of the other steroids found in the body are hormones. Hormones act as chemical messengers between different parts of the body, and regulate growth and development. The sex hormones, for instance, are steroids that promote the development of male and female sexual characteristics.

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[B]Proteins:Proteins are formed when large numbers of amino acids are linked together through dehydration synthesis. (The bonds between amino acids are known as peptide bonds, so chains of linked amino acids are sometimes called polypeptides.) Proteins have a great many functions in living cells. Many proteins function as enzymes and so ensure that the chemical reactions that sustain life take place at a rate sufficient to keep us alive. Proteins are important structural components of cells. Many hormones are proteins. Antibodies are proteins that help the body fight disease.

To a first approximation, a living cell could be described as proteins dissolved in water and surrounded by a phospholipid bilayer. Not only are proteins important components of living cells, but many cells manufacture proteins for use in making non-living structures. For instance, spider silk is made up of proteins. Your hair and fingernails are largely made up of the protein keratin.


An amino acid consists of a central (“alpha”) carbon covalently bound to an amino group (NH2) on one side and a carboxyl (carboxylic acid) group (COOH) on the other. The carbon’s third bond is to a hydrogen atom. Its fourth bond is to what is known as a reactant group. The exact makeup of the reactant group is what determines the identity of the specific amino acid. Though there are a great many amino acids, living organisms use only about 20 of them to make up their proteins.


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[b]Protein Structure:
When long chains of amino acids are linked together, they form proteins. The specific sequence of amino acids that are linked together forms what is known as the primary structure of a protein. This is “coded for” by the DNA molecules in the nucleus of the cell.

Once a long chain of amino acids is assembled (a polypeptide), hydrogen bonding between different parts of the chain will cause sections of it to fold into a helixes and pleated sheets. This is known as the secondary structure of the protein.

After the polypeptide folds into its secondary structure, hydrogen bonding and disulfide bridges between cysteine units will cause the protein to fold up into a distinct, three-dimensional shape. This is the protein’s tertiary structure.

The amino acid cysteine has sulfur as part of the makeup of its reactant group, and if two cysteine subunits in a protein come close-enough together, their sulfur atoms will bond to each other. This is an important part of why proteins fold up into 3-D shapes. The ultimate shape of a protein molecule is vitally important, because it will determine the protein’s function.

Finally, some proteins join up with other proteins to form larger complexes. These complex proteins have quaternary structure. For example, the protein hemoglobin consists of four globin proteins bound to a central, iron-containing heme group.


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The levels of structure of a protein


Since the shape of a protein is so vital to its function, anything that changes a protein’s shape will alter or destroy its function. When a protein’s shape is changed and it can no longer function properly, it is said to be denatured. Acids, bases, and excess heat are examples of agents that can cause proteins to denature. This is part of the reason why it’s so important for living organisms to maintain their body temperatures and the pH of body tissues within narrow limits.


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When you cook an egg, the heat causes the egg’s
proteins to denature, which is why it hardens.


[B]Nucleic Acids:Nucleic acids are polymers of subunits known as nucleotides. Nucleic acids store and transmit genetic information, and are important in protein synthesis.

A nucleotide consists of a pentose (a 5-carbon sugar) with a phosphate group bound on one side, and a nitrogenous base bound on the other. The bases are either purines, which consist of two interlocked carbon-nitrogen rings, or pyrimidines, each of which consists of a single carbon-nitrogen ring. Nucleotides can be linked by dehydration synthesis to form extraordinarily large molecules. In fact, a single nucleic acid can contain literally millions of nucleotides.

The two major types of nucleic acids are DNA and RNA.


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A Typical Nucleotide


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Cytosine, a Nitrogenous Base (a Pyrimidine)


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Guanine, a Nitrogenous Base (a Purine)


[b]DNA:In DNA, the central pentose is deoxyribose. This is why the proper name for DNA is deoxyribonucleic acid. Each nucleotide in a DNA molecule contains one of four nitrogenous bases. The two purines that can be found in DNA molecules are adenine and guanine, and the two pyrimidines are cytosine and thymine.

What makes DNA such a useful molecule for storing genetic information is that once a string of nucleotides is linked together to form a polynucleotide strand, the assembled strand automatically assembles a complementary strand. This happens because each cytosine-containing nucleotide attracts and bonds to a nucleotide containing guanine, and each guanine-containing nucleotide in the assembled strand attracts and bonds to a cytosine-containing nucleotide. Similarly, each adenine-containing nucleotide in the assembled strand attracts and bonds to a thymine-containing nucleotide, while each thymine-containing nucleotide attracts and bonds to an adenine-containing nucleotide.


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The basic structure of a DNA molecule. Deoxyribose and phosphate groups form
the “backbone” of a DNA strand. Hydrogen bonds cause thymine-containing
nucleotides to bind to adenine-containing nucleotides, and guanine-containing
nucleotides to bind to cytosine-containing nucleotides. In this way, a strand of DNA
serves as a “template” for the assembly of a complementary strand.


A DNA molecule consists of two strands of nucleotides bound together. The strands wrap around each other to form the famous “double helix.” Because each strand is complementary to the other and forms a “mirror image” of it, DNA is easy to copy. Each half of a DNA molecule serves as a template for the other half, so if a DNA molecule is “unzipped” down the middle, each half automatically assembles its missing half. This is how cells copy their DNA before reproducing. Since each half of a DNA molecule is a template for the other half, DNA is also self-repairing if damaged.


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A small segment of a DNA molecule.


[b]DNA and the Genetic Code:
The exact sequence of nucleotides in a DNA molecule is a “code” of sorts that specifies the sequence of amino acids that will make up a protein. A cluster of three DNA nucleotides is called a triplet and specifies a particular amino acid. For example, the triplet CTG (Cytosine, Thymine, Guanine) specifies the amino acid leucine. Since there are four different nucleotides, there are 64 (43) possible nucleotide combinations in a given triplet. Since there are only 20 amino acids used by living organisms, this means the genetic code is degenerate – that is, most of the amino acids are coded for by more than one DNA triplet. For example, the amino acid leucine is coded for by six different DNA triplets.

A segment of DNA that specifies the sequence of amino acids that will make up a particular protein is known as a gene. When information is copied from DNA to manufacture a protein, copying begins at the triplet TAC (Thymine, Adenine, Cytosine), which is called the “START” triplet. TAC happens to code for the amino acid methionine, so every protein starts with methionine. The DNA triplets ATT, ATC, and ACT don’t code for any amino acids, so information-copying stops when one of these triplets is reached. These triplets are known as “STOP” triplets.


[b]RNA:
Whereas DNA is used to store genetic information, RNA is used to transfer genetic information to structures called ribosomes, where that information is used to manufacture proteins. In RNA (ribonucleic acid), the central pentose is ribose. (A deoxyribose molecule contains one less oxygen atom than does a ribose molecule.)

As in DNA, each nucleotide that makes up an RNA molecule can contain one of four nitrogenous bases. RNA contains the same purines as does DNA (adenine and guanine), but it has a different pair of pyrimidines. In RNA, the pyrimidines are cytosine and uracil.

An RNA molecule can bind to an “unzipped” DNA molecule, because the cytosine of RNA binds to the guanine of DNA and the guanine of RNA binds to the cytosine of DNA. The adenine of RNA binds to thymine in a DNA molecule, and uracil in RNA binds to adenine in DNA. In this way, when a double-stranded DNA molecule is partially “unzipped,” the information it contains can be copied to form a single, complementary strand of RNA. The RNA can then transfer the protein-assembly information to the region of the cell where protein synthesis takes place.

The process in which DNA is copied to make RNA is known as transcription, and the process in which the information “encoded” in the RNA sequence is used to assemble an amino acid chain that will ultimately form a protein is known as translation.


[b]Other Nucleotides:In addition to the five nucleotides that make up DNA and RNA, there are nucleotides that perform other functions in the body. For instance, some nucleotides function as coenzymes. A coenzyme is a nucleotide or other non-protein molecule that binds to an enzyme and assists in its function.

A well-known example of a nucleotide that is part of neither RNA nor DNA is adenosine triphosphate or ATP. ATP transports the energy generated by decomposition of glucose and other carbohydrates to the specific region of the cell where it is needed.


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An ATP molecule consists of three phosphate groups (in
blue, on the left) bound to the 5-carbon sugar ribose
(center, in purple). The ribose is bound to the nitrogenous
base adenine (top, in red) on the other side.