Goldfarb D. Biophysics DeMYSTiFied

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142 BiophysiCs DemystifieD

Rule 1. Carbon atoms have four valence electrons to share. Therefore, in a

molecule, carbon atoms will form four covalent bonds with other atoms.

It is this rule that allows us to write skeletal formulas for hydrocarbons and

other biomolecules as in Fig. 7-1. A skeletal formula is a short cut way of showing

a molecular structure. A skeletal formula shows each carbon covalent bond as a

line segment, except that the covalent bonds directly between carbon atoms and

hydrogen atoms are not shown (as a shortcut). A skeletal formula also does not

show the carbon atoms themselves, nor does it show the hydrogen atoms that are

directly connected to the carbon atoms.

By this definition of a skeletal formula, each carbon atom is positioned where

any two line segments meet (i.e., where there is sharp bend or angle between

two line segments in the skeletal formula) or wherever a line segment comes

to an end.

(c)

(b)(a)

CHH

–

Figure 7-1 • Example hydrocarbons.

(a) Hexane. (b) 2-Octene. Shown using a

structural formula (left) and skeletal formula

(right). Notice there is one double bond

between the first and second carbon.

skeletal formulas. The third diagram on the

right shows the skeletal formula with a circle in

the middle. This is a special way of indicating

aromatic rings in skeletal formulas so as to

indicate that the bonding electrons are

delocalized (see Chap. 6).

Chapter 7 BiomoleCules 101 143

Also, by this definition, hydrogen atoms connected directly to carbon atoms

are not shown. So how do we know how many hydrogen atoms are connected

to each carbon atom? This is not a problem because we can use Rule 1. For

example, where two line segments meet, we know we have a carbon atom with

two covalent bonds to atoms other than hydrogen. Since Rule 1 tells us that

carbon forms four covalent bonds, we know that there must be two hydrogen

atoms covalently bonded to that carbon. As another example, at the end of the

chain, where a single line segment comes to a point, we again use Rule 1 that

each carbon has four covalent bonds. Since only one bond is shown (the last

line segment), we know that the end carbon atom must have three hydrogen

atoms attached. You can see this in Fig. 7-1 by comparing the skeletal formulas

with the corresponding structural formula.

Sometimes carbon atoms form double bonds. A double bond involves sharing

two electron pairs (i.e. four electrons) in the same covalent bond between two

atoms. In the structural and skeletal formula, double bonds are shown as two paral-

lel line segments. Sometimes, but less often, carbon atoms even form triple bonds.

As you might expect, a triple bond involves sharing three electron pairs (i.e., six

electrons) in the same covalent bond between two atoms, and a triple bond is

shown as three parallel line segments in structural and skeletal formulas.

Rule 2. When counting covalent bonds for a carbon atom, double bonds count

as two covalent bonds and triple bonds count as three covalent bonds.

Sometimes we need to use Rule 2 in conjunction with Rule 1 to deter-

mine how many hydrogen atoms are directly connected to a carbon atom.

You can see an example of this in Fig. 7-1. Notice that where there are some

carbon atoms that are shown to have a double bond on one side and a single

bond on the other side. That makes three covalent bonds shown for each of

those carbon atoms. Since each carbon atom must have four covalent bonds,

we know that those particular carbon atoms each have only one hydrogen

atom directly attached.

Functional groups

A functional group is a specific group of atoms within a molecule that confers

certain characteristics to that molecule. There are several functional groups that

are quite common in biomolecules. To help us speak about of the composition

and structure of various biomolecules, it will be helpful to first review some

common functional groups.

144 BiophysiCs DemystifieD

Hydroxyl Group

A hydroxyl group is an oxygen atom with one hydrogen atom covalently attached.

The hydrogen atom is attached only to the oxygen atom, whereas the oxygen

atom attaches the hydroxyl group to the rest of the molecule. Figure 7-2 shows

a hydroxyl group. The R in the figure indicates the rest of the molecule. The rest

of the molecule can be one, several, hundreds, or even thousands of atoms. The

oxygen atom of the hydroxyl group, however, is always bonded to only one atom

of the rest of the molecule. In biomolecules the hydroxyl oxygen is most often

bonded to a carbon atom. But it can be attached to other atoms, for example, to

phosphorous, in the case of a phosphate functional group. Hydroxyl groups are

polar, with the hydrogen atom having a slightly positive charge allowing it to

participate in hydrogen bonding with other atoms (see Chap. 6).

Figure 7-2 • A hydroxyl group is an oxygen

atom covalently bonded to a hydrogen atom. In a

hydroxyl group, the hydrogen is bonded only to

the oxygen, whereas the oxygen atom connects

the hydroxyl group to the rest of the molecule.

Ketone

Aldehyde

Carboxyl

OHR

Figure 7-3 • Three types of carbonyl groups.

Carbonyl Group

A carbonyl group is carbon atom with a double covalent bond to an oxygen

atom. In addition to the double bond with the oxygen, the carbon atom also

has two covalent single bonds to other atoms. At least one of these single bonds

is always connected to the rest of the molecule. There are various types of car-

bonyl groups depending on what atom or functional group is connected to each

of the two single bonds. Figure 7-3 shows three common types of carbonyl

Chapter 7 BiomoleCules 101 145

groups. When both single bonds are connected to the rest of the molecule, the

group is called a ketone. When one of the two single bonds is connected only to

a hydrogen atom, then the group is called an aldehyde. When it is connected to

a hydroxyl group, then the carbonyl is called a carboxyl group.

The double bond between the carbon and oxygen is a polar bond, so the

oxygen has a slightly negative charge and the carbon has a slightly positive

charge. Carbonyl oxygen atoms often participate in hydrogen bonding.

Carboxyl Group

A carboxyl group is a type of carbonyl group. We discuss it here in a section of

its own because it is so common in biomolecules. In a carboxyl group, the car-

bon atom has a double covalent bond to an oxygen atom and a single covalent

bond to a hydroxyl group. The remaining single covalent bond attaches the

carboxyl group to the rest of the molecule (see Fig. 7-4a).

The chemical formula for a carboxyl group is usually written as COOH.

Molecules that contain a carboxyl functional group are called carboxylic acids.

The hydrogen atom of the carboxyl group has a slightly positive charge, and the

doubly bonded oxygen has a slightly negative charge, making them both able

to participate in hydrogen bonding (see Fig. 7-4b). Carboxyl groups are also

easily ionized to form COO

–

and H

ions.

(a)

(b)

Figure 7-4 • A carboxyl group is carbon atom

doubly bonded to an oxygen atom, and singly

bonded to a hydroxyl group. (a) Molecules

containing carboxyl groups are called

carboxylic acids. (b) In carboxyl groups, both

the doubly bonded oxygen and the hydroxyl

hydrogen are able to participate in hydrogen

bonding. The figure shows two carboxylic acids

hydrogen bonding to each other.

Amine Group

An amine group is a nitrogen atom bonded in such a way as to have a pair of

nonbonded valence electrons. For our purposes, you can think of an amine as a

146 BiophysiCs DemystifieD

nitrogen atom that has three single covalent bonds to three other atoms. Typically

two of the other atoms are hydrogen, while the third atom is a carbon atom link-

ing the amine group to the rest of the molecule. This is called a primary amine,

because it has one connection to the rest of the molecule. See Fig. 7-5. A second-

ary amine has only one hydrogen atom attached and two covalent bonds to the

rest of the molecule. Tertiary amines exist but are less common. In a tertiary

amine the nitrogen has three connections to the rest of the molecule, with no

hydrogen atoms directly connected to the nitrogen.

Amine groups are polar with a slightly negative charge on the nitrogen atom

and (for primary and secondary amines) a slightly positive charge on the hydro-

gen atoms. Amines can participate in hydrogen bonding, on either the positive

or negative side of the bond. One amine group can thus participate in up to

three hydrogen bonds at once. Amines can form positive ions by covalently

binding to an extra hydrogen atom without its electron (i.e., by covalently

bonding to a proton). Thus, when ionized, we have NH

for a primary amine

ion, NH

for a secondary amine ion, and NH

for a tertiary amine ion.

Phosphate

A phosphate group is a phosphorous atom with four oxygen atoms attached.

One oxygen atom always shares a double bond with the phosphorous. The

remaining three oxygen atoms either are covalently bonded to the rest

of the molecule or are part of hydroxyl groups. Figure 7-6 shows a phos-

phate group with only one oxygen atom connecting it to the rest of the

molecule. Thus two of the four oxygen atoms are part of hydroxyl groups.

Phosphate groups are highly polar and so can form hydrogen bonds, as we

Primary amine

Secondary

amine

Tertiary amine

Figure 7-5 • An amine group is a nitrogen

atom with a pair of nonbonded valence

electrons. The amines that concern us most are

primary and secondary amines which have two

and one hydrogen atom, respectively.

Chapter 7 BiomoleCules 101 147

saw with the other functional groups discussed. Phosphate groups also

easily form negative ions by losing the hydrogen atom from one or both of

its hydroxyl groups.

Acids, Bases, and pH

Aqueous solutions always contain some hydrogen ions (H

) and hydroxyl ions

(OH

–

). Since a hydrogen atom is just one proton and one electron, a hydrogen

cation (H

) is really just a proton in solution. Molecules or functional groups

that increase the concentration of protons in solution are called acids. Those

that decrease the concentration of protons are called bases.

For example, amines easily bind protons (because of their nonbonded

valence electrons). Binding protons reduces the proton concentration in solu-

tion, and so amines are considered basic. Phosphates easily release protons

and so phosphates are considered acidic. Sometimes bases decrease the con-

centration of protons by increasing the concentration of hydroxyl ions (OH

–

The hydroxyl ions bind to protons and thereby decrease the concentration of

protons.

We measure the concentration of protons in units of pH (pronounced “pee-

aych”). The pH is approximately equal to the negative base-ten logarithm of

the proton concentration. A pH of 7 means H

is at a concentration of 10

–7

moles per liter. Pure water has a pH of 7 and is considered neutral. A pH less

than 7 means a higher concentration of H

(e.g., pH = 3 means 10

–3

moles per

liter which is greater than 10

–7

moles per liter). Acidic substances (those that

increase H

) therefore lower the pH, whereas bases increase pH. Since water,

with a pH of 7, is considered neutral, measurement of pH is considered to range

from pH = 0 for the most acidic substances to pH = 14 for the most basic

substances.

Figure 7-6 • A phosphate group is a

phosphorous atom with four oxygen atoms

attached. One oxygen atom always shares a

double bond with the phosphorous. The

remaining three oxygen atoms either are

covalently bonded to the rest of the molecule

or are part of hydroxyl groups.

148 BiophysiCs DemystifieD

Many biochemical and biophysical processes are sensitive to the concentra-

tion of protons and hydroxyl ions. These ions also affect the forces that deter-

mine the conformation of biomolecules, especially where other ions or hydrogen

bonds are involved.

We’ve just finished learning the main functional groups that are significant in

biomolecules, as well as some other important background information relevant

to our understanding of molecular and subcellular biophysics. Next we use this

information to discuss the four major classes of biomolecules: carbohydrates,

lipids, proteins, and nucleic acids.

still struggling

The bulk of this chapter is all about nomenclature, building up a vocabulary so

that we can talk about the physics of biomolecules and how it relates to their func-

tion. you may need to review this chapter more than once if the names don’t stick

right away. To make it easier, focus on the section headings. These are the main

terms that you need to know. Look over the figures. You don’t need to memorize

the chemical structures, but you should know what elements are in them and

what that means from a physical point of view. For example, you should know that

hydrocarbons contain only hydrogen and carbon. And molecules, or portions of

molecules, that are purely hydrocarbon are hydrophobic (avoid water). on the

other hand, functional groups that contain oxygen and nitrogen tend to be hydro-

philic, and may participate in hydrogen bonding. Acids and bases also tend to be

hydrophilic because they easily ionize. Structures that contain aromatic rings are

relatively stiff and inflexible. Above all, use this chapter as a reference. When you

see these terms in later chapters, there will usually be enough information to jog

your memory, but if not simply return here.

Carbohydrates

Carbohydrates are molecules made of carbon, hydrogen, and oxygen. They are

the most abundant biomolecules on Earth. Carbohydrates are used for energy

storage (food). They also serve as structural material, for example, cellulose.

Carbohydrates are components of nucleic acids (the genetic material) and of

Chapter 7 BiomoleCules 101 149

some coenzymes. Carbohydrates also play a role in recognition when one cell

or molecule needs to recognize another.

In biochemistry, carbohydrates are also called saccharides and in common

language sugars. The simplest of all carbohydrates are monosaccharides, simple,

single-unit carbohydrates. The chemical formula of a monosaccharide is

This formula tells us that monosaccharides contain equal amounts of carbon

atoms and oxygen atoms, and twice as many hydrogen atoms. Monosaccharides

contain from 3 to 8 carbon atoms. Figure 7-7 shows the structure of a simple

monosaccharide, glucose.

When two monosaccharides are covalently bonded together into a single

molecule, the molecule is called a disaccharide. Sucrose, or table sugar, is a com-

mon disaccharide. When a carbohydrate polymer contains between 2 and

20 monosaccharides, we call it an oligosaccharide. We usually reserve the term

polysaccharide to refer to carbohydrate molecules containing greater than

(a)

Chain form glucose

(b)

Circular form glucose

Figure 7-7 • The monosaccharide glucose

has the chemical formula C

. Two

structures of glucose are shown. (a) Chain form

glucose. (b) Circular form glucose. The circular

form is most common in biological systems.

150 BiophysiCs DemystifieD

20 monosaccharides. Although all saccharides are commonly called sugars,

polysaccharides are also called starches. Figure 7-8 shows a portion of the poly-

saccharide cellulose, which is composed of glucose residues linked together.

Derivatives of Carbohydrates

Some molecules, strictly speaking, are not classified as carbohydrates, but are

derived from and are similar to carbohydrates. For example, if a given carbohy-

drate molecule has one less oxygen atom than normally found in carbohydrates,

so that its chemical formula is C

n –1

, we call it a deoxycarbohydrate. The

most studied deoxycarbohydrate is deoxyribose (C

), which is a major

component of the residues making up DNA (deoxyribonucleic acid).

Other derivatives of carbohydrates include sugar alcohols such as sorbitol,

which are used as low-calorie sweeteners. (They also reduce tooth decay

because, unlike sugars, they cannot be digested by the bacteria in the mouth.)

Sugar acids are also derived from carbohydrates. Ascorbic acid, or vitamin C, is

one such example.

Lipids

Lipids as a class of biomolecules do not dissolve in water, but they do dissolve

in nonpolar solvents. Lipid molecules are all either hydrophobic or amphip-

athic. Some lipids are polymers, or may form polymers. Other lipids are never

found as polymers.

Figure 7-8 • The polysaccharide cellulose is composed of glucose residues. (Courtesy of

Biochemistry Demystified.)

Chapter 7 BiomoleCules 101 151

Probably the most important job that lipids do is to serve as the main

structure of cell membranes. Membranes protect and compartmentalize the

insides of cells. They also help decide what gets into and out of the cell.

Another role for lipids is energy storage. Excess energy from the food we eat

can be stored in the chemical bonds that make up a lipid polymer. Later, this

energy can be released and used by the organism. Lipids, in the form of

stored fat, also provide a layer of thermal insulation and protection for many

organisms.

Figure 7-9 shows an example of a polymeric lipid and nonpolymeric lipid.

As you can see, the two categories of lipid are significantly different in struc-

ture. Polymeric lipids typically contain long chain hydrocarbon structures. Non-

polymeric lipids often contain one or more ring structures. What they have in

common, what makes them both lipids, is that they do not dissolve in water but

they do dissolve in nonpolar solvents.

(b)

C O

(a)

Palmitic acid

Cortisone

Figure 7-9 • Example structures of two classes of lipid: polymeric

and nonpolymeric. (a) The fatty acid palmitic acid (a major

component of palm tree oil). Fatty acids are long chain

hydrocarbons with a carboxyl group at one end. (b) Cortisone, a

steroid.

steroids are a class of nonpolymeric lipids characterized by

four covalently attached ring structures.