SAT Biology E/M Subject Test

Part II: Subject Review

Chapter 3 Molecules of Biology

To understand the complex topics covered in the Biology E/M Subject Test, you must first have a general understanding of basic organic chemistry. In this chapter, we will look at organic chemistry at its most basic level—atoms, molecules, compounds—and see how it directly applies to the biological concepts you will learn about.

Atoms, Molecules, and Compounds

Atoms are the fundamental units of the physical world. Individual atoms combine in chemical reactions to form molecules:

atom + atom → molecule

H + H   →   H2

Thus, a molecule is just a combination of atoms. Molecules can also react with other atoms or other molecules to form larger molecules:

     reactants → product

2 H2 + O2 → 2 H2O

If a molecule contains different types of atoms (as does the molecule above), it is called a compound. For example, CCl4 is a compound because the molecule has both carbon and chlorine in it. On the other hand, H2 is a molecule but is NOT a compound, because the only atoms in the molecule are hydrogen atoms. (If a molecule contains only a single type of atom, it is an element.)

In chemical reactions, the molecules or atoms that are interacting are called reactants and are found on the left side of the arrow. The products (the results of the interactions) are found on the right side of the arrow.

What Organic Chemistry Means

Organic chemistry is simply the chemistry of molecules and compounds that contain carbon. Molecules and compounds that contain carbon are said to be organic, whereas molecules that do not contain carbon are said to be inorganic. There’s a single exception to this rule: carbon dioxide (CO2). Even though carbon dioxide contains carbon, it is an inorganic compound.


Biomolecules

Carbon is the main ingredient of organic molecules. Most molecules within a cell, other than water, are carbon based. Therefore, these molecules are sometimes called biomolecules. Carbon is common in living things because it has only four electrons in the highest energy level of the electron shells that surround the nucleus. Carbon can therefore form up to four bonds with other atoms.


Quick Quiz #1

Check the appropriate boxes:

  1. Water (H2O) is an [  organic  inorganic ] compound.

  2. Cl2 [  is  is not ] a compound.

  3. H2O [  is  is not ] a compound.

  4. Methane (CH4) is an [  organic  inorganic ] compound.

  5. Cl2 [  is  is not ] a molecule.

  6. Carbon dioxide (CO2) is an [  organic  inorganic ] compound.

  7. Products are found on the [  right  left ] side of the arrow in a chemical reaction.

Correct answers can be found in Chapter 15.

There are many organic molecules. Fortunately, as far as biology is concerned, there are only four important types of organic molecules. Most of them are very large, and they’re referred to as macromolecules. The four biologically important macromolecules are the only ones you need to worry about for the SAT Biology E/M Subject Test.


The four important organic molecules are

1. proteins

2. carbohydrates

3. lipids

4. nucleic acids


These four macromolecules are polymers. Polymers are strings of repeated units. The individual units of polymers are called monomers. An example you’re probably more familiar with is a string of pearls. Each individual pearl would be a monomer; strung together, the monomers form a polymer: the whole necklace. Let’s take a look at the first biologically important macromolecule: protein.

Biologically Important Macromolecule #1: Protein

Proteins are polymers of amino acids. In other words, the monomer that makes up a protein is an amino acid. There are 20 different amino acids, and they all have the same basic structure:

The box encloses the backbone of the amino acid. It’s called the backbone because this is the part of the molecule that is constant from amino acid to amino acid. All 20 amino acids contain the same backbone structure.

There are two carbon atoms in the backbone. The first is bonded to a hydrogen (H) atom on one side and an NH2 group on the other side. The NH2 group is called the amino group. The other carbon atom is bonded to an oxygen (O) atom and an OH group. Notice that the oxygen is bonded to the second carbon by a double bond. The COOH group is called the carboxyl group. If you know what the boxed structure looks like, with its amino and carboxyl group, you’ll be able to recognize amino acids on the test. Take a good, long look at the structure in the box, then draw it (three times) on the next page so you’ll really be familiar with it.

•   Draw it:

•   Draw it again:

•   Draw it again:

We’ve already said that all 20 amino acids contain the same backbone structure. But what about the R part of the molecule? The R part of the molecule is called the side-chain, and makes each amino acid different from all the others. All amino acids have the same basic backbone, but different amino acids differ with respect to R. R could be anything from a simple hydrogen atom to a whole long chain of carbon atoms with different groups bonded to them. The side-chain gives the amino acid its identity.

The R-Group

The fourth bond of the
central carbon in an amino
acid is sometimes called
the R-group, or the side
chain. It is this side chain
on an amino acid that
gives the amino acid its
unique chemical
properties.

In the amino acid glycine, R is just a hydrogen atom:

In the amino acid cysteine, R is a carbon atom and a sulfur (S) atom, along with some hydrogen atoms:

Again, there are 20 different possibilities for R groups. You don’t have to know all of them, but you should be able to recognize the backbone of an amino acid.

Amino Acids Combine to Form Proteins

Amino acids bond together in a chain to form a protein. Remember, a long chain of repeated units (monomers; in this case, amino acids) is called a polymer (in this case, a protein). Let’s look at how two amino acids join:

Notice the circles around the OH group of amino acid #1 and around the H of amino acid #2. The carbon from amino acid #1 loses the OH and bonds instead to the nitrogen on amino acid #2. The nitrogen from amino acid #2 loses one H in the process:

The new bond between the amino acids is called a peptide bond. Notice that water (H2O) is removed. Peptide bonds are said to be formed by dehydration synthesis.

When many amino acids join to form a long amino acid chain, this chain is called a protein. Because the amino acids in the chain are all held together by peptide bonds, the protein can also be referred to as a polypeptide.


•   Peptide bonds are formed by dehydration synthesis in which a molecule of water is removed to join two amino acids.

•   Peptide bonds are broken in the reverse process, called hydrolysis, when a water molecule is added to the structure.


Proteins have many different functions. They are enzymes, hormones, channels, structural elements, carriers, messengers, etc. Don’t worry yet about these specific functions. They’ll come up later as we talk about cells and the body. But do remember that proteins have many different three-dimensional shapes and many different functions.

Quick Quiz #2

Fill in the blanks and check the appropriate boxes:

  1. The bond that holds two amino acids together is called a __________bond.

  2. The assembly of a protein from its amino acid constituents involves the [  addition  removal ] of water and is called ______________________________.

  3. An amino acid is a [  monomer  polymer ] of a protein.

  4. Because proteins are essentially chains of amino acids linked together by ________________ bonds, a protein might also be called a ______________________________.

  5. The disassembly of a protein into its component amino acids is called __________________ and involves the [  addition  removal ] of water.

Correct answers can be found in Chapter 15.

Biologically Important Macromolecule #2: Carbohydrate

The monomer for a carbohydrate is a saccharide. The term saccharide refers to “sweetness”; carbohydrates are essentially sugar molecules. All carbohydrates have a common factor: They are made only of carbon, oxygen, and hydrogen.

The carbohydrate is unique among the macromolecules because it is the only macromolecule for which the monomer by itself is considered to be a carbohydrate. A single saccharide can be called a carbohydrate. In fact, there is a whole group of carbohydrates that are made only of a single saccharide. They are called monosaccharides (mono = one).


Carbs

Carbohydrates, or “carbs” as they are sometimes referred to, include the sugar molecules dissolved in a bottle of soda as well as the starch molecules found in pasta and potatoes. Carbohydrates can be used by the body minutes after they are eaten, or they can be stored for use later. Although people involved in athletics seem more concerned with carbs than nonathletes, carbohydrates are an important source of energy for all of us, athlete or not.


Monosaccharides are made of carbon, oxygen, and hydrogen in a fixed ratio. The number of carbon atoms is equal to the number of oxygen atoms, and the number of hydrogen atoms is equal to twice the number of either carbon atoms or oxygen atoms. In other words, the Cs, Hs, and Os exist in a 1:2:1 ratio.


The generic chemical formula for a monosaccharide is

CnH2nOn


The two monosaccharides you need to know for the SAT Biology E/M Subject Test are glucose and fructose. Glucose and fructose have the same chemical formula: C6H12O6. So what is different about them?

Glucose and fructose differ in the arrangement of their atoms:

In the glucose molecule, the double-bonded oxygen is located on the top carbon. In the fructose molecule, it’s located on the second carbon from the top.


Glucose and Fructose: A Quick Review

•   Glucose and fructose are both carbohydrates.

•   Both are monosaccharides.

•   Both have the formula C6H12O6.

•   Glucose and fructose differ in the way the double-bonded oxygen is oriented within the molecule.


One last thing you should know about glucose is that it can also form a ring structure:

Disaccharides

Remember that many carbohydrates are polymers: strings of repeated units. So it makes sense, then, that monosaccharides would link together to form larger carbohydrates. If only two monosaccharides link together, the result is a carbohydrate made of two monomers: a disaccharide (di = two).

The disaccharides you need to know about for the SAT Biology E/M Subject Test are maltose and sucrose. Maltose is formed from two molecules of glucose. When the two molecules bond together, a molecule of water (H2O) is removed. This is dehydration synthesis, just like we saw for peptide bond formation. The chemical formula for maltose is not C12H24O12 (2 × glucose). Remember that two hydrogen atoms and one oxygen atom disappear, so the chemical formula for maltose is C12H22O11.

Sucrose is commonly known as table sugar. It is formed when a molecule of glucose combines with a molecule of fructose in a dehydration synthesis reaction.


The two disaccharides to know are maltose and sucrose.

glucose

+

glucose

water molecule

maltose

C6H12O6

+

C6H12O6

H2O

C12H22O11

glucose

+

fructose

water molecule

sucrose

C6H12O6

+

C6H12O6

H2O

C12H22O11


Polysaccharides

If the number of monosaccharides joined together exceeds two, the molecule is simply known as a polysaccharide (poly = many). There are three polysaccharides to know about for the SAT Biology E/M Subject Test: glycogen, starch, and cellulose. All three of these are polymers of glucose. In other words, they are formed from many, many, many molecules of glucose bonded together.

If glycogen, starch, and cellulose are all polymers of glucose, what’s the difference between them? The difference is in the way the glucose molecules are linked
together, and that’s almost all you have to know.

The other bit of information you need to know about these large polysaccharides is their function. Because they’re large chains of glucose, they act as a good storage form for glucose. We will see later that glucose is the primary form of cellular “food,” so it makes sense that organisms would want to store it. Different organisms store glucose in different forms:

•   Glycogen: the form in which animals (including the human animal) store glucose

•   Starch: the form in which plants store glucose

What about cellulose? Because of the way the glucose molecules are linked together in cellulose, cellulose is a much stronger, more rigid molecule. It is used for plant structures such as stems, leaves, and wood.

•   Cellulose: a structural polysaccharide that forms the plant’s cell walls

Quick Quiz #3

Fill in the blanks and check the appropriate boxes:

  1. Starch serves as a means of storing glucose in [  plants  animals ].

  2. A molecule of maltose is formed from two molecules of __________.

  3. Glucose and fructose [  are  are not ] identical molecules.

  4. A molecule of glucose and a molecule of fructose, both of which are _________________________, combine to form a molecule of ____________, which is a _______________________________.

  5. Cellulose is a _________________________.

  6. Glycogen serves as a means for storing glucose in [  plants  animals ].

  7. The chemical formula for both glucose and fructose is ___________.

  8. The chemical formula for sucrose is _________________________.

  9. Cellulose and glycogen differ in the way that ___________________molecules are bonded together.

10. The chemical formulas for sucrose and maltose [  are  are not ] identical.

Correct answers can be found in Chapter 15.

Biologically Important Macromolecule #3: Lipid

Lipids are fats—oils, butter, lard, and so on. The function of lipids are many: they function as energy storage compounds and components of cell membranes in addition to providing insulation and cushioning. The monomer for a lipid is a hydrocarbon. Simply put, this is just a carbon atom with two hydrogen atoms bonded to it.

Hydrocarbons can link together to form long chains:

The chains can vary in length and are usually between 12 and 24 carbons long. Hydrocarbon chains are very hydrophobic, meaning that they do not interact well with water. Consider what would happen if you put equal amounts of water and cooking oil in a glass and shook it up, then let it sit on the table. The oil and water would begin to separate, and after some time they would be found in separate layers in the glass. The oil (a lipid) is hydrophobic, and it does not want to interact with the water. Another term for hydrophobic is nonpolar. Lipids are also referred to as being nonpolar.

Like Water Off a…

Ever wonder why ducks
and geese survive so well
in wet environments? A
gland just above the tail
produces an oily
(hydrophobic) substance that
the bird spreads over
its outer layer of feathers.
This helps waterproof the
feathers and keeps the
thick down underneath
dry and warm. In a related
manner, humans keep
their skin from becoming
too dry by spreading moisturizers
on it … these
hydrophobic creams keep
water in the skin cells by
forming an oily barrier that
water cannot cross.

The three most common forms in which lipids are found in the body are as triglyceridesphospholipids, and cholesterol. Let’s take a look at each of these molecules.

Triglycerides

Triglycerides consist of three fatty acids (tri = three) bonded to a glycerol molecule (glyc = glycerol). A fatty acid is just a long hydrocarbon chain with a carboxyl group at one end. A glycerol molecule is an alcohol that has three carbon atoms in it.

Most of the fats you eat are in the form of triglycerides, and your body stores fats in the form of triglycerides.

Phospholipids

Phospholipids look very much like triglycerides, except that one of the fatty acid chains is replaced with a phosphate group (–PO32–).

The phosphate group is hydrophilic (can interact with water). Another word to describe it is polar.


Phospholipids are polar on one end (the phosphate end) and nonpolar on the other (the fatty acid end).


A common way to represent phospholipids is something like the figure on the next page.

When phospholipids interact with one another, they align themselves so that their polar phosphate head groups stay together and their nonpolar fatty acid tails stay together:

Often they form a double layer:

This double layer of phospholipids is known as a lipid bilayer. Lipid bilayers form cell membranes. We’ll talk more about cell membranes a little later on.

Cholesterol

Cholesterol is a unique lipid. It is not made of long hydrocarbon chains; instead, the hydrocarbons form rings. Cholesterol is found only in animal cells, in cell membranes along with phospholipids. Additionally, all the steroid hormones in the body (for example, estrogen, testosterone, and progesterone) are derived from cholesterol.


Cholesterol

Cholesterol is probably best known because of its negative reputation. Cholesterol is most infamous for its association with cardiovascular diseases. You may have heard about “good” cholesterol and “bad” cholesterol. “Good cholesterol” is HDL, or a high density lipoprotein. “Bad cholesterol” is LDL, or a low density lipoprotein. Most doctors will recommend that people have an LDL level in their blood of <100 mg/dL, or even considerably less than that for people with a history of heart problems.

Cholesterol does have positive functions. Your body needs cholesterol to build and maintain cell membranes and to produce steroid hormones such as estrogen, testosterone, and progesterone. Cholesterol is found in the body tissues and blood of all animals.


Quick Quiz #4

Fill in the blanks and check the appropriate boxes:

  1. Triglycerides are made of one molecule of _____________________and three _________________________.

  2. Lipids in general are [  hydrophilic  hydrophobic ].

  3. The primary lipid found in cell membranes is __________________.

  4. Steroid hormones are derived from _________________________.

  5. Steroid hormones [  are  are not ] hydrophobic.

  6. Fats are stored in the body in the form of _____________________.

Correct answers can be found in Chapter 15.

Biologically Important Macromolecule #4: Nucleic Acid

Nucleic acids are acidic macromolecules (“acids”) typically found in the nucleus of the cell (“nucleic”). Specifically, they are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). The monomer of a nucleic acid is a nucleotide, so nucleic acids are sometimes referred to aspolynucleotides. A nucleotide is made up of a sugar, a phosphate, and a base:

Let’s consider the structure of DNA first. RNA is very similar to DNA, so once you understand how DNA is constructed, it will be easy to understand how RNA is constructed.

The “base” in the figure above can be replaced by one of four different chemicals referred to as nucleotide bases.


The four possible nucleotide bases for DNA are

Adenine   Guanine   Cytosine   Thymine


Because there are four types of DNA bases, there are really four types of DNA nucleotides:

Notice that the sugar and the phosphate are constant from nucleotide to nucleotide. The sugar and the phosphate are known as the backbone of the nucleotide.

When nucleotides bond to form a long chain (a polynucleotide), the chain is a strand of DNA. Because the four types of nucleotides can bond in any order, many different strands of DNA can be made. Here’s an example of three possible strands:

Each is a strand of DNA, and each is a polymer of nucleotides, but each strand differs from the others because of the order in which the nucleotides are
bonded together.

DNA Is Double-Stranded

As you may already know, DNA is a double-stranded molecule. Two strands of DNA pair up to form a ladder like structure that twists on itself. This double spiral of DNA strands is known as a double helix. The double helix was first discovered in 1956 by two scientists named James Watson and Francis Crick. (They were assisted by the work of Maurice Wilkins and Rosalind Franklin) Here’s how the double helix is formed:

1.   Two strands of DNA line up next to each other.

2.   The sugar-phosphate portions of the two nucleotide chains form the sides of the ladder.

3.   The bases bond to each other and form the rungs of the ladder.

4.   The ladder twists into a spiral to form the double helix.


Rosalind Franklin

James Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize for discovering the double-helix structure of DNA molecules. However, they were assisted by the pioneering work of Rosalind Franklin. She learned X-ray diffraction techniques while working in Paris as a physical chemist. In 1952 she produced X-ray photographs of DNA strands, which showed the “twisted ladder” structure. Watson and Crick used these photographs when they published their model of the structure of DNA.


Below is a drawing of the DNA ladder before it twists into the double helix.

Nucleotide Base Pairing

There is one very important thing you should know about the rungs of the ladder: The bases that form the rungs bond to each other very specifically.


•   Adenine and thymine will bond only with each other.

•   Cytosine and guanine will bond only with each other.


Sometimes the bonding of a nucleotide base with its partner is referred to as forming a base pair or, simply, base pairing.


Base Pair Memory Trick

Here’s a mnemonic device to help you remember how bases pair up. Write down the bases in alphabetical order:

Adenine   Cytosine   Guanine   Thymine

Then remember that

•   the two bases on the ends form a base pair (bond) with each other

•   the two bases in the middle form a base pair (bond) with each other


Two strands of DNA that can form base pairs with each other at each nucleotide are said to be complementary. So the two strands of a double helix are complementary. Each nucleotide base on one strand is bonded to its partner on the other strand.

A common question on the SAT Biology E/M Subject Test involves choosing the correct complementary strand if you’re given a sequence of nucleotide bases. It’s not a difficult question as long as you remember the base pairing rules. Look at the following example:

       If a particular base sequence in DNA is Adenine-Guanine-Cytosine, then the complementary strand has the base sequence

(A)  Cytosine-Adenine-Guanine

(B)  Thymine-Adenine-Guanine

(C)  Cytosine-Thymine-Adenine

(D)  Thymine-Cytosine-Guanine

(E)  Guanine-Adenine-Thymine

Following the base pairing rules (adenine pairs with thymine, and guanine pairs with cytosine), we quickly see that choice D presents the correct order of bases in the complementary strand.

There is one last thing to remember about DNA base pairing: the number of bonds that hold each pair together. The type of bond that holds the base pairs together is a hydrogen bond. Look back at the figure of the “untwisted” ladder. Notice that the A-T base pair is held together by two hydrogen bonds, while the G-C base pair is held together by three hydrogen bonds. What this means is that G-C base pairs are stronger than A-T base pairs. Thus, a DNA double helix that contains many G-C base pairs will be more stable (stronger) than a DNA double helix that contains many A-T base pairs.

RNA

RNA is a polymer of nucleotides that’s similar to DNA. The biggest difference between RNA and DNA is that RNA is a single-stranded molecule whereas DNA is double-stranded (a double helix). Another difference is that RNA does not use thymine as a nucleotide base; instead, it uses a base called uracil. Uracil can form a base pair with adenine in RNA, just like thymine does in DNA (RNA can fold on itself to form base pairs). Below is a summary of the differences between RNA and DNA.

The fact that RNA is single-stranded allows it to assume various unique shapes. There is no second strand to lock it into a double-helix shape. It can form base pairs with itself, and this allows it to fold up into many different three-dimensional shapes. We’ll talk more about RNA later on when we discuss protein synthesis in more detail.

Quick Quiz #5

Fill in the blanks and check the appropriate boxes:

  1. The fact that double-stranded DNA forms a double helix was discovered by __________________ and __________________.

  2. The four DNA nucleotide bases are ______________________, ______________________, _______________________, and
_______________________.

  3. RNA [  is  is not ] a double-stranded molecule.

  4. RNA nucleotides [  do  do not ] contain the exact same bases as DNA nucleotides.

  5. In DNA, guanine forms a base pair with ______________________, whereas adenine forms a base pair with _______________________.

  6. The nucleic acid “backbone” is made up of ____________________and _________________________.

  7. The sugar in DNA is [  ribose  deoxyribose ].

  8. In RNA, adenine can form a base pair with ____________________.

Correct answers can be found in Chapter 15.

Key Words

atoms

molecules

compound

element

reactants

products

organic

inorganic

biomolecules

polymers

monomers

amino acids

amino group

double bond

carboxyl group

protein

peptide bond

dehydration synthesis

polypeptide

hydrolysis

saccharide

monosaccharides

glucose

fructose

disaccharide

maltose

sucrose

polysaccharide

glycogen

starch

cellulose

hydrocarbon

hydrophobic

nonpolar

triglycerides

phospholipids

cholesterol

hydrophilic

polar

lipid bilayer

deoxyribonucleic acid (DNA)

ribonucleic acid (RNA)

nucleotide

polynucleotides

adenine

guanine

cytosine

thymine

double helix

base pairing

complementary

hydrogen bond

uracil

Summary

•   Atoms are the fundamental units of the physical world and combine in chemical reactions to form molecules.

•   An element is any substance that cannot be broken into simpler substances.

•   If two or more elements are combined, they form a compound.

•   The four biologically important macromolecules are proteins, carbohydrates, lipids, and nucleic acids.

•   Proteins are polymers of amino acids. Each of the 20 amino acids has a basic backbone structure with one different R-group.

•   Carbohydrates are made of only carbon, oxygen, and hydrogen. Common carbohydrates include monosaccharides (like glucose and fructose), disaccharides (like sucrose and maltose), and polysaccharides (like glycogen, starch, and cellulose).

•   Lipids are composed of hydrocarbons linked to each other. A hydrocarbon is a carbon atom with two hydrogen atoms bonded to it.

•   The most common forms of lipids are triglycerides, phospholipids, and cholesterol.

•   Nucleic acids are biologically important macromolecules that are found in the nucleus of every cell.

•   DNA and RNA are the nucleic acids that make life possible.