Kelter P., Mosher M., Scott A. Chemistry. The Practical Science

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EXERCISE 22.1 What Exactly Is DNA?

You will very often read and hear the term molecules of DNA. Scientists use the

phrase routinely, and “DNA molecules” have become such a hot news story that

they are referred to regularly in general magazines and newspapers and on TV. But

when we closely examine the structure of DNA as we will do in this chapter,

we will see that the phrase a molecule of DNA is not strictly accurate. Why not?

Solution

Several factors introduce complications here. First of all, the negative charges on the

phosphate groups mean that DNA, in the form in which it exists in living things, is

a multi-charged ion, not a molecule at all. If hydrogen ions combined with all these

negative charges, it would become a molecule, but this is not the structure we ob-

serve in living things. Second, when people speak of “DNA molecules”they are often

referring to double-helical DNA, rather than to the single-stranded form. The DNA

double helix is held together by largely noncovalent forces from hydrogen bonds, so

it is really a complex formed from two intertwined molecules (or multi-charged

ions). It cannot properly be described as a molecule at all.

PRACTICE 22.1

Suppose that a new base, shown in the margin, was discovered by scientists. To

which of the four nitrogenous organic bases would this new base be most likely

to form a stable base pair?

See Problems 3 and 4.

DNA Replication—The Secret of Reproduction

One of the most important characteristics of living creatures (animal or plant) is

that they make more of themselves. In other words, they “reproduce.” Reproduc-

tion in this sense depends on the ability of double-helical DNA to copy itself or

“replicate.”

Because the bases form complementary pairs in a double strand of DNA, the

sequence of nucleotide bases in one strand can be readily determined by examin-

ing the other strand of DNA. In other words, the A on one strand is paired with a

T on the other, each T with an A, each G with a C, and each C with a G. This

means that within a reproducing cell, the double helix can unravel and separate

into individual strands. Then, each strand can serve as the template on which a new

complementary strand assembles, as shown in Figure 22.9. The chemical reactions

involved in this DNA

replication are catalyzed by molecules within the cell known

as enzymes. However, the structure of the existing DNA strands determines the

sequence of the new DNA strands. Nucleotides carrying the appropriate bases are

the only ones that can bind to the existing strand in a manner that allows the en-

zymes to link them up into a new DNA strand. The result of this process is two

identical strands of DNA, one for the original cell and one for the new cell when

it is formed.

EXERCISE 22.2 Using the Template

If the DNA strand shown below serves as the template strand during DNA replica-

tion, what will be the sequence of the new double-helical DNA that results?

AATTGCGGGTCCGACC

938 Chapter 22 The Chemistry of Life

A new base for DNA.

A T

Parent strands

Complementary

new strand

Complementary

new strand

FIGURE 22.9

Single-stranded DNA can serve as a tem-

plate for the creation of a new strand.

22.1 DNA—The Basic Structure

939

Solution

Remember the rules of base-pairing. Only two types of base pairs are allowed:

AT and GC (either way round), so the double-helical DNA will have the following

sequence:

AATTGCGGGTCCGACC

TTAACGCCCAGGCTGG

PRACTICE 22.2

A small piece of one of the strands of DNA is added to a single strand of DNA.

Indicate the correct alignment of the small piece with the long strand.

. . . AAAATGCTGGCATAGCGTTCCAGATACGGACTGACTGC . . .

CTATGC

See Problems 5 and 6.

DNA is located inside cells within a structure known as the nucleus. It is a

beautiful chemical structure with the ability to act as a template on which new

copies of itself are formed.

But what makes DNA so important to life? The answer

is that it carries coded information within its base sequence—information that

can be decoded to specify which molecules are made in a cell. These molecules,

known as

proteins, then perform most of the chemical activities that actually sus-

tain life.

22.2 Proteins

Proteins are polymers that are formed when molecules called amino acids un-

dergo condensation reactions. The amine on one amino acid forms an

amide

bond

with the carboxylic acid on another amino acid. This process is repeated

many times as the protein is formed. Some of the important amino acids found

in living cells are shown in Figure 22.10. Note that all these amino acids contain

very similar arrangements of the carboxylic acid and amine functional groups.

The difference between them can be found in the group of atoms attached to the

same carbon as the amine. The amino acids are often referred to as

residues be-

cause they are what remains after the protein is broken up into its individual

amino acids. Twenty different residues are common within your body, and each

has been given a speciﬁc name.

940 Chapter 22 The Chemistry of Life

The amide bond

FIGURE 22.10

Twenty common

amino acids. The

names of the

amino acids are

also shown with

their three-letter

abbreviation and

one-letter code.

Alanine

(Ala, A)

N CH

OHC

Arginine

(Arg, R)

N CH

OHC

Lysine

(Lys, K)

N CH

OHC

Methionine

(Met, M)

N CH

OHC

Isoleucine

(Ile, I)

N CH

CH CH

OHC

Leucine

(Leu, L)

N CH

OHC

Serine

(Ser, S)

N CH

OHC

Threonine

(Thr, T)

N CH

Valine

(Val, V)

N CH

Tryptophan

(Trp, W)

N CH

OHC

Asparagine

(Asn, N)

N CH

OHC

Aspartic acid

(Asp, D)

N CH

OHC

Glutamic acid

(Glu, E)

N CH

OHC

Glutamine

(Gln, Q)

N CH

OHC

Glycine

(Gly, G)

N CH

OHC

Histidine

(His, H)

N CH

OHC

Cysteine

(Cys, C)

N CH

OHC

Phenylalanine

(Phe, F)

N CH

OHC

Proline

(Pro, P)

OHC

Tyrosine

(Tyr, Y)

N CH

OHC

Video Lesson: Proteins

Proteins are made in living cells by the sequential addition of amino acids to

a lengthening

polypeptide chain. This sequence of the protein constitutes the ﬁrst

level of structure of the protein. As indicated in Figure 22.11, it is often called the

primary structure of the protein. Just like every individual person, each type of

protein within a living cell is unique thanks to its amino acid sequence. The se-

quence of the amino acids determines the resulting shape of the protein and the

resulting function of the protein.

We can now appreciate that both DNA and proteins are chemicals whose

structure is determined by the sequence in which monomer units are bonded into

polymers. Each DNA polymer has a unique base sequence (also know as its nu-

cleotide sequence). Each protein has a unique amino acid sequence. The key to

understanding how DNA can specify which proteins a living thing contains is to

understand how the base sequence of DNA can specify the amino acid sequence of a

protein. This is achieved by the operation of a simple chemical code.

22.3 How Genes Code for Proteins

A gene is a section of DNA that encodes a speciﬁc protein molecule.

This means that the base sequence of the gene determines the amino

acid sequence of the resulting protein. The whole process of convert-

ing the genetic code into a particular protein is known as gene expres-

sion, which occurs in two distinct phases:

transcription, in which an

RNA copy of the gene is made, and

translation, in which the RNA copy

directs production of the protein.

What is RNA?

Ribonucleic acid (RNA) is a substance that bears a

close resemblance to DNA. In fact, there are only two main differences

between DNA and RNA (see Figure 22.12). The sugar in RNA is ribose,

which carries one more oxygen atom than the deoxyribose found in

22.3 How Genes Code for Proteins 941

FIGURE 22.11

Primary structure of a protein. The

primary structure is the order of the

amino acid monomers in the strand of

the protein.

N CCN

Amino-terminal

residue

Primary structure of protein

Carboxyl-terminal

residue

NCC

–

N O

Phosphate

Ribose sugar

Nitrogenous organic base

Nucleoside

Nucleotide

–

HC C

The basic components of the monomers that

make up RNA.

DNA

RNA

FIGURE 22.12

The difference between DNA and RNA

lies in the ribose sugar.

Hydrogen bonds

Adenosine

942 Chapter 22 The Chemistry of Life

DNA. Also, in RNA the nitrogenous base uracil, shown in Figure 22.13, is found

in place of the thymine of DNA. Uracil can participate in an A–U base pair as

shown in Figure 22.14, in the same way that thymine can participate in an A–T

base pair. The result is that RNA can form base pairs with a complementary

strand of DNA.

Transcription—Making the Message

The process of gene transcription occurs in a very similar way to DNA replica-

tion. Inside the nucleus of the cell, the DNA unwinds into the individual strands

of DNA, and a new, complementary strand of RNA is made. The complementary

strand is manufactured using enzymes via condensation reactions in much the

same manner as in the manufacture of DNA. The single-stranded RNA copy of a

gene that is produced in transcription is known as

messenger RNA (mRNA). This

copy carries the genetic “message” from the nucleus to the ribosomes (see below)

in the cytoplasm, where the message is used (decoded) to make protein. mRNA

gets its name from the fact that it takes the message held within the genes to the

site of protein synthesis, as illustrated in Figure 22.15.

FIGURE 22.15

mRNA is made in the nucleus and then

transferred to the cytoplasm for protein

synthesis.

Transcription

Nucleus

DNA

mRNA

Cytoplasm

Uridine

FIGURE 22.14

An A–U base pair. Note that the hydrogen bond-

ing is similar to that found in an A–T base pair.

Uracil and adenine attached to a ribose sugar

unit (without a phosphate) are known as uri-

dine and adenosine, respectively.

FIGURE 22.13

The different monomer used in RNA,

shown here without the attached phos-

phate group, is similar in structure to

thymidine.

22.3 How Genes Code for Proteins 943

Translation—Making Proteins

Once at the site of protein synthesis, the mRNA is read by another class of RNA

molecules known as

transfer RNA (tRNA). Each tRNA molecule includes a set of

three nitrogenous bases that can form base pairs with three sequential bases of

mRNA. Each set of three sequential bases within the mRNA is known as a

codon.

The codon binds to the complemetary

anticodon on the tRNA. What is the pur-

pose of the tRNA? Each tRNA also carries a speciﬁc amino acid at its amino acyl

binding site. When the tRNA anticodon binds to the codon on the mRNA, the

amino acid on that tRNA becomes incorporated into the growing protein chain.

If the anticodon and codon are not complementary, the tRNA leaves without

donating its amino acid to the protein. The code, indicating the relationship

between each speciﬁc codon and amino acid is called the genetic code and is

summarized in Table 22.1. The entire process of translation is outlined in

Figure 22.16.

The mRNA contains a special“start” sequence that identiﬁes the beginning of

a protein. In fact, every protein that is made begins with the amino acid methion-

ine. From that point onward, the amino acids are identiﬁed by each codon until

the ﬁnal “stop” codon is reached. Sometimes all of the mRNA is translated into a

protein.Some genes make an mRNA that contains a lot of extraneous nucleotides.

The Genetic Code

The three-letter codes listed are mRNA codons. For example, AAA is the mRNA codon for the amino acid lysine.

Second letter

TABLE 22.1

First letter

Third letter

Phenyl-

alanine

Leucine

Isoleucine

Methionine,

initiation

codon

Valine

UCU

UCC

UCA

UCG

CCU

CCC

CCA

CCG

ACU

ACC

ACA

ACG

GCU

GCC

GCA

GCG

Serine

Proline

Threonine

Alanine

Tyrosine

Stop codon

Histidine

Glutamine

Asparagine

Lysine

Aspartic acid

Glutamic

acid

Cysteine

Stop codon

Tryptophan

Arginine

Serine

Arginine

Glycine

Not all of the mRNA is used to

create a protein.

Mature mRNA

“Stop”

signal

UGU

UGC

UGA

UGG

CGU

CGC

CGA

CGG

AGU

AGC

AGA

AGG

GGU

GGC

GGA

GGG

UAU

UAC

UAA

UAG

CAU

CAC

CAA

CAG

AAU

AAC

AAA

AAG

GAU

GAC

GAA

GAG

UUU

UUC

UUA

UUG

CUU

CUC

CUA

CUG

AUU

AUC

AUA

AUG

GUU

GUC

GUA

GUG

944 Chapter 22 The Chemistry of Life

FIGURE 22.16

The overall process of translation.

Nucleus

DNA

mRNA

Ribosome aligns tRNA

with mRNA and constructs

the protein

Ribosome

Protein

tRNA brings

amino acids

to ribosome

Amino

acids

tRNA

Cytoplasm

To hold the molecules close together and to assist in catalyzing the process of

adding amino acids into the protein, the process of translation takes place on

giant assemblies of protein and RNA known as

ribosomes (see Figure 22.17). As

the ribosome moves along an mRNA molecule, the appropriate tRNAs are able to

bind to special sites on the ribosome, allowing enzymes to link the amino acids

they carry into a new protein chain. The end result is the translation of the base

sequence of the gene (via the mRNA) into the amino acid sequence of the protein.

EXERCISE 22.3 Examining the Genetic Code

Examine the genetic code shown in Table 22.1. Do all codons encode amino acids?

Does each codon specify a unique amino acid?

First Thoughts

Because there are four different bases and three positions, we can ﬁgure out the pos-

sible number of arrangements of these bases into the three positions.

FIGURE 22.17

The ribosome slides along the mRNA.

tRNAs then bring speciﬁc amino acids to

the ribosome and allow the protein chain

to be constructed. In this ﬁgure, the

amino acids (aa) and the tRNAs are num-

bered to indicate their position.

Movement

of ribosome

Growing

polypeptide chain

tRNA

Ribosome

tRNA

leaving

– tRNA

arriving

Codon

mRNA

CCG GUA

GGGGGCCCCCCAAAAAAUUUUUUU

GUA

Solution

There are 64 possible codons—different ways to arrange the four bases into sets of

three. There are only about 20 amino acids found in proteins, so there must be more

codons available than amino acids. Examining the genetic code reveals that each

amino acid can be encoded by several alternative codons. It also reveals that three

codons act as “stop” signals, indicating the point at which the synthesis of a protein

chain should end.

Further Insights

Damage to DNA can result in changes to the genetic code. For example, a speciﬁc

base within a codon could be changed as a result of the damage. Some of these

changes have no effect on the protein encoded by the DNA, because they change a

codon into one of the other codons specifying the same amino acid. Other such

changes cause a different amino acid to appear in the encoded protein. This can

cause problems with the resulting protein that is made using the mutant codon.

PRACTICE 22.3

What is the primary structure of a protein made using the following mRNA

sequence?

AUGUGGCCAAAAUUGGACAUGUUCGACUAG

See Problems 15 and 16.

The human genome contains between about 20,000 and 30,000 genes. These

genes are able to encode an even greater number of proteins, because the RNAs

that are originally made from the genes can be edited to make many different

proteins in a kind of enzymic “cut-and-paste” process. The way in which genes

encode proteins is an astonishing demonstration of the power of chemistry to

sustain the complex processes that underpin all life. To understand more fully

just how powerfully genes inﬂuence the chemistry of life, we need to look at the

proteins encoded by our genes and investigate the things these proteins can do.

Protein Folding

As soon as a protein chain begins to be formed, it

starts to fold into a speciﬁc three-dimensional con-

formation. The folding process is governed princi-

pally by noncovalent interactions among the amino

acids themselves, and also among the amino acids

and the water molecules surrounding the protein.

Localized regions within a polypeptide chain that

fold in a particular way are examples of a protein’s

secondary structure. The most signiﬁcant secondary

structures are the alpha helix ( helix) and the beta

pleated sheet ( sheet), shown in Figure 22.18. The 

helix forms as a consequence of hydrogen bonds

between the NOH and CPO groups of the

polypeptide chain, holding the chain in the form of

a helix. The  sheet is also held together by hydro-

gen bonds between NOH and CPO groups, but

with the hydrogen bonding occurring between

neighboring portions of a polypeptide chain.

Regions of speciﬁc secondary structure are linked

by turns in the polypeptide chain, and by less ordered

structures, to form the overall three-dimensional

22.3 How Genes Code for Proteins 945

FIGURE 22.18

Two common types of secondary struc-

tures: the alpha helix and the beta sheet.

These structures are held together by hy-

drogen bonding (shown as dotted lines).

Hydrogen

bonds

Alpha helix

Beta sheet

conformation of a protein. The folding of the secondary structures

into a three-dimensional conformation is known as the protein’s

ter-

tiary structure

. Just as is true of  helices and  sheets, there are many

common tertiary structures. Some of these are shown in Figure 22.19.

However, many proteins have what can loosely be described as a

“globular” tertiary structure; see the example shown in Figure 22.20.

This is the general three-dimensional shape found for most of the

proteins that act as enzymes.Other proteins have linear tertiary struc-

tures, largely composed of one or more extended helices or sheets.

Many such proteins form strong ﬁbers that contain several protein

molecules intertwined. For example, the protein

collagen, shown in

Figure 22.21, gives strength to connective tissues such as tendons, lig-

aments, and bones. The structural strength of collagen is a result of

three helical proteins wound around one another to form a triple

helix.

When several polypeptide chains are held together by forces of

attraction, as in collagen, we say that a protein with

quaternary structure has been

formed. Many globular proteins also possess quaternary structure. For example,

hemoglobin, the protein that carries oxygen to your muscles, is made of four

polypeptide chains that have folded around each other as shown in Figure 22.22.

Not all proteins have quaternary structure. For example, myoglobin, the oxygen

storage protein that resides in your muscles, consists of only a single polypeptide

chain. The precisely folded structure of proteins can be disrupted, or

denatured,

by heat or by variations in the chemical surroundings, including changes in pH

and in the concentration of salt ions. Denaturation reduces or destroys a protein’s

biochemical activity, depending on how severe it is. This explains, for example,

why the protein albumin in an egg comes out of solution and turns white upon

heating.

946 Chapter 22 The Chemistry of Life

FIGURE 22.19

Some common tertiary structures. These structures are held in place by intermolecular forces of

attraction such as London forces, dipole–dipole interactions, and hydrogen bonding.

Helix-turn-helix Beta-alpha-beta Hairpin Greek key

Collagen

FIGURE 22.21

Collagen is a ﬁbrous protein.

FIGURE 22.20

Lactate dehydrogenase is a globular enzyme

involved in the biochemical process of harvesting

energy from sugars.

22.4 Enzymes 947

FIGURE 22.22

Hemoglobin. There are four subunits, each with its own

iron-containing heme, that come together to form hemo-

globin. The subunits are held together to form the quater-

nary structure of the protein.

Subunit B

Heme groups

Subunit A

Subunit D

Subunit C

Myoglobin. The green ribbons represent the

backbone of the chain of amino acids. Note

the curled structures in the ribbons. They

illustrate the alpha helix secondary structure

in this protein.

HERE’S WHAT WE KNOW SO FAR

■

DNA is a polymer of nucleotides made from two complementary single

strands wrapped around each other to form a double helix.

■

Proteins are polymers of amino acids linked through an amide bond. They

contain primary, secondary, tertiary, and sometimes quaternary structure.

■

Proteins are made by translating the genetic code from mRNA. tRNA supplies

the speciﬁc amino acids to the growing polypeptide chain. The construction

occurs at the ribosomes within the cytoplasm of a cell.

■

Primary structure is the sequence of amino acids that make up the protein.

■

Secondary structures are the speciﬁc regions of a polypeptide chain that fold

into an  helix or a  sheet.

■

Tertiary structures result from folding of the secondary structures within a

polypeptide chain into a three-dimensional shape. They can be globular or

linear in arrangement.

■

Quaternary structure results when two or more polypeptide chains are folded

into a speciﬁc shape. Not all proteins have quaternary structure.

22.4 Enzymes

The covalent bond that links glucose and fructose together in a molecule of su-

crose can be hydrolyzed by water, although the reaction is quite slow. In the lab-

oratory, we can speed the reaction by adding a little acid to an aqueous solution

of sucrose. The reaction can be monitored and the rate of the catalyzed reaction

measured.

Why is this reaction important? In the body, much of the “fuel” that we

ingest is sucrose. This sugar is broken down into its components, glucose and

fructose. As we noted in Chapter 14, both of the sugars are metabolized to pro-

vide energy to operate other biological processes and sustain life. Because these

molecules are vital to our existence, any reaction that makes them, or metabolizes

them, needs to be very rapid. Therefore, almost every chemical reaction within