1

chapter 1 Biomolecules

BIOMOLECULESChapter

1

Organic molecules are carbon containing molecules and are central to living systems.

Proteins, carbohydrates, lipids, and nucleic acids are four key groups of biological

macromolecules. Condensation and hydrolysis reactions are important in building and

breaking apart biological molecules. The molecular structure of these biological macro-

molecules and their building blocks determine their ability to interact with water mole-

cule, that is essential to life. Depending on their hydrophobicity and hydrophilicity, biolog-

ical macromolecules show functional diversity, and play different roles in living systems.

CHAPTER OUTLINE

LEARNING OBJECTIVES• Understand that the polar nature of water and

its physical and chemical properties are crucial

in biological systems.

• Identify, describe and draw the molecular

structure of proteins, carbohydrates, lipids,

and nucleic acids.

• Distinguish between monomers and polymers.

• Describe the synthesis of macromolecules

by condensation and their breakdown

by hydrolysis.

• Identify the bonds formed or broken in each

case.

• Understand and explain the structure and

functional diversity of biomolecules.

Astrobiology studies the origins, evolution and

distribution of life in the universe; the central goal

of this new science is to find evidence of past or

present life beyond Earth, if it ever existed. For

decades NASA and ESA have sent orbiters, landers

and rovers on Mars to increase their knowledge

of the Red Planet and to search for specific

biomolecules that would be conclusive evidence

of life. The link between space exploration and

astrobiology was first highlighted by the American

molecular biologist Joshua Lederberg, who, even

before the official foundation of NASA, was

studying the possibilities of finding life beyond

Earth. In 1958 (the year in which NASA was

founded), Lederberg, aged 33, won the Nobel

Prize for discoveries about bacterial genetics.

2

Amino Acids and Proteins

Unit

1Keywords:

• Protein

• Amino acid

• Zwitterion

• Isoelectric point

• Disulfide bridge

• Peptide linkage

In this unit you will

• Learn about amino acids

• Discuss the chemical structure

and properties of amino acids

• Find out how amino acids bind

together to build proteins

• Discover terms, verbs and

expressions related to this topic

PAIR WORK

A. Define the chemical bonds (ionic and covalent), and describe the factors that favor their formation. Provide an example for each of them, and write their Lewis symbols. Compare and discuss your answers with your classmate.

Ionic Bond Lewis symbol

Definition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Covalent Bond Lewis symbol

Definition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

PAIR WORK

B. The diagram shows the structural formula of the water molecule. Indicate its polarity, and explain the importance of its dipole nature in the chemistry of life. Compare and discuss your answers with your classmate.

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

PAIR WORK

C. Provide the definition of acid and base and write the reactions of an acid and a base in water. Compare and discuss your answers with your classmate.

Acid (definition)

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Acid + Water

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Base (definition)

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Base + Water

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

WARM UP

Interleukin 23 protein molecule.

3

chapter 1 Biomolecules

Figure 1 The Structure of an Amino Acid All amino acids have the same basic structure.

READING AND LISTENING

Amino Acids and Proteins

Introduction

Proteins are large, complex molecules that consist of over 100 amino acid residues

joined by peptide bonds.

Depending on their chemical composition, proteins are defined as:

• Simple proteins: they contain only amino acids and no other chemical groups.

• Conjugated proteins: they function in interaction with other chemical groups

attached by covalent bonding or weak interactions, such as lipids (lipoproteins),

oligosaccharide chains (glycoproteins), and nucleic acids, either DNA or RNA

(nucleoproteins).

Proteins play many critical roles in the body, and they do most of the work in cells and are

required for the structure, function, and regulation of the body’s tissues and organs. Pro-

teins are classified by their biological function (see Table 1).

Proteins and Their Functions

Category Function

Enzymes Catalyze (speed up) biochemical reactions

Structural proteins Provide physical stability and movement

Defensive proteins Recognize and respond to nonself substances (e.g., antibodies)

Signaling proteins Control physiological processes (e.g., hormones)

Receptor proteins Receive and respond to chemical signals

Membrane transporters Regulate passage of substances across cellular membranes

Storage proteins Store amino acids for later use

Transport proteins Bind and carry substances within the organism

Gene regulatory proteins Determine the rate of expression of a gene

All proteins are polymers made up of 20 amino acids in different proportions and sequenc-

es. Proteins range in size from small ones such as insulin, which has 51 amino acids and a

molecular weight of 5733 Daltons (Da), to huge molecules such as the muscle protein titin,

with 26926 amino acids and a molecular weight of 2993451 Da. Proteins consist of one or

more polypeptide chains — unbranched (linear) polymers of covalently linked amino ac-

ids. Variation in the sequences of amino acids in the polypeptide chains allows for the vast

diversity in protein structure and function. Each chain folds into a particular three-dimen-

sional shape specified by the sequence of amino acids present in the chain.

The Structure of Amino AcidsEach amino acid has both a carboxyl functional group and an amino functional group

(Figure 1) attached to the same carbon atom, called the a (alpha) carbon. Also, attached to

the a carbon atom, are a hydrogen atom and a side chain, or R group, designated by the

letter R.

TABLE 1

Read the text and listen to Track 1.

LANGUAGE FOCUS

range in size from … to … (V)

vary in size from ... to ...

stretch from … to…

allows for (V)

enables something to happen

consents

attached to (V)

joined, connected to something

(not to be confused with... to attack (V)

to damage: rust attacks metals)

Side chain

α carbon

Aminogroup

Carboxylgroup

C COO–H3N+

H

R

α C

R

COO–H3N+

H

4

The a carbon is asymmetrical because it is bonded to four different atoms or groups of at-

oms. Therefore, amino acids can exist as optical isomers called D-amino acids and L-amino

acids. D and L are abbreviations of the Latin terms for right (dextro) and left (levo). Only

L-amino acids (with the configuration shown in Figure 1) are commonly found in the pro-

teins of most organisms, and their presence is an important chemical “signature” of life. At

the pH levels typically found in cells (usually about pH 7), both the carboxyl and amino

groups of amino acids are ionized, forming a dipolar ion or zwitterion:

the carboxyl group has lost a hydrogen ion:

—COOH —COO– + H+

and the amino group has gained a hydrogen ion:

—NH2 + H+ —NH3+

Thus, amino acids show amphoteric behaviour (from the Greek word amphoteroi, which

means both), i.e. amino acids can react both as an acid as well as a base. If you increase the

pH of a solution of an amino acid by adding hydroxide ions, the hydrogen ion is removed

from the -NH3+ group:

If you decrease the pH by adding an acid to a solution of an amino acid, the -COO- part of

the zwitterion picks up a hydrogen ion.

The isoelectric point is the pH at which the amino acid has a net charge of zero, i.e. the

zwitterion form is dominant. At pH values below the pI, the amino acid carries a net posi-

tive charge; above the pI, it carries a net negative charge.

H2N H

2O+C

COO–

R

HH3N+ OH–+C

COO–

R

H

H3N+ H

2O+C

COOH

R

HH3N+ H

3O++C

COO–

R

H

H3N+

H3O+

C

COOH

CH3

H H3N+

OH–

C

COO–

CH3

H H2N C

COO–

CH3

H

Isoelectric Point

Low pH High pH

LANGUAGE FOCUS

it is bonded to (V)

it is held together by a chemical bond

Every amino acid has a different isoelectric point: fifteen of the twenty amino acids have

isoelectric points in the range of 4.8-6.3. The lowest isoelectric point is 3.0 (aspartic acid)

and the highest is 10.8 (arginine).

5

chapter 1 Biomolecules

The Twenty Amino AcidsTABLE 2

The side chains (or R groups) of amino acids contain functional groups that are important

in determining the three-dimensional structure and thus the function of the protein. As

Table 2 shows, the 20 amino acids found in living organisms are grouped and distinguished

by their side chains:

• Five amino acids have electrically charged (ionized) side chains at pH levels typical of

living cells. These side chains attract water (are hydrophilic) and attract oppositely

charged ions of all sorts.

• Five amino acids have polar side chains. They are also hydrophilic and attract other

polar or charged molecules.

• Seven amino acids have side chains that are nonpolar and thus hydrophobic. In the

watery environment of the cell, these hydrophobic groups may cluster together in the

interior of the protein.

• Three amino acids — cysteine, glycine, and proline — are special cases, although the

side chains of the latter two are generally hydrophobic.

C C

C C C

CCCCCCC

C C C C C

Amino acids have

both three-letter

and single-letter

abbreviations.

The general

structure of all

amino acids is

the same…

…but each

has a different

side chain.

H2N+

CH2

CH2

H2CCH2

H3N+

C

CH2

CH3

H3N+

H3C CH3

CH

H3N+

CH2

H3N+

H3N+

CH2OH H

H3N+

H3N+

CH2

COO–

CH2

COO–

CH2

O

C

H2N

OH2N

CH2

H3N+

CH3

CH

H3N+

H3C

H3N+

CH2

CH2

S

CH3

H3N+

H3N+

C

CH2

CH2

CH

H3N+

CH2

OH

HC

NH

NH

CH2

CH2

CH2

+NH3

H3N+

CH2

CH2

CH2

NH

C

NH2

NH2

+

H3N+

H3N+

CH3

CH2

SH

H C OH

H3N+

CH2

CH3

CH3CH

H3N+

CH2

H3N+

CH2

C CH

NH

+

H

COO–

H

COO–

H

COO–

H

COO–

H

COO–

H

COO–

H

COO–

H

COO–

H

COO–

H

COO–

H

COO–

H

COO–

H

COO–

H

COO–

H

COO–

H

COO–

H

COO–

H

COO–

H

COO–

H

COO–

Proline(Pro; P)

Tyrosine(Tyr; Y)

Glutamine(Gln; Q)

A. Amino acids with electrically charged hydrophilic side chains

B. Amino acids with polar but uncharged side chains (hydrophilic)

D. Amino acids with nonpolar hydrophobic side chains

C. Special cases

Leucine (Leu; L)

Serine(Ser; S)

Glycine(Gly; G)

Glutamic acid(Glu; E)

Aspartic acid(Asp; D)

Asparagine(Asn; N)

Valine(Val; V)

Methionine(Met; M)

Arginine(Arg; R)

Lysine(Lys; K)

Threonine(Thr; T)

Cysteine(Cys; C)

Histidine (His; H)

Positive Negative

Phenylalanine(Phe; F)

Tryptophan(Trp; W)

–+

Alanine(Ala; A)

Isoleucine(Ile; I)

C C C

LANGUAGE FOCUS

cluster (V)

gather, assemble

6

The cysteine side chain, which has a terminal —SH group, can react with another cysteine

side chain in an oxidation reaction to form a covalent bond (Figure 2). This bond, called a

disulfide bridge or disulfide bond (—S—S—), helps determine how a polypeptide chain

folds. Cysteine can usually be synthesized by the human body, but it may also be obtained

from the diet. Foods rich in proteins are an important source of cysteine: meat, eggs, dairy

products and soy beans. This amino acid is an important source of sulfide in human me-

tabolism.

2 H

H

C

S H H S

N

C

H

H

C

H

H

C H

C

N

C

H

C

S S

N

C

H

H

C

H

H

C H

C

N

C

…resulting in the formation

of a disulfide bridge.

The —SH groups of

two cysteine side

chains react to form a

covalent bond between

the two sulfur atoms…

Side chains

Cysteine molecules

in polypeptide chain

Figure 2 Disulfide Bridge Two cysteine molecules in a polypeptide chain can form a disulfide bridge (—S—S—) by oxidation

(removal of H atoms).

The glycine side chain consists of a single hydrogen atom, H. It is the simplest amino acid

and small enough to fit into tight corners in the interiors of protein molecules where larger

side chains cannot fit. Since the side chain, R, is a single hydrogen atom, glycine is a non-op-

tical amino acid. Glycine is a non-essential amino acid, implying that our bodies are able

to produce it. Most proteins contain small quantities of glycine, except for collagen, which

contains almost 35% glycine. In the genetic code, glycine is coded by all codons starting

with GG (GGU, GGC, GGA and GGG).

Proline possesses a modified amino group that lacks a hydrogen and instead forms a cova-

lent bond with the hydrocarbon side chain, resulting in a ring structure. This limits both

its hydrogen-bonding ability and its ability to rotate about the a carbon. Thus proline is of-

ten found where a protein bends or loops. Moreover, due to its rigidity, proline is abundant

in the proteins of thermophilic organisms.

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chapter 1 Biomolecules

N

H

C

H

O–

O

C N

O

H

H

O–

H

H

N+

C

OH

H

N

H

C

H

O–

O

C O–

O

H

H

H

N+

H

H

H

H2O

H2O

+

H

H

N

H

C

H

O–

O

+

C N

O

H

H H

C

O

N+

H

H

H

Repetition of this

reaction links

many amino acids

together into a

polypeptide.

The amino group of

one amino acid reacts

with the carboxyl group

of another to form a

peptide linkage.

A molecule of water is

lost (condensation) as

each linkage forms.

R

C

N terminus (+H3N)

Amino group Carboxyl group

Peptide linkage

C terminus (COO–)

+

+

R

R

R

R

C C

R

CC C

N terminus (+H3N)

C terminus (COO–)

R R

C C

Figure 3 Formation of Peptide Linkages In living things, the reaction leading to a peptide

linkage has many intermediate steps, but the

reactants and products are the same as those

shown in this simplified diagram.

Just as a sentence begins with a capital letter and ends with a period, polypeptide chains

have a beginning and an end. The “capital letter” marking the beginning of a polypeptide

is the amino group of the first amino acid added to the chain and is known as the N termi-

nus. The “period” is the carboxyl group of the last amino acid added; this is the C terminus.

Two characteristics of the peptide bond are especially important in the three-dimensional

structures of proteins:

• In the C—N linkage, the adjacent a carbons (a-C—C—N— a-C) are not free to rotate

fully. In fact two resonance structures exist:

C

O

NH

–

+C

O

NH

LANGUAGE FOCUS

terminus (N)

the last stop or station at the end of a bus or a

train route

adjacent (A)

next to; touching

Peptide LinkagesWhen amino acids polymerize, the carboxyl and amino groups attached to the a carbon

are the reactive groups. The carboxyl group of one amino acid reacts with the amino group

of another, undergoing a condensation reaction that forms a peptide linkage (also called a

peptide bond). Figure 3 gives a simplified description of this reaction.

8

Thus, the bond between the carbonyl carbon and the nitrogen has a partial double bond

character, and as a consequence rotation around this bond is restricted. Thus, the peptide

unit is a rigid structure and rotation is restricted to the bonds involving the a carbon:

• The oxygen bound to the carbon (C=O) in the carboxyl group carries a slight negative

charge (δ–), whereas the hydrogen bound to the nitrogen (N—H) in the amino group

is slightly positive (δ+). This asymmetry of charge favours hydrogen bonding within

the protein molecule itself and between molecules. These bonds contribute to the

structures and functions of many proteins.

In addition to these characteristics of the peptide linkage, the particular sequence of amino

acids—with their various R groups—in the polypeptide chain also plays a vital role in de-

termining a protein’s structure and function.

CHEMISTRY RECALL

Resonance Structures

If more than one Lewis structure can be drawn for a specific compound, the molecule or ion is said

to have resonance, and each individual Lewis structure is then known as a contributing resonance

structure.

Resonance structures are used to show that electrons are delocalized, i.e. they are able to move

between atoms to stabilize the molecule. Two or more resonance structures are used to describe the

hybrid structure that is intermediate between the contributing Lewis structures shown below.

By convention, the double-headed arrow shows contributing resonance structures.

C

O

NH CH C

O

NH

R

Rotation possible

Rotation restricted

S

O

O O

S

O

O O

S

O

O O

9

chapter 1 Biomolecules

Task 1a

PAIR WORK

A. Answer the questions; then compare and discuss your answers with your classmate.

1. Discuss the biological roles of amino acids.

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

2. Describe what makes each of the 20 amino acids found in proteins unique.

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

3. Explain the amphoteric behaviour of amino acids.

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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4. List the attributes that would make an amino acid’s R group either hydrophobic or hydrophilic.

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5. Explain why cysteine, glycine and proline are considered special amino acids.

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6. Describe the process by which amino acids are joined together.

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B. Fill in the blanks using the words given below.

condensation – isoelectric point – proteins – asymmetrical – carbon – peptide linkages – polypeptide chains – side chain – amino acids – zwitterion

The functions of (a) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . include support, protection, catalysis, transport, defence, regulation, and movement.

Proteins consist of one or more (b) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . which are polymers of (c) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Four atoms or groups are attached to a central (d) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . atom: a hydrogen atom, an amino group, a carboxyl group, and a variable R group. The particular properties of each amino acid depend on its (e) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . , or R group, which may be charged, polar, or hydrophobic.

The a carbon is (f) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . because it is bonded to four different atoms or groups of atoms.

The (g) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . is the pH at which the amino acid is neutral, i.e. the (h) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . form is dominant.

(i) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . , also called peptide bonds, covalently link amino acids into polypeptide chains. These bonds form by (j) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . reactions between the carboxyl and amino groups.

C. Provide a definition for the terms listed below.

a) Protein . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

b) Amino acid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

c) Zwitterion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

d) Isoelectric point . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

e) Disulfide bridge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

f) Peptide linkage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

g) Glycine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

UNDERSTANDING AND DEFINING

10

OH

OH

2N

RH

Task 1b

UNDERSTANDING

B. Now watch the second part of the video (06:28 to 10:05). After watching, write down the two Fischer projections of the generic amino acids and explain the origin of the names and how to recognize the two molecules.

A. Watch the first part of the video (to 06:27). After watching, answer the following questions.

1. Describe the function of haemoglobin.

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2. Describe the function of cell tissues.

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3. What are amino acids? How many of them are there?

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4. Label the structural formula below.

The Structure of Amino Acids (15:32 min) Watch the online video and answer the following questions step by step.

WATCH AND ANSWER

5. Explain why each of the twenty amino acids is different from each other.

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6. What is a chiral carbon? Are there any exceptions among amino acids?

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L – amino acid D – amino acid

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PAIR WORK

C. Finally, watch the third part of the video (10:06 to the end), and complete the text that lists the main ideas discussed in the video. Compare your answers with your classmate.

We are now going to review the main ideas that have been discussed in this video. Firstly, we have learnt where (a) . . . . . . . . . . . . . . . . . fit in a larger metabolic process, such as in the example of (b) . . . . . . . . . . . . . . . . . . Secondly, we have found out about the structure of an amino acid, and the fact that the central (c) . . . . . . . . . . . . . . . . . is a chiral carbon with (d) . . . . . . . . . . . . . . . . . activity. The only exception to this rule is the amino acid (e) . . . . . . . . . . . . . . . . . , which has the simplest side chain of a (f) . . . . . . . . . . . . . . . . . , and therefore cannot be considered a chiral molecule. Thirdly, we have learnt about the Fischer projections for amino acids, and the fact that the (g) . . . . . . . . . . . . . . . . . of an amino acid is the only one that can be found within the (h) . . . . . . . . . . . . . . . . . .

Video 1

11

chapter 1 Biomolecules

Task 2

APPLYING

A. After reading the text in task 1a or watching the video in task 1b, you are now familiar with the structure of amino acids. The table below shows the structural formulas of the twenty amino acids. Circle the unique side chain of each amino acid, and then group the amino acids into: - amino acids with electrically charged (ionized) side chains; - amino acids with polar side chains; - amino acids with non polar (and thus hydrophobic) side chains. Find and label cysteine, glycine and proline.

B. The picture below shows the amino acid alanine. Write down the acid-base equilibria that lead to the three forms of the amino acid: at low pH, at the isoelectric point, and at high pH.

C. Pick two amino acids of your choice, and write down the structural formulas in the zwitterionic form. Write down the condensation reaction that leads to the formation of the peptide linkage between the two amino acids.

GROUP WORK

D. From a historical point of view, phenylalanine (pictured below in its molecular formula) is an interesting amino acid. Search the web and prepare a presentation with slides to point out:

1. The genetic codon(s) for phenylalanine and the historically relevant experiment that kick-started the discovery of the genetic code.

2. The role of phenylalanine in the human body.

3. The genetic disease caused by the inability to metabolize phenylalanine. Specify name, causes, effects and therapy of this metabolic disease.

COOH

HH2N

CH3

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