1

Chapter 5

The Structure and Function of

Macromolecules

2

Root Words• con- = together (condensation reaction: a

reaction in which two molecules become covalently bonded to each other through the loss of a small molecule, usually water)

• di- = two (disaccharide: two monosaccharides joined together )

• glyco- = sweet (glycogen: a polysaccharide sugar used to store energy in animals)

• hydro- = water; -lyse = break (hydrolysis: breaking chemical bonds by adding water)

3

More Roots• macro- = large (macromolecule: a large

molecule)• meros- = part (polymer: a chain

made from smaller organic molecules)• mono- = single; -sacchar = sugar

(monosaccharide: simplest type of sugar)poly- = many (polysaccharide: many monosaccharides joined together)

• tri- = three (triacylglycerol: three fatty acids linked to one glycerol molecule)

4

The Molecules of Life

• Overview:– Another level in the hierarchy

of biological organization is reached when small organic molecules are joined together

– Atom ---> molecule --- macromolecule

5

Macromolecules– Are large molecules composed of

smaller molecules– Are complex in their structures

Figure 5.1

6

Macromolecules

•Most macromolecules are polymers, built from monomers• Four classes of life’s organic molecules are polymers

– Carbohydrates– Lipids– Proteins– Nucleic acids

7

– Is a long molecule consisting of many similar building blocks called monomers

– Specific monomers make up each macromolecule

– E.g. amino acids are the monomers for proteins

Polymer

8

The Synthesis and Breakdown of Polymers

• Monomers form larger molecules by condensation reactions called dehydration synthesis

(a) Dehydration reaction in the synthesis of a polymer

HO H1 2 3 HO

HO H1 2 3 4

H

H2O

Short polymer Unlinked monomer

Longer polymer

Dehydration removes a watermolecule, forming a new bond

Figure 5.2A

9

The Synthesis and Breakdown of Polymers

• Polymers can disassemble by– Hydrolysis (addition of water

molecules)

(b) Hydrolysis of a polymer

HO 1 2 3 H

HO H1 2 3 4

H2O

HHO

Hydrolysis adds a watermolecule, breaking a bond

Figure 5.2B

10

• Although organisms share the same limited number of monomer types, each organism is uniquely based on the arrangement of monomers into polymers

• An immense variety of polymers can be built from a small set of monomers

11

Carbohydrates

• Serve as fuel and building material

• Include both sugars and their polymers (starch, cellulose, etc.)

12

Sugars

• Monosaccharides– Are the simplest sugars– Can be used for fuel– Can be converted into other

organic molecules– Can be combined into polymers

13

• Examples of monosaccharides

Triose sugars(C3H6O3)

Pentose sugars(C5H10O5)

Hexose sugars(C6H12O6)

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

HO C H

H C OH

H C OH

H C OH

H C OH

HO C H

HO C H

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

C OC O

H C OH

H C OH

H C OH

HO C H

H C OH

C O

H

H

H

H H H

H

H H H H

H

H H

C C C COOOO

Ald

oses

Glyceraldehyde

RiboseGlucose Galactose

Dihydroxyacetone

Ribulose

Keto

ses

FructoseFigure 5.3

14

• Monosaccharides– May be linear– Can form rings in aqueous solution

H

H C OH

HO C H

H C OH

H C OH

H C

O

C

H

1

2

3

4

5

6

H

OH

4C

6CH2OH 6CH2OH

5C

HOH

C

H OH

H

2 C

1C

H

O

H

OH

4C

5C

3 C

H

HOH

OH

H

2C

1 C

OH

H

CH2OH

H

H

OHHO

H

OH

OH

H5

3 2

4

(a) Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5.

OH3

O H OO

6

1

Figure 5.4

15

• Disaccharides–Consist of two monosaccharides

–Are joined by a glycosidic linkage

16

Dehydration reaction in the synthesis of maltose. The bonding of two glucose units forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide.

Dehydration reaction in the synthesis of sucrose. Sucrose is a disaccharide formed from glucose and fructose.Notice that fructose,though a hexose like glucose, forms a five-sided ring.

(a)

(b)

H

HO

H

HOH H

OH

O H

OH

CH2OH

H

HO

H

HOH

H

OH

O H

OH

CH2OH

H

O

H

HOH H

OH

O H

OH

CH2OH

H

H2O

H2O

H

H

O

H

HOH

OH

O H

CH2OH

CH2OH HO

OHH

CH2OH

HOH

H

H

HO

OHH

CH2OH

HOH H

O

O H

OHH

CH2OH

HOH H

O

HOH

CH2OH

H HO

O

CH2OH

H

H

OH

O

O

1 2

1 41– 4

glycosidiclinkage

1–2glycosidic

linkage

Glucose

Glucose Glucose

Fructose

Maltose

Sucrose

OH

H

H

Figure 5.5

17

Polysaccharides

• Polysaccharides– Are polymers of sugars– Serve many roles in organisms

18

Storage Polysaccharides

• Starch– Is a polymer

consisting entirely of glucose monomers

– Is the major storage form of glucose in plants

Chloroplast Starch

Amylose Amylopectin

1 m

(a) Starch: a plant polysaccharideFigure 5.6

19

• Glycogen– Consists of glucose monomers– Is the major storage form of glucose in

animals Mitochondria Giycogen granules

0.5 m

(b) Glycogen: an animal polysaccharide

Glycogen

Figure 5.6

20

Structural Polysaccharides

• Cellulose– Is a polymer of glucose

21

– Has different glycosidic linkages than starch

(c) Cellulose: 1– 4 linkage of glucose monomers

H O

O

CH2OH

HOH H

H

OH

OHH

H

HO

4

C

C

C

C

C

C

H

H

H

HO

OH

H

OH

OH

OH

H

O

CH2OH

HH

H

OH

OHH

H

HO

4 OH

CH2OH

O

OH

OH

HO41

O

CH2OH

O

OH

OH

O

CH2OH

O

OH

OH

CH2OH

O

OH

OH

O O

CH2OH

O

OH

OH

HO4

O1

OH

O

OH OHO

CH2OH

O

OH

O OH

O

OH

OH

(a) and glucose ring structures

(b) Starch: 1– 4 linkage of glucose monomers

1

glucose glucose

CH2OH

CH2OH

1 4 41 1

Figure 5.7 A–C

22

Plant cells

0.5 m

Cell walls

Cellulose microfibrils in a plant cell wall

Microfibril

CH2OH

CH2OH

OH

OH

OO

OHOCH2OH

O

OOH

OCH2OH OH

OH OHO

O

CH2OH

OO

OH

CH2OH

OO

OH

O

O

CH2OHOH

CH2OHOHOOH OH OH OH

O

OH OH

CH2OH

CH2OH

OHO

OH CH2OH

OO

OH CH2OH

OH

Glucose monomer

O

O

O

O

O

O

Parallel cellulose molecules areheld together by hydrogenbonds between hydroxyl

groups attached to carbonatoms 3 and 6.

About 80 cellulosemolecules associate

to form a microfibril, themain architectural unitof the plant cell wall.

A cellulose moleculeis an unbranched glucose polymer.

OH

OH

O

OOH

Cellulosemolecules

Figure 5.8

– Is a major component of the tough walls that enclose plant cells

23

• Cellulose is difficult to digest– Cows have microbes in their stomachs

to facilitate this process

Figure 5.9

24

• Chitin, another important structural polysaccharide– Is found in the exoskeleton of

arthropods– Can be used as surgical thread

(a) The structure of the chitin monomer.

O

CH2OH

OHHH OH

H

NH

CCH3

O

H

H

(b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emergingin adult form.

(c) Chitin is used to make a strong and flexible surgical

thread that decomposes after the wound or incision heals.

OH

Figure 5.10 A–C

25

Lipids

• Lipids are a diverse group of hydrophobic molecules

• Lipids– Are the one class of large biological

molecules that do not consist of polymers– Share the common trait of being

hydrophobic

26

Fats– Are constructed from two types of smaller

molecules, a single glycerol and usually three fatty acids

– Vary in the length and number and locations of double bonds they contain

27

Fats– Are constructed from two types of smaller

molecules, a single glycerol and usually three fatty acids

– Vary in the length and number and locations of double bonds they contain

28

Fats• Are constructed from two types of smaller

molecules, a single glycerol and usually three fatty acids

29

Fats• Vary in the length and number and

locations of double bonds they contain

30

• Saturated fatty acids– Have the maximum number of

hydrogen atoms possible– Have no double bonds

(a) Saturated fat and fatty acid

Stearic acid

Figure 5.12

31

• Unsaturated fatty acids– Have one or more double bonds

(b) Unsaturated fat and fatty acidcis double bondcauses bending

Oleic acid

Figure 5.12

32

• Phospholipids– Have only two fatty acids– Have a phosphate group instead of

a third fatty acid

33

• Phospholipid structure– Consists of a hydrophilic “head”

and hydrophobic “tails”CH2

O

PO O

O

CH2CHCH2

OO

C O C O

Phosphate

Glycerol

(a) Structural formula (b) Space-filling model

Fatty acids

(c) Phospholipid symbol

Hyd

rop

hob

i c t

ails

Hydrophilichead

Hydrophobictails

–

Hyd

rop

hi li c

head

CH2 Choline+

Figure 5.13

N(CH3)3

34

• The structure of phospholipids– Results in a bilayer arrangement found

in cell membranes

Hydrophilichead

WATER

WATER

Hydrophobictail

Figure 5.14

35

Steroids

• Steroids– Are lipids characterized by a carbon

skeleton consisting of four fused rings

36

• One steroid, cholesterol– Is found in cell membranes– Is a precursor for some hormones

HO

CH3

CH3

H3C CH3

CH3

Figure 5.15

37

Proteins

• Proteins have many structures, resulting in a wide range of functions

• Proteins do most of the work in cells and act as enzymes

• Proteins are made of monomers called amino acids

38

• An overview of protein functions

Table 5.1

39

• Enzymes– Are a type of protein that acts as a

catalyst, speeding up chemical reactions

Substrate(sucrose)

Enzyme (sucrase)

Glucose

OH

H O

H2O

Fructose

3 Substrate is convertedto products.

1 Active site is available for a molecule of substrate, the

reactant on which the enzyme acts.

Substrate binds toenzyme.

22

4 Products are released.Figure 5.16

40

Polypeptides

• Polypeptides– Are polymers (chains) of amino

acids

• A protein– Consists of one or more

polypeptides

41

• Amino acids– Are organic molecules possessing

both carboxyl and amino groups– Differ in their properties due to

differing side chains, called R groups

42

Twenty Amino Acids

• 20 different amino acids make up proteins

O

O–

H

H3N+ C C

O

O–

H

CH3

H3N+ C

H

C

O

O–

CH3 CH3

CH3

C C

O

O–

H

H3N+

CH

CH3

CH2

C

H

H3N+

CH3CH3

CH2

CH

C

H

H3N+

C

CH3

CH2

CH2

CH3N+

H

C

O

O–

CH2

CH3N+

H

C

O

O–

CH2

NH

H

C

O

O–

H3N+ C

CH2

H2C

H2N C

CH2

H

C

Nonpolar

Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)

Methionine (Met) Phenylalanine (Phe)

C

O

O–

Tryptophan (Trp) Proline (Pro)

H3C

Figure 5.17

S

O

O–

43

O–

OH

CH2

C C

H

H3N+

O

O–

H3N+

OH CH3

CH

C C

HO–

O

SH

CH2

C

H

H3N+ C

O

O–

H3N+

C C

CH2

OH

H H H

H3N+

NH2

CH2

OC

C CO

O–

NH2 O

C

CH2

CH2

C CH3N

+

O

O–

O

Polar

Electricallycharged

–O O

C

CH2

C CH3N

+

H

O

O–

O– O

C

CH2

C CH3N

+

H

O

O–

CH2

CH2

CH2

CH2

NH3+

CH2

C CH3N

+

H

O

O–

NH2

C NH2+

CH2

CH2

CH2

C CH3N

+

H

O

O–

CH2

NH+

NHCH2

C CH3N

+

H

O

O–

Serine (Ser) Threonine (Thr)Cysteine

(Cys)Tyrosine

(Tyr)Asparagine

(Asn)Glutamine

(Gln)

Acidic Basic

Aspartic acid (Asp)

Glutamic acid (Glu)

Lysine (Lys) Arginine (Arg) Histidine (His)

44

Amino Acid Polymers

• Amino acids– Are linked by peptide bonds

45

Protein Conformation and Function

• A protein’s specific conformation (shape) determines how it functions

46

Four Levels of Protein Structure

• Primary structure– Is the unique

sequence of amino acids in a polypeptide

Figure 5.20–

Amino acid

subunits

+H3NAmino

end

oCarboxyl end

oc

GlyProThrGlyThr

Gly

GluSeuLysCysProLeu

MetVal

Lys

ValLeu

AspAlaValArgGly

SerPro

Ala

Gly

lle

SerProPheHisGluHis

Ala

GluValValPheThrAla

Asn

AspSer

GlyProArg

ArgTyrThr

lleAla

Ala

Leu

LeuSer

ProTyrSerTyrSerThr

Thr

Ala

ValVal

ThrAsnProLysGlu

ThrLys

SerTyrTrpLysAlaLeu

GluLleAsp

47

O C helix

pleated sheetAmino acid

subunitsNCH

C

O

C N

H

CO H

R

C NH

C

O H

C

R

N

HH

R C

O

R

C

H

NH

C

O H

NCO

R

C

H

NH

H

C

R

C

O

C

O

C

NH

H

R

C

C

ON

HH

C

R

C

O

NH

R

C

H C

ON

HH

C

R

C

O

NH

R

C

H C

ON

HH

C

R

C

O

N H

H C R

N HO

O C N

C

RC

H O

CHR

N HO C

RC

H

N H

O CH C R

N H

CC

N

R

H

O C

H C R

N H

O C

RC

H

H

C

RN

H

CO

C

NH

R

C

H C

O

N

H

C

• Secondary structure– Is the folding or coiling of the

polypeptide into a repeating configuration

– Includes the helix and the pleated sheet

H H

Figure 5.20

48

• Tertiary structure– Is the overall three-dimensional shape

of a polypeptide– Results from interactions between

amino acids and R groups

CH2CH

OH

O

CHO

CH2

CH2 NH3+ C-O CH2

O

CH2SSCH2

CH

CH3

CH3

H3C

H3C

Hydrophobic interactions and van der Waalsinteractions Polypeptid

ebackbone

Hyrdogenbond

Ionic bond

CH2

Disulfide bridge

49

• Quaternary structure– Is the overall protein structure that

results from the aggregation of two or more polypeptide subunits

Polypeptidechain

Collagen

Chains

ChainsHemoglobin

IronHeme

50

Review of Protein Structure

+H3NAmino end

Amino acidsubunits

helix

51

Sickle-Cell Disease: A Simple Change in Primary Structure

• Sickle-cell disease– Results from a single amino

acid substitution in the protein hemoglobin

52

Fibers of abnormalhemoglobin deform cell into sickle shape.

Primary structure

Secondaryand tertiarystructures

Quaternary structure

Function

Red bloodcell shape

Hemoglobin A

Molecules donot associatewith oneanother, eachcarries oxygen.Normal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen

10 m 10 m

Primary structure

Secondaryand tertiarystructures

Quaternary structure

Function

Red bloodcell shape

Hemoglobin SMolecules interact with one another tocrystallize into a fiber, capacity to carry oxygen is greatly reduced.

subunit subunit

1 2 3 4 5 6 7 3 4 5 6 721

Normal hemoglobin

Sickle-cell hemoglobin . . .. . .

Figure 5.21

Exposed hydrophobic

region

Val ThrHis Leu Pro Glul Glu Val His Leu Thr Pro Val Glu

53

What Determines Protein Conformation?

• Protein conformation Depends on the physical and chemical conditions of the protein’s environment

• Temperature, pH, etc. affect protein structure

54

•Denaturation is when a protein unravels and loses its native conformation(shape)

Denaturation

Renaturation

Denatured protein

Normal protein

Figure 5.22

55

The Protein-Folding Problem

• Most proteins– Probably go through several

intermediate states on their way to a stable conformation

– Denaturated proteins no longer work in their unfolded condition

– Proteins may be denaturated by extreme changes in pH or temperature

56

• Chaperonins– Are protein molecules that assist in the

proper folding of other proteins

Hollowcylinder

Cap

Chaperonin(fully assembled)

Steps of ChaperoninAction: An unfolded poly- peptide enters the cylinder from one end.

The cap attaches, causing the cylinder to change shape insuch a way that it creates a hydrophilic environment for the folding of the polypeptide.

The cap comesoff, and the properlyfolded protein is released.

Correctlyfoldedprotein

Polypeptide

2

1

3

Figure 5.23

57

• X-ray crystallography– Is used to determine a protein’s three-

dimensional structure X-raydiffraction pattern

Photographic filmDiffracted X-

raysX-ray

source

X-ray

beam

CrystalNucleic acid Protein

(a) X-ray diffraction pattern(b) 3D computer modelFigure 5.24

58

Nucleic Acids

• Nucleic acids store and transmit hereditary information

• Genes– Are the units of inheritance– Program the amino acid

sequence of polypeptides– Are made of nucleotide

sequences on DNA

59

The Roles of Nucleic Acids

• There are two types of nucleic acids– Deoxyribonucleic acid (DNA)– Ribonucleic acid (RNA)

60

Deoxyribonucleic Acid

• DNA– Stores information for the

synthesis of specific proteins– Found in the nucleus of cells

61

DNA Functions– Directs RNA synthesis (transcription)– Directs protein synthesis through RNA

(translation)

1

2

3

Synthesis of mRNA in the nucleus

Movement of mRNA into cytoplasm

via nuclear pore

Synthesisof protein

NUCLEUSCYTOPLASM

DNA

mRNA

Ribosome

AminoacidsPolypeptide

mRNA

Figure 5.25

62

The Structure of Nucleic Acids

• Nucleic acids– Exist as polymers called

polynucleotides

(a) Polynucleotide, or nucleic acid

3’C

5’ end

5’C

3’C

5’C

3’ endOH

Figure 5.26

O

O

O

O

63

• Each polynucleotide– Consists of monomers called nucleotides– Sugar + phosphate + nitrogen base

Nitrogenousbase

Nucleoside

O

O

O

O P CH2

5’C

3’CPhosphate

group Pentosesugar

(b) NucleotideFigure 5.26

O

64

Nucleotide Monomers

• Nucleotide monomers – Are made up of

nucleotides (sugar + base) and phosphate groups

(c) Nucleoside componentsFigure 5.26

CHCH

Uracil (in RNA)U

Ribose (in RNA)

Nitrogenous bases Pyrimidines

CN

NC

OH

NH2

CHCH

OC

NH

CHHN

CO

CCH3

N

HNC

C

HO

O

CytosineC

Thymine (in DNA)T

NHC

N C

CN

C

CH

N

NH2 O

NHC

NHH

C C

N

NH

C NH2

AdenineA

GuanineG

Purines

OHOCH2

HH H

OH

H

OHOCH2

HH H

OH

H

Pentose sugars

Deoxyribose (in DNA)Ribose (in RNA)OHOH

CH

CH

Uracil (in RNA)U

4’

5”

3’OH H

2’

1’

5”

4’

3’ 2’

1’

65

Nucleotide Polymers

• Nucleotide polymers– Are made up of nucleotides linked

by the–OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next

66

Gene

• The sequence of bases along a nucleotide polymer– Is unique for each gene

67

The DNA Double Helix

• Cellular DNA molecules– Have two polynucleotides that spiral

around an imaginary axis– Form a double helix

68

• The DNA double helix– Consists of two antiparallel nucleotide

strands3’ end

Sugar-phosphatebackbone

Base pair (joined byhydrogen bonding)

Old strands

Nucleotideabout to be added to a new strand

A

3’ end

3’ end

5’ end

Newstrands

3’ end

5’ end

5’ end

Figure 5.27

69

A,T,C,G

• The nitrogenous bases in DNA– Form hydrogen bonds in a

complementary fashion (A with T only, and C with G only)

70

DNA and Proteins as Tape Measures of Evolution

• Molecular comparisons – Help biologists sort out the

evolutionary connections among species

71

The Theme of Emergent Properties in the Chemistry of

Life: A Review

• Higher levels of organization– Result in the emergence of

new properties

• Organization– Is the key to the chemistry of

life