Chapter 1Chapter 1The Structure and The Structure and

Function of BiomoleculesBiomolecules

(Macromolecules)

1

The Molecules of LifeThe Molecules of Life• Overview:Overview:

– Another level in the hierarchy of biological organization is of biological organization is reached when small organic molecules are joined togethermolecules are joined together

– Atom ---> molecule ---dcompound

2

MacromoleculesMacromolecules– Are large molecules composed of smaller Are large molecules composed of smaller

molecules– Are complex in their structuresmp

3Figure 5.1

MacromoleculesMacromolecules

M l l l •Most macromolecules are polymers, built from monomers

F l f lif ’ i• Four classes of life’s organicmolecules are polymers

Carbohydrates– Carbohydrates– Proteins

N l i id– Nucleic acids– Lipids

4

• A polymer– Is a long molecule consisting of Is a long molecule consisting of

many similar building blocks called monomersmonomers

– Specific monomers make up each macromoleculemacromolecule

– E.g. amino acids are the monomers f t ifor proteins

5

The Synthesis and Breakdown of Polymers

• Monomers form larger molecules by Monomers form larger molecules by condensation reactions called dehydration synthesis

HO H1 2 3 HOH

Short polymer Unlinked monomer

H2O

Short polymer Unlinked monomer

Dehydration removes a watermolecule, forming a new bond

(a) Dehydration reaction in the synthesis of a polymer

HO H1 2 3 4

Longer polymerFigure 5.2A

6

The Synthesis and Breakdown of Polymers

• Polymers can disassemble byPolymers can disassemble by– Hydrolysis (addition of water molecules)

HO H1 2 3 4

H2OHydrolysis adds a watermolecule, breaking a bond

(b) Hydrolysis of a polymer

HO 1 2 3 H HHO

Figure 5 2B

7

(b) Hydrolysis of a polymerFigure 5.2B

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

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

8

CarbohydratesCarbohydrates• Serve as fuel and building Serve as fuel and building

materiall d b h d • Include both sugars and

their polymers (starch, p y (cellulose, etc.)

9

SugarsSugars

Monosaccharides• Monosaccharides– Are the simplest sugars

C b d f f l– Can be used for fuel– Can be converted into other

i l lorganic molecules– Can be combined into polymers

10

Ex mpl s f m n s h id s• Examples of monosaccharidesTriose sugars

(C H O )Pentose sugars

(C H O )Hexose sugars

(C H O )(C3H6O3) (C5H10O5) (C6H12O6)

H C OHH C OH

H C OH

H C OH

HO C H

H C OH

HO C H

H C OH

H H H HC C C C

OOOO

es H C OH H C OH

H C OH

H C OH

HO C H

H C OH

H C OH

H C OH

HO C H

HO C H

H C OH

H C OH

H

H

H HAldos

e

Glyceraldehyde

Ribose

H C OH H C OH

C OC O

H C OH

C O

H H H

HGlucose Galactose

H C OH

H C OH

H C OHH C OH

H C OHH C OH

H C OHHO C H

H

HDihydroxyacetone

b l

Keto

ses

11

HRibuloseFructoseFigure 5.3

• MonosaccharidesMonosaccharides– May be linear– Can form rings– Can form rings

H OC1

2

6CH2OH 6CH2OHCH OHH C OH

HO C H

H C OH

2

3

4

H

OH

4C

5C

HOH H

1CH

O

H

OH

4C

5C

HOH H

1 C

HCH2OH

HOH

HO

H

OH

H5

3 2

4

O H OO

6

1

H C OH

H C

H

5

6

OH C

H OH

2 C OH 3 C

H OH

2C OHH OH

OH 3

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

Figure 5.4

12

D h d• Disaccharides– Consist of two Consist of two

monosaccharidesA j i d b l sidi – Are joined by a glycosidic linkage

13

Dehydration reaction in the synthesis of maltose. The bonding of two glucose units

(a)

OCH2OH

OCH2OH CH2OH

OCH2OH

Oof 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.

H

HO

H

HOH H

OH

O H

OH

H

O

H

HOH H

OH

O H

OHH

H

HO

OHH

HOH H

O H

OHH

HOH H

O H

OHO

1 41–4

glycosidiclinkage

OH

H

gJoining the glucose monomers in a different way would result in a different disaccharide. CH2O

H

H2O

CH OHCH2OH CH OH

Glucose Glucose Maltose

Dehydration reaction in the synthesis of sucrose. Sucrose is a disaccharide f rmed

(b)

H

HO

H

HOH

H

O

O H

OH

H

H

H

O

H

HOH

OH

O HCH2OH

CH2OH HO

OHH

HOH H

O

HOH

CH2OH

H HO

O

CH2OH

H

O

1 21–2

glycosidiclinkage

H

a disaccharide formed from glucose and fructose.Notice that fructose,though a hexose like glucose, forms a five-sided ring.

H OH

H2OHOH OHH HOH

Glucose Fructose Sucrose

14

Figure 5.5

PolysaccharidesPolysaccharides• PolysaccharidesPolysaccharides

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

15

Storage PolysaccharidesStorage Polysaccharides• Starch

Chloroplast Starch

Starch– Is a polymer

consisting consisting entirely of glucose

1 μmgmonomers

– Is the major

1 μm

storage form of glucose in plants

Amylose Amylopectin

16

(a) Starch: a plant polysaccharideFigure 5.6

• Glycogen• Glycogen– Consists of glucose monomers

Is th j st f f l s i – Is the major storage form of glucose in animals Mitochondria Giycogen

granules

0.5 μm

Glycogen

17(b) Glycogen: an animal polysaccharideFigure 5.6

Structural PolysaccharidesStructural Polysaccharides• CelluloseCellulose

– Is a polymer of glucose

18

– Has different glycosidic linkages than starch

H O

O

CH2OH

HHH

C

CHH

OH O

CH2OH

HOH

HHOH H O

HOHH

HO

4 C

C

C

C

H

H

HO

HHOHOHO

H

HH

H

H

OHH

HO

4 OH

1

α glucose β glucoseCH H

CH2OH

O

CH2OH

O

CH2OH

O

CH2OH

O

(a) α and β glucose ring structures

α glucose β glucose

OOH

OH

HO

41O

OOH

OH

O

OOH

OH

OOH

OH

O O

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

1 4 41 1

CH2OH

OOHH

O4

O1

OH

O

OH

OHO

CH2OH O

O OH

O

OH

OH

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

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

OH

O OOH

O HCH2O

HCH2O

HFigure 5.7 A–C

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

Cell walls

Cellulose microfibrils in a plant cell wall Microfibril

About 80 cellulosemolecules associate

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

0.5 μm

Plant cells

CH2OH

OHO

OO

OHOCH OH

OO

OHO

CH2OH OH

OH OHO

CH OHOHO

O

C ll l

CH2OH

OH

CH2OH

O

CH2OHO

O OH

CH2OHO

O

CH2OHOH

CH2OHOHOOH OH OH OH

OH OH

CH2OHOHO O

OH CH2OH

OH

O

O

O

OParallel cellulose molecules areheld together by hydrogenbonds between hydroxyl

groups attached to carbon

OH

OH

O

OH

Cellulosemolecules

20

OOH

OOH OH

CH2OH

OH

OH CH2OHO

β Glucose monomer

Ogroups attached to carbon

atoms 3 and 6. A cellulose moleculeis an unbranched βglucose polymer.

OOH

Figure 5.8

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

facilitate this processfacilitate this process

21

Figure 5.9

• Chitin, another important structural , mp u upolysaccharide– Is found in the exoskeleton of arthropodsIs found in the exoskeleton of arthropods– Can be used as surgical thread

OCH2O

H

OHHH OHOH

HNHCCH3

O

H

HOH

(a) The structure of thechitin monomer.

(b) Chitin forms the exoskeleton of arthropods. This cicada is molting shedding its old

(c) Chitin is used to make a strong and flexible surgicalthread that decomposes after

22

is molting, shedding its old exoskeleton and emergingin adult form.

thread that decomposes afterthe wound or incision heals.

Figure 5.10 A–C

LipidsLipids

Lipids are a diverse group of • Lipids are a diverse group of hydrophobic moleculesLi id• Lipids– Are the one class of large biological

l l h d i f molecules that do not consist of polymersSh th t it f b i – Share the common trait of being hydrophobic

23

Fats d f f ll – 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

24

Fats d f f ll – 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

25

Fats• Are constructed from two types of smaller

molecules, a single glycerol and usually three fatty , g g y y yacids

26

Fats• Vary in the length and number and locations

of double bonds they contain

27

• Saturated fatty acids• Saturated fatty acids– Have the maximum number of

hydrogen atoms possiblehydrogen atoms possible– Have no double bonds

Stearic acid

28(a) Saturated fat and fatty acidFigure 5.12

• Unsaturated fatty acids– Have one or more double bonds

Oleic acid

(b) Unsaturated fat and fatty acidcis double bondcauses bendingFigure 5.12

29

g

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

third fatty acid

30

• Phospholipid structurep p– Consists of a hydrophilic “head” and

hydrophobic “tails”hydrophobic tailsCH2

OPO O Phosphate–

CH2 Choline+N(CH3)3

PO OOCH2CHCH2

OO

C O C O

Glycerol

Fatty acids

Hydrophilichead

Hydrophobictails

31(a) Structural formula (b) Space-filling model (c) Phospholipid

symbolFigure 5.13

• The structure of phospholipidsu u f p p p– Results in a bilayer arrangement found in

cell membranes

H d hiliWATER

Hydrophilichead

WATER

Hydrophobic

32

y ptail

Figure 5.14

SteroidsSteroids• SteroidsSteroids

– Are lipids characterized by a carbon skeleton consisting of four fused ringsskeleton consisting of four fused rings

33

On st id h l st l• One steroid, cholesterol– Is found in cell membranes

f h– Is a precursor for some hormones

H3C CH

CH3

H3 CH3

CH3

CH3

HOFigure 5.15

34

ProteinsProteins• Proteins have many structures Proteins have many structures,

resulting in a wide range of functionsfunctions

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

• Proteins are made of monomers ll d i idcalled amino acids

35

• An overview of protein functionsAn overview of protein functions

Table 5.1

36

• EnzymesE zym– Are a type of protein that acts as a

catalyst, speeding up chemical reactionsy , p g p

Substrate(sucrose)

1 Active site is available fora molecule of substrate, the

reactant on which the enzyme acts.

Substrate binds toenzyme.

22

(sucrose)

GlucoseEnzyme (sucrase)

Glucose

OH H2OFructose

H O

37

3 Substrate is convertedto products.

4 Products are released.Figure 5.16

PolypeptidesPolypeptides• PolypeptidesPolypeptides

– Are polymers (chains) of amino acidsA protein• A protein– Consists of one or more polypeptides

38

• Amino acidsm– Are organic molecules possessing both carboxyl and amino groupsy g p

– Differ in their properties due to differing side chains, called R groupsg g p

39

Twenty Amino AcidsTwenty Amino Acids• 20 different amino acids make up CH3CH3

CH320 different amino acids make up proteinsH

H3N+ C CO

O–

CH3

H3N+ C C

O

O–

CH3 CH3

CH3

C C

O

O–

H3N+

CH

CH3

CH2

CH3N+

CH3

CH2

CH

CH3N+ CC

O

O–

H3C O

O–OH H

O OH H H

Nonpolar

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

O O

O

O–

CH3

CH2

CH CH CH

NH

CH2

H2C

H2N C

CH2

C

S

OCH2

CH3N+

H

C

O

O–

CH2

CH3N+

H

CO

O–

CH2

H

CO

O–

H3N+ CH

Methionine (Met) Phenylalanine (Phe) Tryptophan (Trp) Proline (Pro)

40Figure 5.17

OH OH CH3SH

OH

NH2 OC

NH2 OC

CH2Polar

O–

CH2

C C

H

H3N+

O

O–

H3N+

3

CH

C C

H O–

O CH2

C

H

H3N+ C

O

O–

H3N+ C C

CH2

H H H

H3N+

CH2

C CO

O–

CH2

C CH3N+

O

O–

OPolar

Serine (Ser) Threonine (Thr) Cysteine (Cys)

Tyrosine(Tyr)

Asparagine(Asn)

Glutamine(Gln)

NH + NH NH+

( ) ( ) (Cys) (Tyr) (Asn) (Gln)

Acidic Basic

Electricallycharged

–O OC

CH2

C CH3N+

O

O–

O– OC

CH2

C CH3NOCH2

CH2

CH2

CH2

NH3

CH2 O

NH2

C NH2+

CH2

CH2

CH

NH

NHCH2

C CH3N+

H

O

O–

HC C3

+

HO–

CH2

C CH3N+

H

O

O–

CH2

C CH3N+

H

O

O–

CH2

H

Aspartic acid Glutamic acid Lysine (Lys) Arginine (Arg) Histidine (His)

41

p(Asp) (Glu)

Amino Acid PolymersAmino Acid Polymers• Amino acidsAmino acids

– Are linked by peptide bonds

42

Protein Conformation and Protein Conformation and Function

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

43

Four Levels of Protein StructureFour Levels of Protein Structure• Primary structure Amino +H3N

GlyProThrGlyThrPrimary structure

– Is the unique sequence of amino

acid subunits

H3NAmino end

Gly

GluSeuLysCysProLeu

MetVal

Lys

ValLeuAsp

AlaValArgGlySer

ProAlasequence of amino

acids in a polypeptide

GlylleSerProPheHisGluHis

AlaGlu

ValValPheThrAl

ThrLysSer

TyrTrpLysAlaLeu

GluLle Asp

–oo

c

ValPheThrAlaAsn

AspSer

GlyProArgArgTyrThrlle

AlaAlaLeu

LeuSerProTyrSerTyrSerThr

ThrAlaVal

ValThrAsnProLysGlu

44

Figure 5.20o

Carboxyl end

• Secondary structureSecondary structure– Is the folding or coiling of the polypeptide

into a repeating configurationinto a repeating configuration– Includes the α helix and the β pleated

sheetβ pleated sheet

Amino acidsubunits NC

H

CO

C NH

CO H

RC N

H

CO H

CR

NHH

R CO

RCH

NH

CO H

NCO

RCH

NH

H

CR

CO H

CR

NH

CO

C

sheet

H O H H O H H O H H

CO

C

NH

H

RC

CO

NH

H

CR

CO

NH

RCH C

ONH H

CR

C

ONH

RCH C

ONH H

CR

CO

R H R H

O

NH

RCH C

ONH

C

O C α helixN H

H C RN H O

O C N

CH O

CHR

N HO C

RC H

N H

O CH C R

N H

C N HO C

H C R

N HO C

RC

H

45

O C N

RC

H O CC

N

R

H

H H

Figure 5.20

• Tertiary structureTertiary structure– Is the overall three-dimensional shape of

a polypeptidep yp p– Results from interactions between amino

acids and R groupsg p

CH2CH

O CH3H3C

Hydrophobic interactions and van der Waalsinteractions CH2

OHOCHOCH2 CHSSCH

CH

CH3CH3

3

H3C Polypeptidebackbone

Hyrdogenbond

2

CH2 NH3+ C-O CH2

O

CH2SSCH2

Ionic bond

Disulfide bridge

46

• Quaternary structureQu y u u– Is the overall protein structure that

results from the aggregation of two or gg gmore polypeptide subunits

Polypeptidechain

Collagenβ Ch iβ Chains

IronH

47α Chains

Hemoglobin

Heme

Review of Protein StructureReview of Protein Structure

+H3NAmino end

Amino acidsubunits

α helix

48

Sickle-Cell Disease: A Simple Change Sickle-Cell Disease: A Simple Change in Primary Structure

• Sickle-cell diseaseSickle cell disease– Results from a single amino acid

substitution in the protein substitution in the protein hemoglobin

49

P i Normal hemoglobin Sickle-cell hemoglobinPrimary

structure

Secondaryand tertiary

Primary structure

Secondaryand tertiaryβ subunit β subunit

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

Normal hemoglob n Sickle cell hemoglobin. . .. . . Exposed

hydrophobic region

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

structures

Quaternary structure

Hemoglobin Aα

β

βα

β

βα

ystructures

Quaternary structure Hemoglobin S

Function Molecules donot associate

ith n

β α βFunction

Molecules interact with one another tocrystallize into a fiber capacity

Red bloodcell shape

with oneanother, eachcarries oxygen.Normal cells arefull of individual

10 μm 10 μm

Red blood

fiber, capacity to carry oxygen is greatly reduced.

Fibers of abnormalhemoglobin d f ll

cell shape full of individualhemoglobinmolecules, eachcarrying oxygen

cell shape

Figure 5.21

50

deform cell into sickle shape.

What Determines Protein What Determines Protein Conformation?

• Protein conformation Depends pon the physical and chemical conditions of the protein’s penvironment

• Temperature, pH, etc. affect Temperature, pH, etc. affect protein structure

51

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

Renaturation

Denatured proteinNormal protein

Figure 5.22

52

g

The Protein-Folding ProblemThe Protein-Folding Problem• Most proteinsMost proteins

– Probably go through several intermediate states on their way to a intermediate states on their way to a stable conformation

– Denaturated proteins no longer work Denaturated proteins no longer work in their unfolded condition

– Proteins may be denaturated by y yextreme changes in pH or temperature

53

• Chaperonins– Are protein molecules that assist in the

proper folding of other proteins

Cap

CorrectlyfoldedproteinPolypeptide

Hollowl dcylinder

St f Ch i The cap attaches causing The cap comesChaperonin(fully assembled)

Steps of ChaperoninAction:

An unfolded poly-peptide enters the cylinder from one

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

The cap comesoff, and the properlyfolded protein is released.

2

1

3

Fi 5 23

54

y f mend.

y pthe folding of the polypeptide. Figure 5.23

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

dimensional structure X raydimensional structure X-raydiffraction pattern

Photographic filmDiffracted X-

raysraysX-raysource

X-raybeam

Crystal Nucleic acid Protein

55(a) X-ray diffraction pattern(b) 3D computer model

Figure 5.24

Nucleic AcidsNucleic Acids

Nucleic acids store and transmit • Nucleic acids store and transmit hereditary informationG• Genes– Are the units of inheritance– Program the amino acid sequence of

polypeptides– Are made of nucleotide sequences

on DNA

56

The Roles of Nucleic AcidsThe Roles of Nucleic Acids• There are two types of nucleic acidsThere are two types of nucleic acids

– Deoxyribonucleic acid (DNA)– Ribonucleic acid (RNA)– Ribonucleic acid (RNA)

57

Deoxyribonucleic AcidDeoxyribonucleic Acid• DNADNA

– Stores information for the synthesis of specific proteinsof specific proteins

– Found in the nucleus of cells

58

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

(translation)1 S nth sis f

DNA

1 Synthesis ofmRNA in the nucleus

NUCLEUS

mRNA

2 Movement of

NUCLEUSCYTOPLASM

mRNA

Rib

3

mRNA into cytoplasm via nuclear pore

Synthesisof protein

Ribosome

59

p

AminoacidsPolypeptideFigure 5.25

The Structure of Nucleic The Structure of Nucleic Acids

5’ end

• Nucleic acids– Exist as polymers called

5 end

5’C

3’C

O

Exist as polymers called polynucleotides

3 C

O

O

3’C

5’C O

60(a) Polynucleotide,

or nucleic acid

3 C3’ end

OH

Figure 5.26

• Each polynucleotideE p y u– Consists of monomers called nucleotides– Sugar + phosphate + nitrogen baseSugar + phosphate + nitrogen base

Nucleoside

Nitrogenousbase

O 5’C

O

O−

−O P CH2

3’CPhosphate

O

3’CPhosphategroup Pentose

sugar

(b) NucleotideFigure 5.26

61

Nucleotide MonomersM m

• Nucleotide monomers• Nucleotide monomers– Are made up of

nucleosides (sugar + CHCH

Nitrogenous basesPyrimidines

CN

NCO

NH2

CHCH

OC

N CHHN C

O

C CH3

N

HNC

CO

O

CHCHnucleosides (sugar +

base) and phosphate groups

Uracil (in RNA)U

OH

O NH

NH

O

CytosineC

Thymine (in DNA)T

NH2 OPurines

Uracil (in RNA)U

groupsN

HCN C

C N

C

CHN

2

NHC

NHH

C C

N

NHC NH2

AdenineA

GuanineG

OHOCH2

HH H

OH

H

OHOCH2

HH H

OH

H

Pentose sugars

OHOH

4’

5”

3’OH H

2’

1’

5”

4’

3’ 2’

1’

62(c) Nucleoside componentsFigure 5.26

Ribose (in RNA)Deoxyribose (in DNA) Ribose (in RNA)OHOHOH H

Nucleotide PolymersNucleotide Polymers• Nucleotide polymersNucleotide polymers

– Are made up of nucleotides linked by the–OH group on the 3´ carbon of one the OH group on the 3 carbon of one nucleotide and the phosphate on the 5´carbon on the next

63

GeneGene• The sequence of bases along a The sequence of bases along a

nucleotide polymer– Is unique for each gene– Is unique for each gene

64

The DNA Double HelixThe DNA Double Helix• Cellular DNA moleculesCellular DNA molecules

– Have two polynucleotides that spiral around an imaginary axisan imaginary axis

– Form a double helix

65

• The DNA double helix• The DNA double helix– Consists of two antiparallel nucleotide

strandsstrands3’ end

Sugar-phosphatebackbone

5’ end

Base pair (joined byhydrogen bonding)Old strands

Nucleotideb t t b about to be

added to a new strand

A 3’ end

3’ end New

5’ end

663’ end

3 end

5’ end

strands

Figure 5.27

A T C GA,T,C,G• The nitrogenous bases in DNAThe nitrogenous bases in DNA

– Form hydrogen bonds in a complementary fashion (A with T only and C with G only)fashion (A with T only, and C with G only)

67

DNA and Proteins as Tape DNA and Proteins as Tape Measures of Evolution

• Molecular comparisons Molecular comparisons – Help biologists sort out the

evolutionary connections among evolutionary connections among species

68

The Theme of Emergent Properties The Theme of Emergent Properties in the Chemistry of Life: A Review

• Higher levels of organizationR lt i th f – Result in the emergence of new properties

O i ti• Organization– Is the key to the chemistry of

liflife

69

70