1

The Structure and Function of

Macromolecules

Chapter 3

2

Are large molecules (polymers) composed of smaller molecules (monomers)

Are complex in their structures

Macromolecules

Protein

3

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

CarbohydratesProteinsNucleic acidsLipids

Macromolecules

4

A polymerIs a long molecule consisting of

many similar building blocks called monomers

Specific monomers make up each macromoleculeAmino acids are the monomers for

proteinsMonosaccharides make up

carbohydratesGlycerol and Fatty acids for LipidsNucleotides for Nucleic acids

5

Monomers form larger molecules by condensation reactions called Dehydration synthesis or Condensation

Is an anabolic reaction (building up)

The Synthesis and Breakdown of Polymers

(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 5.2ACondensation of amino acids

6

Dehydration Synthesis of Carbohydrates

7

Polymers can disassemble byHydrolysis (addition of water molecules)Is a catabolic or breakdown reaction

The Synthesis and Breakdown of Polymers

(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

8

Hydrolysis of a Disaccharide

9

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 small set of monomers

How many words can be made using the English alphabet?

10

C, H, O w/ a H:O ratio of 2:1Serve as fuel and building material

Sugars and their polymers (starch, cellulose, etc.)

Tend to end in “ose”

Carbohydrates

11

MonosaccharidesAre the simplest sugarsMost are: C6H12O6Can be used for fuelCan be converted into other organic molecules

Can be combined into polymers

Glucose, Galactose, Fructose, Ribose…

Sugars

Examples of monosaccharides

12

Triose sugars(C3H6O3)

Pentose sugars

(C5H10O5)Hexose sugars

(C6H12O6)

H C OHH C OHH C OHH C OHH C OH

H C OHHO C H

H C OHH C OHH C OH

H C OHHO C HHO C H

H C OHH C OH

H C OH

H C OH

H C OH

H C OHH C OHH C OH

H C OHC OC O

H C OHH C OHH C OH

HO C H

H C OHC O

H

H

H

H H H

H

H H H H

HH H

C C C COOOO

Aldo

ses

Glyceraldehyde

RiboseGlucose Galactose

Dihydroxyacetone

Ribulose

Keto

ses

Fructose

Figure 5.3

13

MonosaccharidesMay be linearCan form rings in solution

H

H C OH

HO C H

H C OH

H C OH

H C

OC

H

12

34

5

6

H

OH

4C

6CH2OH

6CH2OH5C

HOH

CH OH

H2 C

1CH

O

H

OH

4C

5C

3 CH

HOH

OH

H2C

1 C

OH

HCH2OH

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.

OH 3

O H O O6

1

Figure 5.4

14

DisaccharidesC12H22O11Consist of two monosaccharides

Are joined by a glycosidic linkage

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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.

H

HOH

HOH H

OH

O H

OH

CH2OH

H

HO

H

HOH H

OH

O HOH

CH2OH

H

O

H

HOH H

OH

O H

OH

CH2OH

H

H2O

H2O

H

H

O

H

HOH

OH

O HCH2OH

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

1– 2glycosidic

linkage

MaltoseGlucose Glucose

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PolysaccharidesAre polymers of sugars

Serve many roles in organisms

Starch, glycogen, cellulose, chitin

Polysaccharides

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Starch - AmyloseIs a polymer consisting entirely of glucose monomers

Is the major storage form of glucose in plants

in amyloplasts

Storage PolysaccharidesChloroplas

t Starch

Amylose Amylopectin

1 m

(a) Starch: a plant polysaccharideFigure 5.6

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GlycogenConsists of glucose monomersIs the major storage form of glucose in animal

livers Mitochondria Giycogen granules

0.5 m

(b) Glycogen: an animal polysaccharide

Glycogen

Figure 5.6

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CelluloseIs a polymer of glucose

Structural Polysaccharides

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Has different glycosidic linkages than starch

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

H O

OCH2OH

HOH H

H

OHOHH

H

HO4

CCCCCC

H

H

H

HOOHHOHOHOH

H

OCH2OH

HH

H

OH

OHH

H

HO4 OH

CH2OHO

OH

OH

HO41

O

CH2OHO

OH

OH

O

CH2OHO

OH

OH

CH2OHO

OH

OH

O O

CH2OHO

OH

OH

HO 4O

1

OH

OOH OHO

CH2OHO

OH

O OHO

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

– C6 is on the top left on both monomers– C6 is flipped from top to bottom

OH OH

OH OH

Plant cells

About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall.

A cellulose moleculeis an unbranched glucose polymer.

Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6.

Cellulosemolecules

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

21Hydrogen bonds

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Cellulose is difficult to digestCows have microbes in their stomachs to

facilitate this process

Figure 5.9

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Chitin, another important structural polysaccharideIs found in the exoskeleton of arthropodsCan be used as surgical thread

(a) The structure of the chitin monomer.

OCH2O

H

OHHH OH

HNHCCH3

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

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Lipids are a diverse group of hydrophobic molecules

LipidsAre the one class of large biological molecules

that do not consist of polymersNot considered a true macromoleculesMade up mostly of chains of hydrocarbonsShare the common trait of being hydrophobicFats, oils, waxes, phospholipids and steroidsCarbon, Hydrogen & Oxygen with

H:O ratio >2:1Involved in long term energy storage

Lipids

25

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

Fats

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Saturated fatty acidsHave the maximum number of hydrogen atoms

possibleHave no double bondsLard, butter, animal fat, palm oil, coconut oil, palm

kernel oil

(a) Saturated fat and fatty acid

Stearic acid

Figure 5.12

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Unsaturated fatty acidsHave one or more double bondsOlive oil

(b) Unsaturated fat and fatty acid

cis double bondcauses bending

Oleic acid

Figure 5.12

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The following foods are high in monounsaturated fats: peanut butter olives nuts – almonds, pecans, pistachios, cashews avocado seeds – sesame oils – olive, sesame, peanut, canola

The following foods are high in polyunsaturated fats:walnuts seeds – pumpkin, sunflower flaxseed fish – salmon, tuna, mackerel oils – safflower, soybean, corn

What to eat?

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PhospholipidsHave only two fatty acidsHave a phosphate group instead of a

third fatty acidTypical of a cell membrane

***The kink in the H-C chain due to a double bond is what gives the cell membrane its fluidity

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Phospholipid structureConsists of a hydrophilic “head”

and hydrophobic “tails”CH2

OPO OOCH2CHCH

2OO

C O C O

Phosphate

Glycerol

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

Fatty acids

(c) Phospholipid symbol

Hyd

r oph

obic

tai

ls

Hydrophilichead

Hydrophobictails

–

Hyd

r oph

ilic

h ead CH2 Choline+

Figure 5.13

N(CH3)3

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The structure of phospholipidsResults in a bilayer arrangement found in cell

membranes

Hydrophilic head

WATER

WATER

Hydrophobic tail

Figure 5.14

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SteroidsAre lipids characterized by a carbon skeleton

consisting of four fused rings

Steroids

One steroid, cholesterolIs found in cell membranesIs a precursor for some hormones like estrogen

& testosterone

HO

CH3

CH3

H3C CH3

CH3

Figure 5.15

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36

Proteins have many structures, resulting in a wide range of functionsBuilding and regulatory functions

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

Most hormones are protein derivedProteins are made of monomers called amino

acidsMade up of Carbon, Hydrogen, Oxygen,

Nitrogen & sometimes Sulfur

Proteins

37

An overview of protein functions

38

EnzymesAre a type of protein that acts as a catalyst,

speeding up chemical reactions (by reducing the amount of activation energy needed)

Substrate(sucrose)

Enzyme (sucrase)

Glucose

OH

H O

H2OFructose

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

39

PolypeptidesAre polymers (chains) of amino acids

A proteinConsists of one or more polypeptides

Polypeptides

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Amino acidsAre organic molecules possessing both

carboxyl and amino groupsDiffer in their properties due to differing

side chains, called R groups

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20 different amino acids make up proteins

Twenty Amino Acids (you do not need to memorize these!!)

O

O–

H

H3N+ C CO

O–

H

CH3

H3N+ C

H

CO

O–

CH3 CH3

CH3

C CO

O–

H

H3N+

CH

CH3

CH2

C

H

H3N+

CH3

CH3

CH2

CH

C

H

H3N+ C

CH3

CH2CH2

CH3N+

H

CO

O–

CH2

CH3N+

H

CO

O–

CH2

NH

H

CO

O–

H3N+ C

CH2H2C

H2N C

CH2

H

C

Nonpolar -

Hydrophobic

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

Methionine (Met) Phenylalanine (Phe)

CO

O–

Tryptophan (Trp) Proline (Pro)

H3C

Figure 5.17

S

O

O–

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O–

OH

CH2

C C

H

H3N+

O

O–

H3N+

OH CH3

CH

C C

H O–

O

SH

CH2

C

H

H3N+ CO

O–H3N+ C C

CH2

OH

H H H

H3N+

NH2

CH2

OC

C CO

O–

NH2 OC

CH2

CH2

C CH3N+O

O–

O

Polar - Hydrophili

c

Electrically

Charged - Ionic

–O OC

CH2

C CH3N+

H

O

O–

O– OC

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)

43

Amino acidsAre linked by peptide bonds through Dehydration

synthesis

Amino Acid Polymers

44

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

Protein Conformation and Function

45

The specific order of amino acids in a polypeptide interacts with the environment to determine the overall structure of the protein.

The interactions of the R group of the amino acid determines structure and function of the R region of the protein.Hydrophobic, hydrophilic or

ionic

Primary structure Is the unique sequence of

amino acids in a polypeptide Linear

Four Levels of Protein Structure

Figure 5.20

–

Amino acid

subunits

+H3NAmino

end

oCarboxyl end

oc

GlyProThrGlyThr

GlyGluSeuLysCysProLeu

MetVal

LysVal

LeuAspAlaValArgGlySerProAla

GlylleSerProPheHisGluHis

AlaGlu

ValValPheThrAlaAsnAsp

SerGlyProArg

ArgTyrThr lleAla

AlaLeu

LeuSerProTyrSerTyrSerThr

ThrAlaVal

ValThrAsnProLysGlu

ThrLysSer

TyrTrpLysAlaLeu

GluLleAsp

46

Secondary structureIs the folding or coiling of the

polypeptide into a repeating configuration due to Hydrogen bonds

Includes the helix and the pleated sheet

O C helix

pleated sheetAmino acid

subunitsNCH

CO

C NH

CO H

RC N

H

CO H

CR

NHH

R CO

RCH

NH

CO H

NCO

RCH

NH

HCR

CO

CO

CNH

H

RC

CO

NH H

CR

CO

NH

RCH C

ONH H

CR

CO

NH

RCH C

ONH H

CR

CO

N H

H C RN H O

O C NC

RC

H O

CHR

N HO C

RC H

N H

O CH C R

N H

CC

NR

HO C

H C R

N HO C

RC H

HCR

NH

CO

C

NH

RCH C

ONH

C

H H

Figure 5.20

47

Tertiary structure Is the overall three-dimensional shape of a

polypeptide Results from interactions between amino

acids and R groups - Disulfide bridge formed

CH2CH

OHOCHOCH2

CH2NH3+ C-O CH2

O

CH2SSCH2

CH

CH3CH3

H3CH3C

Hydrophobic interactions and van der Waalsinteractions Polypepti

debackbone

Hyrdogenbond

Ionic bond

CH2

Disulfide bridge

48

Quaternary structureIs the overall protein structure that results

from the aggregation of two or more polypeptide subunits

Polypeptidechain

Collagen Chains

ChainsHemoglobin

IronHeme

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50

Review of Protein Structure

+H3NAmino end

Amino acidsubunits

helix

51

Sickle-cell diseaseResults from a single

amino acid substitution in the protein hemoglobin

Valine for Glutamic acidCaused by a point

mutation

Sickle-Cell Disease: A Simple Change in Primary Structure

Primary structure

Secondaryand tertiarystructures

Quaternary structure

Function

Red bloodcell shape

Hemoglobin A

Molecules donot associatewith oneanother, eachcarries oxygen.

Normal cells are full of individualhemoglobinmolecules, eachcarrying oxygen

10 m 10 m

Primary structure

Secondaryand tertiarystructures

Quaternary structure

Function

Red bloodcell shape

Hemoglobin S

Molecules 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 ProGlulGlu Val His Leu Thr Pro Val Gl

u

52

Fibers of abnormalhemoglobin deform cell into sickle shape.

53

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

Temperature, pH, [salt], etc. influence protein structure

What Determines Protein Conformation?

54

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

Denaturation

Renaturation

Denatured proteinNormal protein

Figure 5.22

55

Amino acid sequences of 875,000 proteins are known.

3D shapes of 7,000 are known.aka, Scientists don’t know the structure of most

proteinsMost 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

The Protein-Folding Problem

56

Chaperonins (aka, chaperone proteins)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.

CorrectlyfoldedproteinPolypeptide

2

1

3

Figure 5.23

57

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

dimensional structure Rosalind Franklin & DNA X-ray

diffraction pattern

Photographic film

Diffracted X-rays

X-raysource

X-ray

beam Crystal

Nucleic acidProtein

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

58

Nucleic acids store and transmit hereditary informationPolymers of nucleotides

GenesAre the units of inheritanceProgram the amino acid sequence of polypeptidesAre made of nucleotide sequences on DNA

Nucleic Acids

59

There are two types of nucleic acidsDeoxyribonucleic acid (DNA)Ribonucleic acid (RNA)

The Roles of Nucleic Acids

60

DNAStores information for the synthesis of specific

proteinsFound in the nucleus of cells

Deoxyribonucleic Acid

61

Directs RNA synthesis (transcription)Directs protein synthesis through RNA

(translation)

DNA Functions

1

2

3

Synthesis of mRNA in the nucleus

Movement of mRNA into cytoplasm

via nuclear pore

Synthesisof protein

NUCLEUSCYTOPLASM

DNA

mRNARibosome

AminoacidsPolypeptide

mRNA

Figure 5.25

62

Nucleic acidsExist as polymers called

polynucleotides

The Structure of Nucleic Acids

(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 polynucleotideConsists of monomers called

nucleotides5C Sugar + phosphate group +

nitrogen base

Nucleotide monomers Are made up

of nucleosides (sugar + base) and phosphate groups

64Nucleotide Monomers

65

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

Nucleotide Polymers5`

5`3`

3`

66

The sequence of bases along a nucleotide polymerIs unique for each gene

Gene

67

Cellular DNA moleculesHave two polynucleotides that spiral around an

imaginary axisForm a double helix

The DNA Double Helix

68

The DNA double helixConsists of two antiparallel nucleotide strandsLook at the C’s on the ribose molecule. The 5th

C bonded to the Phosphate group is the 5` end.

3’ 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

The nitrogenous bases in DNAForm hydrogen bonds in a complementary

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

A,T,C,G

70

Molecular comparisons Help biologists sort out the

evolutionary connections among species

DNA and Proteins as Tape Measures of Evolution