The Molecules of Life

• Within cells, small organic molecules are joined together to form larger molecules

• Macromolecules are large molecules composed of thousands of covalently connected atoms

Most macromolecules are polymers, built from monomers

• A polymer is a long molecule consisting of many similar building blocks called monomers

• Three of the four classes of life’s organic molecules are polymers:

– Carbohydrates

– Proteins

– Nucleic acids

The Synthesis and Breakdown of Polymers

• Monomers form larger molecules by condensation reactions called dehydration reactions

• Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction

Short polymer Unlinked monomer

Dehydration removes a watermolecule, forming a new bond

Dehydration reaction in the synthesis of a polymer

Longer polymer

Hydrolysis adds a watermolecule, breaking a bond

Hydrolysis of a polymer

The Diversity of Polymers

• Each cell has thousands of different kinds of macromolecules

• Macromolecules vary among cells of an organism, vary more within a species, and vary even more between species

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

1 2 3 HOH

Carbohydrates serve as fuel and building material

• Carbohydrates include sugars and the polymers of sugars

• The simplest carbohydrates are monosaccharides, or single sugars

• Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks

Sugars

• Monosaccharides have molecular formulas that are usually multiples of CH2O

• Glucose is the most common monosaccharide

• Monosaccharides are classified by location of the carbonyl group and by number of carbons in the carbon skeleton

Triose sugars(C3H6O3)

GlyceraldehydeAld

ose

sK

eto

s es

Pentose sugars(C5H10O5)

Ribose

Hexose sugars(C6H12O6)

Glucose Galactose

Dihydroxyacetone

Ribulose

Fructose

• Monosaccharides serve as a major fuel for cells and as raw material for building molecules

• Though often drawn as a linear skeleton, in aqueous solutions they form rings

Linear andring forms

Abbreviated ringstructure

• A disaccharide is formed when a dehydration reaction joins two monosaccharides

• This covalent bond is called a glycosidic bond

• Lactose = Glu + Gal

• Maltose = Glu + Glu

• Sucrose = Glu + Fru

Glucose

Maltose

Fructose Sucrose

Glucose Glucose

Dehydrationreaction in thesynthesis of maltose

Dehydrationreaction in thesynthesis of sucrose

1–4glycosidic

linkage

1–2glycosidic

linkage

Polysaccharides

• Polysaccharides, the polymers of sugars, have storage and structural roles

• The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages

Starch granulesin a potato tuber cell

Cellulose microfibrilsin a plant cell wall

Glycogen granulesin muscletissue

Cellulosemolecules

Hydrogen bondsbetween —OH groups(not shown) attached tocarbons 3 and 6

Starch (amylose)

Glycogen

Cellulose

Glucosemonomer

Storage Polysaccharides

• Starch, a storage polysaccharide of plants, consists entirely of glucose monomers

• Plants store surplus starch as granules within chloroplasts and other plastids

Chloroplast Starch

1 µm

Amylose

Starch: a plant polysaccharide

Amylopectin

• Glycogen is a storage polysaccharide in animals

• Humans and other vertebrates store glycogen mainly in liver and muscle cells

Mitochondria Glycogen granules

0.5 µm

Glycogen

Glycogen: an animal polysaccharide

Structural Polysaccharides

• Cellulose is a major component of the tough wall of plant cells

• Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ

• The difference is based on two ring forms for glucose: alpha () and beta ()

a Glucose

a and b glucose ring structures

b Glucose

Starch: 1–4 linkage of a glucose monomers.

Cellulose: 1–4 linkage of b glucose monomers.

• Polymers with alpha glucose are helical

• Polymers with beta glucose are straight

• In straight structures, H atoms on one strand can bond with OH groups on other strands

• Parallel cellulose molecules held together this way are grouped into microfibrils, which form strong building materials for plants

Cellulosemolecules

Cellulose microfibrilsin a plant cell wall

Cell walls Microfibril

Plant cells

0.5 µm

Glucosemonomer

• Enzymes that digest starch by hydrolyzing alpha linkages can’t hydrolyze beta linkages in cellulose

• Cellulose in human food passes through the digestive tract as insoluble fiber

• Some microbes use enzymes to digest cellulose

• Many herbivores, from cows to termites, have symbiotic relationships with these microbes

• Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods

• Chitin also provides structural support for the cell walls of many fungi

• Chitin can be used as surgical thread

Lipids are a diverse group of hydrophobic molecules

• Lipids are the one class of large biological molecules that do not form polymers

• The unifying feature of lipids is having little or no affinity for water

• Lipids are hydrophobic becausethey consist mostly of hydrocarbons, which form nonpolar covalent bonds

• The most biologically important lipids are fats, phospholipids and steroids

Fats

• Fats are constructed from two types of smaller molecules: glycerol and fatty acids

• Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon

• A fatty acid consists of a carboxyl group attached to a long carbon skeleton

Dehydration reaction in the synthesis of a fat

Glycerol

Fatty acid(palmitic acid)

• Fats separate from water because water molecules form hydrogen bonds with each other and exclude the fats

• In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride

Ester linkage

Fat molecule (triacylglycerol)

• Fatty acids vary in length (number of carbons) and in the number and locations of double bonds

• Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds

• Unsaturated fatty acids have one or more double bonds

• The major function of fats is energy storage

(a) Saturated fat (b) Unsaturated fat

Structuralformula of asaturated fatmolecule

Structuralformula of anunsaturated fat molecule Space-filling

model ofstearic acid,a saturatedfatty acid

Space-fillingmodel of oleicacid, an unsaturatedfatty acid Double bond

causes bending.

• Fats made from saturated fatty acids are called saturated fats

• Most animal fats are saturated

• Saturated fats are solid at room temperature

• A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits

Saturated fat and fatty acid.

Stearic acid

• Fats made from unsaturated fatty acids are called unsaturated fats

• Plant fats and fish fats are usually unsaturated

• Plant fats and fish fats are liquid at room temperature and are called oils

Unsaturated fat and fatty acid.

Oleic acid

cis double bondcauses bending

Phospholipids

• In a phospholipid, two fatty acids and a phosphate group are attached to glycerol

• The two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head

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

Hydrophilichead

(d) Phospholipid bilayer

(c) Phospholipid symbol

Hydrophobictails

Choline

Phosphate

Glycerol

Fatty acids

Hyd

rop

hil

ic h

ead

Hyd

rop

ho

bic

tai

ls

• When phospholipids are added to water, they self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior

• The structure of phospholipids results in a bilayer arrangement found in cell membranes

• Phospholipids are the major component of all cell membranes

WATERHydrophilichead

Hydrophobictails

WATER

Steroids

• Steroids are lipids characterized by a carbon skeleton consisting of four fused rings

• Cholesterol, an important steroid, is a component in animal cell membranes

• Although cholesterol is essential in animals, high levels in the blood may contribute to cardiovascular disease

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

• Proteins account for more than 50% of the dry mass of most cells

• Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances

Enzymatic proteins

Storage proteins

Defensive proteins

Transport proteins

Enzyme

Function: Selective acceleration of chemical reactions

Function: Storage of amino acids

Example: Digestive enzymes catalyze thehydrolysis of bonds in food molecules.

Ovalbumin Amino acidsfor embryo

Examples: Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants have storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo.

Examples: Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules across cell membranes.

Function: Transport of substances

Transportprotein

Cell membrane

Antibodies

BacteriumVirus

Function: Protection against disease

Example: Antibodies inactivate and help destroy viruses and bacteria.

Hormonal proteins

Contractile and motor proteins

Receptor proteins

Structural proteins

Example: Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration.

Function: Coordination of an organism’s activities

Normalblood sugar

Highblood sugar

Insulinsecreted

Examples: Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contraction of muscles.

Function: Movement

Muscle tissue

Actin Myosin

30 m Connective tissue 60 m

Collagen

Examples: Keratin is the protein of hair, horns, feathers, and other skin appendages.Insects and spiders use silk fibers to make their cocoons and webs, respectively. Collagen and elastin proteins provide afibrous framework in animal connective tissues.

Function: Support

Signaling molecules

Receptorprotein

Example: Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells.

Function: Response of cell to chemical stimuli

• Enzymes are a type of protein that acts as a catalyst, speeding up chemical reactions

• Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life

Substrate(sucrose)

Enzyme(sucrose)

Fructose

Glucose

Defensive proteins

Antibodies

BacteriumVirus

Function: Protection against disease

Example: Antibodies inactivate and help destroy viruses and bacteria.

Storage proteins

Function: Storage of amino acids

Ovalbumin Amino acidsfor embryo

Examples: Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants have storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo.

Transport proteins

Examples: Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules across cell membranes.

Function: Transport of substances

Transportprotein

Cell membrane

Hormonal proteins

Example: Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration.

Function: Coordination of an organism’s activities

Normalblood sugar

Highblood sugar

Insulinsecreted

Receptor proteins

Signaling molecules

Receptorprotein

Example: Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells.

Function: Response of cell to chemical stimuli

Contractile and motor proteins

Examples: Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contraction of muscles.

Function: Movement

Muscle tissue

Actin Myosin

30 m

Structural proteins

Connective tissue 60 m

Collagen

Examples: Keratin is the protein of hair, horns, feathers, and other skin appendages.Insects and spiders use silk fibers to make their cocoons and webs, respectively. Collagen and elastin proteins provide afibrous framework in animal connective tissues.

Function: Support

Polypeptides

• Polypeptides are polymers of amino acids

• A protein consists of one or more polypeptides

Amino Acid Monomers

• Amino acids are organic molecules with carboxyl and amino groups

• Amino acids differ in their properties due to differing side chains, called R groups

• Cells use 20 amino acids to make thousands of proteins

Aminogroup

Carboxylgroup

carbon

Nonpolar side chains; hydrophobicSide chain (R group)

Glycine (Gly or G)

Alanine (Ala or A)

Methionine (Met or M)

Phenylalanine (Phe or F)

Leucine (Leu or L)

Isoleucine (le or )

Tryptophan (Trp or W)

Proline (Pro or P)

Valine (Val or V)

Polar side chains; hydrophilic

Serine (Ser or S)

Threonine (Thr or T)

Tyrosine (Tyr or Y)

Asparagine (Asn or N)

Cysteine (Cys or C)

Glutamine (Gln or Q)

Aspartic acid (Asp or D)

Glutamic acid (Glu or E)

Arginine (Arg or R)

Lysine (Lys or K)

Histidine (His or H)

Electrically charged side chains; hydrophilic

Acidic (negatively charged)

Basic (positively charged)

Amino Acid Polymers

• Amino acids are linked by peptide bonds

• A polypeptide is a polymer of amino acids

• Polypeptides range in length from a few monomers to more than a thousand

• Each polypeptide has a unique linear sequence of amino acids

• Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus)

• NCC-NCC-NCC-NCC

New peptidebond forming

Peptide bond

Side chains

Back-bone

Amino end (N-terminus)

Carboxyl end(C-terminus)

Peptide bond

Protein Conformation and Function

• A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape

• The sequence of amino acids determines a protein’s three-dimensional conformation

• A protein’s conformation determines its function

• Ribbon models and space-filling models can depict a protein’s conformation

Antibody protein Protein from flu virus

Four Levels of Protein Structure

• The primary structure of a protein is its unique sequence of amino acids

• Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain

• Tertiary structure is determined by interactions among various side chains (R groups)

• Quaternary structure results when a protein consists of multiple polypeptide chains

Secondarystructure

Tertiarystructure

Quaternarystructure

Transthyretinpolypeptide

Transthyretinprotein

pleated sheet

helix

• Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word

• Primary structure is determined by inherited genetic information

Primary structure

Amino end

Carboxyl end

Primary structure of transthyretin

125

95

90

100105110

120

115

80

70 60

85

75

6555

504540

2530

35

20 15

1051

Amino acids

• The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone

• Typical secondary structures are a coil called an alpha helix and a folded structure called a beta pleated sheet

Secondary structure

Hydrogenbond

pleated sheet

helix

Hydrogen bond

strand

Tertiary structure

Transthyretinpolypeptide

Hydrophobicinteractions andvan der Waalsinteractions

Polypeptidebackbone

Disulfide bridge

Ionic bond

Hydrogenbond

Quaternary structure

Transthyretinprotein

• Quaternary structure results when two or more polypeptide chains form one macromolecule

• Collagen is a fibrous protein consisting of three polypeptides coiled like a rope

• Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains

Chains

ChainsHemoglobin

IronHeme

CollagenPolypeptide chain

Polypeptidechain

Sickle-Cell Disease: A Simple Change in Primary Structure

• A slight change in primary structure can affect a protein’s conformation and ability to function

• Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin

Red bloodcell shape

Normal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen.

10 µm 10 µm

Red bloodcell shape

Fibers of abnormalhemoglobin deformcell into sickleshape.

Figure 3.22

subunit

subunit

Function Red Blood CellShape

QuaternaryStructure

Secondaryand TertiaryStructures

PrimaryStructure

Normal hemoglobin

Sickle-cell hemoglobin

Exposed hydro-phobic region

Molecules crystallizedinto a fiber; capacity tocarry oxygen is reduced.

Molecules do notassociate with oneanother; each carriesoxygen.

12

345

67

12

345

67

No

rmal

Sic

kle-

cell

5 m

5 m

What Determines Protein Conformation?

• In addition to primary structure, physical and chemical conditions can affect conformation

• Alternations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel

• This loss of a protein’s native conformation is called denaturation

• A denatured protein is biologically inactive

Denaturation

Renaturation

Denatured proteinNormal protein

The Protein-Folding Problem

• It is hard to predict a protein’s conformation from its primary structure

• Most proteins probably go through several states on their way to a stable conformation

• Chaperonins are protein molecules that assist the proper folding of other proteins

Chaperonin(fully assembled)

Hollowcylinder

Cap

Polypeptide

Correctlyfoldedprotein

An unfolded poly-peptide enters thecylinder from oneend.

Steps of ChaperoninAction:

The cap comesoff, and theproperly foldedprotein is released.

The cap attaches, causingthe cylinder to changeshape in such a way that it creates a hydrophilicenvironment for thefolding of the polypeptide.

• Scientists use X-ray crystallography to determine a protein’s conformation

• Another method is nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization

Photographic film

Diffracted X-rays

X-raysource X-ray

beam

X-raydiffraction pattern

Crystal

Nucleic acid

3D computer modelX-ray diffraction pattern

Protein

Digital detectorCrystal

Experiment

Results

X-raysource X-ray

beam

X-ray diffractionpattern

DiffractedX-rays

DNARNA

RNApolymerase

Nucleic acids store and transmit hereditary information

• The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene

• Genes are made of DNA, a nucleic acid

The Roles of Nucleic Acids

• There are two types of nucleic acids:

– Deoxyribonucleic acid (DNA)

– Ribonucleic acid (RNA)

• DNA provides directions for its own replication

• DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis

• Protein synthesis occurs in ribosomes

NUCLEUS

DNA

CYTOPLASM

mRNA

mRNA

Ribosome

Aminoacids

Synthesis ofmRNA in the nucleus

Movement ofmRNA into cytoplasmvia nuclear pore

Synthesis of protein

Polypeptide

The Structure of Nucleic Acids

• Nucleic acids are polymers called polynucleotides

• Each polynucleotide is made of monomers called nucleotides

• Each nucleotide consists of a nitrogenous base, a pentose sugar and a phosphate group

• The portion of a nucleotide without the phosphate group is called a nucleoside

Sugar-phosphate backbone(on blue background)

(a) Polynucleotide, or nucleic acid

(b) Nucleotide

(c) Nucleoside components

5 end

3 end

5C

5C

3C

3C

Phosphategroup Sugar

(pentose)

Nitrogenousbase

Nucleoside

Nitrogenous bases

Pyrimidines

Cytosine (C) Thymine(T, in DNA)

Uracil(U, in RNA)

Purines

Adenine (A) Guanine (G)

Sugars

Deoxyribose (in DNA) Ribose (in RNA)

5 end

3 end

Nucleoside

Nitrogenousbase

Phosphategroup

Nucleotide

Polynucleotide, ornucleic acid

Pentosesugar

Sugar-phosphatebackbones

5

5

3

3 Base pair joinedby hydrogen bonding

Hydrogen bonds

Nucleotide Monomers

• Nucleotide monomers are made up of nucleosides and phosphate groups

• Nucleoside = nitrogenous base + sugar

• There are two families of nitrogenous bases:

– Pyrimidines have a single six-membered ring

– Purines have a six-membered ring fused to a five-membered ring

• In DNA, the sugar is deoxyribose

• In RNA, the sugar is ribose

Nitrogenous bases

Pyrimidines

Purines

Pentose sugars

CytosineC

Thymine (in DNA)T

Uracil (in RNA)U

AdenineA

GuanineG

Deoxyribose (in DNA)

Nucleoside components

Ribose (in RNA)

Nucleotide Polymers

• Nucleotide polymers are linked together, building a polynucleotide

• Adjacent nucleotides are joined by covalent bonds that form between the –OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next

• These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages

• The sequence of bases along a DNA or mRNA polymer is unique for each gene

The DNA Double Helix

• A DNA molecule has two polynucleotides spiraling around an imaginary axis, forming a double helix

• In the DNA double helix, the two backbones run in opposite 5´ to 3´ directions from each other, an arrangement referred to as antiparallel

• One DNA molecule includes many genes

• The nitrogenous bases in DNA form hydrogen bonds in a complementary fashion: A always with T, and G always with C

Sugar-phosphatebackbone

3 end5 end

Base pair (joined byhydrogen bonding)

Old strands

Nucleotideabout to beadded to anew strand

5 end

New strands

3 end

5 end3 end

5 end

DNA and Proteins as Tape Measures of Evolution

• The linear sequences of nucleotides in DNA molecules are passed from parents to offspring

• Two closely related species are more similar in DNA than are more distantly related species

• Molecular biology can be used to assess evolutionary kinship

Animations and Videos

• Macromolecules – 1

• Macromolecules – 2

• Polymers

• Biomolecules – Carbohydrates

• Carbohydrates

• Glucose in Water

• Dehydration and Hydrolysis

Animations and Videos

• Disaccharides

• Polysaccharides

• Bozeman – Carbohydrates

• Fats

• Lipids

• Biomolecules – Lipids

• Bozeman - Lipids

Animations and Videos

• Proteins

• Protein Structure – 1

• Protein Structure – 2

• Life Cycle of a Protein

• Peptide Bond Formation

• Dehydration Synthesis of Amino Acids

• Protein Folding - 1

Animations and Videos

• Protein Folding – 2

• Protein Organization

• Protein Denaturation

• Bozeman – Proteins

• How Enzymes Work

• Enzyme Action and the Hydrolysis of Sucrose

• Enzyme Catalysis - 1

Animations and Videos

• Enzyme Catalysis – 2

• Allosteric Regulation of Enzymes

• Allosteric Enzyme

• Enzyme Changing Shape

• Bozeman – Enzymes

• Bozeman - Nucleic Acids

• Testing Organic Substances

• Chapter Quiz Questions – 1

Animations and Videos

• Chapter Quiz Questions – 2