05 macromolecules

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1 Chapter 5 The Structure and Function of Macromolecules

Transcript of 05 macromolecules

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Chapter 5The Structure and

Function of Macromolecules

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The Molecules of Life• Overview:

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

– Atom ---> molecule --- compound

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Macromolecules– Are large molecules composed of smaller

molecules– Are complex in their structures

Figure 5.1

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Macromolecules

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

– Carbohydrates– Proteins– Nucleic acids– Lipids

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• A polymer– 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

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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

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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

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• 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

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Carbohydrates• Serve as fuel and building

material• Include both sugars and

their polymers (starch, cellulose, etc.)

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Sugars

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

organic molecules– Can be combined into polymers

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• Examples of Monosaccharides

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

Triose sugars(C3H6O3)

Pentose sugars(C5H10O5)

Hexose sugars(C6H12O6)

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• Monosaccharides– May be linear– Can form rings

H

H C OH

HO C H

H C OH

H C OH

H C

OC

H

1

2

3

4

5

6

H

OH

4C

6CH2OH 6CH2OH

5C

HOH

C

H OH

H2 C

1CH

O

H

OH

4C

5C

3 C

H

HOH

OH

H2C

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.

OH 3

O H OO6

1

Figure 5.4

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• Disaccharides– Consist of two

monosaccharides– Are joined by a glycosidic

linkage (a bond between an O atom and two different H atoms from different base molecules – see diagram on nest slide)

Dehydration Synthesis (Condensation) Reactions & Hydrolysis Reactions

• These are the two most common types of reactions that occur in living organisms.

• Dehydrations (Condensation) reactions join monomers (or small molecules) together to form larger molecules by removing a water molecule

• Hydrolysis reactions break apart larger, macromolecules in to smaller molecules (monomers) by adding a water molecule and breaking a glycosidic linkage. 14

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.

H2O

CH2OH

Glucose Fructose Sucrose

H

HO

H

HOH

H

OH

O H

OH

CH2OH

H

H

O

H

HOH

OH

O HCH2OH

CH2OH HO

OHH

CH2OH

HOH H

O

HOH

CH2OH

H HO

OH

O

1 21–2

glycosidiclinkage

H

H

HO

H

HOH H

OH

O H

OH

CH2OH

H

O

H

HOH H

OH

O H

OH

CH2OH

H

H2O

H

HO

OHH

CH2OH

HOH H

O H

OHH

CH2OH

HOH H

O H

OHO

1 41– 4

glycosidiclinkage

Glucose Glucose Maltose

OH

H

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Polysaccharides• Polysaccharides

– Are polymers of sugars– Serve many roles in organisms

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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 µm

(a) Starch: a plant polysaccharideFigure 5.6

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

animals Mitochondria Giycogen granules

0.5 µm

(b) Glycogen: an animal polysaccharide

Glycogen

Figure 5.6

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Structural Polysaccharides• Cellulose

– Is a polymer of glucose

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– Has different glycosidic linkages than starch

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

H O

O

CH2OH

HOH H

H

OHO

HH

H

HO

4

C

C

C

C

C

C

H

H

H

HO

OH

HOHOHOH

H

O

CH2OH

HH

H

OH

OHH

H

HO

4 OH

CH2OH O

OH

OH

HO

41O

CH2OH

OOH

OH

O

CH2OH

OOH

OH

CH2OH

OOH

OH

O O

CH2OH O

OH

OH

HO

4O

1

OH

O

OH

OHO

CH2OH O

OH

O OH

O

OH

OH

(a) α and β glucose ring structures

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

1

α glucose β glucose

CH2OH

CH2OH

1 4 41 1

Figure 5.7 A–C

Plant cells

0.5 µm

Cell walls

Cellulose microfibrils in a plant cell wall

Microfibril

CH2OH

CH2OH

OHOH

OO

OHOCH2OH

OO

OHO

CH2OH OH

OH OHO

O

CH2OHO

O OH

CH2OH

OO

OH

O

O

CH2OHOH

CH2OHOHOOH OH OH OH

O

OH OH

CH2OH

CH2OHOHO

OH CH2OH

OO

OH CH2OH

OH

β 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 associateto form a microfibril, the main architectural unit of the plant cell wall.

A cellulose moleculeis an unbranched βglucose polymer.

OH

OH

O

OOH

Cellulosemolecules

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

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

facilitate this process

Figure 5.9

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

(c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals.

(a) The structure of the chitin monomer.

O

CH2OH

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.

OH

Figure 5.10 A–C

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Lipids

• Lipids are a diverse group of hydrophobic molecules

• Lipids– Are the one class of large biological

molecules that do not always consist of polymers

– Share the common trait of being hydrophobic

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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

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Fats– Are constructed from two types of smaller

molecules, a single glycerol and usually three fatty acids

– Fatty Acids have a “carboxyl” group at the end of the chain

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Fats• Glycerol forms the “backbone” of the fat

molecule

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“Fatty” Acids• Vary in the length, number and locations of

double bonds they contain

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• 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

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• Unsaturated fatty acids– Have one or more double bonds

(b) Unsaturated fat and fatty acidcis double bondcauses bending

Oleic acid

Figure 5.12

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

third fatty acid

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• Phospholipid structure– Consists of a hydrophilic “head” and a

hydrophobic “tail”CH2

OPO OOCH2CHCH2

OO

C O C O

Phosphate

Glycerol

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

Fatty acids

(c) Phospholipid symbol

Hyd

roph

obic t

ails

Hydrophilichead

Hydrophobictails

Hyd

roph

ilic

head CH2 Choline+

Figure 5.13

N(CH3)3

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

Hydrophilichead

WATER

WATER

Hydrophobictail

Figure 5.14

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Steroids• Steroids are lipids characterized by a

carbon skeleton consisting of four fused rings

HO

CH3

CH3

H3C CH3

CH3

Figure 5.15

Steroids• Steroids include estrogen, progesterone and

testosterone.

• Estrogen and progesterone are made primarily in the ovary and in the placenta during pregnancy

• Testosterone is made in the testes.Testosterone is also converted into estrogen to regulate the supply of each, in the bodies of both females and males.

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• One steroid, cholesterol– Is found in cell membranes and prevents

them “freezing”– Is a precursor for some hormones

HO

CH3

CH3

H3C CH3

CH3

Figure 5.15

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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

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• An overview of protein functions

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

catalyst, speeding up chemical reactions

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.

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4 Products are released.Figure 5.16

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Polypeptides• Polypeptides

– Are polymers (chains) of amino acids

• A protein– Consists of one or more polypeptides

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• Amino acids– Are organic molecules possessing both carboxyl and amino groups

– Differ in their properties due to differing side chains, called R groups

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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

CO

O–

CH2

NH

H

CO

O–

H3N+ C

CH2

H2C

H2

NC

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–

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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–

OPolar

Electricallycharged

–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)

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Amino Acid Polymers• Amino acids

– Are linked by peptide bonds

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Protein Conformation and Function

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

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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

ValLeuAsp

AlaValArgGlySer

ProAla

GlylleSerProPheHisGluHis

AlaGlu

ValValPheThrAlaAsn

AspSer

GlyProArgArgTyrThrlle

AlaAlaLeu

LeuSerProTyrSerTyrSerThr

ThrAlaVal

ValThrAsnProLysGlu

ThrLysSer

TyrTrpLysAlaLeu

GluLle Asp

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O C α helix

β 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

CO

C

NH

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 N

C

RC

H O

CHR

N HO C

RC H

N H

O CH C R

N H

CC

N

RH

O C

H C R

N HO C

RC

H

H

CR

NH

CO

C

NH

RCH C

ONH

C

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

into a repeating configuration– Includes the α helix (coiled) and the β

pleated (folded) sheet

H H

Figure 5.20

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

a polypeptide– Results from interactions between amino

acids and R groupsCH2

CH

OHOCHOCH2

CH2 NH3+ C-O CH2

O

CH2SSCH2

CH

CH3

CH3

H3CH3C

Hydrophobic interactions and

van der Waalsinteractions

Polypeptidebackbone

Hyrdogenbond

Ionic bond

CH2

Disulfide bridge

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• Quaternary structure– Is the overall protein

structure that results from the aggregation of two or more polypeptide subunits

Polypeptidechain

Collagenβ Chains

α ChainsHemoglobin

IronHeme

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Review of Protein Structure

+H3NAmino end

Amino acidsubunits

α helix

Primary Secondary Tertiary Quaternary

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Sickle-Cell Disease: A Simple Change in Primary Structure

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

substitution in the protein hemoglobin

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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

α

β

β

α

10 µm 10 µm

α

β

β α

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.

β subunit β 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

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What Determines Protein Conformation?

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

• Temperature, pH, etc. affect protein structure

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

Denaturation

Renaturation

Denatured proteinNormal protein

Figure 5.22

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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

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• 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.

CorrectlyfoldedproteinPolypeptide

2

1

3

Figure 5.23

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

dimensional structure X-raydiffraction pattern

Photographic filmDiffracted X-

raysX-raysource

X-ray beam

Crystal Nucleic acid Protein

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

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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

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

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

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Deoxyribonucleic Acid• DNA

– Stores information for the synthesis of specific proteins

– Found in the nucleus of cells

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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

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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

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

Nitrogenousbase

Nucleoside

O

O

O−

−O P CH2

5’C

3’CPhosphategroup Pentose

sugar

(b) NucleotideFigure 5.26

O

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Nucleotide Monomers

• Nucleotide monomers – Are made up of

nucleosides (sugar + base) and phosphate groups

(c) Nucleoside componentsFigure 5.26

CHCH

Uracil (in RNA)U

Ribose (in RNA)

Nitrogenous bases Pyrimidines

CN

NCO

H

NH2

CHCH

OC

NH

CHHN C

O

CCH3

N

HNC

CH

O

O

CytosineC

Thymine (in DNA)T

NHC

N C

C N

C

CHN

NH2 ON

HCNHH

C C

N

NHC NH2

AdenineA

GuanineG

Purines

OHOCH2

HH H

OH

H

OHOCH2

HH H

OH

H

Pentose sugars

Deoxyribose (in DNA) Ribose (in RNA)OHOH

CHCH

Uracil (in RNA)U

4’

5”

3’OH H

2’

1’

5”

4’

3’ 2’

1’

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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

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Gene• The sequence of bases along a

nucleotide polymer– Is unique for each gene

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The DNA Double Helix• Cellular DNA molecules

– Have two polynucleotides that spiral around an imaginary axis

– Form a double helix

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• The DNA double helix– Consists of two antiparallel nucleotide

strands 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

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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)

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DNA and Proteins as Tape Measures of Evolution

• Molecular comparisons – Help biologists sort out the

evolutionary connections among species

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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