Chapter 5

The Structure and Function of Macromolecules
PowerPoint Lectures for Biology, Seventh Edition
Neil Campbell and Jane Reece

Lectures by Chris Romero
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• Overview: The Molecules of Life
– Another level in the hierarchy of biological organization is reached when small organic molecules are joined together

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• Macromolecules
– Are large molecules composed of smaller molecules – Are complex in their structures

Figure 5.1
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Concept 5.1: Most macromolecules are polymers, built from monomers • Three of the classes of life’s organic molecules are polymers
– Carbohydrates – Proteins – Nucleic acids

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

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The Synthesis and Breakdown of Polymers • Monomers form larger molecules by condensation reactions called dehydration reactions
1

HO

2

3

H

HO

H

Short polymer Dehydration removes a water molecule, forming a new bond HO Figure 5.2A 1 2 3

Unlinked monomer
H2O

4

H

Longer polymer (a) Dehydration reaction in the synthesis of a polymer

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• Polymers can disassemble by
– Hydrolysis
HO 1 2 3 4

H

Hydrolysis adds a water molecule, breaking a bond

H2O

HO

1

2

3

H

HO

H

Figure 5.2B (b) Hydrolysis of a polymer

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The Diversity of Polymers • Each class of polymer
– Is formed from a specific set of monomers 1
2 3
H HO

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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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• Concept 5.2: Carbohydrates serve as fuel and building material • Carbohydrates
– Include both sugars and their polymers

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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
Triose sugars Pentose sugars (C3H6O3) (C5H10O5)
H C H C C H OH OH H H H H O H C C C C C H OH OH OH OH H HO H H H O H C C C C C C H OH H OH OH OH H HO HO H H

Hexose sugars (C6H12O6)
O H C C C C C C H OH H H OH OH O

Aldoses

H

Glyceraldehyde

Ribose
H H C OH C O H H H H H C OH C O

Glucose
H H

Galactose
C OH C O

Ketoses

H

C OH H

C OH C OH C OH H

HO H H H

C H C OH C OH C OH H

Dihydroxyacetone

Figure 5.3

Ribulose

Fructose

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• Monosaccharides
– May be linear – Can form rings
H
1C

O
6

CH2OH O
1

6

CH2OH O
1

H HO H H H

2 3 4 5

C C

OH H OH OH OH H
4

5C

H H C O

5

H
4

C H OH

CH2OH H C OH HO
6

C C C H

C
3

H OH C H
2

H
4

H C OH

C
3

H
2

H OH
3 2

5

O
1

H OH

OH

OH

C H

C OH

H

OH

6

Figure 5.4 (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.

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• Disaccharides
– Consist of two monosaccharides – Are joined by a glycosidic linkage

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• Examples of disaccharides
(a) 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.

CH2OH H HO O H OH H H OH H2O
Glucose

CH2OH H OH HO H O H OH H H OH H OH OH H HO

CH2OH H O H H O H OH
Maltose

CH2OH H
1– 4 1 glycosidic linkage

H
4

O

H O H H

O H

H OH

OH

Glucose

CH2OH H
(b) Dehydration reaction H in the synthesis of O sucrose. Sucrose is a disaccharide formed from glucose and fructose. Notice that fructose, though a hexose like glucose, forms a five-sided ring.

H O H H

O H O H

CH2OH H O H HO H

CH2OH O HO H H CH2OH H HO H O H H O H OH
Sucrose

H

1–2 glycosidic 1 linkage

CH2OH O
2

H CH2OH

O

H

HO

OH H2O

OH H

Glucose

Fructose

Figure 5.5
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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

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– Is the major storage form of glucose in plants
Chloroplast Starch

1 µm

Amylose

Amylopectin

Figure 5.6 (a) Starch: a plant polysaccharide
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• Glycogen
– Consists of glucose monomers – Is the major storage form of glucose in animals
Mitochondria Giycogen granules

0.5 µm

Glycogen Figure 5.6 (b) Glycogen: an animal polysaccharide
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Structural Polysaccharides • Cellulose
– Is a polymer of glucose

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– Has different glycosidic linkages than starch
H CH2O H O H OH H H OH C H OH H HO H H H C C C C C OH H OH OH OH O H
4

HO

CH2O H H O OH H 4 1 OH H HO H H OH

α glucose

β glucose

(a) α and β glucose ring structures CH2O H O HO OH OH
1 4

CH2O H O O OH OH
1

CH2O H O O
4

CH2O H O
1

OH OH

O

4

OH OH

1

O

Figure 5.7 A–C

(b) Starch: 1– 4 linkage of α glucose monomers CH2O CH2O OH OH H H O O O O OH OH OH OH 1 4 O HO OH O O CH2O CH2O OH OH H H (c) Cellulose: 1– 4 linkage of β glucose monomers

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– Is a major component of the tough walls that enclose plant cells
Cell walls Cellulose microfibrils in a plant cell wall Microfibril About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall.

0.5 µm

Plant cells
CH2OH OH CH2OH OH O O O O OH OH OH OH O O O O O O CH OH CH2OH OH 2 H CH2OH OH CH2OH OH O O O O OH OH OH OH O O O O O O CH OH CH2OH OH 2 H CH2OH OH OH CH2OH O O O O OH OH OH O O OH O O O O CH OH OH CH2OH 2 H

Cellulose molecules

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

Figure 5.8

β Glucose
monomer

A cellulose molecule is an unbranched β glucose polymer.

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

Figure 5.9
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• Chitin, another important structural polysaccharide
– Is found in the exoskeleton of arthropods – Can be used as surgical thread
CH2O HO OH H H OH H OH H H NH C
CH3

O

(a) The structure of the (b) Chitin forms the exoskeleton of arthropods. This cicada chitin monomer. is molting, shedding its old exoskeleton and emerging Figure 5.10 A–C in adult form.
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(c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals.

• Concept 5.3: 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

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Fats • Fats
– Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids
H H H H C C C H OH OH OH O HO C H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H

Fatty acid (palmitic acid)

Glycerol (a) Dehydration reaction in the synthesis of a fat Ester linkage
H H C O O C H C H O H C O C H C H O H C H O C H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H H H

Figure 5.11

(b) Fat molecule (triacylglycerol)

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• Fatty acids
– Vary in the length and 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

Stearic acid

Figure 5.12 (a) Saturated fat and fatty acid
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• Unsaturated fatty acids
– Have one or more double bonds

Oleic acid

Figure 5.12

(b) Unsaturated fat and fatty acid

cis double bond causes bending

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Phospholipids • 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 hydrophobic “tails”
Hydrophilic head
CH2 CH2 O CH2 O C CH O O C O O P O CH2 O–

+ ) N(CH

3 3

Choline Phosphate Glycerol

Hydrophobic tails

Fatty acids
Hydrophilic head Hydrophobic tails

Figure 5.13

(a) Structural formula

(b) Space-filling model

(c) Phospholipid symbol

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• The structure of phospholipids
– Results in a bilayer arrangement found in cell membranes
WATER Hydrophilic head

WATER Hydrophobic tail

Figure 5.14
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Steroids • Steroids
– Are lipids characterized by a carbon skeleton consisting of four fused rings

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• One steroid, cholesterol
– Is found in cell membranes – Is a precursor for some hormones
H3C CH3 CH3

CH3

CH3

Figure 5.15

HO

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• Concept 5.4: Proteins have many structures, resulting in a wide range of functions
– Proteins • Have many roles inside the cell

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• An overview of protein functions

Table 5.1

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• Enzymes
– Are a type of protein that acts as a catalyst, speeding up chemical reactions
1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts.
Substrate (sucrose)

2 Substrate binds to enzyme.

Glucose OH Fructose H O Enzyme (sucrase)

H2O

4 Products are released. Figure 5.16
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3 Substrate is converted to products.

Polypeptides • Polypeptides
– Are polymers of amino acids

• A protein
– Consists of one or more polypeptides

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Amino Acid Monomers • 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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• 20 different amino acids make up proteins
CH3 CH3 H H3N
+

CH3

CH3 CH2 O H3C H3N O
– +

CH3 CH3 O C O

CH CH2 H3N
+

O C O

CH3 H3N+ C C

O H3N O
– +

CH C C

O O–

C

C

C

C

H Glycine (Gly) Nonpolar

H Alanine (Ala)

H Valine (Val)

H Leucine (Leu)

H Isoleucine (Ile)

CH3 S CH2 CH2 H3N+ C H C O– O H3N+ CH2 C H C O– O H3N+ CH2 C H C O– NH H2C H2N O

CH2 CH2 C H C O– O

Methionine (Met)

Phenylalanine (Phe)

Tryptophan (Trp)

Proline (Pro)

Figure 5.17
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OH NH2 O C O C O– H3N
+

NH2 O C CH2 O C H3N O–
+

Polar
H3N
+

OH CH2 C H C O– O

OH H3N+ C H

CH3 CH C O– O H3N+

SH CH2 C H CH2 C H C O– O H3N
+

CH2 C H

CH2 C H C

O O–

Serine (Ser)

Threonine (Thr)

Cysteine (Cys)

Tyrosine (Tyr)

Asparagine (Asn)

Glutamine (Gln)

Acidic

Basic
O– C O CH2 CH2 O C O– H3N+ NH3+ CH2 CH2 CH2 CH2 C H C O

O C

O CH2

NH2 C CH2 CH2 O H3N+ CH2 CH2 C H C O– O H3N+ NH2+

NH+ NH CH2 C H C O–

Electrically charged

O C O– H3N
+

O

H3N+

C H

C H

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
Peptide bond OH CH2 H H N C C H O (a) OH DESMOSOMES DESMOSOMES OH CH2 H H N C C H O H N C C H O SH Side chains H H O OH SH CH2 H C OH O DESMOSOMES H
H2O

CH2

N C C OH H N C

Peptide CH2 bond CH2 H N C C OH H O

Backbone

Figure 5.18

(b)

Amino end (N-terminus)

Carboxyl end (C-terminus)

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Determining the Amino Acid Sequence of a Polypeptide

• The amino acid sequences of polypeptides
– Were first determined using chemical means – Can now be determined by automated machines

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Protein Conformation and Function • A protein’s specific conformation
– Determines how it functions

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• Two models of protein conformation

Groove

(a) A ribbon model

Groove

Figure 5.19

(b) A space-filling model

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Four Levels of Protein Structure • Primary structure
– Is the unique sequence of amino acids in a polypeptide HN Amino acid
+ 3
Gly ProThr Gly Thr Gly

Amino end

Glu Cys LysSeu LeuPro Met Val Lys Val Leu Asp AlaVal Arg Gly Ser Pro Ala

subunits

Glu Lle

Asp Thr Lys

Leu Ala Gly

Ser Lys Trp Tyr

lle Ser ProPheHis Glu

His Ala

Ala Thr PheVal Asn

Glu Val lle Ala Ala Leu

Thr Asp Tyr Arg Ser Arg GlyPro

Thr Ser Thr Ala

Tyr

Leu Ser Pro SerTyr

Val Val Glu ThrAsnProLys

c

o o–

Figure 5.20
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Carboxyl end

• Secondary structure
– Is the folding or coiling of the polypeptide into a repeating configuration – Includes the α helix and the β pleated sheet
β pleated sheet
Amino acid subunits
C N H O H H C C N R R O C H O R C C N O H H O H H C C N R R O R C C N OH H O H H C C N R R O C H H NH C N C H O C R R C C N OH H O H H C C N R R H C N HC N H O C C C O

R N H

C H H H C N HC C N HC N C N H H C O C C O R R C H R C H

O C O C N H N H N H O C O C H C R H C R H C R H C R N H O C N H O C O C H O C N H N C C H R H R

α helix

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 groups Hydrophobic
Hyrdogen bond
CH CH22 O H O CH2 H3C CH CH3 H3C CH3 CH

interactions and van der Waals interactions Polypeptide backbone

HO C CH2 S S CH2

Disulfide bridge O
CH2 NH3+ -O C CH2 Ionic bond

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• Quaternary structure
– Is the overall protein structure that results from the aggregation of two or more polypeptide subunits
Polypeptide chain

Collagen β Chains

Iron Heme α Chains Hemoglobin
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• The four levels of protein structure

H3N Amino end
+

Amino acid subunits α helix

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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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• Hemoglobin structure and sickle-cell disease
Primary structure Secondary and tertiary structures Quaternary Hemoglobin A structure α β α Normal hemoglobin
Val His Leu Thr Pro Glul Glu

. . . Primary

Sickle-cell hemoglobin
Val His Leu Thr Pro Val Glu

1 2 3 4 5 6 7

structure 1 2 3 4 5 6 7

...

Secondary β subunit and tertiary structures β Quaternary structure Function α β

Exposed hydrophobic region

β subunit

β α

Hemoglobin S Molecules interact with one another to crystallize into a fiber, capacity to carry oxygen is greatly reduced. Fibers of abnormal hemoglobin deform cell into sickle shape.

Function

Molecules do not associate with one another, each carries oxygen. Normal cells are full of individual hemoglobin molecules, each carrying oxygen

10 µm Red blood cell shape

10 µm

Red blood cell shape

Figure 5.21

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What Determines Protein Conformation? • Protein conformation
– Depends on the physical and chemical conditions of the protein’s environment

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• Denaturation
– Is when a protein unravels and loses its native conformation
Denaturation

Normal protein Renaturation

Denatured 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

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• Chaperonins
– Are protein molecules that assist in the proper folding of other proteins
Polypeptide Cap Correctly folded protein

Hollow cylinder

Chaperonin (fully assembled)

Figure 5.23

2 The cap attaches, causing 3 The cap comes Steps of Chaperonin the cylinder to change shape in off, and the properly Action: such a way that it creates a folded protein is 1 An unfolded polyhydrophilic environment for the released. peptide enters the cylinder from one end. folding of the polypeptide.

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• X-ray crystallography
– Is used to determine a protein’s threeX-ray dimensional structure diffraction
pattern Photographic film Diffracted X-rays X-ray X-ray beam source Crystal Nucleic acid Protein

Figure 5.24

(a) X-ray diffraction pattern

(b) 3D computer model

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• Concept 5.5: Nucleic acids store and transmit hereditary information • Genes
– Are the units of inheritance – Program the amino acid sequence of polypeptides – Are made of nucleic acids

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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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• DNA
– Stores information for the synthesis of specific proteins

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– Directs RNA synthesis – Directs protein synthesis through RNA
DNA 1 Synthesis of mRNA in the nucleus

mRNA

NUCLEUS CYTOPLASM mRNA 2 Movement of mRNA into cytoplasm via nuclear pore 3 Synthesis
of protein

Ribosome

Figure 5.25

Polypeptide

Amino acids

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The Structure of Nucleic Acids • Nucleic acids
– Exist as polymers called polynucleotides
5’ end 5’C 3’C O O

O

5’C 3’C OH

O 3’ end

Figure 5.26

(a) Polynucleotide, or nucleic acid

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• Each polynucleotide
– Consists of monomers called nucleotides
Nucleoside Nitrogenous base

O

5’C O CH2 O

O

P O−

Phosphate group

3’C

Pentose sugar

Figure 5.26

(b) Nucleotide

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Nucleotide Monomers • Nucleotide monomers
– Are made up of nucleosides and phosphate groups
Nitrogenous bases Pyrimidines NH2 O O C CH3 C C N C CH HN HN CH CH C CH C C CH N N O N O O H H H Cytosine Thymine (in DNA) Uracil (in RNA) Uracil (in RNA) U C U T Purines NH2 O N C C N CC NH N HC HC C CH N C N NH2 N N H H Adenine Guanine A G
5”

Pentose sugars H H

HOCH2 O OH
4’ 1’

HOCH2 O OH
4’

5”

H H

1’

H H H 3’ 2’ H 3’ 2’ OH H OH OH Deoxyribose (in DNA) Ribose (in RNA)

Figure 5.26

(c) Nucleoside components

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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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• 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
5’ end 3’ end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) Old strands Nucleotide about to be added to a new strand

A

3’ end

5’ end

3’ end

New strands 3’ end

Figure 5.27

5’ end

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• 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

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