ch 05 macromolecules-104

7/25/2019 Ch 05 Macromolecules-104

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Lecture Outline

1. Macromolecules are polymers, built frommonomers

2. Carbohydrates serve as fuel and building material

3. Lipids are a diverse group of hydrophobic

molecules4. Proteins include a diversity of structures, resulting

in a wide range of functions

5. Nucleic acids store, transmit, and help expresshereditary information

6. Genomics and proteomics have transformedbiological inquiry and applications

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Macromolecules are polymers, built

from monomers

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The Diversity of Mcromolecules

Monomers Polymer

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A polymeris a long molecule consisting of many similar

building blocks.

The repeating units that serve as building blocks are called monomers

Three of the four classes of lifes organic molecules are polymers:

Carbohydrates

, Proteins

,Nucleic acids

Each cell has thousands of different macromolecules, which vary among

cells of an organism, vary more within a species, and vary even more

between species.


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(a) Dehydration reaction: synthesizing a polymer

Short polymer Unlinked monomer

Dehydration removesa water molecule,forming a new bond.

Longer polymer

(b) Hydrolysis: breaking down a polymer

Hydrolysis addsa water molecule,breaking a bond.

1

1

1

2 3

2 3 4

2 3 4

1 2 3

The Synthesis and Breakdown of Polymers

Fig 5.2

Dehydration reaction/

Condensation reaction

Hydrolysis

Enzymesrequired

Diverse Polymers

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Carbohydrates serve as fuel and

building material

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(Carbonyl group)

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Aldoses (Aldehyde Sugars) Ketoses (Ketone Sugars)

Glyceraldehyde

Trioses: 3-carbon sugars (C3H6O3)

Dihydroxyacetone

Pentoses: 5-carbon sugars (C5H10O5)

Hexoses: 6-carbon sugars (C6H12O6)

Ribose Ribulose

Glucose Galactose Fructose

aldoseketose

D- form

epimers at C-4

dextrose = D-(+)-Glc

Figure 5.3 The structure and

classification of some monosaccharides

Sugars

Monosaccharides molecular formulas:

(CH2O)n Glucose (C6H12O6):

the most common

classification

The location of thecarbonyl group: aldose

ketose

number of carbons

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-

-

anomer, anomeric carbon

(~ 2/3)

(a) Linear and ring forms of glucose

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11

-D-glucopyranose-D-glucopyranose

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Disaccharide

nonreducing end reducing endGal

(14)Glc

reducing sugarhydrolyzed by lactase (human), -galactosidase (bacteria)

Lactose intolerance

The covalent bond joins two monosaccharides is

called a glycosidic linkage

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(a) Dehydration reaction in the synthesis of maltose

(b) Dehydration reaction in the synthesis of sucrose

Glucose Glucose

Glucose

Maltose

Fructose Sucrose

14glycosidiclinkage

12glycosidic

linkage

1 4

1 2

Examples of disaccharide synthesis(glycosidic linkage)

reducing sugar

non-reducing sugar13


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Polysaccharides (Glycans)

Serve as storage and structural roles

The architecture and function of a polysaccharide

are determined by its sugar monomers and the

positions of its glycosidic linkages

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Storage Polysaccharides

Starch,polymers of glucoses in plants: (14)

amyloseThe simplest form,& amylopectin

Plants store surplus starch as granules within chloroplasts

and other plastids

Glycogen, polymers of glucosesin animals

Is stored mainly in liver and muscle cells

They are hydrolyzed to release glucose when the demandfor sugar increases

Structural Polysaccharides

Cellulose,polymers of glucoses in plant cell walls. but the glycosidic linkages differ from starch; (14)

Chitin, in the exoskeleton of arthropods and cell walls

of many fungi

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Amylopectin, glycogen: (14) & (16) linkage,

branched

Cellulose:(14)

(14)

(16)

Amylases

Cellulases

16

( glucose monomer)

( glucose monomer)

Figure 5 6


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Figure 5.6

Storage structures(plastids)containing starchgranules in a potatotuber cell

50 m

(a) Starch

Amylose (unbranched)

Amylopectin(somewhatbranched)

Glucosemonomer

Glycogengranules inmuscletissue Glycogen (branched)

1 m

(b) Glycogen

Cellwall

Plant cell,surroundedby cell wall

10 m

0.5 m

(c) Cellulose

Microfibril

Cellulose microfibrilsin a plant cell wall Cellulose molecule (unbranched)

Hydrogen bonds

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largely helical


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The cellulose in human food passes through the digestivetract as insoluble fiber

Many herbivores, from cows to termites, have symbiotic

relationships with some microbes that use enzymes

(cellulases) to digest cellulose

What would happen if a cow were given antibiotics

that killed all the prokaryotes in its stomach?

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Figure 5 8


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Figure 5.8

The structureof the chitinmonomer

Chitin, embedded in proteins,

forms the exoskeleton ofarthropods

.

Chitin is used to

make a strongand flexiblesurgicalthread.

N-acetylglucosamine

units, in -1,4 linkage

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Chitin also provides

structural support for the

cell walls of many fungi


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N-link (Asn) & O-link (Ser)

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Glycoproteins


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proteoglycan glycosaminoglycan, GAG )

heparin


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proteoglycan

glycosaminoglycanGAG

(Hyaluronic acid)

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Lipids are a diverse group of

hydrophobic molecules

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Energy storage

Cell membrane Signaling molecule

Lipid Functions


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Lipids

the one class of large biological molecules that does not

include true polymers

consist mostly of hydrocarbons; hydrophobic

The most biologically important lipids are fats, phospholipids,

and steroids


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Fats separate from water because watermolecules hydrogen-bond to each other andexclude the fats

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

The fatty acids in a fat can be all the same or of

two or three different kinds Fatty acids vary in length (number of carbons)

and in the number and locations of double bonds

Saturated fatty acidshave the maximum number

of hydrogen atoms possible and no double bonds Unsaturated fatty acidshave one or more double

bonds


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Fats are

constructedfrom glycerol

and fatty acids

A fatty acid

consists of a

carboxyl group

attached

to a long carbon

skeleton

(a) One of three dehydration reactions in the synthesis ofa fat

(b) Fat molecule (triacylglycerol)

Fatty acid

(in this case, palmitic acid)

Glycerol

Ester linkage

Fig 5.10

The synthesis and

structure of a fat, or

triacylglycerol

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Fats

(,or triglyceride

F tt id i l th ( b f b ) d


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Figure 5.11

(a) Saturated fatStructuralformula of asaturated fatmolecule

Space-filling model of stearicacid, a saturated fatty acid

Structuralformula of anunsaturated fatmolecule

Cisdouble bondcauses bending.

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Fatty acids vary in length (number of carbons) and

in the number and locations of double bonds

(b) Unsaturated fat

Space-filling model of oleicacid, an unsaturated fatty acid


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Nomenclatures of fatty acids

Trans-fatty acid cis-fatty acid

monounsaturated fatty acids, MUFA

polyunsaturated fatty acids, PUFA

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Fats made from saturated fatty acids are called

saturated fats and are solid at room temperature

Most animal fats are saturated Fats made from unsaturated fatty acids are

called unsaturated fats or oils and are liquid at room

temperature

Plant fats and fish fats are usually unsaturated

Essential fatty acids

These must be supplied in the diet, not

synthesized in the human body include the omega-3 fatty acids, required for

normal growth, and thought to provide protection

against cardiovascular disease.


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The major function of fats is energy storage Humans and other mammals store their long-

term food reserves in adipose cells Adipose tissue also cushions vital organs and

insulates the body


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A diet rich in saturated fats may contribute to

cardiovascular disease through plaque deposits

Hydrogenationis the process of convertingunsaturated fats to saturated fats by adding

hydrogen

Hydrogenating vegetable oils also creates

unsaturated fats with transdouble bonds

These t rans fatsmay contribute more than

saturated fats to cardiovascular disease

Successful diets usually involve three things:

decreasing the amounts of carbohydrates

and fats; exercise; and behavior modification.


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Phospholipids

Choline

Phosphate

Glycerol

Fatty acids

Hydrophilichead

Hydrophobictails

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

Hydrophilichead

Hydrophobictails

Fig 5.12 The structure of a phospholipid.

In a phospholipid, two

fatty acids and a

phosphate group areattached to glycerol

The two fatty acid tails

are hydrophobic, but the

phosphate group and its

attachments form a

hydrophilic head

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When phospholipids are added to water, they

self-assemble into double-layered structures

called bilayers At the surface of a cell, phospholipids are also

arranged in a bilayer, with the hydrophobic tails

pointing toward the interior

The structure of phospholipids results in a

bilayer arrangement found in cell membranes

The existence of cells depends on phospholipids


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The structure of phospholipids results in a bilayer

arrangement found in cell membranes

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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

Fig 5.14 Cholesterol, a steroid

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Cholesterol and Membrane Fluidity


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Sex hormones


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Proteins include a diversity of structures,

resulting in a wide range of functions

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Proteins are all constructed from the same set of

20 amino acids

Polypeptidesare unbranched polymers built

from these amino acids

A proteinis a biologically functional molecule

that consists of one or more polypeptides Proteins account for more than 50% of the dry

mass of most cells.

Diverse protein functions


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Classification

A i f t i f ti


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Enzymatic proteins Defensive proteins

Storage proteins Transport proteins

Enzyme Virus

Antibodies

Bacterium

Ovalbumin Amino acidsfor embryo

Transportprotein

Cell membrane

Function: Selective acceleration ofchemical reactions

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

Function: Protection against disease

Example: Antibodies inactivate and help destroy

viruses and bacteria.

Function: Storage of amino acids Function: Transport of substances

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 or the developing embryo.

Examples: Hemoglobin, the iron-containing

protein of ertebrate blood, transports oxygen

from the lungs to other parts of the body. Other

proteins transport molecules across

cell membranes.

An overview of protein functions

Figure 5.15

Figure 5.15-b


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Hormonal proteins

Function: Coordination of an organisms activities

Example: Insulin, a hormone secreted by the

pancreas, causes other tissues to take up glucose,

thus regulating blood sugar concentration

Highblood sugar

Normalblood sugar

Insulinsecreted

Signalingmolecules

Receptorprotein

Muscle tissue

Actin Myosin

100 m 60

m

Collagen

Connectivetissue

Receptor proteinsFunction: Response of cell to chemical stimuli

Example: Receptors built into the membrane of a

nerve cell detect signaling molecules released by

other nerve cells.

Contractile and motor proteinsFunction: MovementExamples: Motor proteins are responsible for the

undulations of cilia and flagella. Actin and myosin

proteins are responsible for the contraction of

muscles.

Structural proteinsFunction: SupportExamples: 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.

Enzymes are a type of protein that acts as a catalyst to


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Enzyme(sucrase)

Substrate(sucrose)

Fructose

Glucose

OH

HO

H2O

Products

Active site

The catalytic cycle

of an enzyme

Enzymes are a type of protein that acts as a catalyst to

speed up chemical reactions

Enzymes can perform their functions repeatedly, functioning

as workhorses that carry out the processes of life.


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Amino Acid Monomers

Amino acids are

organic molecules

with carboxyl and

amino groups

Amino acids differ inside chains, called R

groups

Side chain (R group)

Aminogroup

Carboxylgroup

carbon

Figure 5.16

Nonpolar side chains; hydrophobic


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p ; y p

Side chain(R group)

Glycine(Gly or G)

Alanine(Ala or A)

Valine(Val or V)

Leucine(Leu or L)

Isoleucine(Ile or I)

Methionine(Met or M)

Phenylalanine(Phe or F)

Tryptophan(Trp or W)

Proline(Pro or P)

Polar side chains; hydrophilic

Serine(Ser or S)

Threonine(Thr or T)

Cysteine(Cys or C)

Tyrosine(Tyr or Y)

Asparagine(Asn or N)

Glutamine(Gln or Q)

Electrically charged side chains; hydrophilic

Acidic (negatively charged)

Basic (positively charged)

Aspartic acid(Asp or D)

Glutamic acid(Glu or E)

Lysine(Lys or K)

Arginine(Arg or R)

Histidine(His or H)


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Polypeptides (Amino Acid Polymers)

Amino acids are linked by covalent bondscalled peptide bonds

A polypeptide is a polymer of amino acids

Polypeptides range in length from a few tomore than a thousand monomers

Each polypeptide has a unique linear

sequence of amino acids, with a carboxyl end(C-terminus) and an amino end (N-terminus)

Making a


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Peptide bond

New peptidebond forming

Side chains

Back-bone

Amino end

(N-terminus)

Peptidebond

Carboxyl end

(C-terminus)

Figure 5.17 Making a

polypeptide chain

Peptide bond


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Protein Structure and Function

The specific activities of proteins result from theirintricate three-dimensional architecture

A functional protein consists of one or morepolypeptides precisely twisted, folded, and coiled

into a unique shape The sequence of amino acids determines a

proteins three-dimensional structure

A proteins structure determines its function

The function of a protein usually depends on itsability to recognize and bind to some othermolecule

Figure 5.16


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(a) A ribbon model (b) A space-filling model (c) A wireframe model

GrooveGroove

Targetmolecule

Structure of a protein, the enzyme lysozyme

Figure 5.17


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Antibody protein Protein from flu virus


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Levels of Protein Structure

The primary structureof a protein is itsunique sequence of amino acids

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

chain Tertiary structureis determined byinteractions among various side chains (Rgroups)

Quaternary structureresults when a proteinconsists of multiple polypeptide chains

Primary structure


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Aminoacids

Amino end

Carboxyl end

Primary structure of transthyretin

the sequence ofamino acids in a

protein

is determined by

inherited genetic

information

Primary structure


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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 helixand a folded structure called a pleated sheet


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Tertiary structure, the overall shape of a

polypeptide, results from interactions between

R groups, rather than interactions between

backbone constituents

These interactions include hydrogen bonds,

ionic bonds, hydrophobic interactions, andvan der Waals interactions

Strong covalent bonds called disulfidebridges

may reinforce the protein

s structure

Four Levels of Protein Structure


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Four Levels of Protein Structure

Secondary

structure

Tertiary

structure

Quaternary

structureHydrogen bond

helix

pleated sheet

strand

Hydrogenbond

Transthyretinpolypeptide

Transthyretinprotein

Secondary structure


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Secondary structure

Hydrogen bond

helix

pleated sheet

strand, shown as aflat arrow pointingtoward the carboxyl end

Hydrogen bond

Figure 5.20c

Figure 5.20e

T ti t t


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Tertiary structure

Transthyretin

polypeptide

Hydrogen

bond

Disulfide

bridge

Polypeptidebackbone

Ionic bond

Hydrophobic

interactions and

van der Waals

interactions

Quaternary structure results when two or more


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Transthyretin protein(four identical polypeptides)

Collagen-- triple helix structure

Quaternary structureresults 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.

Heme


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Hemoglobin

Iron

subunit

subunit

subunit

subunit

Si kl C ll Di A Ch i P i


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Sickle-Cell Disease: A Change in Primary

Structure

A slight change in primary structure can affect

a proteins structure and ability to function

Sickle-cell disease, an inherited blood

disorder, results from a single amino acid

substitution in the protein hemoglobin

A single amino acid substitution in a protein causes sickle-cell disease


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PrimaryStructure

Secondaryand TertiaryStructures

QuaternaryStructure

FunctionRed BloodCell Shape

subunit

subunit

Exposedhydrophobicregion

Molecules do notassociate with oneanother; each carriesoxygen.

Sickle-cellhemoglobin

Normalhemoglobin

10 m

10 m

Sickle-cellhemo

globin

No

rmalhemoglobin

1

23

4

5

6

7

1

2

3

4

5

6

7

Molecules interact withone another andcrystallize into a fiber;capacity to carryoxygen is reduced.

What Determines Protein Structure?


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What Determines Protein Structure?

Alterations in pH, salt concentration, temperature, or other

environmental factors can cause a protein to unravel This loss of a proteins native structure is called

denaturation (2, 3, 4)

A denatured protein is biologically inactive

Figure 5.22

Denaturation

and renaturation

of a protein.

Protein Folding in the Cell


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Protein Folding in the Cell

Chaperonins are proteinmolecules that assist the proper

folding of other proteins

Diseases such as Alzheimers,

Parkinsons, and mad cowdisease are associated with

misfolded proteins

Cap

Chaperonin(fully assembled)

Hollow

cylinder

Fig 5.23

It is hard to predict a proteins

structure from its primary structure

Most proteins probably go through

several stages on their way to a

stable structure

Figure 5.23 A chaperonin in action.


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

Polypeptide

Correctlyfoldedprotein

Steps of ChaperoninAction:

An unfolded poly-peptide enters thecylinder fromone end.

The cap comesoff, and theproperly foldedprotein isreleased.

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1


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Scientists use X-ray crystallographyto

determine a proteins structure

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

protein crystallization

Bioinformatics is another approach to prediction

of protein structure from amino acid sequences

EXPERIMENTDetermine a


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DiffractedX-rays

X-ray

source X-raybeam

Crystal Digital detector X-ray diffractionpattern

RNA DNA

RNApolymerase II

RESULTS

Figure 5.24 Inquiry: What

can the 3-D shape of the

enzyme RNA polymerase II

tell us about its function?

X-ray

crystallography

nuclear magnetic

resonance (NMR)

spectroscopy Bioinformatics

proteins

structure


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Nucleic acids store, transmit, andhelp express hereditary information

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Nucleic acids store transmit and help


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Nucleic acids store, transmit, and help

express hereditary information

The amino acid sequence of a polypeptide is

programmed by a unit of inheritance called

a gene

Genes consist of DNA, a nucleic acidmade ofmonomers called nucleotides

There are two types of nucleic acids

Deoxyribonucleic acid (DNA)

Ribonucleic acid (RNA)

The Roles of Nucleic Acids


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The Roles of Nucleic Acids

DNA provides directions for its own replication

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

This process is called gene expression

Each gene along a DNA molecule directs synthesisof a messenger RNA (mRNA)

The mRNA molecule interacts with the cellsprotein-synthesizing machinery to direct

production of a polypeptide

The flow of genetic information can besummarized as DNA RNA protein

DNA DNA: Genetic materials


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Synthesis of

mRNA mRNA

NUCLEUS

CYTOPLASM

mRNA

Ribosome

AminoacidsPolypeptide

Movement ofmRNA intocytoplasm

Synthesisof protein

1

2

3

DNA RNA Protein

RNA: Gene expression

r-RNA, mRNA, rRNA,

& others

(some as enzymes)

Figure 5.25-3

The Components of Nucleic Acids


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Nucleoside = nitrogenous base + sugar

There are two families of nitrogenous bases

Pyrimidines (cytosine, thymine, and uracil)have

a single six-membered ring Purines (adenine and guanine) have a six-

membered ring fused to a five-membered ring

In DNA, the sugar is deoxyribose; in RNA, the sugar

is ribose Nucleotide= nucleoside + phosphate group

Nucleotide Monomers

The Components of Nucleic Acids

Components of nucleic acidsSugar-phosphate backbone Nitrogenous bases


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Sugar phosphate backbone5end

5C

3C

5

C

3C

3end

(a) Polynucleotide,or nucleic acid

(b) Nucleotide

Phosphategroup Sugar

(pentose)

NucleosideNitrogenous

base

5C

3

C

1C

Nitrogenous bases

Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA)

Adenine (A) Guanine (G)

Sugars

Deoxyribose (in DNA) Ribose (in RNA)

(c) Nucleoside components

Pyrimidines

Purines

Figure 5.26

Nucleotide Polymers


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Nucleotide Polymers

Nucleotides are linked together to build a

polynucleotide Adjacent nucleotides are joined by a

phosphodiester linkage, which consists of aphosphate group that links the sugars of two

nucleotides These links create a backbone of sugar-phosphate

units with nitrogenous bases as appendages

The sequence of bases along a DNA or mRNApolymer is unique for each gene

The Structures of DNA and RNA Molecules


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e St uctu es o a d o ecu es

DNA molecules have two polynucleotides spiralingaround an imaginary axis, forming a double helix

The backbones run in opposite 5 3directionsfrom each other, an arrangement referred to asantiparallel

One DNA molecule includes many genes Only certain bases in DNA pair up and formhydrogen bonds: adenine (A) always with thymine(T), and guanine (G) always with cytosine (C)

This is called complementary base pairing This feature of DNA structure makes it possible togenerate two identical copies of each DNAmolecule in a cell preparing to divide

RNA i t t t DNA i i l t d d


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RNA, in contrast to DNA, is single stranded

Complementary pairing can also occur

between two RNA molecules or between partsof thesame molecule

In RNA, thymine is replaced by uracil (U) soA and U pair

While DNA always exists as a double helix,RNA molecules are more variable in form

Figure 5.27

The structures of DNA and tRNA molecules


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Sugar-phosphatebackbones

Hydrogen bonds

Base pair joinedby hydrogen bonding

Base pair joinedby hydrogen

bonding

(b) Transfer RNA(a) DNA

5

3

5

3


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Genomics and proteomics have

transformed biological inquiry and

applications

Figure 5.26

MAKE CONNECTIONSC t ib ti f G i d P t i t Bi l


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Contributions of Genomics and Proteomics to Biology

Paleontology Evolution

Hippopotamus Short-finned pilot whale

Medical Science Conservation BiologySpeciesInteractions

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Genomics and proteomics have transformed


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biological inquiry and applications

Once the structure of DNA and its relationship toamino acid sequence was understood, biologistssought to decode genes by learning their basesequences

The first chemical techniques for DNA sequencing were

developed in the 1970s and refined over the next 20years

It is enlightening to sequence the full complement ofDNA in an organisms genome

The rapid development of faster and less expensivemethods of sequencing was a side effect of the HumanGenome Project

Many genomes have been sequenced, generatingreams of data

Bioinformatics uses computer software and


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Bioinformatics uses computer software andother computational tools to deal with thedata resulting from sequencing manygenomes

Analyzing large sets of genes or evencomparing whole genomes of different

species is called genomics A similar analysis of large sets of proteins

including their sequences is called proteomics

DNA and Proteins as Tape Measures


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p

of Evolution

Sequences of genes and their protein productsdocument the hereditary background of anorganism

Linear sequences of DNA molecules arepassed from parents to offspring

We can extend the concept of moleculargenealogy to relationships between species

Molecular biology has added a new measureto the toolkit of evolutionary biology

DNA and Proteins as Tape Measures


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of Evolution

Human GibbonRhesusmonkey

Summary


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Summary

An immense variety of biological polymers with

diverse functions can be built from a small numberof specific class of monomers.

Carbohydrates, lipids, proteins, and nucleic acids

are four major categories of biological

macromolecules in living organisms.

Can you compare the common and diverse

characteristics of the four major large biological

molecules in terms of structure and function? Importance of genomics and proteomics


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(1)

(2)DNAdouble helix Helix Sheetconformation

(3)

(4)

(5)

ch 05 macromolecules-104

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