The Structure and The Structure and Function of Function of

MacromoleculesMacromoleculesChapter 5Chapter 5

3 -- Proteins3 -- Proteins

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Macromolecules: Macromolecules: The Molecules of LifeThe Molecules of Life

CarbohydratesCarbohydrates Nucleic AcidsNucleic Acids ProteinsProteins LipidsLipids

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ProteinsProteins Polypeptides -- polymers of amino acidsPolypeptides -- polymers of amino acids Protein -- one or more polypeptidesProtein -- one or more polypeptides

Proteins -- many structures with wide range of Proteins -- many structures with wide range of functionsfunctions

Proteins -- more than 50% of the dry mass of Proteins -- more than 50% of the dry mass of most cellsmost cells

Proteins -- include structural support, storage, Proteins -- include structural support, storage, transport, cellular communications, movement, transport, cellular communications, movement, and defense against foreign substancesand defense against foreign substances

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Amino Acid MonomersAmino Acid Monomers Organic molecules with carboxyl and Organic molecules with carboxyl and

amino groupsamino groups Different properties due to differing side Different properties due to differing side

chains, called R groupschains, called R groups 20 amino acids to make thousands of 20 amino acids to make thousands of

proteinsproteins

LE 5-UN78LE 5-UN78

Aminogroup

Carboxylgroup

carbon

LE 5-17aLE 5-17a

Isoleucine (Ile)

Methionine (Met) Phenylalanine (Phe) Tryptophan (Trp) Proline (Pro)

Leucine (Leu)Valine (Val)Alanine (Ala)

Nonpolar

Glycine (Gly)

LE 5-17bLE 5-17b

Asparagine (Asn) Glutamine (Gln)Threonine (Thr)

Polar

Serine (Ser) Cysteine (Cys) Tyrosine (Tyr)

LE 5-17cLE 5-17c

Electricallycharged

Aspartic acid (Asp)

Acidic Basic

Glutamic acid (Glu) Lysine (Lys) Arginine (Arg) Histidine (His)

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Amino Acid PolymersAmino Acid Polymers

Amino acids -- linked by peptide bondsAmino acids -- linked by peptide bonds A polypeptide -- polymer of amino acidsA polypeptide -- polymer of amino acids Polypeptide length -- few monomers to Polypeptide length -- few monomers to

more than a thousandmore than a thousand Each polypeptide has a unique linear Each polypeptide has a unique linear

sequence of amino acidssequence of amino acids

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Determining the Amino Determining the Amino Acid Sequence of a Acid Sequence of a

PolypeptidePolypeptide First determined by chemical methodsFirst determined by chemical methods Now? Mostly automated – DNA Now? Mostly automated – DNA

sequencersequencer

LE 5-20aLE 5-20a

Amino acidsubunits

Carboxyl end

Amino end

Primary structure Primary structure

unique sequence of unique sequence of amino acidsamino acids

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LE 5-LE 5-20b20b

Secondary structureSecondary structure Interactions between backbone Interactions between backbone

componentscomponents Hydrogen bondsHydrogen bonds Typical secondary structures are coils (alpha helix) Typical secondary structures are coils (alpha helix)

and a folded structure (beta pleated sheet)and a folded structure (beta pleated sheet)

Amino acidsubunits

pleated sheet

helix

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LE 5-20dLE 5-20d

Hydrophobicinteractions andvan der Waalsinteractions

Polypeptidebackbone

Disulfide bridge

Ionic bond

Hydrogenbond

Tertiary Tertiary StructureStructure

Interactions Interactions between R groupsbetween R groupsInclude hydrogen Include hydrogen bonds, ionic bonds, bonds, ionic bonds, hydrophobic hydrophobic interactions, and interactions, and van der Waals van der Waals interactionsinteractions

Disulfide bridges Disulfide bridges may reinforce the may reinforce the protein’s protein’s conformationconformation

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Four Levels of Protein Four Levels of Protein StructureStructure

Primary structure -- unique sequence Primary structure -- unique sequence of amino acidsof amino acids

Secondary structure – interactions Secondary structure – interactions between backbone componentsbetween backbone components

Tertiary structure -- interactions Tertiary structure -- interactions between various side chains (R groups)between various side chains (R groups)

Quaternary structure – proteins Quaternary structure – proteins consisting of multiple polypeptide consisting of multiple polypeptide chainschains

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

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

Proteins with Quaternary Proteins with Quaternary StructureStructure

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Sickle-Cell Disease: A Sickle-Cell Disease: A Simple Change in Primary Simple Change in Primary

StructureStructure A slight change in primary structure A slight change in primary structure

can affect a protein’s conformation and can affect a protein’s conformation and ability to function ability to function

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

cell shapeNormal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen.

10 µm 10 µm

Red bloodcell shape

Fibers of abnormalhemoglobin deformcell into sickleshape.

LE 5-21bLE 5-21b

Primarystructure

Secondaryand tertiarystructures

1 2 3

Normal hemoglobin

Val His Leu

4Thr

5Pro

6Glu Glu

7Primarystructure

Secondaryand tertiarystructures

1 2 3

Sickle-cell hemoglobin

Val His Leu

4Thr

5Pro

6Val Glu

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Quaternarystructure

Normalhemoglobin(top view)

Function Molecules donot associatewith oneanother; eachcarries oxygen.

Quaternarystructure

Sickle-cellhemoglobin

Function Molecules interact withone another tocrystallize intoa fiber; capacityto carry oxygenis greatly reduced.

Exposedhydrophobicregion subunit subunit

LE 5-19LE 5-19

A ribbon model

Groove

Groove

A space-filling model

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Conformation and Conformation and FunctionFunction

Conformation – 3-D shapeConformation – 3-D shapeFunctional protein -- one or more Functional protein -- one or more

polypeptides twisted, folded, and coiled polypeptides twisted, folded, and coiled into a unique shapeinto a unique shape

Sequence -- determines a protein’s Sequence -- determines a protein’s three-dimensional conformationthree-dimensional conformation

Conformation -- determines its functionConformation -- determines its functionRibbon models and space-filling models Ribbon models and space-filling models

can depict a protein’s conformationcan depict a protein’s conformation

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What Determines Protein What Determines Protein Conformation?Conformation?

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

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

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

A denatured protein is biologically inactiveA denatured protein is biologically inactive

LE 5-22LE 5-22

Denaturation

Renaturation

Denatured proteinNormal protein

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The Protein-Folding The Protein-Folding ProblemProblem

Prediction of conformation is non-trivialPrediction of conformation is non-trivial Thousands of possible conformations!Thousands of possible conformations!

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

Chaperonins assist the proper folding Chaperonins assist the proper folding of other proteinsof other proteins

LE 5-23aLE 5-23a

Chaperonin(fully assembled)

Hollowcylinder

Cap

LE 5-23bLE 5-23b

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.

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

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

3D computer modelX-ray diffraction pattern

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The Flow of Genetic The Flow of Genetic InformationInformation

The information content -- DNA The information content -- DNA sequencesequence

DNA – directs synthesis of proteinsDNA – directs synthesis of proteins Gene manufactureGene manufacture

Transcription Transcription Translation Translation

Ribosome -- where translation Ribosome -- where translation happenshappens

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LE 17-4LE 17-4

DNAmolecule

Gene 1

Gene 2

Gene 3

DNA strand(template)

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TRANSCRIPTION

Codon

mRNA

TRANSLATION

Protein

Amino acid

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Nutritional Mutants in Nutritional Mutants in NeurosporaNeurospora

Beadle and Tatum – irradiated mold Beadle and Tatum – irradiated mold resulting in inability to synthesize resulting in inability to synthesize certain moleculescertain molecules Three classes of arginine-deficient Three classes of arginine-deficient

mutantsmutants 3 different enzymes necessary for 3 different enzymes necessary for

synthesizing argininesynthesizing arginine ““One gene–one enzyme” hypothesisOne gene–one enzyme” hypothesis

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The Products of Gene The Products of Gene Expression: A Developing Expression: A Developing

StoryStory Not all proteins are enzymes!Not all proteins are enzymes! One gene–one proteinOne gene–one protein

Quaternary structure -- each component needs its Quaternary structure -- each component needs its own geneown gene ATP synthase has 16 subunits!ATP synthase has 16 subunits!

Now -- Beadle and Tatum’s hypothesis “one gene–one Now -- Beadle and Tatum’s hypothesis “one gene–one polypeptide”polypeptide”

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Basic Principles of Basic Principles of Transcription and Transcription and

TranslationTranslation Transcription -- synthesis of RNA under the Transcription -- synthesis of RNA under the

direction of DNAdirection of DNA produces messenger RNA (mRNA)produces messenger RNA (mRNA) ““language” of DNA to “language” of RNAlanguage” of DNA to “language” of RNA

Translation -- synthesis of a polypeptide under Translation -- synthesis of a polypeptide under the direction of mRNAthe direction of mRNA Ribosomes are the sites of translationRibosomes are the sites of translation ““language” of Nucleic Acids to “language” of Amino language” of Nucleic Acids to “language” of Amino

AcidsAcids

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LE 17-4LE 17-4

DNAmolecule

Gene 1

Gene 2

Gene 3

DNA strand(template)

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TRANSCRIPTION

Codon

mRNA

TRANSLATION

Protein

Amino acid

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DNA to RNADNA to RNA

DNA in eukaryotes is in the nucleusDNA in eukaryotes is in the nucleus Protein synthesis occurs at ribosomes Protein synthesis occurs at ribosomes

in the cytoplasmin the cytoplasm DNA information -- from nucleus to DNA information -- from nucleus to

cytoplasmcytoplasm intermediaryintermediary ( (RNARNA))

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RNA IntermediariesRNA Intermediaries

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A ribosome has A ribosome has three binding three binding sites for tRNA:sites for tRNA: P site -- holds the P site -- holds the

tRNAtRNA The A site -- holds The A site -- holds

the tRNA with the tRNA with next amino acidnext amino acid

The E site -- exit The E site -- exit site, where site, where discharged tRNAs discharged tRNAs leave the leave the ribosomeribosome