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Lecture 4:Lecture 4:

MacromoleculesMacromolecules

And Protein StructureAnd Protein Structure

A large part of modernbiology is understanding large molecules like Proteins

A large part of modernbiology is understanding large molecules like Proteins

Chapter 3: Peptide Chapter 3: Peptide Structure: peptide bonds Structure: peptide bonds

and side chainsand side chains

Websites:

http://www.ncl.ox.ac.uk/dp/jjones1.html

http://wizard.pharm.wayne.edu/biochem/prot.html.html

Websites:

http://www.ncl.ox.ac.uk/dp/jjones1.html

http://wizard.pharm.wayne.edu/biochem/prot.html.html

Goals:Goals:

1. Study polypeptides, peptide bonds & proteins.1. Study polypeptides, peptide bonds & proteins.

2. Introduce 3-D, quaternary protein structure.2. Introduce 3-D, quaternary protein structure.

3. Relate proteins to genetics, science, agriculture

and health.

3. Relate proteins to genetics, science, agriculture

and health.

Assignment:Assignment: Read: chapters 3 & 5Read: chapters 3 & 5

Review: Molecule Building BlocksReview: Molecule Building Blocks

Small Molecules Chemical Bonds MacromoleculesSmall Molecules Chemical Bonds Macromolecules

Sugars Covalent PolysaccharidesSugars Covalent Polysaccharides

Glycerol and fatty acids

Glycerol and fatty acids CovalentCovalent Lipids (fats)Lipids (fats)

Amino acids Covalent and peptide ProteinsAmino acids Covalent and peptide Proteins

Chapter 3: Chapter 3: 22ndnd topic: topic:

Peptide Bonding Peptide Bonding

Side chains (R groups) determine 20 different amino acidsSide chains (R groups) determine 20 different amino acids

-Central carbon atom

-Central carbon atom

C -Amino group-Amino group

HH

HH

NN

Amino groupAmino group

-Carboxyl group-Carboxyl group

OHOHCC

OO

Carboxyl groupCarboxyl group

R

-Side chain (R)HH

-Hydrogen atom-Hydrogen atom

Amino Acid StructureAmino Acid Structure

Peptide bonds link Amino Acids together

Peptide bonds link Amino Acids together

OH

H

H

C CN

O

RH

H

C CN

O

R

H

H

H

C CN

O

R

A Polypeptide = long chain of amino acids joined by peptide bondsA Polypeptide = long chain of amino acids joined by peptide bonds

Dehydration synthesis = losing a waterDehydration synthesis = losing a water

Protein conformation = 3-D Structure, peptide bonding is the Primary structure Protein conformation = 3-D Structure, peptide bonding is the Primary structure

Protein = chain of amino acidsProtein = chain of amino acids

Chemical ReactionChemical Reaction

Protein Conformation or Structure Determines FunctionProtein Conformation or Structure Determines Function

Chapter 3: Chapter 3: ““R” structures &R” structures &

Primary StructurePrimary StructurePrimary Structure =

AA’s make the Chain…

AA Type

Amino AcidsAmino AcidsBuilding Blocks for ALL Proteins Building Blocks for ALL Proteins

Non-Essential Amino AcidsGlycineAlanine

AspartateGlutamateAsparagineGlutamineArginineTyrosineSysteineSerineProline

Non-Essential Amino AcidsGlycineAlanine

AspartateGlutamateAsparagineGlutamineArginineTyrosineSysteineSerineProline

Assignment: Look up the essential amino acidsAssignment: Look up the essential amino acids

Essential Amino AcidsPhenylalanine

ValineThreonine

TryptophanIsoleucine

MethionineHistidineLeucineLysine

Essential Amino AcidsPhenylalanine

ValineThreonine

TryptophanIsoleucine

MethionineHistidineLeucineLysine

Side Chains: “R”Side Chains: “R”

H|

GlycineGlycine AsparagineAsparagine

CysteineCysteine

Glutamic AcidGlutamic Acid

GlutamineGlutamine

ArginineArginine

Aspartic AcidAspartic Acid

SerineSerineAlanineAlanine

LysineLysine

ProlineProline

IsoleucineIsoleucine

LeucineLeucine

ThreonineThreonine

MethionineMethionine

HistidineHistidine

TyrosineTyrosine

TryptophanTryptophan

ValineValine

PhenylalaninePhenylalanine

Amino Acids

Polarity or

Charge helps

Determine

Binding…

Polarity or

Charge helps

Determine

Binding…

Amino Acids

Each AA has aunique 1-letter and 3-lettercode identifying it in the Protein’s chain…

Each AA has aunique 1-letter and 3-lettercode identifying it in the Protein’s chain…

Each AA has a unique 1-letter or a 3-letter code to identifying the Protein’s AA-chain

Each AA has a unique 1-letter or a 3-letter code to identifying the Protein’s AA-chain

3-Letter Code in AA chain

Protein AA Chain Sequence

The backgroundshadow indicates similar binding or folding function.

Single letter codeSingle letter code

Primary StructurePrimary Structure

Amino acid sequenceAmino acid sequence

Peptide bondingPeptide bonding

H H

HH

C C

O

N

R H

H

C C

O

N

R H

H

C C

O

N

R

H

C C

O

OH

R

Protein Secondary StructureProtein Secondary Structure

Is the pattern of hydrogen bonding in one polypeptide

• Pattern yields folding:

1- helix or

2- - pleated sheets

Is the pattern of hydrogen bonding in one polypeptide

• Pattern yields folding:

1- helix or

2- - pleated sheets

1. Hydrogen bonds1. Hydrogen bonds2. Disulfide bonds (cysteine)2. Disulfide bonds (cysteine)3. Hydrophobic forces3. Hydrophobic forces4. Ionic interactions4. Ionic interactions

Types of Bonding:Types of Bonding:

Types of BondsTypes of Bonds

Hydrogen bondsHydrogen bonds Disulfide bondsDisulfide bonds

Hydrophobic forcesHydrophobic forcesIonic interactionsIonic interactions

Tertiary Structure = Folding Side Chains (R-groups)Tertiary Structure = Folding Side Chains (R-groups)

Bonds:

1. Hydrogen bonds1. Hydrogen bonds2. Disulfide bonds (cysteine)2. Disulfide bonds (cysteine)3. Hydrophobic forces3. Hydrophobic forces4. Ionic interactions4. Ionic interactions

Quaternary StructureQuaternary Structure>1 polypeptide chain folded

Multiple Proteins Folded Together

>1 polypeptide chain folded

Multiple Proteins Folded Together

1. Hydrogen bonds1. Hydrogen bonds

2. Disulfide bonds (cysteine)2. Disulfide bonds (cysteine)

3. Hydrophobic forces3. Hydrophobic forces

4. Ionic interactions4. Ionic interactions

Bonds:

The core histone octamer: from Arents et al. (1991).

Proteins are Complex and SpecificProteins are Complex and Specific

• The complex primary sequence of amino acids in the protein’s chain can be symbolically represented as a “molecular language” that determines the “meaning” or structure of the protein. Protein structure specifies its function.

• Proteins function by binding to and interacting with their substrates to effect chemical reactions, cellular communication, pore formation, catalysis, etc.

• The complex primary sequence of amino acids in the protein’s chain can be symbolically represented as a “molecular language” that determines the “meaning” or structure of the protein. Protein structure specifies its function.

• Proteins function by binding to and interacting with their substrates to effect chemical reactions, cellular communication, pore formation, catalysis, etc.

“Life is a wave,in which no two consecutive moments of its existence is

composed of the same particles.”

“Life is a wave,in which no two consecutive moments of its existence is

composed of the same particles.”

-- John Tyndall (1820 - 1893)British draftsman, surveyor, physics professor, mathematician, geologist,

atmospheric scientist, public lecturer, and mountaineer

-- John Tyndall (1820 - 1893)British draftsman, surveyor, physics professor, mathematician, geologist,

atmospheric scientist, public lecturer, and mountaineer