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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