BIOCH200 Lecture Notes - Lecture 10: Hydrolysis, Tripeptide, Amide

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Introductory to Biochemistry: Protein Structure and Function
Formation of a Peptide Bond
Two amino acids joined by one peptide → “dipeptide” with two A.A residues
Condensation Reaction → Water is lost.
3 Amino Acids Joined → tripeptide with 2 peptide bonds
4 A.A joined → Tetrapeptide with 3 peptide bonds.
Bond is broken through hydrolysis
Oligopeptides→ large number of A.A referring to synthetic peptides
Polypeptide → long chains produced naturally.
Protein → Large polypeptide (more than one) with biological function.
Only terminal alpha-amino and alpha-carboxylate regain charge → Others lose charge due to
peptide formation.
Some R groups may also be charged!
Peptide bonds go from C to N while a protein goes from N-terminus to C-terminus.
Primary Structure
Sequence of amino acids in polypeptide that determines structure which determines function.
Joined together by covalent peptide bonds
Properties of Peptide Bonds
Amide bonds
Electrons are delocalized to generate two resonance forms.
Peptide bonds exhibit double bond character → no rotation around C-N
Functional groups are potential H-bond acceptors or donors
Peptide bonds are polar and short.
Peptide Bonds
Rigid and Planar
Rotation occurs between C-(alpha)C and N-(alpha)C
Backbone includes alpha carbons and those involved in peptide bond → Does not include R
groups.
Secondary Structure
Local folding of backbone → Zooming in at a region of the protein
Hydrogen bonding of groups in polypeptide backbone
Alpha-helix, Beta-sheets and loops
N to C terminus
Regular Secondary Structure
1. Alpha-helix
2. Beta Sheets
Irregular Secondary Structure
1. Loops.
Alpha Helix
Right handed twist
Carbonyl oxygen of each residue forms Hydrogen bond with backbone NH four residues down.
C1 w/ N5
C2 w/ N6
First 4 NH at N-terminus and last 4 CO groups at C-terminus do not form H-Bonds
Side Chains are outside of helix and face down towards the N-terminus.
Stabilized by H-bonds in backbone CO and NH in same helices.
Beta Sheets
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Document Summary

Two amino acids joined by one peptide dipeptide with two a. a residues. 3 amino acids joined tripeptide with 2 peptide bonds. 4 a. a joined tetrapeptide with 3 peptide bonds. Oligopeptides large number of a. a referring to synthetic peptides. Protein large polypeptide (more than one) with biological function. Only terminal alpha-amino and alpha-carboxylate regain charge others lose charge due to peptide formation. Some r groups may also be charged! Peptide bonds go from c to n while a protein goes from n-terminus to c-terminus. Sequence of amino acids in polypeptide that determines structure which determines function. Electrons are delocalized to generate two resonance forms. Peptide bonds exhibit double bond character no rotation around c-n. Functional groups are potential h-bond acceptors or donors. Backbone includes alpha carbons and those involved in peptide bond does not include r. Local folding of backbone zooming in at a region of the protein. Hydrogen bonding of groups in polypeptide backbone.

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