Chapter 24 Lecture Notes - CEM252 at MSU Fall 1996


Chapter 24: Amino Acids and Proteins

Amino Acid
Compound with amino functional group and carboxylic acid functional group
a-amino acids
amine and carboxyl separated by 1 carbon atom
b-amino acids
amine and carboxyl separated by 2 carbon atoms... Chapter 24 - Slide 1


Protein-Derived Amino Acids

Protein - biological polymer of a-amino acids

Simplest protein derived amino acid (aa) - glycine (only achiral protein-derived aa)

Chapter 24 - Slide 2



Chirality of amino acids

Only one configuration found naturally

Chapter 24 - Slide 3


Natural AA Sidechains (R groups): Non-polar


Chapter 24 - Slide 4


Natural AA Sidechains (R groups): Polar, neutral


Chapter 24 - Slide 5


Natural AA Sidechains (R groups): Polar, acidic


Chapter 24 - Slide 6


Natural AA Sidechains (R groups): Polar, basic


Chapter 24 - Slide 7


Acid-Base Properties of Amino Acids

Amino AcidpKa a-CO2HpKa b-CO2HpKa a-NH3+
Aspartic Acid2.103.869.82

Chapter 24 - Slide 8


Significance of pKa


Chapter 24 - Slide 9


Forms of Amino Acid Present as a Function of pH


Chapter 24 - Slide 10


Buffer Regions


Chapter 24 - Slide 11


Challenge:

Tyrosine has an a-CO2H pKa of 2.20, and a-NH3+ pKa of 9.11, and a sidechain pKa of 10.07 - sketch a titration curve and give the structure of the major form or forms present at all equivalence and half-equivalence points.

Chapter 24 - Slide 12



Isoelectric Point

Isoelectric point (pI) - pH at which molecule has no net charge
(find by averaging pkas on either side of neutral form)
Chapter 24 - Slide 13



Isoelectric Precipitation

Amino acids with net charges repel each other and do not easily crystallize from solution - solubility is lowest at the isoelectric point

Chapter 24 - Slide 14



Electrophoresis

A method for separating charged compounds in an electric field

Chapter 24 - Slide 15



Nutrition

Dietary protein provides aas not made in our systems - these are called essential
tyrosine
Essential Amino AcidsNonessential Amino Acids
arginineglycine
histidinealanine
lysinecysteine
isoleucineaspartic acid
leucineglutamic acid
valineasparagine
threonineglutamine
methionineproline
phenylalanine
tryptophanserine
Chapter 24 - Slide 16



Polypeptides and Proteins

Proteins and polypeptides are chains of aa's

Dipeptide - 2 amino acids
Tripeptide - 3 amino acids ...
Polypeptides have 10 or more amino acids
Proteins have 100s or more amino acids

Chapter 24 - Slide 17


Amino Acid Connections



Chapter 24 - Slide 18


Peptide Bond Geometry

Peptide bonds are planar due to conjugation of nitrogen lone pair with carbonyl
Peptide bond movie

Chapter 24 - Slide 19



Protein Structural Descriptions

Primary Structure
sequence of amino acids
Secondary Structure
local three-dimensional patterns
Tertiary Structure
three-dimensional shape of an amino acid chain
Quaternary Structure
three-dimensional shape of multiple amino acid chains
Chapter 24 - Slide 20


Primary Structure Determination

Step 1: Amino Acid Analysis
Protein is hydrolyzed in strong acid or base at high temperatures
Mixture of amino acids generated by protein hydrolysis is analyzed by chromatography

Step 2: Sequence Analysis
protein cleaved into polypeptides
polypeptides subjected to amino acid analysis or Edman degradation

Chapter 24 - Slide 21



Sample Hydrolysis


Chapter 24 - Slide 22


Sequence Analysis

Chapter 24 - Slide 23


Cyanogen Bromide Cleavage


Chapter 24 - Slide 24


Edman Degradation

This process can be repeated ~20-30 times
Long polypeptides require cleavage to small units which can be individually sequenced

Chapter 24 - Slide 25



Challenge

Given:

What is the structure of the original peptide?

Chapter 24 - Slide 26



Secondary Structure

Common local conformations:

Stabilized by:

Chapter 24 - Slide 27


Alpha-Helix

alpha helix movie
Chapter 24 - Slide 28


Beta-Pleated Sheet

beta sheet movie
Chapter 24 - Slide 29


Tertiary Structure

Stabilized by:


Chapter 24 - Slide 30


Quaternary Structure

Forces holding protein chains together:

Chapter 24 - Slide 31


Polypeptide Synthesis

Problems:

Chapter 24 - Slide 32


Polypeptide Synthesis

Chapter 24 - Slide 33


Linear Polypeptide Synthesis


Chapter 24 - Slide 34


Convergent Polypeptide Synthesis


Chapter 24 - Slide 35


Solid-Phase Polypeptide Synthesis: (Merrifield Synthesis)

Chapter 24 - Slide 36


Amino Protecting Groups

Amino groups commonly protected as carbamates

Chapter 24 - Slide 37



Carboxyl Protecting Groups

Methyl, ethyl, and benzyl esters

Chapter 24 - Slide 38



Peptide Bond Forming Reaction

Chapter 24 - Slide 39




Last modified 12/26/96

Dr. Abby Parrill
Department of Chemistry
Michigan State University

These pages may be downloaded and linked from other pages freely for academic and educational purposes. Questions, problems, and errors should be sent to parrill@argus.cem.msu.edu.