Biochemistr

Amino Acid
Structure
Abigail Jopling

Biochemistry

Objectives
Identify

20 amino acids and classify them as essential or

nonessential

Define

zwitterion, isoelectric point, stereoisomers, enantiomers

and chiral

Characterize

amino acid side chains/functional groups and the

hydrophobic effect

Describe
Name

acid/base properties of amino acids

polypeptide amino acid sequences and identify their

terminal ends

Biochemistry

Amino Acid Introduction

Building blocks of proteins

Linear polymers are formed by linking the

carboxyl group of one amino acid to the
amino group of another

All living organisms form proteins from the

same 20 amino acids

Essential amino acids can only be derived

from diet, the rest can be synthesized

Biochemistry

Amino Acid Structure

Fisher

projection shows constituent atoms

Stereochemical projection shows function

Tetrahedral carbon is
chiral (except in glycine)

Variable R groups display

different characteristics

Size
Shape
Charge
H bond
Hydrophobic character
Chemical reactivity

Source

Biochemistry

Amino Acid Structure

Fisher
Projection

Source

Stereochemical
Projection

Source

Biochemistry

Amino Acid Structure

Exist

in two mirror image forms (L and D

stereoisomers)

Only L isomers exist in animals

Dipolar

ions/Zwitterion

Ion carrying both a positive and negative

charge
Exist mainly in this state at physiologic pH

L vs D

Biochemistry

L vs D

Biochemistry

Zwitterion

Biochemistry

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Zwitterion

Biochemistry

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Alanine Titration

Sourc
e

Biochemistry

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Alanine Titration

Biochemistry

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Biochemistry

Nomenclature
Each

amino acid has a

full name, three letter
abbreviation and single
letter abbreviation

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Biochemistry

Side Chain Properties

Key

to protein structure and function

based on

Size
Shape
Charge
Hydrogen bond
Acid/Base

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Biochemistry

Functional Group Classification

Amino

acids with nonpolar side chains (R groups)

Polar

amino acids with neutral R groups that

show unevenly distributed charges

Positively

charged amino acids with positively

charged R groups around pH 7.4

Negatively

charged amino acids with negatively

charged R groups around pH 7.4

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Biochemistry

Nonpolar R Groups
Hydrophobic

amino acids

Tend

to cluster together inside the

protein and away from the aqueous
environment of the cell (hydrophobic
effect)

Comprise the driving force for 3D

architecture of water soluble proteins
Proline ring limits ability to rotate

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Nonpolar R Groups

Biochemistry

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Biochemistry

Neutral Polar R Groups

Have zero net charge at neutral pH, but R group has

an electronegative atom

Side chains are hydrophilic and reactive

Cluster on surface of membrane proteins

The SH group in Cysteine is much more reactive than

the OH group

Entirely loses proton at slightly basic pH to form

reactive thiolate group

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Neutral Polar R Groups

Biochemistry

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Acidic R Groups
Negatively

charged at neutral pH

Biochemistry

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Acidic R Groups

Biochemistry

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Biochemistry

Basic R Groups
Positively

charged at neutral pH

Histidines

aromatic ring can be either

positively charged or uncharged at
neutral pH

Important

for acid base catalysis

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Basic R Groups

Biochemistry

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Histidine Ionization

Biochemistry

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Derived Amino Acids

Found in proteins, but not coded in DNA

Formed by post translational modification

4-hydroxyproline
5-hydroxylysine
-N-methyl-lysine
3-methylhistidine
-carboxyglutamate
desmosine
isodesmosine

Biochemistry

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Biochemistry

Post-Translational Modifications

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Biochemistry

Essential vs. Nonessential

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Kawashiorkor
Disease

of the displaced

child
Inadequate

intake disrupts
oncotic pressure

Reversible

if treated early

Biochemistry

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Biochemistry

Acid/Base Properties
Amphoteric

Contain weakly acidic -carboxyl groups

and weakly basic -amino groups
Each acidic or basic amino acid has a side
chain with an ionizable group

Acid-base

catalysis

Ability to donate or accept protons to

facilitate reactions

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Biochemistry

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Biochemistry

Peptide Bond

Amide bond=peptide bond

Condensation reaction betweenamino group

of one amino acid and thecarboxyl group of
another
Composed of six atoms (C, O, N, H, C)
Planar

Polypeptides are formed by linking amino

acids together with peptide bonds

N-C-C-N-C-C pattern forms the backbone

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Biochemistry

Peptide Bond Formation

Sourc

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Biochemistry

Peptide Bond Formation

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Polypeptide Formation

Source

Biochemistry

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Biochemistry

Amino Acid Sequences

Specific

direction

Amino terminal residue to carboxyl

terminal residue

Naming

All amino acid residues have suffixes

changed to yl with the exception of the
C-terminal amino acid

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Biochemistry

Polypeptide Directionality

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Biochemistry

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Putting It All
Together

Biochemistry