VARIATIONS OF “R”

PROTEINS
 Size
CHARACTERISTICS OF PROTEINS
 Shape
Protein – Naturally occurring, unbranched Polymer in
which the Monomer units are Amino Acids  Charge
 Most abundant molecules in the cells after
water  Acidity

 Account for 15% of cell’s overall mass  Functional Groups Present

 Has an Average Nitrogen Content of 15.4% by  Hydrogen-Bonding Ability

mass
 Chemical Reactivity

AMINO ACID STRUCTURE
Amino Acids – Building blocks of protein

 Monomer Units of Protein Side Chain

ELEMENTAL COMPOSITION OF PROTEIN

 Carbon (C)
R  -Carbon Atom
 Hydrgen (H)

 Nitrogen (N) H2N C COOH

 Oxygen (O) -Carboxyl
-Amino H
Group
 Sulfur (S) Group
 Iron (Fe) – Present in Specialized Protein
Amino and Carboxyl Group – Constant in Amino Acids
 Phosphorous (P) – Also present in Specialized R Group – Gives the characteristics of Amino Acids
Protein
 Helps distinguish what type of Amino Acid
AMINO ACIDS
Amino Acids - Organic compound that contains both an
Amino (-NH2) and Carboxyl (-COOH) groups attached to
same Carbon Atom

 The position of the carbon atom is ALPHA (a)

Alpha Carbon (a) – Found at the terminal side

NH2 (Amino Group) – Attached to the Alpha carbon

-COOH (Hydroxyl Group) – Attached to the Alpha Carbon ** All Amino Acids differ from one another because of
their R-GROUPS **
 Highest Priority
** Amino Acids are BIPOLAR **
R – Side Chain Carbon
Standard Amino Acids – Divided into 4 groups based on
 >700 Amino Acids are known properties of R-groups

 Based on common R groups, there are 20 GMRL | 10-07-20

standard amino acids
Non Polar Amino Acids – R groups are non-polar Polar Basic - Contain Amino Group as part of the side
chain
 8 out of 20 amino acids are non-polae
 2 Amino Acids belong to this category
 When present in protein, they are located in the
INTERIOR of the protein, where there is no NOMENCLATURE
polarity ** Common Names assigned to Amino Acids are
Hydrophobic Amino Acids – Amino acids that are currently used **
“water-fearing” Three Letter Abbreviations – Widely used for naming
 Insoluble in water  First letter of amino acids should be capitalized
NON-POLAR AMINO ACIDS
 The next two letters should not be capitalized
 Hydrophobic
EXCEPT:
 Water-fearing  Asparagine (ASN)
SUBTYPES
 Glutamine (GLN)
 Alkyl
 Tryptophan (TRP)
 Aromatic
One Letter Symbols - Commonly used for comparing
POLAR AMINO ACIDS
amino acid sequences of proteins
 Hydrophilic
 Usually the first letter of the name
 Water-loving
 When more than one amino acid has the same
letter, The most abundant amino acid gets the
SUBTYPES 1st letter

 Neutral
NON-POLAR AMINO ACIDS
 Acidic

 Basic

Polar Amino Acids - R-groups are polar

THREE TYPES OF POLAR AMINO ACIDS

 Polar Neutral

 Polar Acidic

 Polar Basic

Polar Neutral - Contains POLAR but NEUTRAL side

chains

 7 Amino Acids belong to this category

Red Part – R group that gives the Amino Acid its own
Polar Acidic - Contain Carboxyl Group as part of the
identity
side chains
Glycine – Only Amino Acid that does not exhibit
CHIRALITY

GMRL | 10-07-20
POLAR NEUTRAL AMINO ACIDS CHIRALITY AND AMINO ACIDS
Chirality in Amino Acids – Four different groups are
attached to the A-Carbon Atom in Standard Amino Acids

 Except Glycine

 Glycine R-Group – Hydrogen

 19 out of 20 Standard Amino Acids contain a

Chiral Center

Chiral Centers – Exhibit Enantiomerism

Enantiomerism – Left and Right handed forms

 Each of the 19 Amino Acids exist in left and right

handed forms

POLAR ACIDIC AMINO ACIDS

L-isomers in Amino Acids – Found in nature as well as

in proteins

Bacteria – Have some D-amino Acids

Monosaccharides – Nature favors D-Amino Acids

RULES FOR DRAWING FISCHER PROJECTION

POLAR BASIC AMINO ACIDS FORMULAS

 The — COOH group is put at the top, the R group

at the bottom to position the carbon chain
vertically

 The — NH2 group is in a horizontal position

 Positioning — NH2 on the left = L isomer

 Positioning — NH2 on the right = D isomer

GMRL | 10-07-20
 Isoelectric Point (pI) – pH at which the concentration of
Zwitterion is maximum

 Net charge is zero

 Different amino acids have different isoelectric

points

At Isoelectric Point - Amino acids are not attracted

towards an applied electric field because they have net
zero charge

CHARGE

 Become +1 as you lower the pH

 Become -1 as you raise the pH

ACID BASE PROPERTIES OF AMINO ACIDS
COOH COO- COO-
Amino Acids in Pure Form – Look like white crystalline + +
H3N C H H2N C H
H3N C H
solids
CH3 CH3 CH3
** Most Amino Acids decompose before they melt **
Low pH High pH
Zwitter Ion
(net + charge) (net - charge)
** Amino Acids are not very soluble in water ** (net neutral charge)

** Can be Basic or Acidic in one structure **

Zwitterion - An ion with + (positive) and – (Negative)
charges on the same molecule with a net zero charge
Carboxyl Groups - Give-up a proton to get negative
charge
Amino Groups - Accept a proton to become positive
COO- COO-
CYSTEINE: A CHEMICALLY UNIQUE AMINO ACID
Cysteine - The only standard amino acid with a
Sulfhydryl Group (— SH group)/(Thiols)
 Dimerizes to form a Cystine Molecule with the
presence of Mild Oxidizing Agents
Sulfhydryl Group - Imparts Cysteine a chemical
property unique among the standard amino acids

Cystine - Two Cysteine Residues linked via a Covalent

+H NH3 +
3N H H Disulfide Bond.

R CH3

L D

ACID-BASE PROPERTIES OF AMINO ACIDS

Amino Acids in Solution - Exist in three different
species

 Zwitterions

 Positive Ion

 Negative Ion

GMRL | 10-07-20
PEPTIDES
Peptides – Combination of 3 amino acids

Dipeptide – Bond between two amino acids

Oligopeptide – Bond between 10-20 amino acids

Polypeptide – Bond between large number of amino

acids

** Every peptide has an N-Terminal end and a C-

Terminal End **

EXAMPLE:

H3N-aa-aa-aa-aa-aa-aa-aa-aa-aa-COO-
+

OH
N-terminal end
O O CH2 O

+H
H H
3N CH C N CH C N CH C O-

CH3 CH2 C-terminal end

Alanine Phenylalanine Serine