Proteins• Proteins are long polymers made up of 20

different amino acid monomers• They are quite large, with molar masses of around

5,000 g/mol to around 100,000 g/mol• They have complex structures with unique 3-D

shapes that determine their functions• They are the most abundant organic compounds in

the body, and also the most diverse in function• Proteins are involved in structure, transport,

storage, metabolism, cell signaling and many other processes

Functions of Proteins

Amino Acids• Amino acids, as the name implies, have both an amine

group and a carboxylic acid group• The 20 amino acids that make up our proteins have the

amine group, the acid group, a hydrogen, and a variable group attached to a central carbon (called the carbon)

• The variable groups (called side chains) are what determine the individual characteristics of the amino acids

General structure of an amino acid:

H2N

R

CH

HO

OH2N COOH

R

H

Acidic and Basic Amino Acids• Amino acids can be classified by the nature of the side-

chain as acidic, basic, polar neutral or nonpolar

Polar Neutral Amino Acids

Nonpolar Amino Acids

Abbreviations for Amino Acids• Each amino acid has standard 3-letter and 1-letter

abbreviations (shown in the table below)

Name 3-Let 1-Let Name 3-Let 1-LetGlycine Gly G Serine Ser SAlanine Ala A Threonine Thr TValine Val V Asparagine Asn NLeucine Leu L Glutamine Gln QIsoleucine Ile I Tyrosine Tyr YPhenylalanine Phe F Aspartic Acid Asp DMethionine Met M Glutamic Acid Glu EProline Pro P Lysine Lys KTryptophan Trp W Arginine Arg RCysteine Cys C Histidine His H

D- and L-Amino Acids• All amino acids besides glycine are chiral• Each amino acid has two possible enantiomers

- these are classified as D or L as with sugars• Amino acids in nature are almost exclusively L-amino acids• When a Fischer projection is written with the acid at the top,

and the R group at the bottom:- if the amine group is on the right, it’s a D-amino acid- if the amine group is on the left, it’s an L-amino acid

COOH

CH3

NH2H

COOH

CH3

H2N H

D-Alanine L-Alanine

Isoelectric Points for Amino Acids• Because the amine group is basic, and the carboxylic acid group

is acidic, amino acids often exist as zwitterions• A zwitterion is a dipolar ion with a net charge of zero• Because zwitterions act like salts, they have high melting points• The isoelectric point (pI) is the pH at which a zwitterion forms

- below pI the amino acid has a net positive charge- above pI the amino acid has a net negative charge

• Acidic amino acids have low pI values and basic amino acids have high pI values (due to side-chain ionization)

Electrophoresis of Amino Acids• Electrophoresis is a technique used to separate charged

molecules with an electric field• The samples are loaded onto a support medium (usually an

agarose or polyacrylamide gel) and separated by mobility- mobility is affected by size, shape, charge and solubility

• A buffered solution is used to conduct the charge and allow the charged molecules to move- negatively charged amino acids move towards the anode (-)- positively charged amino acids move towards the cathode (+)

Peptides• Peptides are two or more amino acids linked together by amide

bonds (called peptide bonds)• A peptide bond is formed when the acid group of one amino

acid reacts with the amine group of another amino acid• When writing the structure of a peptide:

- the amino acid with the free (unreacted) amine group is written on the left and is called the N terminal amino acid- the amino acid with the free (unreacted) acid group is written on the right and is called the C terminal amino acid

• Peptides are usually named using the 3- or 1-letter abbreviations for the amino acids, going from N terminal to C terminal

Synthesis of Peptides and Proteins• In cells, peptides and proteins are synthesized using RNA

catalysts (to be discussed in Chapter 22)• In the laboratory a variety of techniques are used

- most commonly the peptides are synthesized on resin beads using an automated peptide synthesizer- smaller peptides, like dipeptides, are generally synthesized by hand in solution (not on resin)- protecting groups must be used in order to prevent unwanted amino acid couplings

H2N

CH3

OH

O

NH

CH3

OH

O

PProtectamine

H2NOH

O

Protectacid

H2NO

O

P

NH

HN

CH3

O

O

OP P

Deprotect

H2N

HN

CH3

O

OH

O

Structure of Peptide Bonds• Peptides are particularly stable and are also fairly rigid• This is due to the structure of the peptide amide bonds• Through resonance, the lone pair electrons on nitrogen and

the pi electrons of the carbonyl are delocalized- this gives some double bond character to the C-N bond, preventing free rotation around that bond- this also makes the nitrogen less basic, since the lone pair is not very available for bonding, increasing peptide stability

NH2

O

NH2

O

NH2

O

Resonance Structures Resonance Hybrid

Primary Structure of Peptides and Proteins• A polypeptide containing 50 or more amino acids is usually

called a protein• The primary structure of a protein is the sequence of amino

acids in the peptide chain• The higher levels of structure, as well as the function, are

derived from the primary structure- even a single amino acid change can have drastic effects

• For example, the nonapeptides oxytocin and vasopressin only differ in the amino acids at positions 3 and 8

Insulin• Insulin was the first protein whose primary

structure was determined• Human, pig and cow insulin differ only at four

amino acids• Bovine insulin (from cow pancreas) was used

for diabetics, but now it’s made by genetically engineered E. coli

Secondary Structure of Proteins (the Alpha Helix)• The secondary structure of a protein indicates the

conformation of the peptide chain in a given region• There are three main types of secondary structure: the alpha

helix, the beta-pleated sheet and the triple helix- all three are governed by hydrogen bonding

• The alpha helix is coiled due to H-bonding between backbone N-H on one loop to backbone C=O group on next loop• The side chains are all on the outside of the helix, so larger side chain groups favor helix

Secondary Structure of Proteins (the Beta-Pleated Sheet)• Beta-pleated sheets consist of peptide chains side-by-side,

held together by backbone H-bonding• All the side chains point out above and below the sheet

- smaller side chains favor -pleated sheets (larger ones would be too crowded)

Secondary Structure of Proteins (the Triple Helix)• A triple helix consists of three peptide strands in a braid, held

together by H-bonding, both backbone H-bonding and H-bonding between hydroxyl groups on adjacent peptide strands- they contain large amounts glycine, proline, hydroxyproline and hydroxylysine that contain –OH groups for H-bonding

• Triple helices are very strong, and are found in collagen, connective tissue, skin, tendons, and cartilage- several triple helices can form a larger braid for increased strength