Proteins

Proteins(Greek = “of first importance”)

Functions: Structure - skin, bones, hair, fingernails Catalysis - biological catalysts are enzymes Movement - muscle: actin and myosin Transport - hemoglobin, transport thru

membranes

Proteins

Functions: Hormones - insulin, oxytocin, HGH, etc. Protection - antigen-antibody reactions,

fibrinogen in clotting Storage - casein in milk, ovalbumin in eggs,

ferritin in liver-stores iron Regulation - control in expression of genes

Proteins

Protein types: 9000 different proteins in a cell Individual human being >100,000 different

Fibrous Protein Insoluble in H2O Used mainly for structural purposes

Globular Protein Partly soluble in H2O Usually not used for structural purposes

Proteins are Natural Polymers

Proteins are constructed in the body from many repeating units call amino acids

Just like other polymers the amino acids (monomers) are joined together to make long chains (polymers) – but we call them proteins instead

All of the polymer information applies to proteins – cross linking, rings, polarity etc.

Amino Acids

The Building Blocks of proteins Contains an amino group and an acid group Nature synthesizes about 20 common AA All but one (proline) fit this formula:

AA Proline:

COOHC

NH2

R

H

proline

N

COOH

H

Amino Acids

Amino Acids (AA) The twenty common are Called alpha amino acids One and three letter codes given to 20 common AA All but glycine (where R=H)

exist as a pair of enantiomers nature usually produces the

L amino acid

COOHC

NH2

R

H

Amino Acids

Amino Acids (AA) Sometimes classified

as AA with: nonpolar R groups polar but neutral R groups acidic R groups basic R groups

Zwitterions

An acid -COOH andan amine -NH2 groupcannot coexist

The H+ migrates to the-NH2 group

COO- and NH3+ are

actually present, calleda “Zwitterion”

Zwitterions

Zwitterion = compound where both a positive charge and a negative charge exist on the same molecule

AA are ionic compounds

They are internal salts

In solution their form changesdepending on the pH

Zwitterions

COOHC

NH3+

R

HCOO-C

NH3+

R

H

COO-C

NH2

R

H

pH = 1-5

excess H+ excess OH-

pH = 10-14

more basicmore acidic

Zwitterions

COOHC

NH3+

R

H

COO-C

NH3+

R

H COO-C

NH2

R

H

pH = 1-5

excess H+ excess OH-

pH = 10-14

more basicmore acidic

at pI (isoelectric

point)charge = 0

pI

The pI is the “isoelectric point”The pI is the pH where

NO charge is on the AA:

COO-C

NH3+

R

H

at pIcharge = 0

(Not necessarily

at a neutral pH)

Cysteine

The AA Cysteine exists as a dimer:

cysteine

COOHC

NH2

CH2

H

HS[O]

[H]2

HCOO C

NH2

CH2

H

S COOHC

NH2

CH2

H

S

cystine

a disulfide linkage

Peptides

AA are also called peptidesThey can be combined to form peptide

bonds

glycineCCHH2N OH

OH+

alanineCCH

CH3

H2N OH

O-H2O

Peptides

Dipeptides

a peptide bond

CCHH2N

OHCCH

CH3

NH OH

O

glycineCCHH2N OH

OH+

alanineCCH

CH3

H2N OH

O-H2O

a peptide bond

CCHH2N

OHCCH

CH3

NH OH

O

amineend

acidend

glycylalanine (Gly-Ala), a dipeptide

Peptides

Glycylalanine is not the same as Alanylglycine

CCH

CH3

H2N

O

CCHNH OH

OH

CCHH2N

OHCCH

CH3

NH OH

O

glycylalanine

alanylglycine

Peptides

Synthesis of Alanylglycine

alanineCCH

CH3

H2N OH

O

+glycine

CCHH2N OH

OH-H2O

CCH

CH3

H2N

O

CCHNH OH

OH

alanylglycine

Peptides

Addition of peptides (head to tail) Formation of:

dipeptides tripeptides tetrapeptides pentapeptides polypeptides PROTEINS

AA’s

Proteins

Proteins usually contain about 30+ AAAA known as residues

One letter abbreviations G, A, V, L

Three letter abbreviations Gly, Ala, Val, Leu

N terminal AA (amine end) on LEFTC terminal AA (carboxyl end) on RIGHT

glycylalanine Gly-Ala G-A

Polypeptides

Polypeptides

CCHN

R

OH

CCHN

R

OH

CCHN

R

OH

CCHN

R

OH

CCHN

R

OH

CCHN

R

OH

peptide bonds peptide bonds

side chains

amino acidresidues

Solubility

Polypeptides or Proteins If there is a charge on a polypeptide, it is

more soluble in aqueous solution If there is NO CHARGE (neutral at pI), it is

LEAST SOLUBLE in solution

COOHC

NH3+

R

H

COO-C

NH2

R

H

charged charged

Protein Structure

Primary Structure 1o

Linear sequence of AA

Secondary Structure 2o

Repeating patterns ( helix, pleated sheet)

Tertiary Structure 3o

Overall conformation of protein

Quaternary Structure 4o

Multichained protein structure

Protein Structure

Primary Structure 1o

Linear sequence of AA

CCHN

R

OH

CCHN

R

OH

CCHN

R

OH

CCHN

R

OH

CCHN

R

OH

CCHN

R

OH

AA 1 AA 2 AA 3 AA 4 AA 5 AA 6

With any 6 AA residues, the number of possible combinations is

6 x 6 x 6 x 6 x 6 x 6 = 46656AA’s

Protein Structure

Primary StructureCCHN

R

OH

CCHN

R

OH

CCHN

R

OH

CCHN

R

OH

CCHN

R

OH

CCHN

R

OH

AA 1 AA 2 AA 3 AA 4 AA 5 AA 6

With any 6 of the 20 common AA residues, the number of possible combinations is 20 x 20 x 20 x 20 x 20 x 20 = 64,000,000

(and this is not nearly large enough to be a protein!) AA’s

Protein Structure

Primary Structure A typical protein could have 60 AA residues. This

would have 2060 possible primary sequences. 2060 = 1078

This results in more possibilities for this small protein than there are atoms in the universe!

Protein Structure

Primary Structure Sometimes small changes in the

1o structure do not alter the biological function, sometimes they do.

AA’s

Changes and Effect of AA change

Sickle cell anemia – only one change in an amino acid – changes the hemoglobin

Protein Structure

Secondary Structure Repeating patterns

within a region Common patterns

helix pleated sheet

Originally proposed by Linus Pauling Robert Corey

AA’s

Protein Structure

Secondary Structure

helix Single protein chain Shape maintained by

intramolecular H bondingbetween -C=O and H-N-

Helical shape helix is clockwise

Protein Structure

Secondary Structure pleated sheet

Several protein chains Shape maintained by

intramolecular H bondingand other attractive forces between chains

Chains run anti-paralleland make U turns at ends

Protein Structure

Secondary StructureRandom Coils

Few proteins haveexclusively helix or pleated sheet

Many have non-repeatingsections called:Random Coils

Collagen Protein Structure

Secondary StructureTriple Helix of Collagen

Structural protein of connective tissues bone, cartilage, tendon aorta, skin

About 30% of human body’s protein

Triple helix units = tropocollagen

Tertiary Structure

The Three dimensional arrangement of every atom in the molecule

Includes not just the peptide backbone but the side chains as well

These interactions are responsible for the overall folding of the protein

This folding defies its functionand it’s reactivity

Tertiary Structure

The Tertiary structure is formed by the followinginteractions:Covalent BondsHydrogen BondingSalt BridgesHydrophobic InteractionsMetal Ion Coordination

Tertiary Structure –Covalent Bonding

The most common covalent bond in forming the tertiary structure is the disufide bond

It is formed from the disulfideinteraction of cysteine

cysteine

COOHC

NH2

CH2

H

HS[O]

[H]2 HCOO C

NH2

CH2

H

S COOHC

NH2

CH2

H

S

cystine

Tertiary Structure –Hydrogen Bonding

Anytime you have a hydrogen connected to a F O of N – you can get hydrogen bonding

These interactions can occur on the side chain, backbone or both

Tertiary Structure –Salt Bridge

Salt bridges are due to charged portions of the protein.

Opposite charges will attract and form ionic bonds

Some examples are the NH3+ and COO- areas of theprotein

Tertiary Structure –hydrophobic interactions

Because the nonopolar groups will turn away from the water and the polar groups toward it, hydrophobic interactions take place.

These interactions are strong enough to help define the overall structure of a protein

Tertiary Structure –Metal Ion Coordination

Two side chains with the same charge would normally repel each other

However, if a metal is placed between them, they will coordinate to the meal and be connected together.

These metal coordinations are important in tertiary structure formation

Tertiary Structure

Quaternary Structure

Highest level of organization Determines how

sub unit fit together Example Hemoglobin

(4 sub chains) 2 chains 141 AA 2 chains 146 AA

- Example - Collagen

Denaturation

Denaturation Any physical or chemical agent that destroys the

conformation of a protein is said to “denature” it Examples:

Heat (boil an egg) to gelatin Addition of 6M Urea (breaks H bonds) Detergents (surface-active agents) Reducing agents (break -S-S- bonds)

Denaturation

Denaturation Examples:

Acids/Bases/Salts (affect salt bridges) Heavy metal ions (Hg2+, Pb2+)

Some denaturation is reversible Urea (6M) then add to H2O

Some is irreversible Hard boiling an egg

Denaturation

Denaturation