Proteins

Chapter 22

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

ProteinsFunctions:

– 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 theL amino acid COOHC

NH2

R

H

LOOK IN THE BOOK

Amino Acids• Amino Acids (AA)

– Sometimes classifiedas AA with:

• nonpolar R groups• polar but neutral R groups• acidic R groups• basic R groups

Zwitterions• An acid -COOH and

an 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

AA’s

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

AA’s

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

AA’s

pI• The pI is the “isoelectric point”

• The pI is the pH whereNO 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

AA’s

Peptides• AA are also called peptides

• They can be combined to form...

glycine

CCHH2N OH

OH

+

alanine

CCH

CH3

H2N OH

O-H2O

AA’s

Peptides• AA are also called peptides

• They can be combined to form a dipeptide.

a peptide bond

CCHH2N

OH

CCH

CH3

NH OH

O

glycine

CCHH2N OH

OH

+

alanine

CCH

CH3

H2N OH

O-H2O

Peptides• Known as a “dipeptide”

a peptide bond

CCHH2N

OH

CCH

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

OH

CCH

CH3

NH OH

O

glycylalanine

alanylglycine

Peptides• Synthesis of Alanylglycine

alanine

CCH

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

Student Practice

• Show the product for the following combination of amino acids

Glu – Pro – His

Pro – Asn – Leu

Val – Ala – Trp

http://www.youtube.com/watch?v=va0DNJId_CM

Proteins• Proteins usually contain about 30+ AA• AA known as residues

– One letter abbreviations• G, A, V, L

– Three letter abbreviations• Gly, Ala, Val, Leu

• N terminal AA (amine end) on LEFT• C terminal AA (carboxyl end) on RIGHT

glycylalanine Gly-Ala G-A

AA’s

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

AA’s

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 Structure

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 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

• Cattle and hog insulin is used for humans but is different

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

From yahoo images

youtube

• http://www.youtube.com/watch?v=bCOJkpL7MVw

Protein Structure• Secondary Structure

– Repeating patternswithin 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

AA’s

YOUTUBE

http://www.youtube.com/watch?v=yh9Cr5n21EE

http://www.youtube.com/watch?v=XKI0le9e2D8

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

AA’s

Protein Structure• Secondary Structure• Random Coils

– Few proteins haveexclusively helix or pleated sheet

– Many have non-repeatingsections called:Random Coils

AA’s

Collagen Protein Structure

• Secondary Structure• Triple Helix of Collagen

– Structural protein of connective tissues

• bone, cartilage, tendon• aorta, skin

– About 30% of human body’s protein

– Triple helix units = tropocollagen

AA’s

Youtube

http://www.youtube.com/watch?v=YmuFI1jtc8M&feature=PlayList&p=C8887E4E7D367515&index=0&playnext=1

http://www.youtube.com/watch?v=gXeYf9dLT3s

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 function

and it’s reactivity

AA’s

Tertiary Structure

The Tertiary structure is formed by the following

interactions:

Covalent Bonds

Hydrogen Bonding

Salt Bridges

Hydrophobic Interactions

Metal Ion Coordination

AA’s

Tertiary Structure –Covalent Bonding

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

• It is formed from the disulfide

Interaction 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 occure

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 the

protein

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

subunit 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