Chapter 21Chapter 21

ProteinsProteins 4/15/094/15/09

Spider Silk, a fibrous protein. . .tough on bugsNot on you. . .(soft and smooth)

ProteinsProteins• Proteins many have functions:

•1.Structure:1.Structure: collagen and keratin are the chief constituents of skin, bone, hair, and nails.

•2. Catalysts:2. Catalysts: virtually all reactions in living systems are catalyzed by •proteins called enzymes.

•3. Movement:3. Movement: muscles are made up of proteins called myosin and actin.

•4. Transport4. Transport: hemoglobin transports oxygen from the lungs to cells; other proteins transport molecules across cell membranes.

•5. Hormones:5. Hormones: many hormones are proteins, among them insulin, •oxytocin, and human growth hormone.

ProteinsProteins

Proteins are divided into two types:

1. fibrous proteins (e.g. collagen, keratin)

2. globular proteins (e.g. Hemoglobin)

6. Protection:6. Protection: blood clotting involves the protein fibrinogen;the body used proteins called antibodies to fight disease.

7. Storage:7. Storage: casein in milk and ovalbumin in eggs store nutrients for newborn infants and birds; ferritin, a protein in the liver, stores iron.

8. Regulation:8. Regulation: certain proteins not only control the expression of genes, but also control when gene expression takes place.

Amino Acids Amino Acids proteinsproteins

In Nature 20 alpha Amino acidIn Nature 20 alpha Amino acids exist (see table 21.1)s exist (see table 21.1) :

AKA α A.A.s b/c amino group is on the α carbon

•A.A.s contains amino group, carboxyl group, R group.

R- group polarityMost imp.

Chirality of Amino Chirality of Amino AcidsAcids

H NH3+

COO-

CH3

+H3N H

COO-

CH3

D-Alanine L-Alanine

(Fischer projections)

•Except glycine, all protein-derived amino acids have at least one stereocenter (the α-carbon) and are chiral.

•In Nature majority of protein-derived α-amino acids are in the L-form.

NH3 on the “Left” in Fischer proj.

•How do we know when/where it’s L vs D?

H NH3+

COO-

CH3

+H3N H

COO-

CH3

D-Alanine L-Alanine

(Fischer projections)

Chirality of Amino Chirality of Amino AcidsAcids• A comparison of the stereochemistry of

L-alanine and D-glyceraldehyde (as Fischer projections):

H NH3+

COO-

CH3

+H3N H

COO-

CH3

H OH

CHO

CH2OH

HO H

CHO

CH2OH

D-Alanine L-Alanine

D-Glyceraldehyde L-Glyceraldehyde

the naturally occurring form

the naturally occurring form

See table 21.1 R-group polarity classification:

1.Nonpolar (hydrophobic-repel H2O2. Polar (hydrophillic) 3. Basic (hydrophillic) 4. Acidic (hydrophillic)

Determines structure + function of protein

20 Protein-Derived AA 20 Protein-Derived AA

• Nonpolar side chains (at pH 7.0)

NH3+

COO-

NH3+

COO-

NH3+

COO-

NH3+

COO-

NH3+

COO-S

NH3+

COO-

NH H

COO-

NH3+

COO-

NH

COO-

NH3+

Alanine (Ala, A)

Glycine (Gly, G)

Isoleucine (Ile, I)

Leucine (Leu, L)

Methionine (Met, M)

Phenylalanine (Phe, F)

Proline (Pro, P)

Tryptophan (Trp, W)

Valine (Val, V)

Red = R Groups, AKA Side ChainsRed = R Groups, AKA Side Chains

20 Protein-Derived AA20 Protein-Derived AA• Polar side chains (at pH 7.0)

NH3+

COO-

HS

NH3+

COO-

HO

Cysteine (Cys, C)

Tyrosine (Tyr, Y)

NH3+

COO-H2N

O

NH3+

COO-

H2N

O

NH3+

COO-

HO

NH3+

COO-OH

Asparagine (Asn, N)

Glutamine (Gln, Q)

Serine (Ser, S)

Threonine (Thr, T)

Red = R Groups, AKA Side ChainsRed = R Groups, AKA Side Chains

20 Protein-Derived AA20 Protein-Derived AA• Acidic and basic side chains (at pH 7.0)

NH3+

COO--O

O

NH3+

COO--O

O NH3+

COO-

NH

H2N

NH2+

NH3+

COO-

N

NH

NH3+

COO-H3N

Glutamic acid (Glu, E)

Aspartic acid (Asp, D)

Histidine (His, H)

Lysine (Lys, K)

Arginine (Arg, R)

+

Red = R Groups, AKA Side ChainsRed = R Groups, AKA Side Chains

Zwitterions –Zwitterions – molecules that molecules that

havehave::• + charge on one atom• - charge on another atom

R-CH-COH

NH2

OR-CH-CO-

NH3+

O

Un-ionizedform

Zwitterion

COOH (Acid) donates H+ to NH2 (base)

Although amino acids commonly written in the un-ionized form, they are more properly written in the zwitterion zwitterion (internal salt) form.

Zwitterions Zwitterions ADD acid (decrease pH) what happens?

ADD base (increase pH) what happens?

When A.A.s have equal + & - chargesaka: isoelectric point (pI)

Ionization vs pHIonization vs pH• The net charge on an amino acid depends on the pH of the solution in which it is dissolved.• If we dissolve an amino acid in water, it is present in the aqueous solution as its zwitterion.•to summarize:

pH 2.0 pH 5.0 - 6.0 pH 10.0Net charge +1 Net charge 0 Net charge -1

+

RH3N-CH-C-O

-O+

RH3N-CH-C-OH

O

RH2N-CH-C-O

-OOH-

H3O+

OH-

H3O+

Isoelectric PointIsoelectric Point• Isoelectric Isoelectric point, pI:point, pI:The pH at which the majority of molecules of a compound in solution have no net charge.

6.015.41

5.655.976.026.025.745.486.485.685.87

5.895.97

pI

valinetryptophan

threonineserineprolinephenylalaninemethionineleucineisoleucineglycineglutamine

asparaginealanine

Nonpolar &polar side chains

10.76

2.77

5.073.22

7.599.74

5.66

pI

tyrosine

lysinehistidine

glutamic acidcysteine

aspartic acid

arginine

AcidicSide Chains

BasicSide Chains pI

CysteineCysteine• The -SHSH (sulfhydryl) group of cysteine is easily oxidized to an -S-S--S-S- (disulfide).

+

CH2

H3N-CH-COO-

SH

oxidation

reduction

+

CH2

H3N-CH-COO-

S

+H3N-CH-COO

-CH2

S

CysteineCystine

2

a disulfidebond

Peptides and ProteinsPeptides and Proteins• Formation of an amide

The Peptide bond

Peptide named starting @ N-terminus(e.g. Gly-Ala, see Table 21.1)

H2O

PeptidesPeptides• 1902, Emil Fischer proposed proteins are long chains of amino acids joined by amide bonds.

• peptide bondpeptide bond:: amide bond between the -carboxyl group of one amino acid and the -amino group of another.

O

O-H3N

CH3H3N O-

CH2OH

O

H3NN

CH3

O CH2OH

O

O-

H

H2O+

Alanine (Ala) Serine (Ser)

++

+

peptide bond

Alanylserine (Ala-Ser)

+ α

Writing PeptidesWriting Peptides

H3N

OH

NH O

HN

COO-

O-

OC6H5O

+

C-terminalamino acid

N-terminalamino acid

Ser-Phe-Asp

•Start at left, beginning with the free -NH3+ group and ending with the free -COO- group on the right.

•C-terminal amino acid:C-terminal amino acid: the amino acid at the end of the chain having the free -COO- group.

•N-terminal amino acid:N-terminal amino acid: the amino acid at the end of the •chain having the free -NH3+ group.

• What would this tri-peptide be called?Peptides and ProteinsPeptides and Proteins

Note: short chain A.A.s = peptidesLonger chained 10-20 A.A.s = polypeptides

> 30 A.A. chains = proteins (residues)

Other Amino AcidsOther Amino Acids• Hydroxylation (oxidation) of proline, lysine, and tyrosine, and iodination for tyrosine, give these nonstandard amino acids.

NH H

COO-

HO

Hydroxyproline

NH3+

COO-H3N+ OH

Hydroxylysine

C

C-O-

O

HH3N

OII

I IOH

Thyroxine

Properties of peptides and Properties of peptides and proteinsproteins

Note: R groups = AKA Side chains(See table 21.1, previous slides)

1. determine Chem. + phys. Properties acid base behavior = most imp.

Know Which A.A.s:polar?

Non polar?basic? acidic?

~ by LOOKING @ R-group

Determine the chemical nature of these Determine the chemical nature of these A.A.sA.A.s(i.e. R groups as Polar, Non polar, Basic (i.e. R groups as Polar, Non polar, Basic or Acidic)or Acidic)

Tryptophan Glutamic acidserine lysine

Which is the only A.A. that forms di-sulfide bonds?

Peptides and ProteinsPeptides and Proteins• Proteins behave as zwitterions.• Proteins isoelectric point, pIisoelectric point, pI.

• At its pI, the protein has no net charge.• At higher pH (more basic) than its pI, has net (-)charge.

• At lower pH (more acidic) than its pI, has net (+)charge.

• Hemoglobin, almost equal number of acidic and basic side chains; its pI is 6.8. ~ 7

• Serum albumin has acidic side chains; its pI is 4.9.

• Proteins are least soluble in water at their isoelectric points and can be precipitated from solution at this pH.

Changing the pH changes “the Nature” of Protein,)

Denaturing a ProteinDenaturing a Protein

Isoelectric point (pI)neutral

Acidic solut.pH 2

(protonated)

basic solut.pH 10

(deprotonated)NOTE: form/shape changes w/ pH change

Levels of StructureLevels of Structure• Primary structure:Primary structure: the sequence of amino acids in a

polypeptide chain; read from the N-terminal amino acid to the C-terminal amino acid.

• Secondary structure:Secondary structure: conformations of amino acids in localized regions of a polypeptide chain; examples are -helix, -pleated sheet, and random coil.

• Tertiary structure:Tertiary structure: the complete three-dimensional arrangement of atoms of a polypeptide chain.

• Quaternary structure:Quaternary structure: the spatial relationship and interactions between subunits in a protein that has more than one polypeptide chain.

» See Hemoglobin next slide. . .

Structure(s)Structure(s) of Proteins of Proteins