Chemistry 2100

Lecture 10

ProteinsProteins serve many functions, including the following.– 1. Structure:Structure: Collagen and keratin are the chief

constituents of skin, bone, hair, and nails.– 2. Catalysts:Catalysts: Virtually all reactions in living systems

are catalyzed by proteins called enzymes.– 3. Movement:Movement: Muscles are made up of proteins

called myosin and actin.– 4. TransportTransport: Hemoglobin transports oxygen from

the lungs to cells; other proteins transport molecules across cell membranes.

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

Proteins– 6. Protection: Protection: Blood clotting involves the protein

fibrinogen; the body used proteins called antibodies to fight disease.

– 7. Storage: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:Regulation: Certain proteins not only control the expression of genes, but also control when gene expression takes place.

• Proteins are divided into two types:– Fibrous proteins– Globular proteins

• nonpolar

• polar / neutral

• acidic / basic

COOH

R

HH2 N

Chirality of -Amino AcidsWith the exception of glycine, all protein-derived amino acids have at least one stereocenter (the -carbon) and are chiral.– The vast majority of -amino acids have

the L-configuration at the -carbon.

H NH3+

COO-

CH3

+H3N H

COO-

CH3

D-Alanine L-Alanine

(Fischer projections)

• nonpolar

• polar / neutral

• acidic / basic

COOH

R

HH2 N

Protein-Derived -Amino Acids

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)

Protein-Derived -Amino Acids

• 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)

Acidic and basic side chains (at pH 7.0)

Protein-Derived -Amino Acids

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)

+

essential amino acids

Leu, Ile, Lys, Met, Phe, Thr, Trp, Val, His ( Arg, Tyr, Cys )

zwitterion

H2 N H

COO

R

H2 N H

COOH

R

H3 N H

COOH

R

H3O+

OH-

H3

Ionization 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.

– If we add a strong acid such as HCl to bring the pH of the solution to 0.0, the strong acid donates a proton to the -COO- of the amino acid turning the zwitterion into a positive ion.

+

RH3N-CH-C-O

-O

+ H3O+ +

RH3N-CH-C-OH

O+H2O

Ionization vs. pH

– If we add a strong base such as NaOH to the solution and bring its pH to 14, a proton is transferred from the NH3

+ group to the base turning the zwitterion into a negative ion.

– To summarize:

+

RH3N-CH-C-O

-O

+ OH-

RH2N-CH-C-O-

O+H2O

+

RH3N-CH-C-O

-O+

RH3N-CH-C-OH

O

RH2N-CH-C-O-

OOH-

H3O+

OH-

H3O+

Problem: Calculate the net charge of lysine at pH = 3, 7, 11. Estimate pI for lysine.

CH2CH2CH2CH2NH2

H2N H

COOH

CH2CH2CH2CH2NH2

H2N H

COOH

pH = 7

CH2CH2CH2CH2NH2

H2N H

COOH

pH = 7

(–)

CH2CH2CH2CH2NH2

H2N H

COOH

pH = 7

(–)

(+)

CH2CH2CH2CH2NH2

H2N H

COOH

pH = 7

(–)

(+)

(+)

CH2CH2CH2CH2NH2

H2N H

COOH

CH2CH2CH2CH2NH2

H2N H

COOH

pH = 7

(–)

(+)

(+)

CH2CH2CH2CH2NH2

H2N H

COOH

pH = 3

CH2CH2CH2CH2NH2

H2N H

COOH

pH = 7

(–)

(+)

(+)

CH2CH2CH2CH2NH2

H2N H

COOH

pH = 3

(+)

(+)

CH2CH2CH2CH2NH2

H2N H

COOH

pH = 7

(–)

(+)

(+)

CH2CH2CH2CH2NH2

H2N H

COOH

pH = 11

CH2CH2CH2CH2NH2

H2N H

COOH

pH = 3

CH2CH2CH2CH2NH2

H2N H

COOH

pH = 7

(–)

(+)

(+)

(+)

(+)

CH2CH2CH2CH2NH2

H2N H

COOH

pH = 11

CH2CH2CH2CH2NH2

H2N H

COOH

pH = 3

CH2CH2CH2CH2NH2

H2N H

COOH

pH = 7

(–)

(+)

(+)

(+)

(+)

(–)

Isoelectric Point (pI)• 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

5.655.976.025.985.745.486.485.685.87

5.885.97

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

Problem: Predict the electrophoresis behavior at pH 6.0 of a mixture of alanine (pI 6.0), aspartic acid (pI 2.8) and lysine (pI 9.7)

Problem: Predict the electrophoresis behavior at pH 6.0 of a mixture of alanine (pI 6.0), aspartic acid (pI 2.8) and lysine (pI 9.7)

Problem: Predict the electrophoresis behavior at pH 6.0 of a mixture of alanine (pI 6.0), aspartic acid (pI 2.8) and lysine (pI 9.7)

Lys Ala Asp

Problem: Predict the electrophoresis behavior at pH 6.0 of a mixture of alanine (pI 6.0), aspartic acid (pI 2.8) and lysine (pI 9.7)

O

OHCH CH2 N

R

O

OHCH CH2 N

R'

+

O

CH CH2N

R R'

NH CCH OH

O(-HOH)

Peptide Bonds

O

OHCH CH2 N

R

O

OHCH CH2 N

R'

+

O

CH CH2N

R R'

NH CCH OH

O(-HOH)

Peptide Bonds

O

OHCH CH2 N

R

O

OHCH CH2 N

R'

+

O

CH CH2N

R R'

NH CCH OH

O(-HOH)

Peptide Bonds

O

OHCH CH2 N

R

O

OHCH CH2 N

R'

+

O

CH CH2N

R R'

NH CCH OH

O(-HOH)

Peptide Bonds

O

OHCH CH2 N

R

O

OHCH CH2 N

R'

+

O

CH CH2N

R R'

NH CCH OH

O(-HOH)

Peptide Bonds

"

"

"

CC

O

H

R

H

R'

H "R

H

"R

H

R H

H

H O

HO

O

OH

NC

CN

CC

NC

CN

CC

N

"

"

"

CC

O

H

R

H

R'

H "R

H

"R

H

R H

H

H O

HO

O

OH

NC

CN

CC

NC

CN

CC

N

"

"

"

CC

O

H

R

H

R'

H "R

H

"R

H

R H

H

H O

HO

O

OH

NC

CN

CC

NC

CN

CC

N

"

"

"

CC

O

H

R

H

R'

H "R

H

"R

H

R H

H

H O

HO

O

OH

NC

CN

CC

NC

CN

CC

N

"

"

"

CC

O

H

R

H

R'

H "R

H

"R

H

R H

H

H O

HO

O

OH

NC

CN

CC

NC

CN

CC

N

O

CH C NH CCH

O

NH

CH2 COOH

NH CCH

O

CH2 OH CH2 CH2 SCH3

O

NHCCHH2 N

(CH2 )4 NH2

CH C OH

O

(CH2 )3 NHCNH2

NHlysylserylmethionylaspartylarginine [Lys–Ser–Met–Asp–Arg]

(–)

(–)

(N-terminus) (C-terminus)

(+)

(+)

(+)

O

CH C NH CCH

O

NH

CH2 COOH

NH CCH

O

CH2 OH CH2 CH2 SCH3

O

NHCCHH2 N

(CH2 )4 NH2

CH C OH

O

(CH2 )3 NHCNH2

NHlysylserylmethionylaspartylarginine [Lys–Ser–Met–Asp–Arg]

(–)

(–)

(N-terminus) (C-terminus)

(+)

(+)

(+)

O

CH C NH CCH

O

NH

CH2 COOH

NH CCH

O

CH2 OH CH2 CH2 SCH3

O

NHCCHH2 N

(CH2 )4 NH2

CH C OH

O

(CH2 )3 NHCNH2

NHlysylserylmethionylaspartylarginine [Lys–Ser–Met–Asp–Arg]

(–)

(–)

(N-terminus) (C-terminus)

(+)

(+)

(+)

O

CH C NH CCH

O

NH

CH2 COOH

NH CCH

O

CH2 OH CH2 CH2 SCH3

O

NHCCHH2 N

(CH2 )4 NH2

CH C OH

O

(CH2 )3 NHCNH2

NHlysylserylmethionylaspartylarginine [Lys–Ser–Met–Asp–Arg]

(–)

(–)

(N-terminus) (C-terminus)

(+)

(+)

(+)

O

CH C NH CCH

O

NH

CH2 COOH

NH CCH

O

CH2 OH CH2 CH2 SCH3

O

NHCCHH2 N

(CH2 )4 NH2

CH C OH

O

(CH2 )3 NHCNH2

NHlysylserylmethionylaspartylarginine [Lys–Ser–Met–Asp–Arg]

(–)

(–)

(N-terminus) (C-terminus)

(+)

(+)

(+)

O

CH C NH CCH

O

NH

CH2 COOH

NH CCH

O

CH2 OH CH2 CH2 SCH3

O

NHCCHH2 N

(CH2 )4 NH2

CH C OH

O

(CH2 )3 NHCNH2

NH

pH = 7

lysylserylmethionylaspartylarginine [Lys–Ser–Met–Asp–Arg]

(–)

(–)

(N-terminus) (C-terminus)

O

CH C NH CCH

O

NH

CH2 COOH

NH CCH

O

CH2 OH CH2 CH2 SCH3

O

NHCCHH2 N

(CH2 )4 NH2

CH C OH

O

(CH2 )3 NHCNH2

NH

pH = 7

lysylserylmethionylaspartylarginine [Lys–Ser–Met–Asp–Arg]

(–)

(–)

(N-terminus) (C-terminus)

(+)

(+)

(+)

O

CH C NH CCH

O

NH

CH2 COOH

NH CCH

O

CH2 OH CH2 CH2 SCH3

O

NHCCHH2 N

(CH2 )4 NH2

CH C OH

O

(CH2 )3 NHCNH2

NH

pH = 3

lysylserylmethionylaspartylarginine [Lys–Ser–Met–Asp–Arg]

(–)

(–)

(N-terminus) (C-terminus)

(+)

(+)

(+)

O

CH C NH CCH

O

NH

CH2 COOH

NH CCH

O

CH2 OH CH2 CH2 SCH3

O

NHCCHH2 N

(CH2 )4 NH2

CH C OH

O

(CH2 )3 NHCNH2

NH

pH = 3

lysylserylmethionylaspartylarginine [Lys–Ser–Met–Asp–Arg]

(–)

(–)

(N-terminus) (C-terminus)

(+)

(+)

(+)

O

CH C NH CCH

O

NH

CH2 COOH

NH CCH

O

CH2 OH CH2 CH2 SCH3

O

NHCCHH2 N

(CH2 )4 NH2

CH C OH

O

(CH2 )3 NHCNH2

NH

pH = 11

lysylserylmethionylaspartylarginine [Lys–Ser–Met–Asp–Arg]

(–)

(–)

(N-terminus) (C-terminus)

O

CH C NH CCH

O

NH

CH2 COOH

NH CCH

O

CH2 OH CH2 CH2 SCH3

O

NHCCHH2 N

(CH2 )4 NH2

CH C OH

O

(CH2 )3 NHCNH2

NH

pH = 11

lysylserylmethionylaspartylarginine [Lys–Ser–Met–Asp–Arg]

(–)

(–)

(N-terminus) (C-terminus)

(5!) = 120 combinations

(20!) = 2.4 1018 eicosapeptides

(205) = 3.2 106 possible pentapeptides

++++H+ or OH-

Arg Asp Lys Met Ser H2OLys – Ser – Met – Asp – Arg

(5!) = 120 combinations

(20!) = 2.4 1018 eicosapeptides

(205) = 3.2 106 possible pentapeptides

++++H+ or OH-

Arg Asp Lys Met Ser H2OLys – Ser – Met – Asp – Arg

(5!) = 120 combinations

(20!) = 2.4 1018 eicosapeptides

(205) = 3.2 106 possible pentapeptides

++++H+ or OH-

Arg Asp Lys Met Ser H2OLys – Ser – Met – Asp – Arg

(5!) = 120 combinations

(20!) = 2.4 1018 eicosapeptides

(205) = 3.2 106 possible pentapeptides

++++H+ or OH-

Arg Asp Lys Met Ser H2OLys – Ser – Met – Asp – Arg

(5!) = 120 combinations

(20!) = 2.4 1018 eicosapeptides

(205) = 3.2 106 possible pentapeptides

++++H+ or OH-

Arg Asp Lys Met Ser H2OLys – Ser – Met – Asp – Arg

(5!) = 120 combinations

(20!) = 2.4 1018 eicosapeptides

(205) = 3.2 106 possible pentapeptides

++++H+ or OH-

Arg Asp Lys Met Ser H2OLys – Ser – Met – Asp – Arg

oxytocin

vasopressin

Cys

Tyr

Phe Gln

Asn

Cys

SS

H2N

O

NH2CGlyArgPro

Cys

Tyr

Ile Gln

Asn

Cys

SS

H2N

O

NH2CGlyLeuPro

CH C NH CCH OH

O O

CH2

OO

HH

NHCCHNHCCHNH

O

HO

NH2

C

Tyr–Gly–Gly–Phe–MetMethionine enkephalin

CH2 CHCH3

CH3

Morphine

O

N

HO OH

CH3

H

H

Tyr–Gly–Gly–Phe–LeuLeucine enkephalin

Enkephalins

SS

Gly–Ile–Val–Glu–Gln–Cys–Cys–Thr–Ser–Ile–Cys–Ser–Leu–Tyr–Gln–Leu–Glu–Asn–Tyr–Cys–Asn

Phe–Val–Asn–Gln–His–Leu–Cys–Gly–Ser–His–Leu–Val–Glu–Ala–Leu–Tyr–Leu–Val–Cys–Gly–Glu–Arg–Gly–Phe–Phe–Tyr–Thr–Pro–Lys–Thr

S5 10 15 3020 25

5 10 15 20

SS

S

Insulin

Structure of Proteins

"

N CH C

H R

N

O

H

CH

R'

C

O O

R"H

CCHN

" R

O

C

R"

CH

H

O

N

R"H

CCHN N CH C

H

O

"

N CH C

H R

N

O

H

CH

R'

C

O O

R"H

CCHN

" R

O

C

R"

CH

H

O

N

R"H

CCHN N CH C

H

O

"

N CH C

H R

N

O

H

CH

R'

C

O O

R"H

CCHN

" R

O

C

R"

CH

H

O

N

R"H

CCHN N CH C

H

O

"

N CH C

H R

N

O

H

CH

R'

C

O O

R"H

CCHN

" R

O

C

R"

CH

H

O

N

R"H

CCHN N CH C

H

O

Secondary Structure: The -Helix

-Pleated Sheet

Random Coil

-helix

-helix-pleated sheet

-pleated sheet

Protein Tertiary Structure

-helix

-helix-pleated sheet

-pleated sheet

salt bridge

NH3

+

-helix

-helix-pleated sheet

-pleated sheet

C-O

O

hydrogenbond

CH2 O

H

CH2O

H

salt bridge

NH3

+

-helix

-helix-pleated sheet

-pleated sheet

C-O

O

hydrogenbond

CH2 O

H

CH2O

H

NH

H

C

OH

O

hydrogenbond

salt bridge

NH3

+

-helix

-helix-pleated sheet

-pleated sheet

C-O

O

hydrogenbond

CH2 O

H

CH2O

H

NH

H

C

OH

O

hydrogenbond

salt bridge

NH3

+

CH2

HO

hydrophilicinteraction

to water

CH2

C

NH2

O

CH2

HO

-helix

-helix-pleated sheet

-pleated sheet

C-O

O

CH2

CH2

hydrophobicinteraction

hydrogenbond

CH2 O

H

CH2O

H

NH

H

C

OH

O

hydrogenbond

salt bridge

NH3

+

CH2

HO

hydrophilicinteraction

to water

CH2

C

NH2

O

CH2

HO

-helix

-helix-pleated sheet

-pleated sheet

C-O

O

CH

CH3 CH3

CH3

CH2

CH2

hydrophobicinteraction

hydrogenbond

CH2 O

H

CH2O

H

NH

H

C

OH

O

hydrogenbond

salt bridge

NH3

+

CH2

HO

hydrophilicinteraction

to water

CH2

C

NH2

O

CH2

HO

-helix

-helix-pleated sheet

-pleated sheet

C-O

O

CH

CH3 CH3

CH3

CH2

CH2

hydrophobicinteraction

S

S

S

Sdisulfide

bond

hydrogenbond

CH2 O

H

CH2O

H

NH

H

C

OH

O

hydrogenbond

salt bridge

NH3

+

CH2

HO

hydrophilicinteraction

to water

CH2

C

NH2

O

CH2

HO

-helix

-helix-pleated sheet

-pleated sheet

C-O

O

Protein Quaternary Structure

C3032H4816N735O780S8Fe4 (MW 64,450)

Hemoglobin

Sickle-Cell Anemia

Sequence Varies: Ask 23andMe

Proteins

Denaturation

Denaturation… also knownas “Cooking”

Misfolding Diseases

Mutation Impairs Proper Folding

Cystic Fibrosis

Sickle CellAnemia

Contagious Misfolding: Prions