Biomolecules Survey Part 3: Amino Acids, Peptides, and Proteins Lecture Supplement page 238.

Biomolecules Survey Part 3:Amino Acids, Peptides, and Proteins

Lecture Supplement page 238

Why Bother With Protein Structure?

Molecular structure controls function

N

H O

HR

n

Repeating unit

N

H O

N

HR

N

H O

N

HRH

H R

O OH

H R

•Enzyme selectivity•Drug design•Many others

Fundamental protein structure = amide polymer

N

H O

HR

OHH

Amino AcidsThe Fundamental Building Block of Peptides and Proteins

N

O

HR

OH

H H

All amino acids have amine and carboxylic acid groups

•All are primary amines (R-NH2) except proline

Amine (base) + carboxylic acid = proton transfer possible:

Neutral (unionized) form Zwitterionic (ionized) form

Keq > 1 atphysiological pH

-carbon •Side chains (R) vary

•18 are S, 1 is R, 1 is achiral

N

H O

HR

OHH

H2N COOH

HHN

Amino AcidsThe 20 standard amino acids categorized by side chain properties:•Hydrophilic versus hydrophobic

Hydrophobic nonacidic side chains

Glycine (Gly)Achiral

Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)

Proline (Pro)2o amine (HNR2)

Tryptophan (Trp) Phenylalanine (Phe) Methionine (Met)

H2N COOH

HH

•Acidic versus basic versus neither (nonacidic)

H2N COOH

HH3C

H2N COOH

H

H2N COOH

H

H2N COOH

H

COOHN

H

H H2N COOH

H

H2N COOH

H

CH3S

Amino AcidsHydrophobic acidic side chains Side chain more acidic than water

Cysteine (Cys)

Hydrophilic nonacidic side chains

H2N COOH

HHS

H2N COOH

HHO

H2N COOH

H

OH

H2N COOH

H

O

H2N

H2N COOH

H

O

H2N

H2N COOH

HHO

Tyrosine (Tyr)

Serine (Ser) Threonine (Thr) Asparagine (Asp) Glutamine (Gln)

Amino AcidsHydrophilic acidic side chains

Hydrophilic basic side chains Nitrogen lone pairs to accept a proton

H2N COOH

H

O

HO

H2N COOH

H

O

HO

H2N COOH

HH2N

H2N COOH

H

N

H

HN

NH2 H2N COOH

HHN

N

Do I have to memorize amino acid structures?

Aspartic acid (Asp) Glutamic acid (Glu)

Lysine (Lys) Arginine (Arg) Histidine (His)

Amino Acids Form PeptidesAmino acids link via peptide bond (an amide); form chains

N

H O

OHH

CH3

Ala

N

H O

OHH

OH

Ser

N

H O

OHH

Val

N

H O

N

OHH

N

O

CH3

H

H O

OH

Serine side chain configuration?

Verify with model of complete tripeptide

-2 H2O

Amino Acids Form Peptides

•A tripeptide (three amino acids)•Naming: Val-Ser-Ala or Ala-Ser-Val? N-terminus C-terminus

N

H O

N

OHH

N

O

CH3

H

H O

OHN-terminus C-terminus

Ala Ser Val

•Amino acid sequence = primary structure of peptide or protein•Like amino acids, peptides and proteins also have zwitterionic forms:

H2N

O

N

OHH

N COOH

CH3 H O

H3N

O

N

OHH

N CO2

CH3 H O

How Does Peptide Bond Influence Structure?

TransAmino acid chain

opposite sides of C-N bond

CisAmino acid chain

same side of C-N bond

•Torsional strain: Trans < cis; equilibrium favors trans isomer by ~ 2 kcal mol-1

H

N

O

NH

O

Conjugation effects:Barrier to rotation around C-N bond ~16 kcal mol-1

C

H

NC

O

is planar

•Amide is conjugated:

H

N

O -

+

The Protein Conformation Problem

Consider major conformational isomers of a glycine peptide:

•Each glycine has 2 x 3 x 3 = 18 major conformations Verify with models

•A small protein consisting of 14 glycine has 1814 = 3.7 x 1017 major conformations!

•Number of conformations significantly if more amino acids, or side chains present

Problem: Protein function requires well-organized and restricted structure

Solutions: •Local conformational restrictions: Cis/trans isomers and planarity

•Intramolecular hydrogen bondsResults: •Reduced protein flexibility

•Reduced structure randomness

O

N

H Otrans or cis

3 staggered

3 staggered

Secondary Structure•Structural randomness reduced by intramolecular hydrogen bonds

-Helix

•Clockwise spiral down

•H-bonds parallel to axis

•Side chains point out from center

•Elastic coil: Thinkbook binding

N

ON

N

R

H N

H

H

O

O

N

H

O

N

O

O

H

RH

H

R

H

H

R

H

R

H

axis of helix

•Causes three basic motifs: The secondary structures of proteins

There is an H-bond between C=O and N-H of residue 1 and residue 4 (residue 2 and residue 5) (… etc.)

Secondary Structure

-Sheet: Two or more aligned, H-bonded -strands

•Parallel N-termini same end) or antiparallel N-termini opposite ends)•The illustrated -sheet is antiparallel• -Sheet more rigid/less elastic than -helix•Significant component of keratin (hair, wool) and silk•Make your own silk: Thinkbook Appendix C

N-terminus C-terminus

C-terminus N-terminus

N

HRO

N

H

N

RO

N

H

N

RO

N

H

N

R

O

H

N

R O

N

HO

N

R

N

HO

N

R

N

HO

N

R

HROHROHRO

ORHORHORH

HHHH

O O O OHHH

O O O

R R R R R

RRRRR RRRRR

R

R

R R R R R

-Strand: A “fully extended” polypeptide chain (as opposed to being in a helix)

Secondary Structure(Random) Coil: Not really random, just hard to describe

• Key point: Random coils do not have catalytic activity • Denatured proteins adopt the shape of a random coil

Tertiary StructureTertiary structure: Three-dimensional atomic positions

Response to environment: Side chain orientation depends on environment

Polar environment(water)

Nonpolar environment(core of cell membrane)

Hydrophilic side chains point out point in

Hydrophobic side chains point in point out

Disulfide bridges: Form loop within one chain, or bond two separate chains

S H

H S

Cys

Cys

S

S

Found in:•Insulin (3)•Keratin (hair)•Others

•Aspects of protein structure determined by side chain composition

Quaternary StructureQuaternary structure: Association of two or more subunits by noncovalent bonds

•Subunits = proteins, carbohydrates, coenzymes, etc.

•Large surface areas noncovalent forces can be significant magnitude

Quaternary structure = four subunits

Four levels of protein structure• Primary structure: amino acid sequence

• Secondary structure: alpha helix, beta strand / beta sheets

• Tertiary structure: spatial arrangement of amino acid residues and disulfide bonds

• Quaternary structure: spatial arrangement of subunits and nature of their interactions

Insulin – Primary Structure

Insulin – Secondary Structure and Tertiary Structure

To play with an interactive 3D-Model of the insulin monomer: http://www.pdb.org/pdb/101/motm_disscussed_entry.do?id=4ins

-3 alpha helices-1 beta strand

Insulin – Quaternary Structure

Insulin hexamer (inactive form of insulin; long-term storage in the body)

Protein Structure RepresentationsMyoglobin •stores O2 in muscle tissue via heme

•~70% -helix•A globular protein (~spherical shape)

Helix = fuchsiaSheet = yellow

Coil = white

Worldwide Protein Data Bank: http://www.wwpdb.org/

Protein Structure Representations

Retinol Binding ProteinHelix = fuchsiaSheet = yellow

Coil = white

•Important for vision

Protein Structure RepresentationsLactate Dehydrogenase Helix = fuchsia

Sheet = yellowCoil = white

•Quaternary structure = four identical protein subunits•Released in bloodstream by damaged muscles•Indicative of heart damage or failure•Subject of Chem 153L experiments