proteins are polymers of amino acids. there are 20 unique amino acids that make up proteins in...

Proteins are polymers of amino acids.

There are 20 unique amino acids that make up proteins in

general.

Each of the 20 differentamino acids has a different

R group.

Otherwise, the amino acidstructure is the same!Generic structure of an

amino acid

© 2014 John Wiley & Sons, Inc. All rights reserved.

KEY CONCEPTS: Section 4-1

• The 20 amino acids differ in the chemical characteristics of their R groups.

• Amino acids are linked by peptide bonds to form a polypeptide.

• A protein’s structure may be described at four levels, from primary to quaternary.

© 2014 John Wiley & Sons, Inc. All rights reserved.

AminoAcids:

Get toKnowThem!!

AminoAcids:

I’m notKidding. Makethemyourfriends!!

The 20 amino acids differ in the chemical characteristics of their

R groups.

• There are three categories for the R groups.• Hydrophobic amino acids have nonpolar R

groups.• Hydrophilic amino acids have polar R groups.

Nonpolar R groups

Polar R groups

Uncharged Charged

© 2014 John Wiley & Sons, Inc. All rights reserved.

Glycine has a nonpolar side chain.

• Gly is the simplest amino acid.

• Side chain = H

• Each amino acid has:– Full name (e.g., Glycine)– 3 letter code (e.g., Gly)– 1 letter code (e.g., G)

© 2014 John Wiley & Sons, Inc. All rights reserved.

Ala and Phe have hydrophobic R groups.

• Ala has a methyl group for its side chain.

• Phe, as its name suggests, includes a phenyl ring on an Ala residue.

© 2014 John Wiley & Sons, Inc. All rights reserved.

Val, Leu and Ile have hydrophobic R groups.

• Leu has an extra methylene group (-CH2-) than Val. • Ile has the same functional moieties in its R group as

Leu, just arranged differently – hence the prefix iso.• V, L, and I are also referred to as Branched Chain

Amino Acids (BCAAs)

© 2014 John Wiley & Sons, Inc. All rights reserved.

Met has a hydrophobic R group.

• Met is one of only two amino acids with a sulfur in its R-group.

© 2014 John Wiley & Sons, Inc. All rights reserved.

Trp has a hydrophobic R group.

• Trp is the only amino acid with a fused ring system.

© 2014 John Wiley & Sons, Inc. All rights reserved.

Practical Application

• Most proteins have at least one Trp.

• Trp absorbs UV light at 280 nm.

• [Protein] can be determined based on detection of Trp in proteins!

Recall Beer’s Law:

Aλ = ελbc

© 2014 John Wiley & Sons, Inc. All rights reserved.

Pro has a unique R group.

• Pro is the only amino acid whose side chain loops back onto its own backbone!

• Pro induces kinks in a polypeptide sequence.

© 2014 John Wiley & Sons, Inc. All rights reserved.

Hydrophilic Amino Acids

• There are 2 groups of hydrophilic amino acids.– Polar, uncharged– Polar, charged

• Polar amino acids are often found in the active sites of enzymes because they can facilitate chemical catalysis.

© 2014 John Wiley & Sons, Inc. All rights reserved.

Cys residues can form disulfide bonds.

© 2014 John Wiley & Sons, Inc. All rights reserved.

Disulfide bonds facilitate crosslinking.

• Disulfide bonds can form intra-strand crosslinks (as shown).

• When a protein contains more than one polypeptide chain, disulfide bonds can also form inter-chain crosslinks.

3D Structure of the ProteinLysozyme

Only the backbone is shown in blue.

Disulfide bonds are shown in yellowball-and-stick representation.

© 2014 John Wiley & Sons, Inc. All rights reserved.

Ser and Thr have hydroxyl groups in their side chains.

• -OH groups are prominent nucleophiles in biochemical reactions.

• Other chemical groups can covalently bond to proteins via -OH groups.

© 2014 John Wiley & Sons, Inc. All rights reserved.

Tyr has a polar, uncharged R group.

• Tyr is a derivative of Phe.

• Phe and Tyr are precursors of amino acid derivatives that are neurotransmitters.

© 2014 John Wiley & Sons, Inc. All rights reserved.

Asn and Gln have polar, uncharged R groups.

• Gln has 2 methylene groups, Asn has only 1.

© 2014 John Wiley & Sons, Inc. All rights reserved.

His has a polar, uncharged R group.

• Histidine has an imidazole (5-membered ring system with N’s).

• NOTE: Histidine can be charged below its pKa of ~6.

© 2014 John Wiley & Sons, Inc. All rights reserved.

Lys and Arg have positively charged, polar R groups.

• Both Lys and Arg have long side chains with a positively charged amine group.

© 2014 John Wiley & Sons, Inc. All rights reserved.

Asp and Glu have negatively charged, polar R groups.

• Asp and Glu are analogous to Asn and Gln, except Asp and Glu have carboxylate groups!

© 2014 John Wiley & Sons, Inc. All rights reserved.

Amino acids are linked via a condensation reaction.

Here amino acids within the peptide are called

“amino acid residues” because only the residual

atoms remain.

© 2014 John Wiley & Sons, Inc. All rights reserved.

Amino acids are linked by peptide bonds to form a polypeptide

• Example below shows a short peptide.

• Polypeptides have many amino acid residues.

© 2014 John Wiley & Sons, Inc. All rights reserved.

Solution:Look up the pK values for the

ionization states.

Recall the meaning of pK!

© 2014 John Wiley & Sons, Inc. All rights reserved.

pK reveals the cutoff pH for protonation of a species.

pK = 3.5

pK = 9.0

When the pH < 3.5, the structure of a generic amino acid is

Both ends areprotonated at very low pH.

© 2014 John Wiley & Sons, Inc. All rights reserved.

pK reveals the cutoff pH for protonation of a species.

pK = 3.5

pK = 9.0

When the pH > 3.5 and <9.0, the structure of a generic amino acid is

Carboxyl group is deprotonatedat neutral pH.

Amino group is still protonated!

ZwitterionForm of aGeneric

Amino Acid

© 2014 John Wiley & Sons, Inc. All rights reserved.

pK reveals the cutoff pH for protonation of a species.

pK = 3.5

pK = 9.0

When the pH > 9.0, the structure of a generic amino acid is

Carboxyl group is still deprotonated.

Amino group is now deprotonated!

© 2014 John Wiley & Sons, Inc. All rights reserved.

PROBLEM:

How can one deduce the structure of an amino acid or

peptide when the side chain also has an ionizable group?

© 2014 John Wiley & Sons, Inc. All rights reserved.

Solution:Look up the pK values for the ionization

states.

Recall the meaning of pK!

© 2014 John Wiley & Sons, Inc. All rights reserved.

Solution:Analyze side chain pK values.

EXAMPLE: His, pK = 6.0

At pH < 6.0, His side chain is

protonated

At pH > 6.0, His side chain is

deprotonated

© 2014 John Wiley & Sons, Inc. All rights reserved.

There are four different levels of protein structure.

© 2014 John Wiley & Sons, Inc. All rights reserved.

KEY CONCEPTS: Section 4-2

• The polypeptide backbone has limited conformational flexibility.

• The α helix and β sheet are common secondary structures characterized by hydrogen bonding between backbone groups.

© 2014 John Wiley & Sons, Inc. All rights reserved.

Biochemists view macromolecules in a variety of ways!

Space-filling representation of all atoms. Shades of blue = different subunits

Shows that proteins are globular in 3D!

Shows shape of backbone chainin one region of a protein is

alpha helical!

“Ribbon” diagram (red)

Ball-and-stick

atoms are superimposed

Hydrogen bonds =

dashed lines

© 2014 John Wiley & Sons, Inc. All rights reserved.

Hydrogen Bonding in a β Sheet

© 2014 John Wiley & Sons, Inc. All rights reserved.

Some polypeptide chains align in regions with directionality.

Antiparallel Beta Sheetsalign in opposite directions.

Parallel Beta Sheetsalign in the same direction.

© 2014 John Wiley & Sons, Inc. All rights reserved.

Secondary Structures

• The α helix and β sheet are common secondary structures characterized by hydrogen bonding between backbone groups.

• H-bonds form in an α helix between the carbonyl oxygen and the amino hydrogen.

© 2014 John Wiley & Sons, Inc. All rights reserved.

Proteins can have any combination of secondary structures.

α/βprotein

α-helicalprotein

β-protein

Protein with very little 2°

structure

© 2014 John Wiley & Sons, Inc. All rights reserved.

KEY CONCEPTS: Section 4-3

• A folded polypeptide assumes a shape with a hydrophilic surface and a hydrophobic core.

• Protein folding and protein stabilization depend on noncovalent forces.

• Some proteins can adopt more than one stable conformation.

© 2014 John Wiley & Sons, Inc. All rights reserved.

A folded polypeptide assumes a shape with a hydrophilic surface and

a hydrophobic core.

© 2014 John Wiley & Sons, Inc. All rights reserved.

Protein folding and protein stabilization depend on noncovalent forces.

• Key example: the hydrophobic effect

© 2014 John Wiley & Sons, Inc. All rights reserved.

KEY CONCEPTS: Section 4-4

• Proteins containing more than one polypeptide chain have quaternary structure.

© 2014 John Wiley & Sons, Inc. All rights reserved.

Domains vs. Subunits

A single chain can form local 3D structure – domains.

Two or more separate chains (subunits) can orient in 3D space to give quaternary

structure!

© 2014 John Wiley & Sons, Inc. All rights reserved.

KEY CONCEPTS: Section 4-5

• Chromatography is a technique for separating molecules on the basis of size, charge, or specific binding behavior.

• The sequence of amino acids in a polypeptide can be determined.

• The 3D arrangement of atoms in a protein can be deduced by measuring the diffraction of X-rays or by analyzing NMR.

© 2014 John Wiley & Sons, Inc. All rights reserved.

Chromatography is a technique for separating molecules on the basis of

size, charge, or specific binding.

•Common chromatographic methods in biochemistry

– Gel filtration (or size exclusion) chromatography

– Ion exchange chromatography– Affinity chromatography

© 2014 John Wiley & Sons, Inc. All rights reserved.

Gel Filtration Chromatography

Separation based on size

Small Proteins

Large Proteins

© 2014 John Wiley & Sons, Inc. All rights reserved.

Ion Exchange Chromatography

• Separation based on charge

• Resins have either diethylaminoethane or carboxymethyl functional groups.

© 2014 John Wiley & Sons, Inc. All rights reserved.

SDS PAGE Analysis of Proteins

Isoelectric Points of Several Common Proteins.

2D Gel Analysis- combines SDS-

PAGE with Isoelectric Focusing

Crystals of the ProteinStreptavidin

• The 3D arrangement of atoms in a protein can be deduced by measuring the diffraction of X-rays or by analyzing NMR.

• With X-ray crystallography, the protein must first be crystallized.

© 2014 John Wiley & Sons, Inc. All rights reserved.

The NMR Structure ofGlutaredoxin

• The 3D arrangement of atoms in a protein can be deduced by measuring the diffraction of X-rays or by analyzing NMR.

• With NMR spectroscopy, a family of structures is obtained.

© 2014 John Wiley & Sons, Inc. All rights reserved.