Proteins and Amino Acids

1

Biological Functions of Proteins• Facilitate biochemical reactions• Structural support• Storage and Transport• Immune protection• Generate movement• Transmission of nerve impulses• Control growth and differentiation

2

Key Properties of Proteins

• Linear polymers of amino acids• Contains a wide range of functional groups• Forms complex assemblies of more than

one polypeptide chain• Versatile structure – some are rigid while

others are flexible

3

Globular and Fibrous Proteins• Globular protein• Usually water soluble,

compact, roughly spherical

• Hydrophobic interior, hydrophilic surface

• Globular proteins include enzymes,carrier and regulatory proteins

• Fibrous protein• Provide mechanical support• Often assembled into large

cables or threads• α-Keratins: major components

of hair and nails• Collagen: major component of

tendons, skin, bones and teeth

4

General Structure of Proteins• Twenty common a-amino acids have

carboxyl and amino groups bonded to the α-carbon atom• A hydrogen atom and a side chain (R) are

also attached to the α-carbon atom

5

6

Zwitterions • Under normal cellular conditions amino

acids are zwitterions (dipolar ions):Amino group = -NH3+

Carboxyl group = -COO-

7

Stereochemistry of amino acids• 19 of the 20 common amino acids have a

chiral a-carbon atom (Gly does not)

• Threonine and isoleucine have 2 chiral carbons each (4 possible stereoisomers each)

• Mirror image pairs of amino acids are designated L (levo) and D (dextro)

• Proteins are assembled from L-amino acids (a few D-amino acids occur in nature)

8

Amino acid side chains

• Nine non-polar aa• Six polar uncharged aa• Five charged aa• Three basic aa• Two acidic aa• Two aa with sulfur groups• Four ring-forming aa• Three have aromatic rings 9

Hydropathy• Relative hydrophobicity of the

amino acid

• The larger the hydropathy, the greater the tendency of an amino acid to prefer a hydrophobic environment

• Hydropathy affects protein folding: hydrophobic side chains tend to be in the interiorhydrophilic residues tend to be on the surface

10

Acid-base chemistry of amino acids

11

Isoelectric point

12

• pH at which the amino acid bears zero net charge

Titration curve of Histidine

13

Polymer of amino acid• Peptide bond -

linkage between amino acids is a secondary amide bond

• Formed by condensation of the α-carboxyl of one amino acid with the α-amino of another amino acid (loss of H2O molecule)

14

Resonance Structure of the peptide bond

15

Trans and Cis configuration of peptide bond• Usually in the trans configuration

16

Dihedral Angle

17

Dihedral angle of proteins

• The phi angle is the angle around the -N-Cα- bond• The psi angle is the angle around the -Cα-C- bond• The omega angle is the angle around the -C1-N- bond (i.e. the

peptide bond)18

LEVELS OF PROTEIN STRUCTURE 19

Primary structure

20

>2CQG:A|PDBID|CHAIN|SEQUENCEGSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQSQDSGPSSG

Secondary Structure

21

Alpha-helix

22

Right-handed and Left-handed α-Helix

23

Right-handed and Left-handed α-Helix

24

Beta-sheet

25

Determining 2o structure: Ramanchandran Plot

26

Supersecondary structure: Motifs• Secondary

structures often group together to form a specific geometric arrangements known as motifs

• Since motifs contain more than one secondary structural element, these are referred to as super secondary structures 27

Domains• stable, independently folding, compact

structural units within a protein, formed by segments of the polypeptide chain, with relative independent structure and function distinguishable from other regions and stabilized through the same kind of linkages than the tertiary level

• Often each domain has a separate function to perform for the protein, such as:• Bind a small ligand• Spanning the plasma membrane

(transmembrane proteins)• Contain the catalytic site (enzymes)• DNA-binding (in transcription factors)• Providing a surface to bind specifically to

another protein• In some (but not all) cases, each domain in a

protein is encoded by a separate exon in the gene encoding that protein.

28

Tertiary Structure

• Forces holding the tertiary (and higher order) structure together• Salt bridge• Covalent bond

(disulfide bridges)• Hydrophobic

interaction• Hydrogen bonding 29

Quaternary Structure

30

31

Protein Folding

32

33