Amino Acids & Side Amino Acids & Side GroupsGroupsPolar Charged

◦ACIDIC  negatively charged amino acids ASP & GLU

   R group with a 2nd COOH that ionizes above pH 7.0

Polar Charged◦BASIC  positively charged amino acids

LYS, ARG, HIS R group with a 2nd amide* that protonates below

pH 7.0 

Acidic vs. BasicAcidic vs. Basic

Acidic Side Chains Basic Side Chains

Polar ChargedPolar Charged

Amino Acids & Side Amino Acids & Side GroupsGroupsPolar Uncharged

◦THR, TYR, ASN, GLN    (cys) are soluble in water, i.e.,

hydrophilic  (attract H-bonds) Contain hydroxyl or amino functional groups

Polar UnchargedPolar UnchargedHydroxylHydroxyl

Polar Uncharged IIPolar Uncharged IIAmino Functional GroupsAmino Functional Groups

Polar Uncharged Amino Polar Uncharged Amino AcidsAcids

Amino Acids & Side Amino Acids & Side GroupsGroupsNON-POLAR (aliphatic)

◦Includes GLY, ALA, VAL, LEU, ILE, PRO all contain only hydrocarbons groups   =  

hydrophobicity

AROMATIC (hydrophobic non-polars)    ◦PHE & TRP     (TYR)   

all contain R groups with    ring structures* or Sulfur*            

R groups with sulfur◦ MET,  CYS

Non-PolarNon-PolarHydrocarbon R-GroupsHydrocarbon R-Groups

Non-PolarNon-PolarAromatic R-GroupsAromatic R-Groups

Non-PolarNon-PolarSulfur R GroupsSulfur R Groups

Secondary Protein Secondary Protein StructuresStructures

Alpha Helix Beta-pleated sheets

The most common polypeptide helix

Stabilized by extensive hydrogen bonding

Hydrogen bonds extend up from the oxygen from the carbonyl group to the NH group of a peptide linkage◦ This was shown in class via the

visuals

There are approximately 4 peptide bond links up stream between the atoms involved in the hydrogen bonds

Each turn of an alpha helix contains 3.6 amino acids.

• Unlike the alpha helix, composed of two or more peptide chains

• Polypeptide chains are joined by hydrogen bonds

• When the hydrogen bonds are formed between the polypeptide chains they are termed interchains.

• The polypeptide chains can run parallel to each other or anti-parallel– Recall the “ends” of a

polypeptide chain• C-terminus• N-terminus/Amino-terminus

Alpha HelixAlpha Helix

Beta-pleated sheetsBeta-pleated sheets

Beta-pleated Sheets and Beta-pleated Sheets and Alzheimer’s DiseaseAlzheimer’s Disease• The amyloid protein, a class of

fibrous proteins, is deposited in the brain.

• Individuals, that have Alzheimer’s Disease, have the amyloid protein composed of twisted Beta-pleated sheet fibrils whose three-dimentional structure is virtually identical to that of silk fibrils–Silk• Contain Beta-pleated sheet protein structures

Tertiary StructureTertiary StructureInteractions stabilizing Tertiary

Structures◦Four were mentioned in class

Disulfide Bonds Hydrophobic interactions Hydrogen bonds Ionic interactions

Disulfide Bonds Disulfide Bonds • A disulfide bond is a covalent linkage

formed by the sulfhydryl group (-SH) of two cysteine residues to form cystine

• The folding of the polypeptide chain brings the cysteine residues near each other

• Disulfide linkage contributes to the stability of the three-dimensional shape of the protein molecule

• Disulfide bonds are found in proteins that are secreted by cells– Thought that these strong covalent bonds

help stabilize the structure of proteins and help prevent them from becoming denatured in the extra-cellular environment

Hydrophobic InteractionsHydrophobic Interactions• Recall that amino acids with non-

polar side chains tend to be located in the interior of the polypeptide–Here, they associate with other

hydrophobic amino acids• Special Note–Proteins located in non-polar (lipid)

environments such as the phopholipid bilayer, tend to be in an opposite form• Hydrophobic amino acids are located on the

surface• Hydrophilic amino acids are located on the

interior

Ionic InteractionsIonic InteractionsNegatively charged groups

interact with positively charged groups◦Negatively charged groups

(-COO-) in the side chain of aspartate or glutamate

◦Positively charged groups (-NH3

+) in the side chain of lysine

Dipole MomentDipole MomentDipole Moment is

the measure of a molecule’s overall polarity

μ = Q * r◦ μ = Dipole

Moment◦ Q = charge◦ r = distance

between chargesMeasured in

debyes (\də-ˈbī\ )

Van der Waals ForcesVan der Waals ForcesA weak attractive

force between atoms or non-polar molecules caused by a temporary change in dipole moment ◦ Arising from a brief

shift of orbital electrons to one side of one atom or molecule, creating a similar shift in adjacent atoms or molecules.