• Proteins are long chains of repeating amino acids linked via peptide bonds
• The amino acid sequence determines the identity of the protein.
• Proteins have many functions within an organism
– structural components
– regulation of biochemical reactions (hormones and enzymes)
– transport of essential substances (hemoglobin)
– nutrient storage
The zwitterion form of the amino acid has a large dipole
However, the net charge on the molecule is zero.
R group denotes 'any
C – bonded group'
– R group consists of hydrocarbon chain or other
non-polar group (alkyl sulfide or indole)
– R group contains polar groups such as OH, SH, C=O
– R group contains a COOH (COO-) group
– R-group contains a NH2 (NH3
Amino Acid Key Points
•Amino acids exist in zwitterion form.
•All amino acids contained in proteins have the acid function (COOH) and NH2 function attached to the same carbon atom. (a amino acids)
• All the amino acids found in proteins are chiral except for glycine
•Arginine, Histidine, Isoleucine, Leucine, Lysine,meththionine ,Phenylalanine, Threonine, Tryptophan, and Valine cannot be synthesized by humans and must be obtained in the diet. (essential amino acids)
• Amino acids can link to one another via peptide bonds to form peptides and proteins.
•The protein amino acids all have the L-configuration
In the Fischer Projection format, the amino group is on the left of the chain. Amino acids in proteins have the ‘L’ configuration
• Proteins are long chains (~50 to > 500) of amino acids linked by peptide bonds.
• Primary structure is determine by the sequence of amino acids
– Often written as "alphabetical abbreviation" of individual amino acid
Three Dimensional Structure of Proteins
There are Four Levels of Structure:
1. Primary- the order of amino acids in the protein chain
2. Secondary – results from hydrogen bonding between NH2 and CO groups on 'neighboring' amino acids.
3. Tertiary- results from attraction or repulsive forces between R groups on the amino acids. Often 'long range' forces.
4. Quarternary- applies to proteins containing more than one protein subunits.
• Secondary structure describes how the atoms are arranged in space.
– Influenced mainly by hydrogen bonding between N-H and O=C groups
• Three major secondary structures of proteins.
– a helix (alpha helix)
– beta pleated sheet
– triple helix
Hydrogen bonds form between amino acids located 4 amino acids apart in the primary structure.
Chains are held 'side by side' by H- bonds. Amino acids tend to be those
having small R groups. (glycine, alanine, serine) This allows close stacking and strong interaction between chains Most common example is silk.
Three polypeptide chains are woven together A small amount of hydroxy proline and hydroxylysine are present, which result in increased H bonds. Long fibers having exceptional strength result Collagen is a protein having triple helix form. Found in connective tissue.
• Interactions among the R groups of the polypeptide chains are responsible for the tertiary structures
• These structures result in 'folds' and 'bends' in the chains, giving them a three dimensional structure
• Quarternary Structures describe the configuration of proteins which are composed of two or more protein units.
• Hemoglobin is an example
– 4 separate protein chains
– chains held together by intermolecular forces
(same forces as tertiary structures)
• The forces responsible for the secondary, tertiary and quaternary structures are significantly weaker than the covalent bonds responsible for the primary structure.
• Heat, changes in pH, and mechanical agitation disrupt these forces
– protein loses shape and biological function
– "frying an egg"
• Enzymes are biological catalysts
– protein structures
– provide low energy pathway for reactions to occur.
• Active site
– enzyme binds to "substrate". Binding site in the enzyme is called the 'active site'
– shape often determines what substrates may bind to the enzyme
• Lock and Key
– substrate has proper shape and polarity to fit the active site
• Induced Fit
– Several related molecules may interact with the enzyme
– Approach of the substrate can change the geometry of the active site
• Competitive inhibition
– inhibitor has similar shape and polarity
– occupies active site and prevents substrate from complexing
– addition of more substrate can reverse inhibition
• Non competitive inhibition
– inhibitor binds to site other than active site
– binding causes active site to change geometry
– Additional substrate will not reverse inhibition
• Regulatory enzymes
– Reaction sequence in which the product of the last reaction inhibits the enzyme of the first reaction.
– Feedback system to control the production of the end product.