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Amino Acids & Proteins
- • 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
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Amino function
- zwitterion
- 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'
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Classification
- • Non-polar
- – R group consists of hydrocarbon chain or other
- non-polar group (alkyl sulfide or indole)
- • Polar
- – R group contains polar groups such as OH, SH, C=O
- • Acidic
- – R group contains a COOH (COO-) group
- • Basic
- – R-group contains a NH2 (NH3
- +) group
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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
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In the Fischer Projection format, the amino group is on the left of the chain. Amino acids in proteins have the ‘L’ configuration
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Proteins
- • 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
- – Thr-Leu-Phe-Gly-Gly-Phe-etc.
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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.
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Proteins
- • 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
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Alpha Helix
 - Hydrogen bonds form between amino acids located 4 amino acids apart in the primary structure.
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Beta-Pleated Sheet
- 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.
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Triple Helix
- 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.
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Tertiary Structures
- • 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
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Quarternary Structures
- • 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)
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Denaturing Proteins
- • 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"
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Enzymes
- • 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
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Enzyme Mechanisms
- • 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
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Inhibition Mechanisms
- • 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
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Inhibition Mechanisms
- • 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.
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