Basic Biochemistry Amino Acid and Protein PDF

Amino Acid & Protein 2 (a) The  - helix  A lot of hydrogen bonding between C=O and  N-H groups of neighboring peptide bonds  Helix is Right Handed  In a globular protein, on average there are ~11 amino acid (aa) in one helix (can be up to 53aa). (b) The -structure:  like the alpha he...

Amino Acid & Protein 2 (a) The  - helix  A lot of hydrogen bonding between C=O and  N-H groups of neighboring peptide bonds  Helix is Right Handed  In a globular protein, on average there are ~11 amino acid (aa) in one helix (can be up to 53aa). (b) The -structure:  like the alpha helix, has many hydrogen bonds between neighboring peptide bonds of the same or different chain.  2 types; Parallel (chains in same direction) or Anti- parallel (chain in different directions).  Forms the -pleated sheet structure.  In a globular protein there are 2-15 aa in this structure (average = 6).  the anti-parallel is more commonly found.  there is a slight right-handed twist.  usually found in the central core of globular proteins. The - structure  The 3-D structure of a particular protein /polypeptide.  Some include the arrangement of secondary structures – Super secondary structures or motifs  On average 27% are in alpha helix and 23% beta structures  But there are exceptions – there is 75-80% alpha helix in Myoglobin and Hemoglobin  Concanavalin A has only beta structures and no alpha helices. It is a lectin protein that binds selectively to carbohydrates (sugars, glycoproteins) found in plants, human etc. Myoglobi Concanavalin n A  Usually all hydrophobic aa are found in the protein interior (val, leu, met)  Polar and charged aa (glu, asp, his, lys) are found on the surface of the proteins – meets water molecules  Polar aa with no charge can be found inside or on the surface of globular proteins (ser, asn, tyr)  Usually globular proteins that are large (>200aa) have DOMAINs – for example, domain A & B (ex. The enzyme glyceraldehyde 3-P DH, phosphoglycerate kinase)  The fourth level of protein structure is concerned with the interaction of 2 or more polypeptide chains to associate to form a larger protein molecule.  Proteins with more than one polypeptide chain are said to be oligomeric, and the individual chains are called subunits or monomers of the oligomer.  The geometry of the molecule is its quaternary structure. Two subunits forms a dimer, three a trimer, four a tetramer etc.  The subunits (polypeptide chains) may be identical (homogeneous) e.g. muscle creatine kinase is a dimer of 2 identical subunits or non-identical e.g. haemoglobin is a tetramer and contains 2 alpha + 2 beta subunits (heterogeneous).  The central dogma of protein folding – “The primary structure determines the tertiary structure”  Protein folding is spontaneous and probably starts with a local secondary (α-helix or β-structure) structure, which forms the nucleus/centre, around which the rest of the coil folds around.  Recently proteins called molecular chaperone or chaperone proteins have been discovered (originally called heat shocked proteins) which help in protein folding – although exactly how not known.  Probably protect certain exposed non-polar regions of developing polypeptide 1. Fibrous protein: (a) Keratin (b) Collagen 2. Globular protein: (c) Myoglobin (d) Hemoglobin  Main structural component of hair (also nail, skin and horns etc).  Its basic unit is the a-helix polypeptide.  Two a-helices are twisted together to form a coiled- coil.  Two coiled-coils twist together to form a protofilament/protofibril.  Protofilaments are arranged in 9+2 fashion to form a microfibril  Many microfibrils are packed together form a macrofibril  Many macrofibrils pack together to form a fiber (a single hair)  Rich in hydrophobic amino acids that promote a-helix formation.  Because R-groups are directed toward the outside of the helix, keratins are highly insoluble in water.  Lack helix-breaking proline residues.  Structure of protofilaments is stabilized by intermolecular hydrogen bonds and disulfide bridges.  The disulphide bonds can be reductively cleaved by mercaptans (ex. Ethyl or methyl mercaptans).  Hair so treated can be curled and set in a “permanent wave” by an oxidizing agent which reestablishes the disulphide bonds and the hair in a new conformation.  Most abundant protein in vertebrates – 25% of all protein in body  Structural component of extracellular matrix, bone, teeth, tendons and blood vessels.  Basic structural unit is a collagen polypeptide that forms a left-handed helix  No α-helix or β-pleated sheet structure possible  The collagen molecule is a triple helix of three collagen polypeptides – ~ 3000A long  Myoglobin structure was elucidated by John Kendrew & Max Perutz (late 50s) using x-ray crystallography techniques.  Small in size (153 amino acid residues) and crystallizes easily – easy to study.  Has the ability to carry oxygen because it has a prosthetic group – haem (a tetrapyrrole – see below).  Myoglobin is extremely compact.  75% of polypeptide is in alpha helix – 8 helix segments, A, B, C, D, E, F, G & H.  There are 5 non-helical segments between the helices.  i.e.: NA1-NA2, CD, EF, GH and HC1-HC5 (see diagram above).  NA1-NA2 and HC1-HC5 are the 2 other non-helical segments (2aa at the N-terminal and 5aa at the C-terminal).  4 of the helices are terminated by proline (a helix breaker).  There are no empty spaces in the interior of the molecule, which contain, leu, val, met, phe.  There are no glu, asp, gln, lys and arg in the interior of the molecule (except for his only)  Haem is not a protein and is red in colour.  Hemoglobin (or haemoglobin, frequently abbreviated as Hb), which is contained in red blood cells, serves as the oxygen carrier in blood.  Hemoglobin also plays a major role in the transport of carbon dioxide from the tissues back to the lungs.  Each heme group contains an iron atom, and this is responsible for the binding of oxygen.  Has 4 polypeptide chains; 2 α chains (141aa – minus D helix); 2 β chains (146aa – shortened H helix) chains (i.e. has 4 subunits; 574 aa; M.Wt. 63,500)  Each subunit almost spherical.  Each subunit can carry 1 oxygen molecule  Thus the capacity to carry oxygen is high: Hb4 + 4O2  → Hb4(O2)4 oxy-hemoglobin  Fe2+ in the protohaemcan bind to 6 atoms (like myoglobin).  The β subunits has 8 helical segments (A,B,C ….H) – just like myoglobin. The α subunits have 7 helical segments (minus the D segment).  There are two alternative structures of hemoglobin; the relaxed structure (R) which has a greater oxygen affinity, and the tense structure (T) which has lower affinity for oxygen.  The change between the T and R structures is the result of a rotation of 15 degrees between the two alpha-beta dimers.  This rotation changes the bonds between the side chains of the alpha-beta dimers in the F helix and therefore causes the heme molecule to change positions.  In the T structure, the iron ion is pulled out of the plane of the Fe2+ ring and becomes less accessible for oxygen to bind to it, thus reducing its affinity to oxygen.  In the R structure the iron atom is in the plane