Proteins consist of joined amino acids They are joined by a Also called an Amide Bond

Transcription

1 Lecture Two: Peptide Bond & Protein Structure [Chapter 2 Berg, Tymoczko & Stryer] (Figures in Red are for the 7th Edition) (Figures in Blue are for the 8th Edition) Proteins consist of joined amino acids They are joined by a Also called an Amide Bond Figure 2-18, page 34 (2-13, page 33) (2-13, page 35) The equilibrium in this figure favours the left side is required to produce a peptide bond Many joined amino acids are called a Polypeptide Amino acids in a polypeptide are called A protein consists of one or more polypeptide chains Figure 2-19, page 35 (2-14, page 34) (2-14, page 36) A polypeptide chain has direction The order of residues is read from the Terminal to the Carboxyl (C-) [Acid] Terminal The residue order of a protein is called its sequence This sequence is unique to that protein Figure 2-20, page 35 (2-15, page 34) (2-15, page 36) The polypeptide chain has a regular repeating part This region is called the main chain The main chain atoms are N H C H C O Also referred to as the of a polypeptide The variable region of a polypeptide are the side chains of the amino acids Features of the peptide bond Figure 2-23, page 37 (2-18, page 36) (2-18, page 38) The peptide group is found in all proteins It has very important properties [ Note: 1Å = m = 10-8 cm = 10-1 nm ] Figure 2-24, page 38 (2-19, page 36) (2-19, page 38) The peptide bond in a peptide group has partial double bond characteristics This feature shortens the C-N bond from a single bond towards double bond length

2 The partial double bond character means the peptide group is rigid It acts as a Figure 2-25 & Figure 2-26, page 37 (2-20, page 36 and 2-21, page 37) (2-20, page 38 and 2-21, page 39) The peptide bond is in the Trans conformation The Hydrogen of the amino group is nearly always trans to the Oxygen of the carbonyl group Across the peptide bond Only proline can allow Cis conformation bonding Found in the chain as Xaa-Pro Xaa is any other amino acid The side chains of all the other amino acids would clash were they to be in the cis conformation PROTEIN STRUCTURE Figure 2-22, page 36 (2-17, page 35) (2-17, page 37) The residue sequence is unique to that protein Proven by Sanger in 1953 He used insulin in his studies Figure 2-21, page 36 (2-16, page 35) (2-16, page 37) Cysteine residues have a highly reactive SH group In an oxidising environment cysteines can pair to form Disulphide bonds Also know as and Cystine The Primary Structure of a Protein The amino acid sequence (and disulphides if any) The Secondary Structure of a Protein The spatial arrangement of amino acids near to one another in the linear sequence Proteins can contain regular repeating units Proposed by Pauling and Corey in 1951 Two repeating structures were proposed The ( -helix ) The ( -sheet )

3 The -helix The first repeating structure proposed hence The structure is a regular tight coil Figure 2-29, page 41 (2-24, page 39) (2-24, page 41) The structure has an axis central to the coil There is a 100 o rotation about the axis from one residue to the next 3.6 residues per turn For main chain atoms it is ~ 5Å diameter The distance along the axis from one residue to the next is 1.5Å This is called the of the helix The PITCH of a helix Pitch = Number of residues per turn x Rise = 3.6 x 1.5 = 5.4Å The -helix in proteins is Figure 2-30, page 41 (2-25, page 39) (2-13, page 35) The hydrogen bonding pattern in an -helix is very specific The Carbonyl Oxygen of residue (i) is bonded to the Hydrogen of an amide in residue (i+4) Figure 2-48, page 41 (2-43, page 46) (2-25, page 41) Myoglobin is a protein whose secondary structure consists primarily of -helices The -pleated sheet The second type of repeating structure proposed Comprised of strands of polypeptide Known as -strands Figure 2-35, page 42 (2-30, page 40) (2-30, page 42) The residues are almost fully extended in the strands Two forms of -pleated sheet exist

4 Figure 2-36, page 43 (2-31, page 41) (2-31, page 42) -strands in the sheet run in opposing directions to each other Figure 2-37, page 43 (2-32, page 41) (2-32, page 43) -strands run in the same direction to each other Antiparallel sheets are slightly more stable than parallel sheets The hydrogen bonding is slightly distorted in parallel sheets but is not in antiparallel sheets The distance from C to C for a -strand in an antiparallel conformation is 3.5Å Concanavalin A is a protein whose secondary structure consists primarily of -pleated sheets Figure 2-39, page 44 (2-34, page 42) (2-34, page 43) Beta sheets are often twisted rather than flat Figure 2-41, page 44 (2-36, page 43) (2-36, page 44) Sharp turns are found within proteins to keep them as compact and globular structures These are known as -turns Usually four residues and often glycine is in the third position OTHER TYPES OF SECONDARY STRUCTURES Figure 2-47, page 46 (2-42, page 45) (2-42, page 45) THE COLLAGEN HELIX Collagen is the most abundant animal protein Around 1000 residues in a collagen chain Nearly every third residue is The collagen helix has a rise ~2.9Å and three residues per turn The Pitch = 3 x ~2.9 = ~8.7Å Different from the -helix In the collagen structure three helices wind around each other This is a structure Glycine always packs on the inside of the triple helices Steric hindrance bars any other amino acids from being on the inside of the collagen triple helix

5 Hydrogen bonding within the triple helix are between strands 3 10 HELIX Three residues involved linearly in the chain Ten atoms from a Hydrogen bond donor to its Hydrogen bond acceptor Summary of Lecture Two: Amino acids can join together by a peptide bond The peptide bond is rigid and planar A protein consists of one or more polypeptide chains Read in the N- to C- direction Primary Structure The polypeptide sequence (and disulphides, if any) Secondary Structure Unique to each protein The spatial arrangement of residues near to one another in the sequence Periodic structures -helix Also -turns Collagen helix 3 10 helix -pleated sheets Two forms: antiparallel & parallel