Chapter04FALL05 - Chapter 4 - Proteins Proteins can be...

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Chapter 4 - Proteins Proteins can be classified as either: 1) globular - spherical; water-soluble molecules with a hydrophobic interior and hydrophobic surface; have mostly functional roles in the cell, e.g. enzymes 2) fibrous - made into threads or cables with repeating units; water-insoluble molecules that provide mechanical or structural support, e.g. α keratin and collagen Protein Structure There are four levels of protein structure: 1) primary - linear sequence of amino acids 2) secondary - regular patterns formed by primary structure folding 3) tertiary - completely folded polypeptide with one or more domains 4) quaternary - association of multiple polypeptides; not found in all proteins PRIMARY STRUCTURE peptide group - bond plus 4 groups Bond between carbonyl carbon and nitrogen shorter than normal, but longer than C=N bonds ---> partial do bond character ---> no free rotation around bond ---> bond is planar. Peptide group can exist in cis or trans conformation --> nearly all in trans because of steric hinderance. There is rotation around N-C α bond ( φ phi) and C α -C bond ( ψ psi). Figure 4.8 shows how bond angles are measured. Conformation of peptide group can be described by φ and ψ. Only certain angles are permitted. Are shown in a Ramachandran plot ---> also shows recognizable conformations. (Figure 4-9) SECONDARY STRUCTURE There are two common types of secondary structure: 1) α -helix Most common. Can be described by pitch (distance for 1 turn of helix) and rise (distance/a.a. residue). Can be right or left-handed, but all right-handed. Pitch = 0.54 nm ---> 3.6 a.a. 1
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Rise = 0.15 nm Main chain is core, with R-groups sticking out. Stabilized by H-bonds between carbonyl oxygen and amide hydrogen 4 residues toward C- terminus. Some a.a. residues commonly found in α -helices (alanine), whereas some a.a. destabilize helix (e.g. glycine; lots of rotation). Can have variation called 3 10 helix (right handed) - carbonyl oxygen H-bonds with amide hydrogen 3 residues towards C-terminus ---> tighter ring structure with 10 atoms rather than 13, 3 residues/turn and longer pitch > less stable, but usually only a few residues in length. 2) β -structures β -strands (almost fully extended α helix) and β -sheets (multiple β strands in sheets or layers) Stabilized by H-bonds between carbonyl oxygens and amide hydrogens on adjacent ß strands. Can be arranged in either parallel (same N-C direction) or anti-parallel. R-groups alternately point above and below plane when viewed in 3-D (Figure 4-16). Globular proteins contain regions of β structure. Loops and Turns (nonrepetitive regions) Cause directional change in the polypeptide backbone. Bond angles are constrained, so that only certain directional changes are permitted. Loops are often hydrophilic residues found on protein surfaces, where they H-bond with
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Chapter04FALL05 - Chapter 4 - Proteins Proteins can be...

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