Understanding Proteins: Structure, Functions, and Properties, Study notes of Computer Science

Download Understanding Proteins: Structure, Functions, and Properties and more Study notes Computer Science in PDF only on Docsity! 1 The Structure and Functions of Proteins Protein Structure and Function 2 The many functions of proteins • Mechanoenzymes: myosin, actin • Rhodopsin: allows vision • Globins: transport oxygen • Antibodies: immune system • Enzymes: pepsin, renin, carboxypeptidase A • Receptors: transmit messages through membranes • Vitelogenin: molecular velcro • And hundreds of thousands more… Protein Structure and Function 3 Complex Chemistry Tutorial • Molecules are made of atoms! • There is a lot of hydrogen out there! • Atoms make a “preferred” number of covalent (strong) bonds • C – 4 • N – 3 • O, S – 2 • Atoms will generally “pick up” enough hydrogens to “fill their valence capacity” in vivo. • Molecules also “prefer” to have a neutral charge Protein Structure and Function 4 Biochemistry • In the context of a protein… • Oxygen tends to exhibit a slight negative charge • Nitrogen tends to exhibit a slight positive charge • Carbon tends to remain neutral/uncharged • Atoms can “share” a hydrogen atom, each making “part” of a covalent bond with the hydrogen • Oxygen: H-Bond donor or acceptor • Nitrogen: H-Bond donor • Carbon: Neither Protein Structure and Function 5 Proteins are chains of amino acids • Polymer – a molecule composed of repeating units Protein Structure and Function 6 Amino acid composition • Basic Amino Acid Structure: • The side chain, R, varies for each of the 20 amino acids C R Cα H N O OHH H Amino group Carboxyl group Side chain 2 Protein Structure and Function 7 The Peptide Bond • Dehydration synthesis • Repeating backbone: N–Cα –C –N–Cα –C • Convention – start at amino terminus and proceed to carboxy terminus O O Protein Structure and Function 8 Peptidyl polymers • A few amino acids in a chain are called a polypeptide. A protein is usually composed of 50 to 400+ amino acids. • Since part of the amino acid is lost during dehydration synthesis, we call the units of a protein amino acid residues. carbonyl carbon amide nitrogen Protein Structure and Function 9 Side chain properties • Recall that the electronegativity of carbon is at about the middle of the scale for light elements • Carbon does not make hydrogen bonds with water easily – hydrophobic • O and N are generally more likely than C to h-bond to water – hydrophilic • We group the amino acids into three general groups: • Hydrophobic • Charged (positive/basic & negative/acidic) • Polar Protein Structure and Function 10 The Hydrophobic Amino Acids Proline severely limits allowable conformations! Protein Structure and Function 11 The Charged Amino Acids Protein Structure and Function 12 The Polar Amino Acids