Essential Elements of Biochemistry BCHM 3050 Dr Srikripa Chandrasekaran Dr Sri Lecture Notes 1 26 15 Proteins Protein Structure Proteins are extraordinarily complex Levels of protein structure are primary secondary tertiary and quaternary Proteins are made up of amino acids Each aspect of animated proteins means something specific o Ex A twisted ribbon helix arrow beta sheet The distribution of amino acid residues within the protein core 1 3 non polar 1 3 polar uncharged 1 3 charged The hydrophobic amino acids are buried on the inside Proteins can be classified by shape and composition Proteins are classified by shape globular and fibrous o Globular attract with water more rounded spherical have more regulatory functions like hemoglobin functional catalytic transport etc proteins that do certain functions are globular generally soluble in water irregular amino acid sequence more sensitive to changes in heat pH etc examples catalase hemoglobin insulin immunoglobulin o Fibrous do not attract to water more structural importance strength and support generally insoluble in water repetitive amino acid sequence less sensitive to changes in heat pH etc examples collagen myosin fibrin actin keratin elastin Proteins are also classified by composition simple and conjugated o Simple contain only amino acids o Conjugated contain protein and a non protein component examples are glycoprotein and lipoproteins o Lipoproteins are present on the surface and have specific The monomers of a protein are amino acids and they are held together by functions peptide bonds C N R groups are not involved in peptide bonding Primary structure of proteins Primary structure is the specific amino acid sequence of a protein Homologous proteins share a similar sequence and arose from the same ancestor gene and carry out similar functions The primary structure of a protein can tell you a lot about the organism Proteins are the actors in the story of life and DNA is the director Everything is dictated by DNA behind the scenes 1 Proteom all of the proteins of an organism A lot of different life forms use the same proteins for the same specific functions For people with ALS they do not usually feel things like ice being dumped on their heads or the feeling is very delayed Peptide bonds Peptide bonds are very strong and have partial double bond characteristics so they do not break easily Comparing homology of SOD1 protein across species Humans and chimpanzees have very similar protein sequences Many disease can be modeled in rats mice chimps etc so potential treatments and cures can be tested on them and if they work they can usually be affective in humans as well because these animals have many proteins that are also present in humans Protein mutations Amino acid mutations can cause very severe conditions Sickle cell anemia is caused by an amino acid mutation a Glu is replaced with a Val this mutation started in Africa Torsion angles Phi Psi Polypeptide bond rotation between C1 and N Polypeptide Bond rotation between N and C Polypeptide bond rotation between C and C1 Omega A peptide bond is between an amino group and a carboxylic acid group The bond rotation angle between the N and C alpha is called phi The bond rotation angle between the C alpha and C1 is called psi The bond between C1 and N is called omega Secondary structure Most common include the a helix and b pleated sheet Stabilized by hydrogen bonding between the carbonyl and the N H groups of the polypeptide s backbone The a helix is a rigid rod like structure formed by a helical turn a Helix is stabilized by N H hydrogen bonding with a carbonyl four amino acids away Glycine and proline do not foster a helical formation Proline is a helix breaking residue Proline too rigid lacks an N H group for H bonding Glycine too small polypeptide chain very flexible MALEK favors helix formation Glycines and prolines are helix breakers In an alpha helix the first and the fifth amino acids form a hydrogen bond i 4 a hydrogen bond is formed R groups are not involved in alpha helix the backbone is involved in alpha helix 2 Right handed helix negative values goes anticlockwise Both of these helixes generally have L amino acids not usually D amino Left handed helix positive values goes clockwise acids Left handed helix 57 47 Right handed helix 57 47 Right handed helix is more abundant in nature than the left handed helix Right handed alpha helices Alpha helix i 4 310 helix i 3 pi helix i 5 Some proteins form alpha helixes with hydrogen bonds at i 3 and i 5 i 4 is the normal pattern of hydrogen bonds that form alpha helixes Proteins Beta sheets The pleated sheets form when two or more polypeptide chain segments line up side by side Each strand is fully extended and stabilized by hydrogen bonding between N H and carbonyl groups of adjacent strands Parallel sheets are much less stable than antiparallel sheets Beta Pleated Sheets involve forming hydrogen bonds with an amino acid on the opposite side easily in parallel sheets apart in antiparallel sheets Hydrogen bonds are less stable and more random break apart more Hydrogen bonds are more stable and more predictable harder to break Very often parallel and antiparallel sheets are mixed this is called mixed or twisted Parallel 2 arrows pointing in the same direction Antiparallel 2 arrows pointing in opposite directions Phi and psi values are pretty constant alpha L phi 57 psi 47 left handed alpha helix alpha R phi 57 psi 47 right handed alpha helix 3 10 Helix phi 49 psi 26 right handed pi helix phi 57 psi 80 right handed Type II helices phi 79 psi 150 left handed helices formed by polyglycine and polyproline Collagen phi 51 psi 153 right handed coil has 3 left handed helices Beta sheets phi 110 psi 150 parallel and anti parallel Ramachandran Plot 3 A graph that shows the values of phi and psi for antiparallel beta sheets parallel beta sheets collagen triple helix right twisted beta sheets left handed alpha helix and right handed alpha helix Super secondary structures motifs Many proteins form supersecondary structures motifs with patterns of helix and sheet structures o unit o meander o unit o barrel o Greek key These are just arrangements of secondary structures Loops and turns connect different motifs Loops and turns often break helices glycine and proline usually cause these breakages loops and turns are enriched in glycine and proline Glycine and proline also break beta sheets Proteins Domain Large motifs form a domain
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