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Chapter 4

BIO206 Chapter 4.pdf

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University of Toronto Mississauga
George S Espie

Chapter 4 September-19-13 4:36 PM Enzymes Shape of protein is specified by its amino acid sequence - Protein - referred to as polypeptides/ polypeptide chains (arranged in amino acid sequence) Proteins fold into a conformationof lowest energy - Free energy (G) is minimized - Denatured proteins can renature if denaturing solvent is removed - H bonds within a protein moleculehelp stabilize its folded shape - Molecular chaperones - assist in protein folding in living cells Proteins comein a wide variety of complicatedshapes - Average of 50 to 2000amino acids long - Either the use of x-ray crystallography or nuclear magnetic resonance (NMR) spectroscopycan we predict the precise folding pattern of a protein - Protein domain - part of a protein, 100-250amino acids ○ Displayed as:  polypeptide backbone model - shows overall organization of polypeptide in a clean way to comparestructures of related proteins  ribbon model - easy way to visualize secondary structures such as α Helices and β Sheets  wire model that includes amino acid side chains - useful for predicting which AA's might be involved in a protein's activity(especially enzyme)  space-filling model - provides contour map, gives a feel for the shape of protein and shows which AA side chains are exposed on its surface □ Shows how the protein might look to a small molecule(ex. Water) or to another protein α Helix and β Sheet are commonfolding patterns - 1st one - Found in α-keratin (skin) - 2nd one - Found in fibroin (silk) - Commonb/c they result in H bond between N-H and C=O groups - SH2 has both Helices form readily in biological structures - Can be right-handed or left-handed (depending on the twist) - H bond between N-H and C=O groups in every fourth AA - Regular helix = completeturn every 3.6 AA - Hydrophilic backbone, hydrophobic nonpolar side chains - Coiled-coil - when helices wrap around one another or intertwine (most side chains are on one side, minimizing contact with cytosol-aqueousenvironment) β Sheet form rigid structures at the core of many proteins - H bond between segments of polypeptide chains lying side by side - parallel β sheet - neighbouring polypeptide chain run in the same orientation - Antiparallel β sheet - opposite (ex. SH2) - Antifreeze protein - help insects from freezing during winter Proteins have several levels of organization - Primary structure - AA sequence - Secondary structure - α Helix and β Sheet - Tertiary structure - α Helix and β Sheet, ransom coils, any other loops - Quaternary structure - Protein domain - any segment of polypeptide chain that can fold independently into a compact stable structure. Has different functions. - Catabolite activatorprotein (CAP) ○ 2 domains: small one binds to DNA, large one binds cyclic AMP Few of the m
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