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Proteins •Amino acids •Synthesis & Degredation •Structural Levels •Factors for structure •Domains Reading Lipids •Parts of triglyceride •Function of triglycerides •Phospholipids •Steroids Homework Carbohydrates •Characteristics & Isomers •Mono-, di-, & Poly- Homework 1 Ch 4: Proteins Ch 5: Lipids, Carbs, Nucleic acids Ch 6 Prequiz Ch 7 Prequiz Diffusion & Osmosis Prequiz Study Groups! Moodle email Molecules of the body Protein building block monomer Variable side chain (R group) What Kind of Molecule is this? Notice different way of drawing = perspective 1000s exist Only 20 in proteins 20 Amino Acids Essential amino acids p78 Some have charged side chains (depending on pH) Notice different way of drawing = perspective Some side chains are uncharged But polar Some R-groups are hydrophobic Variations in side chains determine how the protein will interact with other molecules or itself Asparagine is: a)Polar b)Charged + c)Charged d)hydrophobic e)None of the above Asparagine is a polar molecule and will likely NOT interact with a)H2O b)Hydrophillic molecules c)Charged molecules d)Hydrophobic molecules - + 3 When amino acids are polymerized Polymerized Chain Added in order aa #1 aa #2 Backbone aa #1 aa #2 Condensation / Amino terminal N-ter = beginning Amino acid, dipeptide, tripeptide, polypeptide Carboxyl Terminal C-ter = end Peptide Bond carboxyl amino amide Proteins have shape: 3D 4 Levels of protein structure Shape is required for function Native = functional Biologically active Primarily Hydrogen bonds But also ionic And covalent – disulfide bonds Cysteine Cysteine Dimeric form of cysteine When amino acids are polymerized Polymerized Chain Added in order aa #1 aa #2 Backbone aa #1 aa #2 Condensation / Amino terminal N-ter = beginning Amino acid, dipeptide, tripeptide, polypeptide Carboxyl Terminal C-ter = end Proteins have shape: 3D 4 Levels of protein structure Shape is required for function Native = functional Biologically active Primarily Hydrogen bonds But also ionic And covalent – disulfide bonds Cysteine Cysteine Dimeric form of cysteine Proteins have shape: 3D 4 Levels of protein structure Primary (1°) - Sequence Secondary (2°) – Features within the overall chain The sequence of amino acids in a protein is: G-Y-T-T-Q. This is an example of what level of protein structure? a)Primary b)Secondary c)Tertiary d)Quatenary e)None of the above Androgen Receptor is a protein that has a helix shape which allows it to fit into DNA. The helix is an example of what level of protein structure? a)Primary b)Secondary c)Tertiary d)Quatenary How does a protein fold? Unknown Determined by Primary sequence Mostly through hydrogen bonding determined by side chains and backbone Shape is required for function Native = functional Biologically active Proof? Protein Denaturation Essentially: build the chain and it will fold itself Finds most thermodynamically stable form • If you denature a protein it can renature Native = functional Biologically active Non-functional Structure = function Interaction with H2O Drives globular form, hydrophobic residues inside, hydrophillic residues on outside Classical example of structure = function What kind of interaction is the most influential in protein shape? a)Covalent b)Ionic c)Hydrogen d)Hydrophobic e)Van der waals Sequence not the whole story Eggs can’t renature 1. 2. Particular proteins Presence of other proteins Chaperones prions Globular X-ray crystallography + -+ + ++ + -+ + ++ + -+ + ++ + -+ + ++ + -+ + +- + -+ + ++ + -+ + ++ + + -+ + ++ + -+ + ++ + -+ + ++ + -+ + ++ + -+ + ++ + -+ + ++ + -+ + ++ + -+ + +- + - + + + -+ + -+ + ++ + + - -+ + - -+ + ++ + + -+ + ++ + -+ + ++ + -+ + ++ + -+ + ++ + -+ + ++ -+ + ++ + +++ -+ + ++ + + + -+ + ++ + -+ + ++ + -+ + ++ -+ + ++ + + -+ + ++ + + -+ + +-+ + ++ + + + -+ + ++ -+ + ++ + + + + -+ + +- -+ ++ + ++ -+ + - + + + -- - - + + + + ++ -+ - - - ++ + + + + + + + - -+ + + + + + - - +- + -+ +- -- + + - + + + -- - - + + ++ + + + + + - +- -+ ++ - - +- + + -+ +- -- + + + + + -+ + + + + ++ + + + + + - +- + + + + - +- +- ++ + -+ - -+ - X-ray crystallography Lysozyme Myoglobin: 1st structure 1958 Kendrew Ball and Stick Ribbon (route of aa’s) Patterns of structure & sequence domains Regions that do something Example region that interacts with Zn have similar structure – now can identify through primary sequence DNA binding domain – helix loop helix Fibrous and Globular Proteins • Fibrous proteins – Extended and strand-like proteins – Water insoluble – Examples: keratin, elastin, collagen, and certain contractile fibers • Globular proteins – Compact, spherical proteins with tertiary and quaternary structures – Water soluble (more or less) – Examples: antibodies, hormones, and enzymes Phenylalanine is: a)Polar b)Charged + c)Charged d)hydrophobic e)None of the above Many Globular proteins change shape This structure is an example of ___ structure? a)1° b)2° c)3° d)4° e)5° Example of a transmembrane domain Highly hydrophobic side chains Binding of the red molecule gives an alternative protein structure. What level of protein structure is this? a)1° b)2° c)3° d)4° e)5° What is breaking and reforming to allow this rearrangement? a)Covalent b)Ionic c)Hydrogen d)Hydrophobic e)Van der waals Shape changes Mostly / usually alters hydrogen bonding pattern Different composition means another more thermodynamically stable shape When O2 binds to hemoglobin, the protein changes shape. This is an example of what level of protein structure? a)Primary b)Secondary c)Tertiary d)Quatenary How would you expect 2 proteins to interact with each other? Primarily through: a)Covalent b)Ionic c)Hydrogen d)Hydrophobic e)Van der waals How would you expect 2 proteins to interact with each other? Primarily through: a)Covalent b)Ionic c)Hydrogen d)Hydrophobic e)Van der waals Lipids •Contain C, H, and O, but the proportion of oxygen in lipids is less than in carbohydrates therefore hydrophobic / Insoluble in water Soluble in other lipids and organic solvents Lipids are therefore a less cohesive / broad category Functional Groups – a)Carboxyl b)Amino c)Ester d)Methyl e)phosphate Lipids: Triglycerides oils (liquid) & fats (solid) For energy storage Lipids: Triglycerides oils (liquid) & fats (solid) Joining is through? a)Condensation b)Hybridization c)Hydrolysis d)redox Lipids: Triglycerides oils (liquid) & fats (solid) Esterify glycerol Ester = derived from alcohol + carboxyl Monoglyceride, diglyceride, tri- NOT a polymer 2 Major categories of Fatty acids Solids = Fats Saturated with H’s H-O Liquids = oils mono-UNsaturated H-O Trans vs Cis Trans bad – determined empirically / statistical analysis II . Phospholipids Phospholids are amphipathic Phosphate choline group Can vary Serine, etc. Esterification Alcohol + acid Phosphodiester bond The Cell Membrane In water/solution phospholipds will spontanesouly form 63 Membrane Lipids • 75% phospholipids (lipid bilayer) – Phosphate heads: polar and hydrophilic – Fatty acid tails: nonpolar and hydrophobic • 5% glycolipids – Lipids with polar sugar groups on outer membrane surface • 20% cholesterol – Increases membrane stability and fluidity Steroid hormones Testosterone Estradiol (Estrogen) chenodeoxycholic acid (bile salt) Lipids Summary Triglycerides Function: food storage composition: 1 glycerol (know structure) 3 Fatty acids (carboxyl on unbranched hydrocarbon) Saturated vs unsaturated (Cis vs Trans) Phospholipids Function: membranes due to amphipathic structure Composition: 1 glycerol, 2 fatty acids, 1 phosphorous group Cholesterol Function: membranes & hormone precursor Know general structure: 4 rings