* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download AP Biology 2007-2008 Chemistry of Carbon Building
Basal metabolic rate wikipedia , lookup
Vectors in gene therapy wikipedia , lookup
Interactome wikipedia , lookup
Two-hybrid screening wikipedia , lookup
Protein–protein interaction wikipedia , lookup
Cryobiology wikipedia , lookup
Point mutation wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
Deoxyribozyme wikipedia , lookup
Fatty acid synthesis wikipedia , lookup
Metalloprotein wikipedia , lookup
Peptide synthesis wikipedia , lookup
Nuclear magnetic resonance spectroscopy of proteins wikipedia , lookup
Genetic code wikipedia , lookup
Fatty acid metabolism wikipedia , lookup
Amino acid synthesis wikipedia , lookup
Nucleic acid analogue wikipedia , lookup
Protein structure prediction wikipedia , lookup
Proteolysis wikipedia , lookup
Chemistry of Carbon Building Blocks of Life AP Biology 2007-2008 Why study Carbon? All of life is built on carbon Cells ~72% H2O ~25% carbon compounds carbohydrates lipids proteins nucleic acids AP Biology ~3% salts Na, Cl, K… Chemistry of Life Organic chemistry is the study of carbon compounds C atoms are versatile building blocks bonding properties 4 stable covalent bonds H H C H AP Biology H Complex molecules assembled like TinkerToys AP Biology Hydrocarbons Combinations of C & H non-polar not soluble in H2O hydrophobic stable very little attraction between molecules a gas at room temperature AP Biology methane (simplest HC) Hydrocarbons can grow AP Biology Isomers Molecules with same molecular formula but different structures (shapes) different chemical properties different biological functions 6 carbons 6 carbons AP Biology 6 carbons Form affects function Structural differences create important functional significance amino acid alanine L-alanine used in proteins but not D-alanine medicines L-version active but not D-version AP Biology sometimes with tragic results… stereoisomers Form affects function Thalidomide prescribed to pregnant women in 50s & 60s reduced morning sickness, but… stereoisomer caused severe birth defects AP Biology Diversity of molecules Substitute other atoms or groups around the carbon ethane vs. ethanol H replaced by an hydroxyl group (–OH) nonpolar vs. polar gas vs. liquid biological effects! AP Biology ethane (C2H6) ethanol (C2H5OH) Functional groups Parts of organic molecules that are involved in chemical reactions give organic molecules distinctive properties hydroxyl carbonyl carboxyl amino sulfhydryl phosphate Affect reactivity makes hydrocarbons hydrophilic increase solubility in water AP Biology Viva la difference! Basic structure of male & female hormones is identical AP Biology identical carbon skeleton attachment of different functional groups interact with different targets in the body different effects Hydroxyl –OH organic compounds with OH = alcohols names typically end in -ol ethanol AP Biology Carbonyl C=O O double bonded to C if C=O at end molecule = aldehyde if C=O in middle of molecule = ketone AP Biology Carboxyl –COOH C double bonded to O & single bonded to OH group compounds with COOH = acids fatty acids amino acids AP Biology Amino -NH2 N attached to 2 H compounds with NH2 = amines amino acids NH2 acts as base ammonia picks up H+ from solution AP Biology Sulfhydryl –SH S bonded to H compounds with SH = thiols SH groups stabilize the structure of proteins AP Biology Phosphate –PO4 P bound to 4 O connects to C through an O lots of O = lots of negative charge highly reactive transfers energy between organic molecules ATP, GTP, etc. AP Biology Macromolecules Building Blocks of Life AP Biology 2007-2008 Macromolecules Smaller organic molecules join together to form larger molecules macromolecules 4 major classes of macromolecules: carbohydrates lipids proteins nucleic acids AP Biology Polymers Long molecules built by linking repeating building blocks in a chain monomers building blocks repeated small units H 2O covalent bonds HO H HO H Dehydration synthesis HO AP Biology H How to build a polymer Synthesis You gotta be open to “bonding! joins monomers by “taking” H2O out one monomer donates OH– other monomer donates H+ together these form H2O H 2O requires energy & enzymes HO H Dehydration synthesis HO H enzyme Condensation reaction AP Biology HO H How to break down a polymer Breaking up is hard to do! Digestion use H2O to breakdown polymers reverse of dehydration synthesis cleave off one monomer at a time H2O is split into H+ and OH– H+ & OH– attach to ends requires enzymes HO releases energy H2O enzyme H Hydrolysis AP Biology Digestion HO H HO H Carbohydrates AP Biology CH2OH H O H OH H H OH HO H OH Carbohydrates energy molecules AP Biology 2006-2007 Carbohydrates Carbohydrates are composed of C, H, O carbo - hydr - ate CH2O (CH22O) O)xx C66H12 O (CH 12 66 Function: energy raw materials materials energy storage structural Monomer: sugars ex: sugars, starches, cellulose AP Biology sugar sugar sugar sugar sugar sugar sugar sugar Sugars Most names for sugars end in -ose Classified by number of carbons 6C = hexose (glucose) 5C = pentose (ribose) 3C = triose (glyceraldehyde) CH2OH H O H OH 6H HO H AP Biology OH Glucose H CH2OH OH C O H HO H 5 OH O H HO H Ribose H H H C OH C 3OH H Glyceraldehyde Functional groups determine function carbonyl aldehyde carbonyl ketone AP Biology Numbered carbons C 6' 5' C O 4' C C1' energy stored in C-C bonds C3' AP Biology C2' Simple & complex sugars Monosaccharides simple 1 monomer sugars glucose Disaccharides 2 monomers sucrose Polysaccharides large polymers starch AP Biology QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. CH2OH H O H OH H H OH HO Glucose H OH Building sugars Dehydration synthesis monosaccharides | glucose AP Biology H2O | glucose disaccharide | maltose glycosidic linkage Building sugars Dehydration synthesis monosaccharides | glucose AP Biology H2O | fructose Let’s go to the videotape! disaccharide | sucrose (table sugar) QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Polysaccharides Polymers of sugars costs little energy to build easily reversible = release energy Function: energy storage QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. starch (plants) glycogen (animals) in liver & muscles structure cellulose (plants) chitin (arthropods & fungi) AP Biology QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Linear vs. branched polysaccharides slow release starch (plant) energy storage What does branching do? glycogen (animal) AP Biology fast release Let’s go to the videotape! Polysaccharide diversity Molecular structure determines function in starch in cellulose isomers of glucose structure determines function… AP Biology Digesting starch vs. cellulose starch easy to digest enzyme cellulose hard to digest enzyme AP Biology Cellulose Most abundant organic compound on Earth herbivores have evolved a mechanism to digest cellulose most carnivores have not that’s why they eat meat to get their energy & nutrients cellulose = undigestible roughage AP Biology But it tastes like hay! Who can live on this stuff?! Helpful bacteria How can herbivores digest cellulose so well? BACTERIA live in their digestive systems & help digest cellulose-rich (grass) meals a dna ™emiTkciuQ rosserpmoced )desserpmocnU( F FIT .erutcip siht ees ot dedeen era Caprophage Ruminants AP Biology Tell Ime about eat the rabbits, WHAT! again, George! QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Lipids: Fats & Oils AP Biology Lipids long term energy storage concentrated energy AP Biology 2006-2007 Lipids Lipids are composed of C, H, O long hydrocarbon chains (H-C) “Family groups” fats phospholipids steroids Do not form polymers big molecules made of smaller subunits not a continuing chain AP Biology Fats Structure: glycerol (3C alcohol) + fatty acid fatty acid = long HC “tail” with carboxyl (COOH) group “head” enzyme H2O dehydration synthesis AP Biology Building Fats Triacylglycerol 3 fatty acids linked to glycerol ester linkage = between OH & COOH hydroxyl AP Biology carboxyl Dehydration synthesis H2O dehydration synthesis enzyme H2O enzyme H2O AP Biology enzyme HO Fats store energy Long HC chain Why do humans like fatty foods? polar or non-polar? hydrophilic or hydrophobic? Function: energy storage concentrated all H-C! 2x carbohydrates cushion organs insulates body AP Biology think whale blubber! Saturated fats All C bonded to H No C=C double bonds long, straight chain most animal fats solid at room temp. contributes to cardiovascular disease (atherosclerosis) = plaque deposits AP Biology Unsaturated fats C=C double bonds in the fatty acids plant & fish fats vegetable oils liquid at room temperature the kinks made by double bonded C prevent the molecules from packing tightly together mono-unsaturated? poly-unsaturated? AP Biology Saturated vs. unsaturated saturated unsaturated AP Biology Phospholipids Structure: glycerol + 2 fatty acids + PO4 PO4 = negatively charged It’s just like a penguin… A head at one end & a tail at the other! AP Biology Phospholipids Hydrophobic or hydrophilic? fatty acid tails = hydrophobic PO4 head = hydrophillic “attracted to water” split “personality” Come here, No, go away! Come here, No, go away! interaction with H2O is complex & very important! AP Biology “repelled by water” Phospholipids in water Hydrophilic heads “attracted” to H2O Hydrophobic tails “hide” from H2O can self-assemble into “bubbles” bubble = “micelle” can also form a phospholipid bilayer early evolutionary stage of cell? water bilayer AP Biology water Why is this important? Phospholipids create a barrier in water define outside vs. inside they make cell membranes! Tell them about soap! AP Biology Steroids Structure: 4 fused C rings + ?? different steroids created by attaching different functional groups to rings different structure creates different function examples: cholesterol, sex hormones cholesterol AP Biology Cholesterol Important cell component animal cell membranes precursor of all other steroids including vertebrate sex hormones AP Biology high levels in blood may contribute to cardiovascular disease Proteins AP Biology Proteins Multipurpose molecules AP Biology 2008-2009 Proteins Most structurally & functionally diverse group Function: involved in almost everything AP Biology enzymes (pepsin, DNA polymerase) structure (keratin, collagen) carriers & transport (hemoglobin, aquaporin) cell communication signals (insulin & other hormones) receptors defense (antibodies) movement (actin & myosin) storage (bean seed proteins) Proteins Structure H2O monomer = amino acids 20 different amino acids polymer = polypeptide protein can be one or more polypeptide chains folded & bonded together large & complex molecules complex 3-D shape hemoglobin AP Biology Rubisco growth hormones Amino acids Structure central carbon amino group carboxyl group (acid) R group (side chain) H O H | || —C— C—OH —N— | H R variable group different for each amino acid confers unique chemical properties to each amino acid like 20 different letters of an AP Biology alphabet can make many words (proteins) Oh, I get it! amino = NH2 acid = COOH Effect of different R groups: Nonpolar amino acids nonpolar & hydrophobic Why are these nonpolar & hydrophobic? AP Biology Effect of different R groups: Polar amino acids polar or charged & hydrophilic AP Biology Why are these polar & hydrophillic? Ionizing in cellular waters AP Biology H+ donors Ionizing in cellular waters AP Biology H+ acceptors Sulfur containing amino acids Form disulfide bridges covalent cross links betweens sulfhydryls stabilizes 3-D structure H-S – S-H You wondered why perms smell like rotten eggs? AP Biology Building proteins Peptide bonds covalent bond between NH2 (amine) of one amino acid & COOH (carboxyl) of another C–N bond H2O dehydration synthesis AP Biology peptide bond Building proteins Polypeptide chains have direction N-terminus = NH2 end C-terminus = COOH end repeated sequence (N-C-C) is the polypeptide backbone can only grow in one direction AP Biology Protein structure & function Function depends on structure 3-D structure twisted, folded, coiled into unique shape pepsin hemoglobin AP Biology collagen Primary (1°) structure Order of amino acids in chain amino acid sequence determined by gene (DNA) slight change in amino acid sequence can affect protein’s structure & its function even just one amino acid change can make all the difference! AP Biology lysozyme: enzyme in tears & mucus that kills bacteria Sickle cell anemia I’m hydrophilic! AP Biology Just 1 out of 146 amino acids! But I’m hydrophobic! Secondary (2°) structure “Local folding” folding along short sections of polypeptide interactions between adjacent amino acids H bonds weak bonds between R groups forms sections of 3-D structure -helix -pleated sheet AP Biology Secondary (2°) structure AP Biology Tertiary (3°) structure “Whole molecule folding” interactions between distant amino acids hydrophobic interactions cytoplasm is water-based nonpolar amino acids cluster away from water H bonds & ionic bonds disulfide bridges covalent bonds between AP Biology sulfurs in sulfhydryls (S–H) anchors 3-D shape Quaternary (4°) structure More than one polypeptide chain bonded together only then does polypeptide become functional protein hydrophobic interactions AP Biology = skin & tendons collagen hemoglobin Protein structure (review) R groups hydrophobic interactions disulfide bridges (H & ionic bonds) 3° multiple polypeptides hydrophobic interactions 1° amino acid sequence peptide bonds determined by DNA AP Biology 4° 2° R groups H bonds Protein denaturation Unfolding a protein In Biology, size doesn’t matter, SHAPE matters! conditions that disrupt H bonds, ionic bonds, disulfide bridges temperature pH salinity alter 2° & 3° structure alter 3-D shape destroys functionality some proteins can return to their functional shape after denaturation, many cannot AP Biology Chaperonin proteins Guide protein folding AP Biology provide shelter for folding polypeptides keep the new protein segregated from cytoplasmic influences Nucleic acids AP Biology 2006-2007 Nucleic Acids Information storage AP Biology 2006-2007 Nucleic Acids Function: genetic material stores information genes blueprint for building proteins DNA DNA RNA proteins transfers information blueprint for new cells blueprint for next generation AP Biology proteins G C T A AP Biology A C G T A C G T A Nucleic Acids Examples: RNA (ribonucleic acid) single helix DNA (deoxyribonucleic acid) double helix Structure: AP Biology monomers = nucleotides DNA RNA Nucleotides 3 parts nitrogen base (C-N ring) pentose sugar (5C) ribose in RNA deoxyribose in DNA phosphate (PO4) group Are nucleic acids charged molecules? AP Biology Nitrogen base I’m the A,T,C,G or U part! Types of nucleotides 2 types of nucleotides different nitrogen bases purines double ring N base adenine (A) guanine (G) pyrimidines single ring N base cytosine (C) thymine (T) uracil (U) AP Biology Purine = AG Pure silver! Nucleic polymer Backbone sugar to PO4 bond phosphodiester bond new base added to sugar of previous base polymer grows in one direction N bases hang off the sugar-phosphate backbone Dangling bases? Why is this important? AP Biology Pairing of nucleotides Nucleotides bond between DNA strands H bonds purine :: pyrimidine A :: T 2 H bonds G :: C 3 H bonds Matching bases? Why is this important? AP Biology DNA molecule Double helix H bonds between bases join the 2 strands A :: T C :: G H bonds? Why is this important? AP Biology Copying DNA Replication 2 strands of DNA helix are complementary have one, can build other have one, can rebuild the whole Matching halves? Why is this a good system? AP Biology When does a cell copy DNA? When in the life of a cell does DNA have to be copied? cell reproduction mitosis gamete production meiosis AP Biology Interesting note… Ratio of A-T::G-C affects stability of DNA molecule 2 H bonds vs. 3 H bonds biotech procedures more G-C = need higher T° to separate strands high T° organisms many G-C parasites many A-T (don’t know why) AP Biology Another interesting note… ATP Adenosine triphosphate modified nucleotide adenine (AMP) + Pi + Pi + AP Biology + Macromolecule Review AP Biology 2006-2007 Carbohydrates Structure / monomer monosaccharide Function energy raw materials energy storage structural compounds glycosidic bond Examples AP Biology glucose, starch, cellulose, glycogen Lipids Structure / building block glycerol, fatty acid, cholesterol, H-C chains Function energy storage membranes hormones Examples AP Biology ester bond (in a fat) fat, phospholipids, steroids Proteins Structure / monomer amino acids levels of structure Function enzymes transport signals defense structure receptors peptide bond Examples AP Biology digestive enzymes, membrane channels, insulin hormone, actin Nucleic acids Structure / monomer nucleotide Function information storage & transfer Examples AP Biology DNA, RNA phosphodiester bond