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Carbon-based compounds

Carbon-based compounds. Chapter 4~ Carbon & The Molecular Diversity of Life. Organic chemistry…. The Chemistry of Carbon. Forms a tetrahedral shape when bound to 4 molecules. Tetravalence - 4 e- in outer shell. Hydrocarbons. Only carbon & hydrogen (petroleum; lipid ‘tails’)

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Carbon-based compounds

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  1. Carbon-based compounds • Chapter 4~ Carbon & The Molecular Diversity of Life

  2. Organic chemistry… The Chemistry of Carbon • Forms a tetrahedral shape when bound to 4 molecules Tetravalence- 4 e- in outer shell

  3. Hydrocarbons • Only carbon & hydrogen(petroleum; lipid ‘tails’) • Covalent bonding; nonpolar • High energy storage • Isomers(same molecular formula, but different structure & properties) • structural~differing covalent bonding arrangement • geometric~differing spatial arrangement • enantiomers~mirrorimages • pharmacological industry (thalidomide)

  4. Prefixes • Organic compounds are named with prefixes • Plain hydrocarbons end with –ane • Double bonds= ene • Side groups change names (ex: -OH = -ol)

  5. Attachments that replace one or more of the hydrogens bonded to the carbon skeleton of the hydrocarbon Each has a unique property from one organic compound to another Hydroxyl Group H bonded to O alcohols polar (oxygen) solubility in water Carbonyl Group C double bond to O At end of H-C: aldehyde Otherwise: ketone Functional Groups

  6. Carboxyl Group O double bonded to C to hydroxyl carboxylic acids (dissociation= H+) covalent bond between O and H Polar Amino Group N to 2 H atoms “amines” acts as a base SulfhydralGroup sulfur bonded to H Thiols Can cross-link with each other

  7. Methyl Group • C bonded to 3 H’s • Affects shape/configuration • Phosphate Group • phosphate ion covalently attached by 1 O to the C skeleton • Negatively charged

  8. ATP= NRG • ATP is the main energy source for cells. • One phosphate group is cleaved off to form ADP and energy is released

  9. Macromolecules Chapter 5~ The Structure & Function of Macromolecules

  10. Polymers • Covalently bonded monomers • Condensation (dehydration) reaction • One provides a –OH while the other provides a H to form a water molecule • Hydrolysis • bonds between monomers are broken by adding water (ex:digestion)

  11. Carbohydrates • Monomer = Monosaccharides • CH2O formula • multiple hydroxyl (-OH) groups and 1 carbonyl (C=O) group: • aldehyde (aldose) sugar- group at end • ketone(ketose) sugar- group in center • broken down during cellular respiration • raw material for amino acids and fatty acids

  12. Putting them together • Disaccharides • glycosidiclinkage (covalent bond between 2 monosaccharides) • Sucrose (table sugar) • most common disaccharide

  13. Storage: Starch=glucose monomers Plants: roots/plastids Animals: glycogen/fat Structure: Cellulose~ most abundant organic compound Chitin~ exoskeletons; cell walls of fungi; surgical thread Functions of Carbohydrates

  14. Lipids • Monomers: Triacyglycerol (triglyceride) • Carboxyl group = fatty acid • Ester linkage: 3 fatty acids to 1 glycerol molecule • Fats, phospholipids, steroids • Hydrophobic • Non-polar C-H bonds in fatty acid ‘tails’ • Saturated vs. unsaturated fats; single vs. double bonds

  15. Saturated vs. Unsaturated

  16. Phospholipids • Two fatty acids instead of three • phosphate group attaches to one -OH • ‘Tails’ = hydrophobic • ‘Heads’ = hydrophilic

  17. Phospholipids in formation • Micelle (phospholipid droplet in water) • Bilayer(double layer) • cell membranes

  18. Steroids • Lipids with 4 fused carbon rings • Ex: cholesterol... • cell membranes • precursor for other steroids (sex hormones) • “Good” (HDL) vs “Bad” (LDL) cholesterol • atherosclerosis

  19. Proteins • Importance: • instrumental in nearly everything organisms do • 50% dry weight of cells • most structurally sophisticated molecules known • Monomer = amino acids (20) • central carbon atom • carboxyl (-COOH) group • amino group (NH2) • H atom • variable group (R)

  20. Amino Acid R- Groups Variable (R-) group characteristics: • R- group interactions determine shape and function • Nonpolar (hydrophobic) • Gly, Ala, Val, Leu, Ile, Met, Phe, Trp, Pro • Polar (hydrophilic) • Ser, Thr, Cys, Tyr, Asn, Gln • Acids • Asp, Glu • Bases • Lys, Arg, His

  21. Putting them together • Polypeptides formed by a dehydration reaction. • peptide bonds~ covalent bond of carboxyl group to amino group

  22. 3-D Structure • Proteins function is determined by their structural conformation • Amino acid sequence determines how it will fold • Affinity of A.A’s for each other, etc. • Chaperonins- proteins that assist in folding of other proteins • Segregate and protect proteins and allow them to fold w/o any “bad influences” • Four levels of protein structure

  23. Primary Structure • Linear structure of Amino Acids • Molecular Biology: • each protein has a unique primary structure of amino acids • Examples: • One amino acid substitution in hemoglobin causes sickle-cell anemia

  24. Secondary Structure Coils & folds caused by hydrogen bonds • Alpha Helix: • Coiling~ every 4th AA • fibrous proteins, keratin • Pleated Sheet: • Parallel sheets w/ H bonding between them • globular proteins, spider silk

  25. Tertiary Structure • Protein takes on irregular contortions from R group bonding • Hydrogen bonds between polar side groups • Hydrophobic molecules undergo van der Waals interactions • Disulfide bridges form between cystine –SH groups • Ionic bonds between + and -

  26. Quaternary Structure • 2 or more polypeptide chains aggregated into 1 macromolecule • Collagen (connective tissue that makes up 40% of body structure) • Hemoglobin (Oxygen binding protein in red blood cells) * 3-D structure of proteins discovered w/ X-ray crystallography and nuclear magnetic resonance (NMR)

  27. Denaturation • If protein shape is changed, it cannot function properly • Heat, pH change, chemical treatment, etc. • Sometimes proteins can be “renatured” if environment is restored to normal (rare)

  28. Nucleic Acids • 2 types: • Deoxyribonucleic acid (DNA) • Ribonucleic acid (RNA) • Storage and transmittance of genetic information • DNA RNA  protein

  29. Monomers= nucleotides • Each nucleotide is composed of: • nitrogenous base • pentose sugar • phosphate group

  30. “Polynucleotides” • Joined by phosphodiester linkages • covalent bonds between phosphate groups

  31. Nitrogenous bases • Purines always pair w/ Pyrimidines • DNA- • A & T • G & C • RNA- • - A & U • - G & C

  32. DNA • In nucleus • Codes for proteins (like blueprints) • Double helix • 2 strands held together by H-bonds between bases • Complimentary base pairing • Sugar = deoxyribose • Bases- A, G, C, T

  33. Watson and Crick • James Watson and Francis Crick discovered the double helix structure of DNA in 1953.

  34. RNA • Single stranded • Several types: • Ex: mRNA, rRNA, tRNA • Acts as messenger between DNA in nucleus and ribosomes in cytoplasm • Sugar= ribose • Bases- A, G, C, U

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