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Organic Molecules of Living Systems (N=4). Principles of carbon chemistry Principle of polymers Hydrocarbons (book; not responsible) Organic chemistry in living systems: biochemistry Carbon metabolism and energy Minerals and vitamins (book; not responsible). Covalent Bonds and Carbon.
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Organic Molecules of Living Systems (N=4) • Principles of carbon chemistry • Principle of polymers • Hydrocarbons (book; not responsible) • Organic chemistry in living systems: biochemistry • Carbon metabolism and energy • Minerals and vitamins (book; not responsible)
Covalent Bonds and Carbon C C – C – C C C C - C 612C is a unique case Valence electrons for C are 4 (one in each orbit of the 2nd shell) C – C: single covalent bond; share orbit + shared electron C – C – C: two covalent bonds for center carbon atom
More Principles of Carbon Chemistry: Functional Groups • Features of C macromolecules • Carbon skeleton (chains, branches, rings) • Groups of atoms attached to carbon skeleton - functionalgroups • Hydroxyl (OH) • Amino (NH2) • Phosphate (PO4) C C – C – OH C C C – C – NH2 C phosphate (what molecule from last week/this week also had phosphate group?)
Principle of Polymers • Small molecules joined together to form large molecules up to 1,000’s of carbon atoms (macromolecules) • Array of combinations, each with its own unique chemistry (e.g., polarity, solution chemistry, three dimensional structure, reactivity, passage through membranes, etc.)
Simple to Complex Polymers of Carbon Methane - 1 C atom Ethane – 2 C atoms Green atoms = Carbon White atoms = Hydrogen Red atoms = Nitrogen Fullerene – 60+ C atoms (Buckyballs)
More Complex Carbon Polymers nicotine caffeine aspirin
Principle of Polymers • Polymers of carbon: four major classes of macromolecules in all cells (N=4) • Carbohydrates • Proteins • Nucleic acids • Lipids • Diversity of carbon polymers: effectively limitless
Functionality of Hydrocarbons • Carbon skeleton • Functional groups (e.g., hydroxyl - OH, amine group – NH2, phosphate or PO4)
Organic Chemistry and Biochemistry • Introduction to organic chemistry • Principles of carbon chemistry • Principle of polymers • Organic chemistry in living systems: biochemistry • Carbon metabolism and energy
Organic Chemistry and Biochemistry: a Template • Keys: • Structure of basic unit (monomer) • Polymer structure (i.e., macromolecule) • Functional group (e.g., OH, PO4 or NH2) • Four types of carbon polymers -macromolecules - in living systems (N=4) • Carbohydrates • Lipids • Proteins • Nucleic acids
Biochemistry Cheat Sheet • Carbohydrates • Monomer: monosaccharide (e.g., glucose or C6H12O6) • Polymer: polysaccharide • Functional unit: hydroxyl or OH- • Proteins • Monomer: amino acid (peptide) • Polymer: polypeptide and protein • Functional unit: amine or NH2 • Nucleic Acids • Monomer: nucleotide • Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) • Functional units: organic N base, carbohydrate and phosphate (PO4) • Lipids • Monomer: fatty acid + glycerol • Polymer: fats, phospholipids and steroids • Functional unit: glycerol (3 OH- groups)
Biochemistry: Carbohydrates • Keys • Monosaccharide (monomer); Glucose (C6H12O6) • Functional unit: hydroxyl or OH-
Biochemistry Cheat Sheet • Carbohydrates • Monomer: monosaccharide (e.g., glucose or C6H12O6) • Polymer: polysaccharide • Functional unit: hydroxyl or OH- • Proteins • Monomer: amino acid (peptide) • Polymer: polypeptide and protein • Functional unit: amine or NH2 • Nucleic Acids • Monomer: nucleotide • Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) • Functional units: organic N base, carbohydrate and phosphate (PO4) • Lipids • Monomer: fatty acid + glycerol • Polymer: fats, phospholipids and steroids • Functional unit: glycerol (3 OH- groups)
Biochemistry: Proteins Monomer = amino acid Keys Amino acid (monomer) Polypeptide (polymer) Functional unit: amine or NH2 Polypeptide bond serine – lysine – arginine – tryptophan – glutamic acid – etc. Polymer called _____?
Amino Acids: The Building Blocks of Proteins • Side group makes each amino acid unique What is distinction between a polypeptide and a protein?
Amino Acids • Bonding • Two amino acids • Forms peptide bond • Polypeptide -not functional … yet (I am getting there!) • Chain of amino acids • Protein – functional now! • Large molecule • Chain of amino acids • Only 20 different amino acids in all living organisms
Proteins: Linear Sequence of Amino Acids (Monomers) GLY Type of bond? LEU VAL LYS LEU ALA
Protein Conformation(1 and 2nd) The “slinky” structure
Organic Chemistry and Biochemistry • Introduction to organic chemistry • Principles of carbon chemistry • Principle of polymers • Organic chemistry in living systems: biochemistry • Carbon metabolism and energy
Biochemistry Cheat Sheet • Carbohydrates • Monomer: monosaccharide (glucose or C6H12O6) • Polymer: polysaccharide • Functional unit: hydroxyl or OH- • Proteins • Monomer: amino acid (peptide) • Polymer: polypeptide and protein • Functional unit: amine or NH2 • Nucleic Acids • Monomer: nucleotide • Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) • Functional units: organic N base, carbohydrate, and phosphate • Lipids • Monomer: fatty acid + glycerol unit • Polymer: fats, phospholipids and steroids • Functional unit: glycerol (3 OH- groups)
Special Proteins Called Enzymes: How They Work • Base case for reactions to occur • Reactants • Products • Activation energy • Energy analysis (thermodynamic) • Energy to cause reaction to occur (“hill” or activation energy) Without enzyme Enzyme mediated
How Enzymes Work • Efficacy of enzymes • “Hill” height/activation energy • Mechanism • Lower the height of the “hill” • Selectivity/specificity • Rate of a reaction • Absence of enzyme: minutes to hours to days to years • Presence of enzyme: 1,000 - 10,000 times per second! • Increase in rate > 106 orders of magnitude (1,000,000)
Biochemistry Cheat Sheet • Carbohydrates • Monomer: monosaccharide (glucose or C6H12O6) • Polymer: polysaccharide • Functional unit: hydroxyl or OH- • Proteins • Monomer: amino acid (peptide) • Polymer: polypeptide and protein • Functional unit: amine or NH2 • Nucleic Acids • Monomer: nucleotide • Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) • Functional units: organic N base, carbohydrate, and phosphate • Lipids • Monomer: fatty acid + glycerol unit • Polymer: fats, phospholipids and steroids • Functional unit: glycerol (3 OH- groups)
Biochemistry: Nucleic Acids Keys Monomer: Nucleotides Functional units (N=3): organic N base, sugar, and phosphate
Nucleic Acids as Polymers:DNA Double Helix BASES A T C G
Biochemistry Cheat Sheet • Carbohydrates • Monomer: monosaccharide (glucose or C6H12O6) • Polymer: polysaccharide • Functional unit: hydroxyl or OH- • Proteins • Monomer: amino acid (peptide) • Polymer: polypeptide and protein • Functional unit: amine or NH2 • Nucleic Acids • Monomer: nucleotide • Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) • Functional units: organic N base, carbohydrate, and phosphate • Lipids • Monomer: fatty acid + glycerol unit • Polymer: fats, phospholipids and steroids • Functional unit: glycerol (3 OH- groups)
Biochemistry: Lipids Keys Monomer: Fatty acids - C16-18 Functional unit: glycerol (3 OH- groups)
Special Case: Cell Membranes • Cell membrane • Hydrophobic (phosphate) • Hydrophilic (lipid) • Lipid bilayer = cell membrane
Organic Chemistry and Biochemistry • Introduction to organic chemistry • Principles of carbon chemistry • Principle of polymers • Organic chemistry in living systems: biochemistry • Carbon metabolism and energy
Carbon Metabolism Biosynthesis (photosynthesis) CO2 + H2O + Energy CH2O + O2 (light) (C - C Bonds/excited electron) Catabolism CH2O + O2 CO2 + H2O + Energy (C - C Bonds/excited electron) (heat + chemical energy) Key: C-C covalent bonding, which in turn is determined by electrons in the valence state, which in turn is underpinned by energy of electrons in their respective shells (remember the granola bar!)