Organic Molecules of Living Systems (N=4)

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

Significance: increases diversity of carbon compounds

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-

Monomer Unit: Monosaccharide

Polymer: Polysaccharide (Glycogen) Monomer

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

Protein Conformation (3rd & 4rd)

Protein Conformation

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: 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

Nitrogen Base

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

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!)

Organic Molecules of Living Systems (N=4)