Organic Molecules of Living Systems (N=4) Principles of carbon chemistry Principles of carbon chemistry Principle of polymers Principle of polymers Hydrocarbons (book; not responsible) Hydrocarbons (book; not responsible) Organic chemistry in living systems: biochemistry Organic chemistry in living systems: biochemistry Carbon metabolism and energy Carbon metabolism and energy Minerals and vitamins (book; not responsible) Minerals and vitamins (book; not responsible)

6 12 C is a unique case 6 12 C is a unique case Valence electrons for C are 4 (one in each orbit of the 2 nd shell) Valence electrons for C are 4 (one in each orbit of the 2 nd shell) C – C: single covalent bond; share orbit + shared electron C – C: single covalent bond; share orbit + shared electron C – C – C: two covalent bonds for center carbon atom C – C – C: two covalent bonds for center carbon atom Covalent Bonds and Carbon C - C C C – C – C C C

Significance: increases diversity of carbon compounds

More Principles of Carbon Chemistry: Functional Groups Features of C macromolecules Features of C macromolecules Carbon skeleton (chains, branches, rings)Carbon skeleton (chains, branches, rings) Groups of atoms attached to carbon skeleton - functional groupsGroups of atoms attached to carbon skeleton - functional groups Hydroxyl (OH) Hydroxyl (OH) Amino (NH 2 ) Amino (NH 2 ) Phosphate (PO 4 ) Phosphate (PO 4 ) C C – C – OH C phosphate (what molecule from last week/this week also had phosphate group?) C C – C – NH 2 C

Principle of Polymers Small molecules joined together to form large molecules up to 1,000’s of carbon atoms (macromolecules) 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.) 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 Fullerene – 60 + C atoms (Buckyballs) Green atoms = Carbon White atoms = Hydrogen Red atoms = Nitrogen

More Complex Carbon Polymers aspirin caffeinenicotine

Principle of Polymers Polymers of carbon: four major classes of macromolecules in all cells (N=4) Polymers of carbon: four major classes of macromolecules in all cells (N=4) CarbohydratesCarbohydrates ProteinsProteins Nucleic acidsNucleic acids LipidsLipids Diversity of carbon polymers: effectively limitless Diversity of carbon polymers: effectively limitless

Functionality of Hydrocarbons Carbon skeleton Carbon skeleton Functional groups (e.g., hydroxyl - OH, amine group – NH 2, phosphate or PO 4 ) Functional groups (e.g., hydroxyl - OH, amine group – NH 2, phosphate or PO 4 )

Organic Chemistry and Biochemistry Introduction to organic chemistry Introduction to organic chemistry Principles of carbon chemistry Principles of carbon chemistry Principle of polymers Principle of polymers Organic chemistry in living systems: biochemistry Organic chemistry in living systems: biochemistry Carbon metabolism and energy Carbon metabolism and energy

Organic Chemistry and Biochemistry: a Template Keys: Keys: Structure of basic unit (monomer)Structure of basic unit (monomer) Polymer structure (i.e., macromolecule)Polymer structure (i.e., macromolecule) Functional group (e.g., OH, PO 4 or NH 2 )Functional group (e.g., OH, PO 4 or NH 2 ) Four types of carbon polymers - macromolecules - in living systems (N=4) Four types of carbon polymers - macromolecules - in living systems (N=4) CarbohydratesCarbohydrates LipidsLipids ProteinsProteins Nucleic acidsNucleic acids

Biochemistry Cheat Sheet Carbohydrates Carbohydrates Monomer: monosaccharide (e.g., glucose or C 6 H 12 O 6 )Monomer: monosaccharide (e.g., glucose or C 6 H 12 O 6 ) Polymer: polysaccharidePolymer: polysaccharide Functional unit: hydroxyl or OH -Functional unit: hydroxyl or OH - Proteins Proteins Monomer: amino acid (peptide)Monomer: amino acid (peptide) Polymer: polypeptide and proteinPolymer: polypeptide and protein Functional unit: amine or NH 2Functional unit: amine or NH 2 Nucleic Acids Nucleic Acids Monomer: nucleotideMonomer: nucleotide Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) Functional units: organic N base, carbohydrate and phosphate (PO 4 )Functional units: organic N base, carbohydrate and phosphate (PO 4 ) Lipids Lipids Monomer: fatty acid + glycerolMonomer: fatty acid + glycerol Polymer: fats, phospholipids and steroidsPolymer: fats, phospholipids and steroids Functional unit: glycerol (3 OH- groups)Functional unit: glycerol (3 OH- groups)

Biochemistry: Carbohydrates Keys Monosaccharide (monomer); Glucose (C 6 H 12 O 6 ) Functional unit: hydroxyl or OH-

Monomer Unit: Monosaccharide

Polymer: Polysaccharide (Glycogen) Monomer

Biochemistry Cheat Sheet Carbohydrates Carbohydrates Monomer: monosaccharide (e.g., glucose or C 6 H 12 O 6 )Monomer: monosaccharide (e.g., glucose or C 6 H 12 O 6 ) Polymer: polysaccharidePolymer: polysaccharide Functional unit: hydroxyl or OH -Functional unit: hydroxyl or OH - Proteins Proteins Monomer: amino acid (peptide)Monomer: amino acid (peptide) Polymer: polypeptide and proteinPolymer: polypeptide and protein Functional unit: amine or NH 2Functional unit: amine or NH 2 Nucleic Acids Nucleic Acids Monomer: nucleotideMonomer: nucleotide Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) Functional units: organic N base, carbohydrate and phosphate (PO 4)Functional units: organic N base, carbohydrate and phosphate (PO 4) Lipids Lipids Monomer: fatty acid + glycerolMonomer: fatty acid + glycerol Polymer: fats, phospholipids and steroidsPolymer: fats, phospholipids and steroids Functional unit: glycerol (3 OH- groups)Functional unit: glycerol (3 OH- groups)

Biochemistry: Proteins Keys Amino acid (monomer) Polypeptide (polymer) Functional unit: amine or NH 2 Polypeptide bond serine – lysine – arginine – tryptophan – glutamic acid – etc. Monomer = amino acid Polymer called _____?

Amino Acids: The Building Blocks of Proteins Side group makes each amino acid unique Side group makes each amino acid unique What is distinction between a polypeptide and a protein?

Amino Acids Bonding Bonding Two amino acidsTwo amino acids Forms peptide bond Forms peptide bond Polypeptide -not functionalPolypeptide -not functional … yet (I am getting there!) … yet (I am getting there!) Chain of amino acids Chain of amino acids Protein – functional now! Protein – functional now! Large moleculeLarge molecule Chain of amino acidsChain of amino acids Only 20 different amino acids in all living organisms Only 20 different amino acids in all living organisms

Proteins: Linear Sequence of Amino Acids (Monomers) GLY LEU VAL LYS LEU ALA Type of bond?

Protein Conformation (1 and 2 nd ) The “slinky” structure

Protein Conformation (3 rd & 4 rd )

Protein Conformation

Organic Chemistry and Biochemistry Introduction to organic chemistry Introduction to organic chemistry Principles of carbon chemistry Principles of carbon chemistry Principle of polymers Principle of polymers Organic chemistry in living systems: biochemistry Organic chemistry in living systems: biochemistry Carbon metabolism and energy Carbon metabolism and energy

Biochemistry Cheat Sheet Carbohydrates Carbohydrates Monomer: monosaccharide (glucose or C 6 H 12 O 6 )Monomer: monosaccharide (glucose or C 6 H 12 O 6 ) Polymer: polysaccharidePolymer: polysaccharide Functional unit: hydroxyl or OH -Functional unit: hydroxyl or OH - Proteins Proteins Monomer: amino acid (peptide)Monomer: amino acid (peptide) Polymer: polypeptide and proteinPolymer: polypeptide and protein Functional unit: amine or NH 2Functional unit: amine or NH 2 Nucleic Acids Nucleic Acids Monomer: nucleotideMonomer: nucleotide Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) Functional units: organic N base, carbohydrate, and phosphateFunctional units: organic N base, carbohydrate, and phosphate Lipids Lipids Monomer: fatty acid + glycerol unitMonomer: fatty acid + glycerol unit Polymer: fats, phospholipids and steroidsPolymer: fats, phospholipids and steroids Functional unit: glycerol (3 OH- groups)Functional unit: glycerol (3 OH- groups)

Base case for reactions to occur Base case for reactions to occur ReactantsReactants ProductsProducts Activation energyActivation energy Energy analysis (thermodynamic) Energy analysis (thermodynamic) Energy to cause reaction to occur (“hill” or activation energy)Energy to cause reaction to occur (“hill” or activation energy) Special Proteins Called Enzymes: How They Work Enzyme mediated Without enzyme

How Enzymes Work Efficacy of enzymes Efficacy of enzymes “Hill” height/activation energy“Hill” height/activation energy Mechanism Mechanism Lower the height of the “hill”Lower the height of the “hill” Selectivity/specificitySelectivity/specificity Rate of a reaction Rate of a reaction Absence of enzyme: minutes to hours to days to yearsAbsence of enzyme: minutes to hours to days to years Presence of enzyme: 1, ,000 times per second!Presence of enzyme: 1, ,000 times per second! Increase in rate > 10 6 orders of magnitude (1,000,000)Increase in rate > 10 6 orders of magnitude (1,000,000)

Biochemistry Cheat Sheet Carbohydrates Carbohydrates Monomer: monosaccharide (glucose or C 6 H 12 O 6 )Monomer: monosaccharide (glucose or C 6 H 12 O 6 ) Polymer: polysaccharidePolymer: polysaccharide Functional unit: hydroxyl or OH -Functional unit: hydroxyl or OH - Proteins Proteins Monomer: amino acid (peptide)Monomer: amino acid (peptide) Polymer: polypeptide and proteinPolymer: polypeptide and protein Functional unit: amine or NH 2Functional unit: amine or NH 2 Nucleic Acids Nucleic Acids Monomer: nucleotideMonomer: nucleotide Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) Functional units: organic N base, carbohydrate, and phosphateFunctional units: organic N base, carbohydrate, and phosphate Lipids Lipids Monomer: fatty acid + glycerol unitMonomer: fatty acid + glycerol unit Polymer: fats, phospholipids and steroidsPolymer: fats, phospholipids and steroids Functional unit: glycerol (3 OH- groups)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

Nitrogen Base

Biochemistry Cheat Sheet Carbohydrates Carbohydrates Monomer: monosaccharide (glucose or C 6 H 12 O 6 )Monomer: monosaccharide (glucose or C 6 H 12 O 6 ) Polymer: polysaccharidePolymer: polysaccharide Functional unit: hydroxyl or OH -Functional unit: hydroxyl or OH - Proteins Proteins Monomer: amino acid (peptide)Monomer: amino acid (peptide) Polymer: polypeptide and proteinPolymer: polypeptide and protein Functional unit: amine or NH 2Functional unit: amine or NH 2 Nucleic Acids Nucleic Acids Monomer: nucleotideMonomer: nucleotide Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) Functional units: organic N base, carbohydrate, and phosphateFunctional units: organic N base, carbohydrate, and phosphate Lipids Lipids Monomer: fatty acid + glycerol unitMonomer: fatty acid + glycerol unit Polymer: fats, phospholipids and steroidsPolymer: fats, phospholipids and steroids Functional unit: glycerol (3 OH- groups)Functional unit: glycerol (3 OH- groups)

Biochemistry: Lipids Keys Monomer: Fatty acids - C Functional unit: glycerol (3 OH - groups)

Special Case: Cell Membranes Cell membrane Cell membrane Hydrophobic (phosphate)Hydrophobic (phosphate) Hydrophilic (lipid)Hydrophilic (lipid) Lipid bilayer = cell membrane Lipid bilayer = cell membrane

Organic Chemistry and Biochemistry Introduction to organic chemistry Introduction to organic chemistry Principles of carbon chemistry Principles of carbon chemistry Principle of polymers Principle of polymers Organic chemistry in living systems: biochemistry Organic chemistry in living systems: biochemistry Carbon metabolism and energy Carbon metabolism and energy

Carbon Metabolism Biosynthesis (photosynthesis) CO 2 + H 2 O + Energy CH 2 O + O 2 CO 2 + H 2 O + Energy CH 2 O + O 2 (light) (C - C Bonds/excited electron) (light) (C - C Bonds/excited electron)Catabolism CH 2 O + O 2 CO 2 + H 2 O + Energy CH 2 O + O 2 CO 2 + H 2 O + 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!)