Organic Molecules of Organic Molecules of Living Systems (N=4) 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: Organic chemistry in living systems: biochemistry biochemistry Carbon metabolism and energy Carbon metabolism and energy Minerals and vitamins (book; not Minerals and vitamins (book; not responsible) responsible)
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Organic Molecules of Living Systems (N=4) Principles of carbon chemistry Principles of carbon chemistry Principle of polymers Principle of polymers Hydrocarbons.
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Organic Molecules of Living Organic Molecules of Living Systems (N=4)Systems (N=4)
Principles of carbon chemistryPrinciples of carbon chemistry Principle of polymersPrinciple of polymers Hydrocarbons (book; not responsible)Hydrocarbons (book; not responsible) Organic chemistry in living systems: Organic chemistry in living systems:
biochemistrybiochemistry Carbon metabolism and energyCarbon metabolism and energy Minerals and vitamins (book; not Minerals and vitamins (book; not
responsible)responsible)
661212C is a unique caseC is a unique case
ValenceValence electrons for C are 4 (one in each electrons for C are 4 (one in each orbit of the 2orbit of the 2ndnd shell) shell)
C – C: single C – C: single covalentcovalent bond; share orbit + bond; share orbit + shared electronshared electron
C – C – CC – C: two covalent bonds for center – C: two covalent bonds for center carbon atomcarbon atom
Covalent Bonds and Carbon
C - C
C
C – C – C
CC
Significance: increases
diversity of carbon
compounds
More Principles of Carbon More Principles of Carbon Chemistry: Functional GroupsChemistry: Functional Groups
Features of C Features of C macromoleculesmacromolecules• Carbon Carbon skeletonskeleton (chains, branches, rings) (chains, branches, rings)• Groups of atoms attached to carbon Groups of atoms attached to carbon
phosphate (what molecule from last week/this week also had
phosphate group?)
C
C – C – NH2
C
Principle of PolymersPrinciple of Polymers
Small molecules joined together to Small molecules joined together to form large molecules up to 1,000’s of form large molecules up to 1,000’s of carbon atoms (carbon atoms (macromolecules)macromolecules)
Array of combinations, each with its Array of combinations, each with its own own uniqueunique chemistry (e.g., polarity, chemistry (e.g., polarity, solution chemistry, three dimensional solution chemistry, three dimensional structure, reactivity, passage structure, reactivity, passage through membranes, etc.)through membranes, etc.)
Simple to Complex Polymers of CarbonSimple 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 PolymersMore Complex Carbon Polymers
aspirin
caffeinenicotine
Principle of PolymersPrinciple of Polymers Polymers of carbon: four major classes Polymers of carbon: four major classes
of macromolecules in all cells (N=4)of macromolecules in all cells (N=4)• CarbohydratesCarbohydrates• ProteinsProteins• Nucleic acidsNucleic acids• LipidsLipids
Diversity of carbon polymers: Diversity of carbon polymers: effectively limitless effectively limitless
Functionality of HydrocarbonsFunctionality of Hydrocarbons
Carbon skeletonCarbon skeleton
Functional groups (e.g., hydroxyl - OH, Functional groups (e.g., hydroxyl - OH, amine group – NHamine group – NH22, phosphate or PO, phosphate or PO44))
Organic Chemistry and Organic Chemistry and BiochemistryBiochemistry
Introduction to organic chemistryIntroduction to organic chemistry Principles of carbon chemistryPrinciples of carbon chemistry Principle of polymersPrinciple of polymers Organic chemistry in living systems: Organic chemistry in living systems:
biochemistrybiochemistry Carbon metabolism and energyCarbon metabolism and energy
Organic Chemistry and Organic Chemistry and Biochemistry: a TemplateBiochemistry: a Template
Keys:Keys:• Structure of basic unit (Structure of basic unit (monomermonomer))• Polymer structure (i.e., Polymer structure (i.e., macromoleculemacromolecule))
• Functional groupFunctional group (e.g., OH, PO (e.g., OH, PO44 or NH or NH22))
Four types of carbon polymers -Four types of carbon polymers -macromolecules - in living systems (N=4)macromolecules - in living systems (N=4)• CarbohydratesCarbohydrates• LipidsLipids• ProteinsProteins• Nucleic acidsNucleic acids
• Monomer: monosaccharide (e.g., glucose or CMonomer: monosaccharide (e.g., glucose or C66HH1212OO66))• Polymer: Polymer: polypolysaccharidesaccharide• Functional unit: hydroxyl or OHFunctional unit: hydroxyl or OH--
ProteinsProteins• Monomer: amino acid (peptide)Monomer: amino acid (peptide)• Polymer: Polymer: polypolypeptide and proteinpeptide and protein• Functional unit: amine or NHFunctional unit: amine or NH22
Nucleic AcidsNucleic Acids• Monomer: nucleotide Monomer: nucleotide • Polymer: Polymer: polypolynucleotide - DNA (deoxyribonucleic acid) and RNA nucleotide - DNA (deoxyribonucleic acid) and RNA
(ribonucleic acid)(ribonucleic acid)• Functional units: organic N base, carbohydrate and phosphate Functional units: organic N base, carbohydrate and phosphate
• Monomer: monosaccharide (e.g., glucose or CMonomer: monosaccharide (e.g., glucose or C66HH1212OO66))• Polymer: Polymer: polypolysaccharidesaccharide• Functional unit: hydroxyl or OHFunctional unit: hydroxyl or OH--
ProteinsProteins• Monomer: amino acid (peptide)Monomer: amino acid (peptide)• Polymer: Polymer: polypolypeptide and proteinpeptide and protein• Functional unit: amine or NHFunctional unit: amine or NH22
Nucleic AcidsNucleic Acids• Monomer: nucleotide Monomer: nucleotide • Polymer: Polymer: polypolynucleotide - DNA (deoxyribonucleic acid) and RNA nucleotide - DNA (deoxyribonucleic acid) and RNA
(ribonucleic acid)(ribonucleic acid)• Functional units: organic N base, carbohydrate and phosphate Functional units: organic N base, carbohydrate and phosphate
Amino Acids: Amino Acids: The Building Blocks of ProteinsThe Building Blocks of Proteins
Side group makes each amino acid Side group makes each amino acid uniqueunique
What is distinction between a polypeptide and a protein?
Amino AcidsAmino Acids BondingBonding
• Two amino acidsTwo amino acids Forms peptide bondForms peptide bond
• Polypeptide -not functional Polypeptide -not functional … … yet (I am getting there!)yet (I am getting there!)
Chain of amino acidsChain of amino acids
Protein – functional now!Protein – functional now!• Large moleculeLarge molecule• Chain of amino acidsChain of amino acids
Only Only 2020 different amino different amino acids in all living acids in all living organismsorganisms
Proteins: Linear Sequence of Proteins: Linear Sequence of Amino Acids (Monomers)Amino Acids (Monomers)
GLY
LEU
VAL
LYS
LEU
ALA
Type of bond?
Protein Protein ConformationConformation (1 and 2(1 and 2ndnd))
The “slinky” structure
Protein Conformation (3Protein Conformation (3rdrd & 4 & 4rdrd))
Protein ConformationProtein Conformation
Organic Chemistry and Organic Chemistry and BiochemistryBiochemistry
Introduction to organic chemistryIntroduction to organic chemistry Principles of carbon chemistryPrinciples of carbon chemistry Principle of polymersPrinciple of polymers Organic chemistry in living systems: Organic chemistry in living systems:
biochemistrybiochemistry Carbon metabolism and energyCarbon metabolism and energy
• Monomer: monosaccharide (glucose or CMonomer: monosaccharide (glucose or C66HH1212OO66))• Polymer: polysaccharidePolymer: polysaccharide• Functional unit: hydroxyl or OHFunctional unit: hydroxyl or OH--
ProteinsProteins• Monomer: amino acid (peptide)Monomer: amino acid (peptide)• Polymer: Polymer: polypolypeptide and proteinpeptide and protein• Functional unit: amine or NHFunctional unit: amine or NH22
Nucleic AcidsNucleic Acids• Monomer: nucleotide Monomer: nucleotide • Polymer: Polymer: polypolynucleotide - DNA (deoxyribonucleic acid) and RNA nucleotide - DNA (deoxyribonucleic acid) and RNA
(ribonucleic acid)(ribonucleic acid)• Functional units: organic N base, carbohydrate, and phosphateFunctional units: organic N base, carbohydrate, and phosphate
• Monomer: monosaccharide (glucose or CMonomer: monosaccharide (glucose or C66HH1212OO66))• Polymer: polysaccharidePolymer: polysaccharide• Functional unit: hydroxyl or OHFunctional unit: hydroxyl or OH--
ProteinsProteins• Monomer: amino acid (peptide)Monomer: amino acid (peptide)• Polymer: Polymer: polypolypeptide and proteinpeptide and protein• Functional unit: amine or NHFunctional unit: amine or NH22
Nucleic AcidsNucleic Acids• Monomer: nucleotide Monomer: nucleotide • Polymer: Polymer: polypolynucleotide - DNA (deoxyribonucleic acid) and RNA nucleotide - DNA (deoxyribonucleic acid) and RNA
(ribonucleic acid)(ribonucleic acid)• Functional units: organic N base, carbohydrate, and phosphateFunctional units: organic N base, carbohydrate, and phosphate
• Monomer: monosaccharide (glucose or CMonomer: monosaccharide (glucose or C66HH1212OO66))• Polymer: polysaccharidePolymer: polysaccharide• Functional unit: hydroxyl or OHFunctional unit: hydroxyl or OH--
ProteinsProteins• Monomer: amino acid (peptide)Monomer: amino acid (peptide)• Polymer: Polymer: polypolypeptide and proteinpeptide and protein• Functional unit: amine or NHFunctional unit: amine or NH22
Nucleic AcidsNucleic Acids• Monomer: nucleotide Monomer: nucleotide • Polymer: Polymer: polypolynucleotide - DNA (deoxyribonucleic acid) and RNA nucleotide - DNA (deoxyribonucleic acid) and RNA
(ribonucleic acid)(ribonucleic acid)• Functional units: organic N base, carbohydrate, and phosphateFunctional units: organic N base, carbohydrate, and phosphate
Organic Chemistry and Organic Chemistry and BiochemistryBiochemistry
Introduction to organic chemistryIntroduction to organic chemistry Principles of carbon chemistryPrinciples of carbon chemistry Principle of polymersPrinciple of polymers Organic chemistry in living systems: Organic chemistry in living systems:
biochemistrybiochemistry Carbon metabolism and energyCarbon metabolism and energy
COCO22 + H + H22O + Energy CHO + Energy CH22O + OO + O22
(light)(light) ( (C - C Bonds/excited electronC - C Bonds/excited electron))
CatabolismCatabolism
CHCH22O + OO + O2 2 COCO22 + H + H22O + EnergyO + Energy((C - C Bonds/excited electronC - C Bonds/excited electron)) (heat + chemical (heat + chemical
energy)energy)
Key: C-C covalent bonding, which in turn is determined by Key: C-C covalent bonding, which in turn is determined by electrons in the valence state, which in turn is underpinned by electrons in the valence state, which in turn is underpinned by energy of electrons in their respective shells (remember the energy of electrons in their respective shells (remember the granola bar!)granola bar!)