organic molecules of living systems (n=4) principles of carbon chemistry principles of carbon...
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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
skeleton - skeleton - functionalfunctional groupsgroups Hydroxyl (OH)Hydroxyl (OH) Amino (NHAmino (NH22)) Phosphate (POPhosphate (PO44))
C
C – C – OH
C
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
Biochemistry Cheat SheetBiochemistry Cheat Sheet CarbohydratesCarbohydrates
• 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
(PO(PO44))
LipidsLipids• 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: CarbohydratesBiochemistry: CarbohydratesKeysKeys
Monosaccharide (Monosaccharide (monomermonomer); Glucose ); Glucose (C(C66HH1212OO66))
Functional unit: hydroxyl or OH-Functional unit: hydroxyl or OH-
Monomer Unit: Monosaccharide
Polymer: Polysaccharide Polymer: Polysaccharide (Glycogen)(Glycogen)
Monomer
Biochemistry Cheat SheetBiochemistry Cheat Sheet CarbohydratesCarbohydrates
• 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
(PO(PO4)4)
LipidsLipids• 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: ProteinsBiochemistry: Proteins
KeysKeys
Amino acid (Amino acid (monomermonomer))
Polypeptide (Polypeptide (polymerpolymer))
Functional unit: Functional unit: amine amine or NHor NH22
Polypeptide bondPolypeptide bond
serine – lysine – arginine – tryptophan – glutamic acid – etc.
Monomer = amino acid
Polymer called _____?
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
Biochemistry Cheat SheetBiochemistry Cheat Sheet CarbohydratesCarbohydrates
• 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
LipidsLipids• 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 Base case for reactions to occurreactions to occur• Reactants Reactants • ProductsProducts• Activation energyActivation energy
Energy analysis Energy analysis (thermodynamic)(thermodynamic)• Energy to cause Energy to cause
reaction to occur reaction to occur (“hill” or activation (“hill” or activation energy)energy)
Special Proteins Called Special Proteins Called EnzymesEnzymes: : How They WorkHow They Work
Enzyme mediated
Without enzyme
How Enzymes WorkHow Enzymes Work
Efficacy of enzymesEfficacy of enzymes• ““Hill” height/activation energyHill” height/activation energy
MechanismMechanism• Lower the height of the “hill”Lower the height of the “hill”• Selectivity/specificitySelectivity/specificity
Rate of a reactionRate of a reaction• Absence of enzyme: minutes Absence of enzyme: minutes
to hours to days to yearsto hours to days to years• Presence of enzyme: 1,000 - Presence of enzyme: 1,000 -
10,000 times 10,000 times per second!per second!• Increase in rate > Increase in rate > 101066 orders orders
of magnitude (1,000,000)of magnitude (1,000,000)
Biochemistry Cheat SheetBiochemistry Cheat Sheet CarbohydratesCarbohydrates
• 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
LipidsLipids• 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 AcidsBiochemistry: Nucleic Acids
KeysKeysMonomer: Nucleotides Monomer: Nucleotides
Functional units (N=3): organic N base, sugar, andFunctional units (N=3): organic N base, sugar, andphosphatephosphate
Nucleic Acids as Polymers:Nucleic Acids as Polymers:DNA Double HelixDNA Double Helix
BASES
A
T
C
G
Nitrogen Base
Biochemistry Cheat SheetBiochemistry Cheat Sheet CarbohydratesCarbohydrates
• 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
LipidsLipids• 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: LipidsBiochemistry: Lipids
KeysKeysMonomer: Fatty acids - Monomer: Fatty acids -
CC16-1816-18
Functional unit: glycerol Functional unit: glycerol (3 OH(3 OH-- groups) groups)
Special Case: Cell MembranesSpecial Case: Cell Membranes
Cell membraneCell membrane• Hydrophobic Hydrophobic
(phosphate)(phosphate)• Hydrophilic Hydrophilic
(lipid)(lipid)
Lipid bilayer = Lipid bilayer = cell membranecell membrane
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
Carbon MetabolismCarbon Metabolism
Biosynthesis (photosynthesis)Biosynthesis (photosynthesis)
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!)
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