organic molecules of living systems (n=4) principles of carbon chemistry principles of carbon...

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


• 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--



(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


• Monomer: monosaccharide (glucose or CMonomer: monosaccharide (glucose or C66HH1212OO66))• Polymer: polysaccharidePolymer: polysaccharide• Functional unit: hydroxyl or OHFunctional unit: hydroxyl or OH--



(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: 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: 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

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!)

organic molecules of living systems (n=4) principles of carbon chemistry principles of carbon...

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c atomethane

c atomsfullerene

shellc c

c atoms buckyballsgreen

ohmonomer unit

hydroxyl oh

proteinfunctional unit

polysaccharidefunctional