CH. 4 & 5

• Chapter 4~Carbon & The Molecular Diversity of

Life

• Chapter 5~The Structure

& Function of Large Molecules

Why study Carbon?

• All of life is built on carbon • Cells

– ~72% H2O

– ~25% carbon compounds• carbohydrates• lipids• proteins • nucleic acids

– ~3% salts • Na, Cl, K…

Chemistry of Life• Organic chemistry is the study of carbon

compounds• C atoms are versatile building blocks

– bonding properties– 4 stable covalent bonds

HHC

H

H

Complex molecules assembled like TinkerToys

Hydrocarbons• Combinations of C & H

– non-polar •not soluble in H2O

•hydrophobic

– stable– very little attraction

between molecules•a gas at room temperature

methane(simplest HC)

Hydrocarbons can grow

Isomers• Molecules with same molecular formula but

different structures (shapes) – different chemical properties– different biological functions

6 carbons

6 carbons

6 carbons

Form affects function• Structural differences create important

functional significance– amino acid alanine

• L-alanine used in proteins• but not D-alanine

– medicines• L-version active• but not D-version

– sometimes withtragic results…

stereoisomersstereoisomers

Form affects function

• Thalidomide – prescribed to pregnant women in 50s & 60s – reduced morning sickness, but…– stereoisomer caused severe birth defects

Diversity of molecules• Substitute other atoms or groups around the

carbon– ethane vs. ethanol

•H replaced by an hydroxyl group (–OH)

•nonpolar vs. polar

•gas vs. liquid

•biological effects!

ethane (C2H6) ethanol (C2H5OH)

Functional groups• Parts of organic molecules that are

involved in chemical reactions– give organic molecules distinctive properties

hydroxyl amino carbonyl sulfhydryl carboxyl phosphate

• Affect reactivity– makes hydrocarbons hydrophilic – increase solubility in water

Viva la difference!• Basic structure of male & female

hormones is identical– identical carbon skeleton – attachment of different functional groups– interact with different targets in the body

• different effects

Hydroxyl

• –OH– organic compounds with OH =

alcohols – names typically end in -ol

• ethanol

Carbonyl• C=O

– O double bonded to C

•if C=O at end molecule = aldehyde

•if C=O in middle of molecule = ketone

Carboxyl • –COOH

– C double bonded to O & single bonded to OH group

•compounds with COOH = acids– fatty acids–amino acids

Amino• -NH2

– N attached to 2 H

•compounds with NH2 = amines– amino acids

•NH2 acts as base

– ammonia picks up H+ from solution

Sulfhydryl • –SH

– S bonded to H

•compounds with SH = thiols•SH groups stabilize the structure of

proteins

Phosphate • –PO4

– P bound to 4 O

•connects to C through an O

• lots of O = lots of negative charge– highly reactive

•transfers energy between organic molecules – ATP, GTP, etc.

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Polymers

– “mer” means unit– “mono” means one

• Monomer-one unit– “poly” means many

• Polymer-many units

• Polymers are made of many monomers

20

Macromolecules•Most macromolecules are polymers, built from monomers• Four classes of life’s organic molecules are polymers

– Carbohydrates– Proteins– Nucleic acids– Lipids

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The Synthesis and Breakdown of Polymers

• Monomers form larger molecules by condensation reactions called dehydration synthesis

(a) Dehydration reaction in the synthesis of a polymer

HO H1 2 3 HO

HO H1 2 3 4

H

H2O

Short polymer Unlinked monomer

Longer polymer

Dehydration removes a watermolecule, forming a new bond

Figure 5.2A

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The Synthesis and Breakdown of Polymers

• Polymers can disassemble by– Hydrolysis (addition of water molecules)

(b) Hydrolysis of a polymer

HO 1 2 3 H

HO H1 2 3 4

H2O

HHO

Hydrolysis adds a watermolecule, breaking a bond

Figure 5.2B

Carbohydrates• MONOSACCHARIDES are simple sugars in a 1:2:1

ratio

• GLUCOSE

• GALACTOSE = sugar found in milk • FRUCTOSE = fruit sugar

• Chemical composition (C6 H12 O6)

Important Monosaccharides

Glucose

Carbohydrates• DISACCHARIDES consist of two single

sugars(monosaccharides) linked together by glycosidic linkageglycosidic linkage (Dehydration synthesis)

• Lactose = Milk sugar

• Sucrose = Table sugar

Carbohydrates

Carbohydrates• POLYSACCHARIDE is a carbohydrate made of long chains of

sugars (3 or more monosaccharides)

• Starch - Plants convert excess sugars into starches for long-term storage (Alpha linkage)

• Glycogen -Animals store glucose in the form of polysaccharide glycogen in the liver and muscles to be used as quick energy

• Cellulose -a structural polysaccharide contained in the cell walls of plants (ß linkage)

• Chitin – a polysaccharide found in the cell walls of fungi and the exoskeletons of insects and arthropods

StarchStarch

Glucose

Lipids• Lipids are large, NONPOLAR organic molecules

that DO NOT dissolve in water

• Oils, fats, waxes, and steroids are lipid based

• Lipid molecules use less OXYGEN than carbohydrates to store energy efficiently

• Used in biological membranes and as chemical messengers

• Monomers – Fatty acids & Glycerol

Lipids• UNSATURATED FATS are a liquid at room

temperature (OILS). Double bonds can have hydrogen added

• SATURATED FATS are solid at room temperature NO double bonds

Saturated or Unsaturated Fatty Acids

Stearic acid

Solid at room temp

Oleic acid

Liquid at room temp

Triacylglycerol

                                             

       

Phospholipids – Make up the cell membrane

Hydrophilic vs Hydrophobic

Hydrophilic = Water loving

Hydrophobic = Water fearing

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Steroids

• Steroids– Are lipids characterized by a carbon skeleton consisting

of four fused rings

HO

CH3

CH3

H3C CH3

CH3

Figure 5.15

Proteins• Chemical composition C-H-O-N-S• Proteins are made up of smaller monomers called AMINO ACIDS• Amino Acids differ ONLY in the type of R group they carry

Amino acids composed of 3 parts1. Amino Group2. Carboxylic group3. R-group (Makes 20 different amino acids)

Peptide Bonds – link amino acids

20 Amino Acids

Protein Conformation

Primary Structure – sequence of amino acids

Secondary structure – Folding and coiling due to H bond formation between carboxyl and amino groups of non-adjacent amino acid. R groups are NOT involved.

Tertiary structure – disulfide bridges, ionic bonding, or h-bonding of R-groups

Quaternary structure – 2+ amino acid chains R- group interactions, H bonds, ionic interactions

Amino Acids

The polar uncharged amino acids are hydrophilic & can form h-bonds

– Serine– Threonine– Glutamine– Asparagine– Tyrosine– Cysteine

Amino Acids

The nonpolar amino acids are hydrophobic and are usually found in the center of the protein. They also found in proteins which are associated with cell membranes.

– Glycine– Alanine– Valine– Leucine– Isoleucine– Methionine– Phenylalanine– Tryptophan– Proline)

Amino Acids

The electrically charged amino acids have electrical properties that can change depending on the pH.

– Aspartic Acid– Glutamic Acid– Lysine– Arginine– Histidine

Amino AcidsThe electrically charged amino acids (Aspartic Acid, Glutamic Acid, Lysine, Arginine, and Histidine) have electrical properties that can change depending on the pH.

–Cysteine can form covalent disulfide bonds –Proline had a unique structure and causes kinks in the protein chain

Denaturing of Protein

Denaturing of Protein• Transfer protein from aqueous solution to

an organic solvent (chloroform)

• Any chemical that disrupts h-bonds, ionic bonds, & disulfide bridges

• Excessive heat

• Changes in pH

EnzymesEnzymes Act as CATALYSTS that can speed up some reactions by

more than a billion times!

Enzymes work by a physical fit (Lock and Key) between the enzyme molecule and its SUBSTRATE, the reactant being catalyzed.

Enzymes reduces the activation energy for the chemical reaction to occur.

After the reaction, the enzyme is released and is unchanged, so it can be used many times

Enzyme names end in -ase

Enzyme & Substrate fit like a lock & key (Shape specific)

pH or temperature can change the active site shape on any enzyme

Active site is where the Active site is where the reactants bind to the reactants bind to the enzymeenzyme

Activation Activation EnergyEnergy

The energy require to start a reaction is The energy require to start a reaction is called Activation Energycalled Activation Energy

Nucleic AcidsNucleic Acids

Nucleic AcidsNucleic Acids•RNA and DNA made of nucleic acids

•C-H-O-N-P atoms

•Polymers of nucleotides

•Nucleotides consist of a 5-carbon sugar, a phosphate group, and a nitrogenous base. •Store and transmit genetic information

Nucleic AcidsNucleic Acids