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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.
19
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
21
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
22
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
36
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