25.S: Organic and Biological Chemistry (Summary)

• organic chemistry – the study of carbon compounds
• biochemistry – the stuyd of the chemistry of living species

25.2: Introduction to Hydrocarbons

• • made of only hydrogen and carbon
  • 4 types: alkanes, alkenes, alkynes, and aromatic hydrocarbons
  • alkanes – only single bonds
  • also called saturated hydrocarbons
  • have the largest amount of hydrogen atoms bonded to a single carbon atom

• • alkenes (olefins) – have double carbon bonds

• • alkynes – triple carbon bonds

• • aromatic hydrocarbons – carbon atoms connected in a planar ring structure, joined by s and p bonds between carbon atoms

• • alkenes, alkynes and aromatic hydrocarbons – unsaturated hydrocarbons
  • less volatile with increasing molar mass
  • very low molecular weight = gas at room temperature
  • moderate molecular weight = liquid
  • high molecular weight = solid

25.3: Alkanes

• methane major part of natural gas
• used in home heating, gas stoves, hot-water heaters
• propane major part of bottled gas
• used for home heating, cooking
• butane – used in disposable lighters, fuel canisters
• alkanes with 5-12 carbon atoms are found in gasoline
• formla for alkanes is called condensed structural formulas

Molecular Formula	Condensed Structural Formula	Name	Boiling point (°C)
CH4	CH4	Methane	-161
C2H6	CH3 CH3	Ethane	-89
C3H8	CH3 CH2 CH3	Propane	-44
C4H10	CH3 CH2 CH2 CH3	Butane	-0.5
C5H12	CH3 CH2 CH2 CH2 CH3	Pentane	36
C6H14	CH3 CH2 CH2 CH2 CH2 CH3	Hexane	68
C7H16	CH3 CH2 CH2 CH2 CH2 CH2 CH3	Heptane	98
C8H18	CH3 CH2 CH2 CH2 CH2 CH2 CH2 CH3	Octane	125
C9H20	CH3 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH3	Nonane	151
C10H22	CH3 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH3	Decane	174

• Lewis Structure

1. Structures of Alkanes

• • tetrahedral geometry
  • carbon-carbon single bond rotates easily at room temperature
  • long chains tend to change shape

1. Structural Isomers

• • straight-chained hydrocarbons – carbons atoms that are joined in a continuous chain
  • branched-chain hydrocarbons – hydrocarbons with branched chains, 4 or more carbon atoms
  • structural isomers – compounds with the same molecular formula but different bonding arrangements

1. Nomenclature of Alkanes

• • 1) Find the longest continuous chain of carbon atoms, and use the name of this chain as the base name of the compound.
  • 2) Number the carbon atoms in the longest chain, beginning with the end of the chain that is nearest to a substituent
  • 3) Name and give the location of each substituent group
  • 4) When two or more substituents are present list them in alphabetical order

1. Cycloalkanes

• • alkanes that form rings or cycles
  • carbon rings with fewer than five carbon atoms are strained
  • more reactive

1. Reactions of Alkanes

• • at room temperature alkanes do not react with acids, bases, or strong oxidizing agents
  • important for it’s combustion in air; bases for fuels

25.4: Unsaturated Hydrocarbons

• Alkenes
• • double carbon bonds
  • ethene or ethylene simplest alkene\
  • nomenclature of alkenes come from the name of the corresponding alkane
  • the –ane ending is changed to –ene
  • geometrical isomers – compounds that have the same molecular formula and the same groups bonded to one another but differ in the spatial arrangement of these groups
  • geometrical isomers have distinct physical properties and differ in chemical behavior
  • the double carbon bond is resistant to twisting
  • rotation about a double bond is a key process in the chemistry of vision

1. Alkynes

• • one or more triple bonds
  • simplest alkyne is acetylene
  • highly reactive
  • named by changing the alkane ending (-ane) to –yne

1. Addition Reactions of Alkenes and Alkynes

• • addition reactions – a reactant is added to the two atoms that form the multiple bond
  • hyrogenation – reaction between al alkene and H₂

1. Aromatic Hydrocarbons

• • simplest is benzene
  • stability comes from the stabilization of the p electrons through delocalization in the p orbitals
  • represented by a hexagon with an inscribed circle
  • substitution reactions – one atom of a molecule is removed and replaced by another atom or group of atoms

25.5: Functional Groups

functional group – site of reactivity in an organic molecule; controls how the molecule behaves or functions

• chemistry of an organic molecule is determined by the functional groups it contains

1. Alcohols (R-OH)

• alcohols – hydrocarbon derivatives in which one ore more hydrogens of a parent hydrocarbon have been replaced by a hydroxyle or alcohol functional group

1. Ethers (R-O-R’)

• • ethers – two hyrocarbon groups are bonded to one oxygen
  • formed from two molecules of alcohol by splitting out a molecule of water
  • condensation reaction – reaction where water is split out from two substances
  • used in solvents

25.6: Compounds with a Carbonyl Group

• • carbon oxygen double bonds

1. 1. 1. Aldehydes and Ketones

• • carbonyl group in aldehydes has at least one attached hydrogen atom

*formaldehyde*

• • carbonyl group in ketones occurs at the interior of a carbon chain

*Acetone*

• • prepared by oxidizing alcohols

1. Carboxylic Acids

• • carboxylic acids contain carboxyl functional group (COOH)
  • important for manufacturing of polymers
  • produced by oxidation in which the OH group is attached to the CH₂

1. Esters

• • carboxylic acids that undergo condensation with alcohols
  • have pleasant odors
  • saponification – hydrolysis of an ester in a base

1. Amines and Amides

• • amines – organic bases; general formula R₃N
  • amides – anines containing a hydrogen bonded to nitrogen that undergoes condensation

25.8: Introduction to Biochemistry

• biosphere – part of the earth where living organisms are formed and living
• includes influences on life of the atmosphere, natural waters, solid earth
• living organisms require a large amount of energy
• biopolymers – three categories: proteins, polysaccharides (carbohydrates), and nucleic acids

25.9: Proteins

• • macromolecular substances
  • 50% body’s dry weight is proteins
  • composed of amino acids

1. Amino Acids

• • differ in the R group
  • building block of all proteins - a -amino acid
  • general form:

• • chiral - any molecule containing a carbon with four different attached groups
  • enantiomers – mirror-image of chiral
  • enantiomers and chiral have the same physical properties
  • differ in chemical reactivity toward other chiral molecules

1. 1. 1. Polypeptides and Proteins

• • peptide bond – condesation reaction between the carboxyl group of one amino acid and the amino group of another amino acid
  • polypeptides – large number of amino acids that are linked together by peptide bonds
  • proteins are polypeptide molecules
  • weighs from 6000 to over 50 million amu

1. Protein Structure

• • primary structure – arrangement of amino acids along a protein chain
  • makes the protein unique
  • secondary structure – the way segments of the protein chain are oriented in a regular pattern
  • a -helix – most important and common secondary structure arrangement
  • first propoesed by Linus Pauling and R. B. Corey
  • tertiary structure – overal shape of a protein
  • globular protein – a protein that folds into a compact spherical shape
  • soluble in water, mobile within cells
  • enzymes – large protein molecules that serve as catalysts

25.10: Carbohydrates

• • written as C_x(H₂O)_y
  • glucose the most abundant carbohydrate C₆H₁₂O₆
  • not really hydrates of carbon but polyhydroxly aldehydes and ketones

1. Disaccharides

• • monosaccharides – simple sugars that can’t be broken into smaller molecules by hydrolysis with aqueous acids
  • disaccharide – two linked monosaccharides
  • two common disaccharides: sucrose, lactose

1. Polysaccharides

• • made of several monosaccharide units
  • starch – group of polysaccharides
  • food storage in plant seeds and tuers
  • glycogen – starchlike substance synthesized in the body
  • 5000 to more than 5 million amu
  • energy bank in the body; muscles and liver
  • cellulose – major strructural unit of plants
  • straight chains of glucose units
  • more than 500,000 amu

25.11: Nucleic Acids

• • nucleic acids – biopolymers that are chemical carriers of an organisn’t genetic information
  • deoxyribonucleic acids (DNA) – huge molecules with molar weights of 6-16million amu
  • ribonucleic acids (RNA) – smaller molecules with molecular weights of 20,000 to 40,000 amu
  • DNA found inside the nucleus of a cell, RNA found outside nucleus in the cytoplasm
  • DNA stores the genetic information of the cell and controls the production of proteins
  • RNA carries information from the DNA out of the nucleus
  • Monomers of nucleic acids (nucleotides) have three parts:
  • 1) A phosphoric acid molecule, H₃PO₄
  • 2) A fice-carbon sugar
  • 3) A nitrogen-containing organic base

*ribose* *deoxyribose*

• • deoxyribose has one less oxygen atom at carbon 2 than ribose
  • nucleic acids are polynucleotides
  • DNA molecules made of two DNA chains that form a double helix