Organic Chemistry Chapters 22.

Organic Chemistry Chapters 22

Hydrocarbons Chapter 22

O-Chem Chemists knew that living organisms were made up of an obscene number of carbon compounds and thus referred to them as “organic” Organic Compound: the term applied to any and all chemical compounds that contain carbon with the only exceptions being carbon oxides, carbides and carbonates (these are inorganic) Why study nothing but carbon for an entire life and centuries? Remember that it is in Group 14 and thus has four valence electrons Therefore, it can make four bonds to complete is stable valence octet Carbon atoms bond with numerous different atoms, including itself! Catenation: the covalent binding of an element to itself to form chains or rings

Hydrocarbons The simplest organic compounds are known as hydrocarbons
These contain only carbon and hydrogen If you think that only a few could be made, think again Thousands of different hydrocarbons exist! Carbon will form four covalent bonds while hydrogen will form only one So the simplest organic hydrocarbon compound is CH4 Carbon tetrahydride – METHANE!

A Review of Models Chemist represent molecules in a variety of ways
They will use molecular formulas but these lack the geometric shape that molecules form A structural formula shows the general arrangement of atoms but again, not the exact geometry of the bonds/atoms Space-filling models give a more realistic picture of what a molecule would look like but the ball-and-stick models give the best geometric shape

Straight-Chain Alkanes
Methane is the smallest member of a series of hydrocarbons known as alkanes Alkanes: hydrocarbons that have only single bonds between atoms These compounds are known as a homologous series because they differ from one another by a repeating unit (number of C and H) Name Molecular Formula Structural Formula Isomers methane CH4 1 hexane C6H14 CH3(CH2)4CH3 5 ethane C2H6 CH3CH3 heptane C7H16 CH3(CH2)5CH3 9 propane C3H8 CH3CH2CH3 octane C8H18 CH3(CH2)6CH3 18 butane C4H10 CH3CH2CH2CH3 2 nonane C9H20 CH3(CH2)7CH3 35 pentane C5H12 CH3(CH2)3CH3 3 decane C10H22 CH3(CH2)8CH3 75

Isomers Compounds that have the same molecular formula but have different structures Structural Isomers: “constitutional isomers” are isomers where the atoms are bonded together in different orders These have different physical and chemical properties

C H H C Methane CH4 Butane C4H10 C H ? H C R R Methyl -CH3 Butyl -C4H9

Isomers Geometric Isomers:
Isomers in which the order of the atom bonding is the same but the arrangement of atoms in space is different

Branched-Chain Alkanes
The first set of alkanes were straight and without side chains Branched-chain alkanes will have one chain that is longer than others This chain, the longest-continuous chain of carbon atoms is called the parent chain All side chains (branches) are called substituent groups because they appear to substitute for a hydrogen atom in the straight chain Be sure to get and keep a copy of your quick reference guide for naming alkanes

Branched-Chain Nomenclature
Similar to naming compounds and molecules, you will use the IUPAC Nomenclature Rules International Union of Pure and Applied Chemistry Count the number of carbon atoms in the longest continuous chain. Use the name of the straight-chain alkane to name the parent chain Number each carbon in the parent chain Locate the end carbon closest to a substituent group Label that carbon position one (This gives all substituent groups the lowest possible number) Name each alkyl group substituent. The names of the groups are placed before the name of the parent chain If the same alkyl group occurs more than once as a branch on the parent structure, use a prefix (di, tri, tetra, etc.) before its name to indicate how many times it appears Then use the number of the carbon to which each is attached to indicate its position Whenever different alkyl groups are attached to the same parent structure, place their names in alphabetical order (prefixes are not included in alphabetical order) Write the entire name using hyphens to separate numbers from words and commas to separate numbers No space is added between the substituent name and the name of the parent chain

Naming Branched Alkanes (IUPAC)
Octane 4-ethyl 6 2 8 4-ethyl-3,5-dimethyloctane 5 4 7 3 1 3-methyl and 5-methyl = 3,5-dimethyl Root name: name of longest continuous C chain (parent chain) Two equally long? Choose the one with more branches Number C atoms in chain, starting at end with first branch Identify substituents, give each a number (C it is connected to) Two or more identical substituents: use prefixes (di-, tri-, tetra-, etc.) List substituents alphabetically before root name Do not alphabetize prefixes Punctuation: commas separate numbers from each other hyphens separate numbers from names no space between last substituent & root name

Structural Isomers: Pentane (C5H12)
2-methylbutane 2,2-dimethylpropane

Structural Isomers: Hexane (C6H14)
2,3-dimethylbutane 2-methylpentane 2,2-dimethylbutane 3-methylpentane

Structural Isomers: Heptane (C7H16)
2,2-dimethylpentane 2-methylhexane 2,3-dimethylpentane 3-methylhexane

Structural Isomers: Heptane C7H16
2,4-dimethylpentane 3-ethylpentane 3,3-dimethylpentane 2,2,3-trimethylbutane

Cyclic Alkanes One reason that there are thousands of carbon compounds is because they don’t always form straight/branched-chains They can form circles or rings Cyclic hydrocarbons Cycloalkanes are hydrocarbons that contain only single covalent bonds Naming these rings involves added the prefix cyclo- before the carbon chain Cyclopropane, cyclohexane, etc.

Naming Substituted Cycloalkanes
Like other alkanes, cycloalkanes can also have substitute chains (groups) They follow the same IUPAC Nomenclature except for a few subtle differences There is no “longest chain” because the parent chain is the ring itself Because there is no beginning or end in a cyclo, the numbering is started on the carbon that is bonded to the substituent group If there are two or more substituent groups, use the combination of numbers that give the lowest possible set If only one group is attached, no number is necessary

Multiple Covalent Bonds
Recall that carbon can also make multiple covalent bonds (2 or 3) If a carbon compound (organic) contains only single covalent bonds, its said to be a saturated hydrocarbon If just one of the carbons in the organic compound contains a double or triple bond, then it will be unsaturated Saturated means that its loaded with the maximum number of atoms because its using all of its bonds for only one other atom

Alkenes Unsaturated hydrocarbons that contain at least one double covalent bond is known as an alkene Alkenes are named in much the same way as alkanes but their suffix will be an – ene instead of – ane Ethane : ethene, propane : propene To name alkenes with four or more carbons, one must first locate the double bond Numbering of the carbons in the parent chain must start at the end that will give the first carbon in the double bond the lowest number – Use only that number in the name The same is true for cycloalkenes

Branched-Chain Alkenes
The same branched-chain IUPAC nomenclature is true for these unsaturated hydrocarbons with only two small differences The parent chain is always the longest chain that contains the double bond, whether or not it’s the longest chain of carbon atoms The position of the double bond, not the branches, determines how the chain is numbered If there are multiple double bonds, then a prefix must be used before the suffix (diene, triene, tetraene) This again will require the carbon atoms to have the lowest number assignments

Cis- vs. Trans-

Alkynes A carbon compound that contains at least one triple bond will be known as an alkyne These unsaturated hydrocarbons will use all the same nomenclature rules as alkenes except the suffix will be changed to – yne

Aliphatic Hydrocarbons
Alkane Alkene Alkyne Alkadiene General formula CnH2n + 2 CnH2n CnH2n - 2 CnH2n - 2 Typical structural formula – C – C – C – C – – C = C – C – C – – C = C – C – C – – C = C – C = C – butane 1-butene 1-butyne 1,3-butadiene Carbon-carbon bond type all single bonds one double bond one triple bond two double bonds Naming suffix -ane -ene -yne -diene

Benzene An Aromatic Compound C6H6 Resonance structures

Shorthand notation of Benzene

Structure of Benzene H H C C H C C H C C H H

Structure of Benzene C H C H

Benzene 3-D VSEPR Diagram

Substituted Hydrocarbons & Their Reactions
Functional Groups

Functional Groups An atom or group of atoms that is responsible for the specific properties of an organic compound The same functional group will undergo the same chemical reactions no matter the parent chain Therefore, compounds that contain the same functional group can be classified together

Functional Groups

Alcohols An organic compound that contains one or more hydroxyl groups
General form is R – OH Name of alcohols will end in –ol Or hydroxy- Hydrogen bonding is possible in alcohols Used today as alternative fuel sources

Alkyl Halides An organic compound that contains one or more halogen atoms General form is R – X Called either “Element-chain” or “chain element” Bromoethane or Ethyl bromide Some of the most commonly used organic compounds CFCs were used in refrigerants and caused the destruction of the ozone layer years ago Banned by most countries One single chlorine atom can destroy thousand of ozone molecules, O3

Ethers An organic compound in which two hydrocarbon groups are bonded together by the same single oxygen atom General form is R – O – R’ Named “Chain-oxy-chain” R’ can be the same hydrocarbon group as the other They are not very reactive so they are used in solvents

Aldehydes and Ketones Aldehydes are compounds that contain a carbon that is bonded to a hydrogen and double-bonded to an oxygen These will be found on the end of the chain These are known as carbonyl groups Named as you would an alcohol but with –al ending Ketones are similar to ethers and aldehydes both but differ because two hydrocarbon groups are attached by a single carbon, which is double-bonded to an oxygen atom These end in –one when naming

Aldehydes and Ketones O Aldehyde R-C-H Ketone R-C-R' O Acetaldehyde
(CH3CH) ethanal, ethyl aldehyde O Formaldehyde (CH2O) methanal Acetone (CH3COCH3) dimethyl ketone, 2-propanone

Amines An organic compound in which a nitrogen atom connects a hydrocarbon group with multiple different other atoms Named as either amino- or -amine This could include other hydrocarbons Thought to be derived from ammonia, NH3 R’ can be the same hydrocarbon group as the other They are not very reactive so they are used in solvents

Carboxylic Acids An organic compound that contain the carboxyl group
These are acids or proton donors! It is a weaker acid as compared to those in inorganic compounds Can be found in citrus fruits (citric acid) Named –oic acid

Esters An organic compound similar to carboxylic acid except the hydrogen atom has been replaced by an alkyl group Considered derivatives of carboxylic acids Common locations are found in the backbone of our DNA Explosives Named alkyl alkanoate

Functional Groups

Order of Priority of Functional Groups
Formula Functional group Formula Carboxylic acid -COOH Sulfonic acid -SO3H Ester -COOR Acid chloride -COCl Amide -CONH2 Nitrile -CN Aldehyde -CHO Ketone -CO Alcohol -OH Phenol -OH Thiol -SH Amine -NH2 Ether -OR Sulfide -SR

Chemistry of Life Chapter 23

Macromolecules Are large molecules composed of smaller molecules
Are complex in their structures

Macromolecules Most macromolecules are polymers, built from monomers Four classes of life’s organic molecules are polymers Carbohydrates Proteins Nucleic acids Lipids A polymer Is a long molecule consisting of many similar building blocks called monomers Specific monomers make up each macromolecule (E.g. amino acids make proteins)

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 H 1 2 3 4 H2O Short polymer Unlinked monomer Longer polymer Dehydration removes a water molecule, forming a new bond

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 4 H2O Hydrolysis adds a water molecule, breaking a bond

Carbohydrates Serve as fuel and building material Include both sugars and their polymers (starch, cellulose, etc.)

Sugars Monosaccharides Are the simplest sugars Can be used for fuel
Can be converted into other organic molecules Can be combined into polymers

Examples of monosaccharides
Triose sugars (C3H6O3) Pentose sugars (C5H10O5) Hexose sugars (C6H12O6) H C OH H C OH HO C H H C OH C O HO C H H C O Aldoses Glyceraldehyde Ribose Glucose Galactose Dihydroxyacetone Ribulose Ketoses Fructose

Monosaccharides May be linear Can form rings 4C 3 2 OH
H C OH HO C H H C O C 1 2 3 4 5 6 OH 4C 6CH2OH 5C H OH 2 C 1C 3 C 2C 1 C CH2OH HO (a) Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5.

Disaccharides Consist of two monosaccharides Are joined by a glycosidic linkage

Dehydration reaction in the synthesis of maltose
Dehydration reaction in the synthesis of maltose. The bonding of two glucose units forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide. Dehydration reaction in the synthesis of sucrose. Sucrose is a disaccharide formed from glucose and fructose. Notice that fructose, though a hexose like glucose, forms a five-sided ring. (a) (b) H HO H OH OH O CH2OH H2O 1 2 4 1– 4 glycosidic linkage 1–2 glycosidic linkage Glucose Fructose Maltose Sucrose

Polysaccharides Polysaccharides Are polymers of sugars
Serve many roles in organisms

Storage Polysaccharides
Chloroplast Starch Amylose Amylopectin 1 m (a) Starch: a plant polysaccharide Starch Is a polymer consisting entirely of glucose monomers Is the major storage form of glucose in plants

(b) Glycogen: an animal polysaccharide
Consists of glucose monomers Is the major storage form of glucose in animals Mitochondria Giycogen granules 0.5 m (b) Glycogen: an animal polysaccharide Glycogen

Structural Polysaccharides
Cellulose Is a polymer of glucose

Has different glycosidic linkages than starch
(c) Cellulose: 1– 4 linkage of  glucose monomers H O CH2OH OH HO 4 C 1 (a)  and  glucose ring structures (b) Starch: 1– 4 linkage of  glucose monomers  glucose  glucose

Is a major component of the tough walls that enclose plant cells
Cell walls Cellulose microfibrils in a plant cell wall  Microfibril CH2OH OH O Glucose monomer Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6. About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. A cellulose molecule is an unbranched  glucose polymer. Cellulose molecules

Cellulose is difficult to digest
Cows have microbes in their stomachs to facilitate this process Figure 5.9

Chitin, another important structural polysaccharide
Is found in the exoskeleton of arthropods Can be used as surgical thread (a) The structure of the chitin monomer. O CH2OH OH H NH C CH3 (b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emerging in adult form. (c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals.

Lipids Lipids are a diverse group of hydrophobic molecules Lipids
Are the one class of large biological molecules that do not consist of polymers Share the common trait of being hydrophobic

Fats Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids Vary in the length and number and locations of double bonds they contain

Fats Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids

Fats Vary in the length and number and locations of double bonds they contain

(a) Saturated fat and fatty acid
Saturated fatty acids Have the maximum number of hydrogen atoms possible Have no double bonds (a) Saturated fat and fatty acid Stearic acid

(b) Unsaturated fat and fatty acid
Unsaturated fatty acids Have one or more double bonds (b) Unsaturated fat and fatty acid cis double bond causes bending Oleic acid

Phospholipids Have only two fatty acids
Have a phosphate group instead of a third fatty acid

(a) Structural formula (b) Space-filling model
Phospholipid structure Consists of a hydrophilic “head” and hydrophobic “tails” CH2 O P CH C Phosphate Glycerol (a) Structural formula (b) Space-filling model Fatty acids (c) Phospholipid symbol Hydrophobic tails Hydrophilic head Hydrophobic tails – Hydrophilic head Choline + N(CH3)3

The structure of phospholipids
Results in a bilayer arrangement found in cell membranes Hydrophilic head WATER Hydrophobic tail

Steroids Steroids Are lipids characterized by a carbon skeleton consisting of four fused rings

One steroid, cholesterol
Is found in cell membranes Is a precursor for some hormones HO CH3 H3C

Proteins Proteins have many structures, resulting in a wide range of functions Proteins do most of the work in cells and act as enzymes Proteins are made of monomers called amino acids

An overview of protein functions

Enzymes Are a type of protein that acts as a catalyst, speeding up chemical reactions Substrate (sucrose) Enzyme (sucrase) Glucose OH H O H2O Fructose 3 Substrate is converted to products. 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. Substrate binds to enzyme. 2 4 Products are released.

Polypeptides Polypeptides A protein
Are polymers (chains) of amino acids A protein Consists of one or more polypeptides

Amino acids Are organic molecules possessing both carboxyl and amino groups Differ in their properties due to differing side chains, called R groups

Twenty Amino Acids 20 different amino acids make up proteins O O– H
H3N+ C CH3 CH CH2 NH H2C H2N Nonpolar Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile) Methionine (Met) Phenylalanine (Phe) Tryptophan (Trp) Proline (Pro) H3C S 20 different amino acids make up proteins

Polar Electrically charged
OH CH2 C H H3N+ O CH3 CH SH NH2 Polar Electrically charged –O NH3+ NH2+ NH+ NH Serine (Ser) Threonine (Thr) Cysteine (Cys) Tyrosine (Tyr) Asparagine (Asn) Glutamine (Gln) Acidic Basic Aspartic acid (Asp) Glutamic acid (Glu) Lysine (Lys) Arginine (Arg) Histidine (His)

Amino Acid Polymers Amino acids Are linked by peptide bonds

Protein Conformation and Function
A protein’s specific conformation (shape) determines how it functions

Four Levels of Protein Structure
Primary structure Is the unique sequence of amino acids in a polypeptide Figure 5.20 – Amino acid subunits +H3N Amino end o Carboxyl end c Gly Pro Thr Glu Seu Lys Cys Leu Met Val Asp Ala Arg Ser lle Phe His Asn Tyr Trp Lle

Secondary structure Is the folding or coiling of the polypeptide into a repeating configuration Includes the  helix and the  pleated sheet O C  helix  pleated sheet Amino acid subunits N H R

Is the overall three-dimensional shape of a polypeptide
Tertiary structure Is the overall three-dimensional shape of a polypeptide Results from interactions between amino acids and R groups CH2 CH O H O C HO NH3+ -O S CH3 H3C Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hyrdogen bond Ionic bond Disulfide bridge

Quaternary structure Is the overall protein structure that results from the aggregation of two or more polypeptide subunits Polypeptide chain Collagen  Chains  Chains Hemoglobin Iron Heme

Review of Protein Structure
+H3N Amino end Amino acid subunits helix

What Determines Protein Conformation?
Protein conformation Depends on the physical and chemical conditions of the protein’s environment Temperature, pH, etc. affect protein structure

Denaturation is when a protein unravels and loses its native conformation (shape)
Renaturation Denatured protein Normal protein

Nucleic Acids Nucleic acids store and transmit hereditary information
Genes Are the units of inheritance Program the amino acid sequence of polypeptides Are made of nucleotide sequences on DNA

The Roles of Nucleic Acids
There are two types of nucleic acids Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA)

Deoxyribonucleic Acid
DNA Stores information for the synthesis of specific proteins Found in the nucleus of cells

Synthesis of mRNA in the nucleus
DNA Functions Directs RNA synthesis (transcription) Directs protein synthesis through RNA (translation) 1 2 3 Synthesis of mRNA in the nucleus Movement of mRNA into cytoplasm via nuclear pore Synthesis of protein NUCLEUS CYTOPLASM DNA mRNA Ribosome Amino acids Polypeptide

The Structure of Nucleic Acids
5’ end 5’C 3’ end OH O Nucleic acids Exist as polymers called polynucleotides (a) Polynucleotide, or nucleic acid

Each polynucleotide Consists of monomers called nucleotides
Sugar + phosphate + nitrogen base Nitrogenous base Nucleoside O O O P CH2 5’C 3’C Phosphate group Pentose sugar (b) Nucleotide

(c) Nucleoside components
Nucleotide Monomers Nucleotide monomers Are made up of nucleosides (sugar + base) and phosphate groups CH Uracil (in RNA) U Ribose (in RNA) Nitrogenous bases Pyrimidines C N O H NH2 HN CH3 Cytosine Thymine (in DNA) T HC NH Adenine A Guanine G Purines HOCH2 OH Pentose sugars Deoxyribose (in DNA) 4’ 5” 3’ 2’ 1’ (c) Nucleoside components

Nucleotide Polymers Nucleotide polymers
Are made up of nucleotides linked by the–OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next

Gene The sequence of bases along a nucleotide polymer
Is unique for each gene

The DNA Double Helix Cellular DNA molecules
Have two polynucleotides that spiral around an imaginary axis Form a double helix

The DNA double helix Consists of two antiparallel nucleotide strands
3’ end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) Old strands Nucleotide about to be added to a new strand A 5’ end New strands

A,T,C,G The nitrogenous bases in DNA
Form hydrogen bonds in a complementary fashion (A with T only, and C with G only)

DNA and Proteins as Tape Measures of Evolution
Molecular comparisons Help biologists sort out the evolutionary connections among species

Organic Chemistry Chapters 22.

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