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1.2 The Chemicals of Life

1.2 The Chemicals of Life. Hydrocarbons. Nonpolar and form straight or branched chains and ring shaped structures. Names reflect the number of carbons, the number and location of any double or triple bonds and any functional groups.

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1.2 The Chemicals of Life

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  1. 1.2 The Chemicals of Life

  2. Hydrocarbons • Nonpolar and form straight or branched chains and ring shaped structures. • Names reflect the number of carbons, the number and location of any double or triple bonds and any functional groups. • Names based on the number of carbons in the longest carbon chain: 1 carbon......meth 6 carbons....hex 2 carbons....eth 7 carbons....hept 3 carbons....prop 8 carbons....oct 4 carbons....but 9 carbons....non 5 carbons....pent 10 carbons..dec

  3. Organic Chemistry • The study of carbon compounds • Most organic compounds are classified as hydrocarbons. • Hydrocarbons (hydrogens bonded to carbons) can be classified as • Saturated • Single bonds between carbons • Do not react with H • Unsaturated • Double or triple bonds between carbons • React with H

  4. Organic Compounds • Hydrocarbons • Derivatives of halogen acids (water and ammonia) • Carbonyl compounds (C=O)

  5. Naming Organic CompoundsNomenclature • The system developed for naming these compounds is the IUPAC. • Hydrocarbons are studied and named based on bond, atom arrangement, and number of atoms.

  6. Alkanes (Paraffins) CnH2n+2 • Saturated • Named according to the number of Carbon atoms • Names end in ‘-ane’

  7. Most organic compounds have side chains or branches known as alkyl’s and the main chain is the parent. • When naming alkyl side chains the same nomenclature seen for the alkanes is used, but the ‘-ane’ ending becomes a ‘-yl’ ending.

  8. Naming branched alkanes • Find the longest continuous carbon chain (parent), this is not always a straight line. • Number the parent chain, starting at the end closest to the branch. • Identify the branch and its numerical position • Attach the number and name of the branch to the name of the parent • When more than one branch exists arrange them in alphabetical order Ex. CH3CH2CHCH2CH2CH2CH3 CH2CH2CH3

  9. 2. Alkenes (Olefins) • Unsaturated • Name ends in ‘-ene’ with one double bond • ‘-adiene’ with 2 double bonds • ‘-atriene’ with 3 double bonds • Ex. CH3CH2CH3 Propane • CH2=CHCH3 Propene • When numbering the carbons in the longest chain, the first carbon is the one closest to the double bond. • Ex. CH3CH=CHCH2CH3 2 pentene • CH3CH=CHCH=CH2 1,3 pentadiene

  10. 3. Alkynes • Unsaturated with at least 1 triple bond • Name ends in ‘-yne’ with 1 triple bond • Name ends in ‘-adiyne’ with 2 triple bonds • Name ends in ‘-atriyne’ with 3 triple bonds • Ex. CH3CH2CH3 Propane • CH = CCH3 Propyne • When numbering the carbons, the chain is numbered to give the lowest number to the triple bond CH3CH2C=CH 1-butyne

  11. 4. Cyclic Hydrocarbons • When naming cyclic hydrocarbons the prefix ‘cyclo-’ is added to the name of the alkane or alkene. • Cyclohexane Cyclohexene • Benzene is a special form of cycloheane with 3 double bonds

  12. Benzene • When side chains are attached to benzene their names become prefixes to benzene when benzene is the parent --CH3 methylbenzene • When benzene is attached to a chain with more than 7 carbons it is now called ‘phenyl-’ or if it is attached to a chain with a functional group. CH3 CH(CH2)5CH3 2-phenyloactane

  13. Structural Isomers • Isomers = 2 or more different compounds with the same molecular formula • Structural Isomers = compounds with the same molecular formula whose atoms bond in different orders • Ex. Structural isomers for C4H10 • CH3CH2CH2CH3 butane • CH3CHCH3 Methylpropane CH3

  14. CH3 • CH3CH2CH2-- or CH3CH propyl (n-propyl) isopropyl n= normal (straight) iso= isometric sec = secondary t = tertiary

  15. CH3CH2CH2CH2 – Butyl (n-butyl) Isobutyl t-butyl

  16. Example • In monosaccharides, the number of isomers that are possible can be determined by the number of chiral carbon atoms. • In a monosaccharide that contains n chiral centers, there are 2n possible isomers. This idea is illustrated below for a monosaccharide that contains 2 chiral carbon atoms; 22 = 4 isomers.

  17. Exercise • How many isomers are there of • How many chiral carbon atoms are there in General Chemistry Online: Isomer Construction Set

  18. Stereoisomers • Compounds that have the same structure but differ in the arrangement of atoms in space • A example of stereoisomers are geometric isomers. Geometric isomers only occur in two types of compounds: • Alkenes • Cyclic compounds

  19. Geometric Isomers • Stereoisomers that differ by having similar compounds on the same side or opposite sides of a rigid molecule (double bond, cyclic compound) • When single bonds exist between carbons, they can move, spin, rotate and flex to adjust their conformation. Carbons attached by double bonds or attached in a cyclic compound are unable to alter their conformation.

  20. Two like groups on the same side of a rigid bond are said to be CIS. Like groups on opposite sides are said to be TRANS. • These molecules are said to be Chiral molecules http://cwx.prenhall.com/petrucci/medialib/media_portfolio/text_images/083_Chirality.MOV

  21. Exercise 1: • Which molecules are mirror images of each other? Hint: Look at the Chiral carbon atoms

  22. Exercise 2 • Which molecule is a mirror image of this one:

  23. Functional Groups • Site of chemical reactivity in a molecule • Include pi bonds (double or triple bonds) or an electronegative/electropositive atom

  24. Common Functional Groups • Carbon with H,O, S and P attachments • More reactive than the hydrocarbon (C and H only) of a molecule • Site of chemical reactions  functional groups

  25. Functional Groups in Biomolecules(Table 1, pp. 25, Nelson Biology 12)

  26. 1. Alcohols • Structure: contains a hydroxyl group (-OH) bonded to a sp3 hybridized carbon • Function: used in alcoholic beverages, gas-line anti-freeze or as bacteriocidal agent • Naming: From the parent chain of alkanes of alkenes, the ‘e’ is replaced with the ending ‘-ol’ • Example: CH3OH  Methanol CH2=CHCH2OH  2-propenol Note: More than one OH group is designated by di-, tri-, etc…

  27. 2. Aldehydes • Structure: Carbonyl compound that contains at least one hydrogen attached to a carbonyl carbon • Functon: Found in living systems in the form of sugars and hormones • Naming: From the parent chain of alkanes or alkenes, the ‘e’ is replaced with the ending ‘-al’ • Example:

  28. 3. Ketones • Structure: Carbonyl compound that contains two alkyl/aryl groups attached to the carbonyl carbon • Function: See aldehydes • Naming: From the parent chain of alkanes or alkenes, the ‘e’ is replaced with the ending ‘-one’ • Example:

  29. 4. Amines • Structure: N bonded to 3 other atoms, H, C or combination of the two • Function: Found in many proteins and nucleic acids. Adrenaline stimulates nervous system. Can be extracted from plants as decongestants • Naming: The alkyl or aryl group is named then given the ending ‘-amine’ • Example

  30. 5. Amides • Structure: N bonded to a carbonyl carbon • Function: in living systems, found in urea • Naming: from the parent chain of alkanes or alkenes, the ‘e’ is replaced with the ending ‘-amide’ • Synthesized from carboxylic acids and ammonia or amine

  31. 6. Thiol • Structure: Sulfhydryl group (SH) • Function: amino acids • Naming: From the parent chain of alkanes or alkenes, the ‘e’ is replaced with the ending ‘-thiol’ • ethanethiol

  32. 7. Ether • Structure: O molecule bonded between 2 carbons. Can be open chain or cyclic (ROR) • Function: made from reactions involving alcohols • Naming: Identify alkyl group to the left of O and alkyl group to the right and end with the suffix ‘-ether’ • Methyl ethyl ether

  33. 8. Esters • Structure: C bonded to 2 O atoms, one of which is bonded to an alkyl group • Naming: Name alkyl group attached to O. Then name parent carboxylic acid with ending changed to ‘-oate’ • Methyl ethanoate

  34. 9. Carboxylic Acid • Structure: contains a carboxylic group (COOH), made of a carbonyl group and a hydroxyl group • Naming: parent alkane is name, ‘e’ is replaced with ‘-oic acid’ • Methanoic acid

  35. Exercise • Identify and name the functional groups in this molecule Functional Groups Video http://www.zerobio.com/videos/functional_circle2.html

  36. Linkage Bonds • Organic macromolecules are composed of many tiny subunits that are linked together • Carbohydrates, lipids, proteins and nucleic acids are all assembled in the same way • To link subunits a covalent bond is formed between two subunits in which: • One molecule contains a hydroxyl group (OH) • One molecule contains a hydrogen (H)

  37. The hydroxyl group combines with the hydrogen in a process called a dehydration reaction where water is removed. • Energy is required to position the two subunits and to apply enough stress on the bonds to break them. This process is called catalysis. • When macromolecules are broken, water is added to separate the linkage groups  hydrolysis reaction.

  38. Macromolecules Carbohydrates Lipids Proteins Nucleic Acids

  39. Macromolecules Dehydration Synthesis (Condensation Reaction)Two subunits link together through the removal of a water molecule. Dehydration synthesis is an anabolic reaction that absorbs energy.

  40. Macromolecules Hydrolysis Reaction Two subunits break apart through the addition of a water molecule. Hydration synthesis is a catabolic reaction that releases energy.

  41. Carbohydrates • Produced through plants and algae through the process of photosysnthesis • Carbohydrates are used for energy, building materials and for cell identification and communication. • Carbohydrates contain carbon, hydrogen and oxygen in a 1:2:1 ratio. General formula – (CH2O)n, n represents the # of C atoms. • Carbohydrates are classified into 3 groups: • Monosaccharides • Oligosaccharides • Polysaccharides

  42. Monosaccharides • Simple sugars, ex. glucose, galactose, fructose • 5 or more carbons – linear in dry state, form ring structure when dissolved in water. • α – glucose, 50% chance OH group of C 1 will be below plane of ring. • β – glucose, 50% chance OH group of C 1 will be above plane of ring.

  43. EXERCISE How many of the structures shown below are ketoses?

  44. MONOSACCHARIDES QUIZ: Select the formula that represents a monosaccharide C4H8O4 C5H10O10 C6H6O12 C6H6O6

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