Chem 131 Final Exam Review: Roadmap 1.Learning Objectives 2.Functional Groups 3.Nomenclature 4.Organic Reactions 5.Drawing Molecules 6.Isomers 7.Chirality

Chem 131 Final Exam Review: Roadmap

1. Learning Objectives2. Functional Groups3. Nomenclature4. Organic Reactions5. Drawing Molecules6. Isomers7. Chirality8. Acetals & Hemiacetals9. Carboxylic Acid acid/base chemistry10.Alkaloids11. Types of Lipids12.Carbohydrates: chirality & cyclic forms13.Amino Acids & Proteins14.Nucleotides & Nucleic Acids15.Protein synthesis16.Coenzymes17.Citric Acid Cycle18.Metabolism Overview19.Glycolysis

Learning Objectives Chapter 11-15

Difference between organic and inorganic molecules Name characteristic features of organic compounds Draw organic compounds, including skeletal structures Identify common bond types, angles, and molecule

shapes Name functional groups Understand polarity and its effect on solubility and

boiling point Explain the difference between fat and water soluble

vitamins Describe alkane characteristics Draw alkanes as full, condensed, and skeletal

structures Bond angle around alkane carbons Draw constitutional isomers and ID longest carbon

chain ID 1°, 2°, 3°, 4° carbons Name simple alkanes and cycloalkanes Predict products of combustion & balance reaction

equations

Identify unsaturated hydrocarbons: alkenes, alkynes,

aromatic compounds Alkene, Alkyne, Aromatic nomenclature Stereoisomers Addition Reactions Polymers Substitution Reactions Name organic compounds with carbon-heteroatom

single bonds (oxygen, halogens, sulfur) Identify 1°, 2°, 3° alcohols and alkyl halides Predict the products or reactants for following reactions:

Alcohol dehydration Alcohol oxidation Sulfur oxidation Sulfur reduction

Understand the difference between Chiral and Achiral molecules

Identify chiral centers Draw the enantiomers & diastereomers of a chiral

molecule (using dashes & wedges to show geometry) Draw fischer projections of chiral molecules Explain the relevance of chiral centers in Biochemistry


Nomenclature for aldehydes & ketones Identify structure and describe bonding of

aldehydes & ketones Aldehyde oxidation without alcohol oxidation Addition reactions at C – O double bond Hemiacetal & acetal formation Identify cyclic hemiacetals

Nomenclature for carboxylic acids, esters, & amides Identify and describe structure of carboxylic acids, esters

& amides Acid-base chemistry of carboxylic acids (think soap!) Substitution reactions of carboxylic acids

Formation of esters Formation of amides

Hydrolysis of acyl compounds Ester hydrolysis Amide hydrolysis

Structure & formation of polyamides & polyesters

Identify amines and describe bonding & structure (1°, 2°, 3°)

Nomenclature for amines Amine hydrogen bonding Alkaloids & Nitrogen heterocycles

Acid-base chemistry of amines Neurotransmitter amines Amines and common drugs

Identify basic structure & function of lipids: Hydrolyzable Lipids:

Waxes Triglycerols Phospholipids (and phospholipid

bilayers) Nonhydrolyzable Lipids

Steroids Fat soluble vitamins (A, D, E, K) Eicosanoids

Identify carbohydrates Draw Fischer projections of carbohydrates

Classify as D or L ID multiple chiral center and draw enantiomers

Draw common monosaccharides: glucose, galactose, fructose

Draw cyclic monosaccharides & identify hemiacetal & isomers draw Haworth projections

Reduction & oxidation of monosaccharides Describe & draw polysaccharides


The 20 common, naturally occurring Amino Acids stereochemistry acid/base chemistry

Peptide Formation Proteins

Primary, Secondary, Tertiary, Quaternary structure

Hydrolysis and denaturation Enzymes: Catalysis & Inhibition

Nucleosides & Nucleotides: structure DNA & RNA base pairs: names & structures Phosphate addition

Nucleic Acids Formation & primary structure

DNA double helix structure, hydrogen bonding Replication, Transcription, Translation RNA

rRNA, mRNA, tRNA Genetic Code: codon & anticodon Protein Synthesis: initiation, elongation, termination Mutations Recombinant DNA: formation & use

Stages of Metabolism ATP: structure, hydrolysis, & formation Coupling reactions Coenzymes

NAD+ & NADH FAD & FADH2

Coenzyme A Citric Acid Cycle: all 8 steps Electron Transport Chain ATP synthesis by Oxidative Phosphorylation

Role in Metabolism of fatty acid oxidation, glycolysis, & Amino acid catabolism

Reactions catalyzed by: kinase, isomerase, dehydrogenase, decarboxylase, carboxylase

Glycolysis: steps & net reaction Pyruvate conversion to acetyl Coenzyme A

Functional Groups Overview

5Smith. General Organic & Biolocial Chemistry 2nd Ed.

Alkane

Alkene

Alkyne

Aromatic

C − C

C = C

C = C

HydrocarbonFunctional

Groups



Alkyl halides

Alcohols

Ethers

Amines

Thiols

Single Bondto a

HeteroatomFunctional

Groups



Aldehydes

Carboxylic Acids

Esters

Ketones

Amides

CarbonylFunctional

Groups

Nomenclature Alkanes

#Greek Root

Straight Chain Alkane Name

1 meth methane2 eth ethane3 prop propane4 but butane5 pent pentane6 hex hexane7 hept heptane8 oct octane9 non nonane

10 dec decane

# Carbons Structure

Alkyl Group Name

1 CH3- methyl2 CH3CH2- ethyl3 CH3CH2CH2- propyl4 CH3CH2CH2CH2- butyl5 CH3CH2CH2CH2CH2- pentyl6 CH3CH2CH2CH2CH2CH2- hexyl

Smith. General Organic & Biolocial Chemistry 2nd Ed.

parent suffixprefix + +

prefix

parent

suffix

What, where are the substituents?Example: 2,4- dimethyl

How many carbons in longest chain?Example: hex

What is the functional group?Example: ane

2,4-dimethylhexane

12

34

5

6


parent suffixprefix + +cyclo- +

prefix

parent

suffix

What, where are the substituents?Example: 1,3- dimethyl

How many carbons in the ring?Example: hex

What is the functional group?Example: ane

1,3-dimethylcyclohexane

Nomenclature Cycloalkanes

#Greek Root



10 dec decane

# Carbons Structure

Alkyl Group Name


12

34

65

Nomenclature Alkenes & Alkynes

#Greek Root



10 dec decane

# Carbons Structure

Alkyl Group Name




prefix

parent

suffix

First give location and type of substituentsSecond give location of double bond

How many carbons in longest chain?

How many of the functional group and what is it? Alkene = ene; Alkyne = yne

hexa

12

34

5

6

diene2,4-dimethyl 1,5-* Note: when we have more then 1 multiple bond the parent name has an “a” added on: hexa instead of hex

Nomenclature Alkenes & Alkynes

#Greek Root



10 dec decane

# Carbons Structure

Alkyl Group Name



prefix

parent

suffix




pent yne4-methyl 2-


123

4

5

Nomenclature Cyclo Alkenes & Alkynes

#Greek Root



10 dec decane

# Carbons Structure

Alkyl Group Name



prefix

parent

suffix




pent ene3-methyl 1-


12

3

4

5

cyclo

Nomenclature Aromatics: Benzene


prefix

parent

Give location, number, and type of substituent. You can also replace location & number with o, m, p

“Benzene”

benzene1,2-dimethyl

parentprefix +

1

2

3

4

5 6

benzeneo-dimethyl

o -

m -

p -

Polysubstituted Benzenes:1. Number to give lowest #s around ring2. Alphabetize substituents3. If part of common root name the

molecule as a derivative of a monosubstituted benzene with common root at C1.

14

Nomenclature Alcohols

#Greek Root



10 dec decane

# Carbons Structure

Alkyl Group Name




prefix

parent

suffix



How many of the functional group and what is it? Alcohol = “ol”

hexan

12

34

5

6

ol2-methyl 4-*Note: after the greek root of the parent use “an”, ie hexan* Second Note: when we have more then 1 multiple bond the parent name has an “a” after the greek root: hexa

OH

15

Nomenclature Ethers

#Greek Root



10 dec decane

# Carbons Structure

Ether Group Name

1 CH3- Methoxy2 CH3CH2- Ethoxy3 CH3CH2CH2- Propoxy4 CH3CH2CH2CH2- Butyoxy5 CH3CH2CH2CH2CH2- Pentoxy6 CH3CH2CH2CH2CH2CH2- hexoxy



prefix

parent

suffix

Use alkyl substitutant naming roots, but drop the “yl” and use “oxy” for the simplest alkyl group bonded to the ether oxygen.


Use alkane ending: ane

but

1

23

4

ane2-ethoxy

O

16

Nomenclature Thiols

#Greek Root



10 dec decane

# Carbons Structure

Alkyl Group Name




prefix

parent

suffix

Give location and type of substituents, then give location of thiol group.


Hydrocarbon functional group suffix + “thiol”

pent

1

2

34

5

anethiol2,4-dimethyl 1-

SH

17

Nomenclature Alkyl Halides

#Greek Root



10 dec decane

Halide Full NameHalide Group

NameCl Chlorine ChloroBr Bromine BromoF Flourine FlouroI Iodine Iodo



prefix

parent

suffix

Give location and type of substituents.Replace “ine” in halide name with “o”, ie Chlorine = chloro


What is the hydrocarbon functional group? If alkane then “ane” suffix

hex

1

2

34

5

ane2-chloro 4-methyl

Cl6

18

Nomenclature Aldehydes

#Greek Root



10 dec decane

# Carbons Structure

Alkyl Group Name




prefix

parent

suffix

First give location and type of substituents.

How many carbons in longest chain?Aldehyde @ C1, Ketone @ lowest # C

What is the functional group? How many?Aldehyde = -al; Ketone = -one

petan

12

3

45

al2,4-dimethyl* Note: when we have more then 1 aldehyde or ketone the parent name has an “a” added on: hexa instead of hex

O

19

Nomenclature Ketones

# Carbons Structure

Alkyl Group Name




prefix

parent

suffix

First give location and type of substituents. Then the location of the ketone

How many carbons in longest chain?Aldehyde @ C1, Ketone @ lowest # C

What is the functional group? How many?Aldehyde = -al; Ketone = -one

hexa

12

34

5

dione2,3 -* Note: when we have more then 1 aldehyde or ketone the parent name has an “a” added on: hexa instead of hex

O

6

O • Ketone is C1 in cyclic ketones• then number to make the

first substituent on the smallest C #

• Common names for ketones:• Name both alkyl groups• Order alphabetically• Add the work ketone

20

Nomenclature Carboxylic Acids



prefix

parent

suffix


How many carbons in longest chain?Carboxylic acid @ C1

What is the functional group? How many?Carboxylic acid: “-oic acid”

petan

12

3

45

oic acid2,4-dimethyl

* Note: when we have more then 1 functional group the parent name has an “a” added on: hexa instead of hex

O

OH

Functional Group Prefix Suffixalkane alkyl anealkene alkenyl enealkyne alkynyl yne

alcohol (OH) hydroxy olether alkoxy

halide

fluoro, chloro, bromo,

iodo thiol (SH) mercapto thiolaldehyde formyl al

ketone oxo one

carboxylic acid carboxy

oic acid carboxylic

acidester oxycarbonyl oate

amide carbamoyl amide

21

Esters



prefix

parent

suffix

First give location and type of substituents. Then give the name of the alky group bonded to the ester functional group

How many carbons in longest chain?Carbonyl carbon @ C1

What is the functional group? How many?Ester: “-oate”

butan

12

34

oatemethyl


O

O



halide



ketone oxo one


oic acid carboxylic



Nomenclature

22

Nomenclature Amide



prefix

parent

suffix



What is the functional group? How many?Amide: “-amide”

butan

12

34

amide3-methyl


O

N



halide



ketone oxo one


oic acid carboxylic



H

H

23

Amide



prefix

parent

suffix

Use “N” to indicate naming amide R groups


What is the functional group? How many?Amide: “-amide”

butan

12

34

amideNN-dimethyl


O

N



halide



ketone oxo one


oic acid carboxylic



Nomenclature

24

Nomenclature Amines



prefix

parent

suffix

Give location and type of substituents. Indicate naming the amine R groups with “N”

How many carbons in longest chain?Amine @ C1

What is the functional group? How many?Amine = “amine”

butan

24

amineN,N-dimethyl


N



halide



ketone oxo one


oic acid carboxylic



amine amino amine

13

Nomenclature Amines

Reactions SummaryH2O

H2SO4

H2O

H2SO4

H2O/H2SO4

H2O

2 eq ROH (alcohol)H2SO4

H2O

ROH (alcohol)H2SO4

Hydration

Dehydration

Hydrolysis ofAcetals & Hemiacetals

Acetal & Hemiacetalformation

Esterification

H OH

H OH

OR

ORRO

ORRO

Δ

HNR2

H2O/H2SO4

H2O/NaOH

Amide Formation

Ester/AmideHydrolysis

Ester/AmideHydrolysis

NR2

OR

NR2

O- Na+

Reactions Summary

Nucleophile

H2SO4

HX(X = Br or Cl)

NucleophilicSubstitution

Hydrohalogenation H X

Nuc

[O]

NH4OH

Ag2O

[O]

[H]

Pd, Pt, or Rh catalyst

[H] or H2Hydrogenation

Reduction

Oxidation

Selective Oxidation

Oxidation

2 RSH RS SR

RS SR 2 RSH

Reactions Summary

X2

HNO3

H2SO4

SO3

Pd, Pt, or Rh catalyst

[H] or H2

FeX3

(X = Cl or Br)

H2SO4

Sulfonation

Nitration

Chlorination orBromination

Reduction

Cl

NO2

SO3H

NH3 NH4

NH3

HCl NaOHAmine Acid/Base

C CCCH HHH

H HHHH

CH3CH2CH2=CH2

..

Drawing Chemical Structures

Lewis Dot Structures

Structural Formula or Complete Structure

Structural Formula or Complete Structure with Geometry Indicated

Condensed Structure

Skeletal Structure

H

H

H

CCC

C

HH

H

H H

Alkanes Longest Carbon Chain


1

2

3

4

5

6

7

1

1

2

3

4

5

6

2

3

4

5

Longest CarbonChain

Alkanes 1°, 2°, 3°, 4°


C

H

H

H R C

R

H

H R C

R

H

R R C

R

R

R R

1° 2° 3° 4°

R = a Carbon atom

Alcohols & Alkyl Halides

1°, 2°, 3°

Structure Amines

Smith, Janice Gorzynski. General, Organic, & Biological Chemistry 2nd Ed.

34

Structure Amides

StereoisomersSpatial Isomers

ConstitutionalIsomers

Structural Isomers

ISOMERS

DiastereomersEnantiomers

Cis/Trans Isomers

ConformationalIsomers

R

R R R

Rotation around C-C single bonds

Different spatial arrangement of atoms but with the same connectivity

Different connectivity between atoms

Same chemical formula

Mirror images of a chiral molecule that are not superimposable

All stereoisomers that are not mirror images of one another

36

A Fischer Projection takes a 3D tetrahedral shape, and re-draws it:

Chiral Molecules Fischer Projections

Smith. General Organic & Biological Chemistry 2nd Ed.

37

Stereo-isomers Multiple Chiral Centers

chemwiki.ucdavis.edu


38

Ketones & Aldehydes

Acetal Formation


39

Ketones & Aldehydes

Acetal Hydrolysis

Carboxylic Acids

Acid/Base Chemistry

Amines Alkaloids

Cocaine

Alkaloids are compounds that contain an amine.

Biochemistry Neurotransmitters

When norepinephrine levels increase, a person feels elated, and then manic if levels go too high.

Dopamine affects the brain processes that control movement, emotions, and pleasure

Serotonin is important in mood, sleep, perception, and temperature regulation.

Acetylcholine is a quaternary ammonium ion that serves as a neurotransmitter between neurons and muscle cells

Lipids Categories of Lipids

Lipids Categories of Lipids

Carbohydrates Monosaccharides

Smith, Janice Gorzynski. General, Organic, & Biological Chemistry 2nd Ed. 45

generally have 3 to 6 C atoms in a chain with an aldehyde or ketone ending and many –OH groups.

Aldehyde monosaccharides are aldoses

ketone monosaccharides are ketoses.

Carbohydrates D vs L Monosaccharides


The configuration of the chirality center farthest from the carbonyl group determines whether a monosaccharide is D or L.

All naturally occurring sugars are D sugars.

Carbohydrates Cyclic Monosaccharides


The C atom that is part of the hemiacetal is a new chirality center, called the anomer carbon.

Haworth projections

Carbohydrates Disaccharides


48

Amino Acids Basic Structure


Peptides Amide Bond Formation


Proteins 1°, 2°, 3°, 4° Structure


Enzymes Function

http://leavingbio.net/enzymes.htm52

Enzymes Inhibition

53http://o.quizlet.com/i/WRLW8kdWLDOY1YZbEdKgyA_m.jpg

Nucleotides Summary of Structure

54

Nucleic Acids Definition


•Nucleic acids (DNA and RNA) are polymers of nucleotides joined by phosphodiester linkages.

DNA Base Pairs


The bases always line up so that a

pyrimidine derivative can

hydrogen bond to a purine

derivative on the other strand.

RNA Translation & Protein Synthesis


MutationsTypes


ADP/ATP Hydrolysis & Phosphorylation

59

•This forms ADP and hydrogen phosphate (HPO42−),

releasing 7.3 kcal/mol of energy.

59

•Phosphorylation is the reverse reaction, where a phosphate group is added to ADP, forming ATP requiring 7.3 kcal/mol of energy.

Coenzymes

Citric Acid Cycle

Overview

61Smith, Janice Gorzynski. General, Organic, & Biological Chemistry 2nd Ed.

Electron Transport

Definition


•The electron transport chain is a multistep process using 4 enzyme complexes (I, II, III and IV) located along the mitochondrial inner membrane.

63

Steps


Metabolism

Biochemical Rxns

Common Enzymes


Glycolysis Energy Investment & Generation


Glycolysis Overall Reaction


•2 ATPs are used in phase one of glycolysis, and 4 ATPs are made in phase two of glycolysis.

•The net result is the synthesis of 2 ATPs from glycolysis

•The 2 NADHs formed are made in the cytoplasm and must be transported to the mitochondria to join the electron transport chain and make ATP.

Pyruvate can be converted into three possibleproducts depending on the conditions and the organism.

under aerobicconditions

under anaerobicconditions

in fermentationby microorganisms

Glycolysis Pyruvate


Glycolysis ATP Yield


Documents

Chem 131 Final Exam Review: Roadmap 1.Learning Objectives 2.Functional Groups 3.Nomenclature 4.Organic Reactions 5.Drawing Molecules 6.Isomers 7.Chirality