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USC / Chemistry / CHEM 102 / Name that longest chain with the appropriate alkane name.

Name that longest chain with the appropriate alkane name.

Name that longest chain with the appropriate alkane name.

Description

School: University of South Carolina
Department: Chemistry
Course: Fundamental Chemistry II
Professor: Daniel taylor-perry
Term: Fall 2015
Tags: Chemistry
Cost: 50
Name: Chem 102 Final Exam Study Guide
Description: These notes cover the main topics of organic and biochemical from the study guides provided from Mr. Sodetz.
Uploaded: 11/28/2016
46 Pages 50 Views 2 Unlocks
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Final Exam Study Guide Wednesday,  November  30, 2016 3:00 PM


Name that longest chain with the appropriate alkane name.



Organic:

Alkanes  


List the groups alphabetically in front of the longest chain name.



○ Nonane = 9 carbons and Decane = 10 carbons

○ Nonane = 9 carbons and Decane = 10 carbons

Naming Alkanes

1.

Find the longest continuous chain of carbon atoms. This  longest chain may not be written in a straight line.

2. Name that longest chain with the appropriate alkane name.

3.

Find the substituents and name each of them with the  appropriate group name. We also discuss several other topics like What controls the respiratory system?

4.

Number the carbons in the chain such that the lowest number is  given to the group nearest one end of the chain.

5.

List the groups alphabetically in front of the longest chain  name.


Divide the name into the name of the branches and the name of the stem.



6.

Precede each group name with a prefix indicating how many of  them are present in the molecule. In front of the prefix, list the  numbers of each group in the molecule and separate the  numbers with a hyphen.

Naming Branched Alkanes ○

Divide the name into the name of the branches  and the name of the stem.

▪ Draw the straight chain alkane stem.

Number the carbon atoms making up the stem's  chain.

Break the rest of the name up into individual  branch names. We also discuss several other topics like What is needed for curiosity and interest to enjoy life for its own sake?

Determine the number of identical branches (if  any).

Determine the location of the carbon atom on the  stem to which each branch (side chain) is  attached.

Note the locations of the branches on the  numbered stem chain you have already drawn. ▪ Don't forget about the age old question of What are the characteristics of the phylum porifera?

Draw the required number of carbon atoms for  each branch at the specified location along the  stem's carbon chain.

Complete the structure by adding a hydrogen  atom at the end of any vacant covalent bond.

Naming Cycloalkanes Parent Chain 

stem's carbon chain.

Complete the structure by adding a hydrogen  atom at the end of any vacant covalent bond.

Naming Cycloalkanes Parent Chain 

a.

Use the cycloalkane as the parent chain if it has  a greater number of carbons than any  

alkylsubstituent.

b.

If an alkyl chain off the cycloalkane has a  greater number of carbons, then use the alkyl  chain as the parent and the cycloalkane as a  cycloalkyl-substituent.

2. Numbering the Cycloalkane 

a.

When numbering the carbons of a cycloalkane,  start with a substituted carbon so that  thesubstituted carbons have the lowest  numbers (sum).

b.

When two or more different substituents are  present, number according to alphabetical  order.

3. Halogen Substituents 

a.

Halogen substituents are treated exactly like  alkyl groups

Properties of Alkanes  

▪ Saturated hydrocarbons If you want to learn more check out What is the meaning of intensifying according to the stage model of relationship development?

▪ Only carbon-carbon single bonds  ▪ CnH2n+2 = molecular formula  

Can exist as solids, liquids, and gases

□ Up to butane = gases

□ Pentane through hexadecane are liquids

Branched alkanes have lower boiling points than unbranched  

alkanes

Greater van der Waals forces between molecules of  

unbranched alkanes because of a greater surface area  

Solid alkanes have low melting points  ▪

Strong repulsive forces between electrons on neighboring  

atoms  

▪ Completely insoluble in water mmn Rin f Alkn  

unbranched alkanes because of a greater surface area  Solid alkanes have low melting points  

Strong repulsive forces between electrons on neighboring  

atoms  

▪ Completely insoluble in water Common Reactions of Alkanes  We also discuss several other topics like How many core vocabulary words are there?

Combustion □ If you want to learn more check out Did any of the romanov family survive?

▪ Monohalogenation

Alkenes

Naming Alkenes

1. The ene suffix (ending) indicates an alkene or cycloalkene.

2.

The longest chain chosen for the root name must include both  carbon atoms of the double bond.

3.

The root chain must be numbered from the end nearest a  double bond carbon atom. If the double bond is in the center of  the chain, the nearest substituent rule is used to determine the  end where numbering starts.

4.

The smaller of the two numbers designating the carbon atoms  of the double bond is used as the double bond locator. If more  than one double bond is present the compound is named as a  diene, triene or equivalent prefix indicating the number of  double bonds, and each double bond is assigned a locator  number.

5.

In cycloalkenes the double bond carbons are assigned ring  locations #1 and #2. Which of the two is #1 may be determined  by the nearest substituent rule.

6. Substituent groups containing double bonds are:

 H2C=CH– Vinyl group

 H2C=CH–CH2– Allyl group

Properties of Alkenes

Hydrocarbons containing a carbon-carbon double bond  

(unsaturated)

Properties of Alkenes ○

Hydrocarbons containing a carbon-carbon double bond  

(unsaturated)

▪ Formed by loss of hydrogen atoms from adjacent carbon atoms  ▪ CnH2n

▪ Planar geometry  

▪ No rotation around double bond

Cis and Trans Isomers ▪

C=C in double bonds cannot rotate freely like C-C single  

bonds; geometric isomers  

Possible whenever an alkene has two different substituent  

groups on each carbon that forms the double bond □

Addition Reactions of Alkenes ○

Hydrogen (H2) (Hydrogenation)

□ Symmetric reagent, requires Pt or Ni as a catalyst Halogenation

□ F2 Cl2 Br2

Addition Reactions of Alkenes ○

Hydrogen (H2) (Hydrogenation)

□ Symmetric reagent, requires Pt or Ni as a catalyst Halogenation

□ F2, Cl2, Br2

□ Symmetric reagent

1-Hexene with Br2 = deep red color is decolorized as it  

reacts with the double bond of 1-Hexene

Hydrohalogenation

□ HCl, HBr, HI

□ Asymmetric reagent  Hydration

□ Asymmetric reagent □ Water  

Adds to double bonds in the presence of a strong acid to  

form an alcohol  

Combustion

Alkenes burn in the presence of oxygen producing carbon  

dioxide and water  

REMEMBER: MAJOR AND MINOR PRODUCTS

□ Major only = if symmetric

□ Major and minor = if asymmetric

Follow Markovnikov's rule □

In an addition reaction of an asymmetric reagent  with an asymmetric alkene, the major product is the  one formed when hydrogen from the asymmetric  reagent (HX) adds to the double-bonded carbon that  initially has the most hydrogens  

Alkynes

Stability of Carbocations

◆ Tertiary > Secondary > Primary  

▪ Carbon-carbon triple bonds  ▪ -yne  

Aromatic Compounds  

▪ Contain a benzene ring  

▪ A "flat" molecule

▪ Trigonal planar structure

Alcohols  

    

▪ Trigonal planar structure Alcohols  

Naming Alcohols

1. OH group is the primary functional group  

2. Use alkane name as parent, remove -e, replace with -ol  

3.

Number the longest chain containing the OH so the OH  groups has the lowest possible number  

4. Indicate OH position on parent chain  

5. Name and number any side chains or other groups  □

Properties of Alcohols  

Hydrogen bonding in alcohols accounts for high boiling  

points  

□ Hydrogen bonding accounts for high solubility in water

Behave like both a weak acid and a weak base at times  

(donate or accept a proton)

Hydrogen bonding in alcohols accounts for high boiling  

points  

□ Hydrogen bonding accounts for high solubility in water

Behave like both a weak acid and a weak base at times  

(donate or accept a proton)

Elimination Reactions ▪

Dehydration  

Acid + high temperature produces an alkene; major  product is one that results in greatest number of  alkyl groups on a double-bonded carbon  

Most favorable for Tertiary>Secondary>Primary  carbocations, thus Tertiary>Secondary>Primary  alcohols are most reactive

Oxidation

Complete

◊ Leads to formation of CO2 and H20 ◆

Mild

Converts primary and secondary alcohols into  

carbonyl-containing compounds  

Two H atoms are removed during the  

reaction; one form -OH, and one from the  carbon bonded to -OH  

Organic oxidation

One that increases the number of C-O bonds  

and/or decrease the number of C-H bonds  

Organic reduction  

One that decreases the number of C-O bonds  

and/or increases the number of C-H bonds  

Primary alcohols converted to aldehydes and further  to carboxylic acids if excess oxidant is used

◆ Secondary alcohols are converted to ketones  

◆ Tertiary alcohols undergo no oxidation reactions Ethers

       Ethers

Naming Ethers

Treat each carbon chain as a branch off the oxygen  

◆ Give each flanking substituent a -yl ending  ◆ Add "ether" to the end of the name  

IUPAC names:

Identify the longest carbon chain and use it as the  parent name with an -ane ending  

◆ Name the shortest carbon chain with an -oxy ending  

Number longest chain so ether bond gets lowest  possible number

Used other IUPAC rules for naming and numbering  substituents  

Properties of Ethers

□ Dipole-dipole interactions  

□ Cannot form hydrogen bonds with other ether molecules  

Can be involved in H-bondng with systems able to donate  

H (water)  

□ Lower melting and boiling points than alcohols □ Solubility similar to alcohols  

Reactions

Can be involved in H-bondng with systems able to donate  

H (water)  

□ Lower melting and boiling points than alcohols □ Solubility similar to alcohols  

Reactions

Formation of Ethers from Alcohols □

Thiols  

Adding an acid to a primary alcohol with make an  alkene at high temperatures (around 180 degrees) At lower temperature (less than 140 degrees  Celsius) an ether will be the major project  

▪ Contains an -SH group  

Naming Thiols  

□ Add -thiol to the parent hydrocarbon name  Reactions  

▪ Contains an -SH group  

Naming Thiols  

□ Add -thiol to the parent hydrocarbon name  Reactions  

□ Oxidation  

□ Reduction  

Aldehydes  

▪ Contain a carbonyl group  ▪ Trigonal planar- flat  

▪ C=O on end  

Nomenclature of Aldehydes ▪

Find longest carbon chain that contains the aldehyde  

group  

□ Change ending of base alkane name from -e to -al  □

Properties  

Higher boiling points than corresponding alkanes but  

lower than similar alcohols  

Alcohols can hydrogen bond with each other but  

aldehydes and ketones cannot  

Higher boiling points relative to alkanes are primarily  

due to dipole-dipole attractions  

Shorter chain aldehydes and ketones (less than 5-6  

carbons) are soluble in water due to ability to accept  hydrogen bonds from water

□ Longer chain molecules are poorly soluble in water Reactions  

Oxidation  

◆ Aldehydes are oxidized to carboxylic acids  ◆ H on C=O is replaced by -OH

Reduction  

Ketones  

Aldehydes are reduced to primary alcohols; uses  H2,Pd as reducing agent  

▪ C=O not on end  

Nomenclature of Ketones

□ Find longest chain that contains C=O  □ Must not be an end or it is an aldehyde

▪ C=O not on end  

Nomenclature of Ketones

□ Find longest chain that contains C=O  

□ Must not be an end or it is an aldehyde

□ Change ending of base alkane name from -e to -one  

Find lowest number to show location of the carbonyl  

C=O  

□ Name and number substituents as before  □

Properties

□ Same as aldehyde  

Reactions

Oxidation  

◆ No reaction

You can not oxidize a ketone no matter how much  oxidant you use  

Amines  ▪

Reduction

◆ A ketone can be reduced to a secondary alcohol  

▪ Organic derivatives of ammonia  

Classified according to the number of carbon atoms attached to  

the nitrogen  

 

▪ Organic derivatives of ammonia  

Classified according to the number of carbon atoms attached to  

the nitrogen  

▪ Lone pair is responsible for properties and chemistry  

Nomenclature  ▪

Primary Amines  

Locate longest carbon chain that contains -NH2 group

Treat -NH2 group like a substituent and call it  amino

◆ Assign location so lowest possible number if used  ◆

Secondary and Tertiary amines  

Parent name is based on longest chain that contains  the amine N  

Each additional alkyl group bonded to the N is  named as an N-alkyl group  

N- is used in front of the alkyl group to indicate the  substituent is on the amine N  

□ Amine Salts  

◆ Name each substituent on the N as a separate alkyl  group and follow with the name ammonium  

◆ Then name the halide  

Properties of Amines

□ Amine Salts  

◆ Name each substituent on the N as a separate alkyl  group and follow with the name ammonium  

◆ Then name the halide  

Properties of Amines

◆ Primary and secondary amines can form H-bonds  with each other using the lone pair of e- on one N  and H on a neighboring N  

◆ Tertiary amines cannot H-bond with each other ◆ All can form H-bonds with water (= good  

solubility)  

◆ B.P. of amines is generally higher than alkanes but  lower than alcohols of similar size  

◆ Nitrogen is very electronegative  

◊ N-H bond is very polar  

◊ Hydrogen bonding is possible  

◊ High boiling points  

◊ Amines act as organic bases  

???? Amines react with acids and accept a H+  

= amine "salt"  

◆ Produced by ammonia and an alcohol  

□ Reactions  

◆ Primary amine made from NH3 and a primary  alcohol

◆ Secondary and Tertiary amines from primary and  secondary amines, respectively + primary alcohol  ◆

○ Carboxylic acids  

▪ Prepared by oxidation of primary alcohols or aldehydes  ▪

Nomenclature of Carboxylic Acids

□ Find the largest carbon chain that contains the -COOH  group

Drop the -e from the end of the alkane name and  

substitute -oic acid  

□ Number and name branches or other substituents  □ #1 carbon is the acid carbon (carbonyl carbon)  

□ Can also be named with alpha and Beta  

◆ The -NH2 group is on the alpha carbon atom  

□ Carboxylate Salts  

◆ Produced by a reaction between a carboxylic acid  and a strong base

◆ The positive ion is named first  

◆ The carboxylate ion is named by changing the  ending of the acid's name from -ic acid to -ate  

▪ Properties of Carboxylic Acids  

□ The presence of two polar groups results in very strong  hydrogen bonding  

□ Carboxylic acids are weak acids and undergo ionization  in water to form a carboxylate ion  

□ The comparative strength of an acid is measured by its  acid dissociation constant (Ka); the smaller the value of  Ka, the weaker the acid  

□ About 1.8 x 10-5 

□ Acetic acid = vinegar  

□ Citric acid = produced by almost all plants and animals  during metabolism  

▪ Reactions

□ Synthesis: oxidation of primary alcohol to aldehyde to a

□ Acetic acid = vinegar  

□ Citric acid = produced by almost all plants and animals  during metabolism  

▪ Reactions

□ Synthesis: oxidation of primary alcohol to aldehyde to a  carboxylic acid  

□ Carboxylate salts formed by reaction with bases  

○ Esters  

▪ -OH of a carboxylic acid is replaced with an -OR group ▪ Naming of Esters

□ Name the R group in -OR like a side chain  

□ Then name acid portion with -ate ending

▪ Reactions of Esters

□ Synthesis: Carboxylic acid + alcohol  

▪ Reactions of Esters

□ Synthesis: Carboxylic acid + alcohol  

□ Hydrolysis:  

◆ With acid  

◊ Reversal of esterification

◊ Produces an acid and an alcohol  

◆ With base

◊ Hydrolysis with a strong base  

◊ Produces a carboxylate salt and an alcohol  

▪ Properties of Esters

□ Aspirin

◆ White, crystalline solid composed to acetylsalicylic  acid, an ester formed between acetic acid and the  

alcohol -OH group of salicylic acid  

◆ Prodrug = inactive in form and metabolized in the  intestine into the active form  

◆ Provides pain relief, reduces fever, and reduces  

inflammation  

◆ Gastric bleeding and gastrointestinal distress  

□ Ibuprofen  

◆ Nonsteroidal anti-inflammatory drug  

◆ Relief of symptoms of arthritis, abdominal cramps,  fever, and as an analgesic  

◆ Lowest incidence of adverse gastrointestinal side  

effects

○ Acid Halides & Anhydrides  

▪ Acid Halides

fever, and as an analgesic  

◆ Lowest incidence of adverse gastrointestinal side  effects

○ Acid Halides & Anhydrides  

▪ Acid Halides

▪ Anhydrides

○ Amides  

▪ Amine derivative of a carboxylic acid  ▪

▪ Nomenclature of Amides

□ Drop -oic acid ending and replace with amide □

▪ Reactions of Amides

□ Synthesis:  

◆ Carboxylic acid + NH2 or primary or secondary  amine  

◆ Acid halide + NH2 or primary or secondary amine  ◊

□ Hydrolysis  

◆ Results in the formation of a carboxylic acid and  amine  

◆ With acid

◆ With base  

□ Properties of Amides

◆ Primary and secondary amides generally have  higher boiling points than similar carboxylic acids  ◆ Amides generally have higher water solubility than  similar carboxylic acids  

◆ Boiling points decrease as the order of amide  substitution increases primary > secondary >  

tertiary

       

◆ Amides generally have higher water solubility than  

similar carboxylic acids  

◆ Boiling points decrease as the order of amide  

substitution increases primary > secondary >  

tertiary  

◆ Reason: Primary and secondary amides can H-bond  

to each other (Tertiary cannot)

◆ Acetaminophen  

◊ Reduces fever and pain

◊ Not an anti-inflammatory agent  

◊ Does not induce internal bleeding  

◊ Can cause kidney and liver damage

◆ Benzocaine

◊ Local anesthetic used in topical preparations;  

blocks transmission of impulses by sensory  

nerves  

◆ Lidocaine  

◊ Most commonly administered by injection to  

prevent pain during dental work  

◆ Polyamides  

◊ Nylons  

???? Produced by reaction of diamines with  

diacids  

???? Nylon 6,6 is made by heating adipic acid  

with hexamethlyenediamine  

???? High strength, abrasion resistance,  

◊ Polyesters  

???? Made from diacids and dialcohols  

◊ Kevlar  

???? Polyamide  

???? Produced from a dicarboxylic acid and a  

diamine  

???? Five times stronger than steel  

???? H-bonding holds the polymer chains  

together  

???? Poor electrical conductor  

???? Bulletproof vests  

Biochemical:

???? Bulletproof vests  

Biochemical:  

Chapter 20 Carbohydrate Learning Objectives

1. What are the different kinds of carbohydrates?

Be able to define monosaccharides, disaccharides, and  polysaccharides, and recognize examples of each.

Monosaccharides  

○ One monomeric unit

○ D-glyceraldehyde  

○ Dihydroxyacetone  

○ Three carbons = trioses ○ Four carbons = tetroses ○ Five carbons = Pentoses  ○ Six carbons = Hexoses  ○ Aldo- or keto-

Disaccharides

Two monosaccharides connected by a glycosidic  bone

Maltose  

▪ Alpha-D- glucose and Alpha- D- glucose  ▪ Alpha (1-4) linkage  

Lactose  

▪ Beta-D- galactose and Beta-D-glucose  ▪ Beta (1-4) linkage  

Sucrose  

▪ D-glucose and D-fructose

▪ Alpha, Beta (1-2) linkage  

Polysaccharides

○ More than 20 monosaccharides  

Cellulose

▪ Plant cell wall structural polysaccharide ○

Starch

▪ Storage form of glucose in plants

Glycogen

▪ Storage form of glucose in animals  

○ All are composed of only glucose  

2. Why are monosaccharides chiral, and how does this  influence the numbers and types of their isomers? Be able to identify the chiral carbon atoms in monosaccharides,  redict the number of isomers for different monosaccharides,

▪ Storage form of glucose in animals  

○ All are composed of only glucose  

2. Why are monosaccharides chiral, and how does this  influence the numbers and types of their isomers? Be able to identify the chiral carbon atoms in monosaccharides,  predict the number of isomers for different monosaccharides,  and identify pairs of enantiomers.

Chiral carbon  

○ Carbon that has four single bonds  

An asymmetric carbon atom (chiral carbon) is  

a carbon atom that is attached to four different  types of atoms or groups of atoms.

Enantiomers

Stereoisomers that are nonsuperimposable mirror  images of each other  

Diastereomers  

Stereoisomers that are not mirror images of each  other  

3. What are the main structural features of  

monosaccharides?

Be able to explain relationships among open-chain and cyclic  monosaccharide structures; describe the isomers of  monosaccharides, and describe how they are represented by  Fischer projections and cyclic structural formulas. Describe  how hemiacetal and hemiketals are formed.

D- Stereoisomer  

○ Predominant in nature

Same configuration as D-glyceraldehyde in the  chiral carbon most distance from the carbonyl  carbon

L-Stereoisomer

-OH group on the chiral carbon most distant from  the carbonyl carbon is on the left  

Cyclization of Aldoses  •

Reaction of an alcohol with an aldehyde yields a  hemiacetal (aldoses >4 C can cyclize when  forming a hemiacetal)  

-          

the carbonyl carbon is on the left  

Cyclization of Aldoses  •

Reaction of an alcohol with an aldehyde yields a  hemiacetal (aldoses >4 C can cyclize when  forming a hemiacetal)  

Glucose  

Exists in two cyclic forms that differ only at  their anomeric carbon

Anomeric carbon  

The most oxidized carbon in a cyclized  monosaccharide; chiral carbon in ring  structures and thus can adopt an alpha or beta  configuration

Cyclization of Ketoses  •

Reaction of an alcohol with a ketone yields a  hemiketal (ketoses >5 C can cyclize when forming  a hemiketal)  

If in an individual cyclic structure, the -OH group is  

pointing down = alpha

• If the -OH group is pointing up = beta  

4. How do monosaccharides react with oxidizing agents and  alcohols?

Glycosidic bond is the bond between the anomeric C of a  

monosaccharide and a -OR group (forms an "acetal")

The sugar anomeric carbon is condensed with an  alcohol, amine, or thiol  

Reducing sugars  •

Aldehydes can be oxidized to carboxylic acids by  oxidizing agents (Cu2+, Ag+) at basic pH  ○

Aldose monosaccharides with a "free" anomeric  carbon (the #1 carbon is not linked to any other  structure) contain a reactive aldehyde and thus are  reducing sugars  

○ Ketoses are also reducing sugars in basic solutions  Reducing vs. Nonreducing sugars

Aldose and ketose monosaccharides can potentially  contain a free aldehyde or ketone group (open  chain) and therefore are reducing sugars  

Disaccharides containing a "free" anomeric  carbon (unlinked to another sugar) are reducing  sugars = maltose, lactose  

Disaccharides with no free anomeric carbon are  

         chain) and therefore are reducing sugars  ○

Disaccharides containing a "free" anomeric  carbon (unlinked to another sugar) are reducing  sugars = maltose, lactose  

Disaccharides with no free anomeric carbon are  nonreducing sugars (sucrose)  

5. What are the main structural features of some important  disaccharides?

Be able to name and identify the monosaccharides combined in  maltose, lactose, and sucrose, and describe the types of  linkages between the monosaccharides. Describe the role of  carbohydrates in the ABO blood type system.

Maltose  

○ Alpha-D- glucose with alpha-D-glucose  ○ Alpha (1-4) linkage  

Lactose  

○ Beta-D-galactose and Beta-D-glucose ○ Beta(1-4) linkage

Sucrose

○ D-glucose and D-fructose

○ Alpha, Beta (1-2) linkage  

• cell-cell recognition.  

carbohydrates allow specific recognition between  cells using relatively small molecules.

People with blood type O can receive only O type  blood but can donate to any blood type. People with  blood type A can receive only A and O type blood  but can donate to A and AB recipients. Similarly,  people with blood type B can receive only B and O  type blood but can donate to B and AB recipients.  People with blood type AB can receive any type of  blood but can only donate to other AB types. All  people synthesize a precursor carbohydrate, called  the H antigen, which is attached to lipids or proteins  on the outer surface of red blood cells. Specific  enzymes synthesized by the ABO genes attach  additional monosaccharides to the H antigen, and  the completed carbohydrate determines that  '

           on the outer surface of red blood cells. Specific  enzymes synthesized by the ABO genes attach  additional monosaccharides to the H antigen, and  the completed carbohydrate determines that  person's blood type.

6. What are the distinguishing structural features and  functions of cellulose, starch and glycogen?

Be able to describe the monosaccharides and linkages in these  polysaccharides, and their biological functions.

Cellulose

○ Plant cell wall structural polysaccharide

Linear polymer of >1,000 Beta-D-glucoses linked  

by Beta (1-4) glycosidic linkages

○ Chair conformation = maximum H-bonding  Starch

○ Storage form of glucose in plants

Amylose  

Linear polymer of 100-1000 alpha-D-glucoses  

linked by alpha (1-4) glycosidic linkages

Amylopectin  

Glycogen

Contains 100-100000 alpha-D-glucoses linked  alpha (1-4) with frequent alpha (1-6) branch  points  

○ Storage form of glucose in animals  

similar structure as amylopectin but larger and  

many more alpha (1-6) branch points  

Chitin

○ Component of shells  

Composed of repeating N-acetly- beta-D

glucosamine  

○ Second most abundant polysaccharide  Fall 16

Chapter 23 Lipids Learning Objectives

Describe the properties of fatty acids?

Describe the structural features and physical properties of the  common fatty acids. Relate the IUPAC names of fatty acids to  their structures and be able to decipher shorthand notations for  fatt acids. Describe saturation and unsaturation and the

Chapter 23 Lipids Learning Objectives

Describe the properties of fatty acids?

Describe the structural features and physical properties of the  common fatty acids. Relate the IUPAC names of fatty acids to  their structures and be able to decipher shorthand notations for  fatty acids. Describe saturation and unsaturation and the  influence on melting points.

Mono-carboxylic acids with long hydrocarbon side  

chains  

• Can either be saturated or unsaturated  

As the fatty acid becomes more unsaturated, the melting  

point decreases because there are less contact points  

Describe the distinguishing structural features and  properties of the major classes of lipids.

Be able to describe key structural features and differences  between fatty acids, waxes, triacylglycerols,  glycerophospholipids and sphingolipids.

Waxes

Mixture of long-chain carboxylic acids esterified  with long-chain alcohols  

Form important protective barriers on plants and  animals

○ Simplest of fatty acid esters

Triacylglycerols

○ Important metabolic fuels  

○ Neutral lipids  

○ 3 fatty acyl residues esterified to glycerol  

Very hydrophobic and are stored in adipose tissue  in anhydrous form  

○ 90% of our dietary lipid intake  

Glycerophospholipids

○ Most abundant lipid in mammalian cell membranes  ○ Contain a glycerol backbone  

Have two FA groups esterified to C-1 and C-2 of  glycerol 3-phosphate  

Phosphate is esterified to both glycerol and a  second compound  

Sphingolipids  

Membrane lipids with one long-chain amino  alcohol called a sphingosine, one long-chain fatty  acid and one polar head group joined by a  glycosidic bond or a phosphodiester bond  

   

Sphingolipids  

Membrane lipids with one long-chain amino  alcohol called a sphingosine, one long-chain fatty  acid and one polar head group joined by a  glycosidic bond or a phosphodiester bond  

○ Second most abundant lipid  

What reactions do triacylglycerols undergo? Be able to describe hydrogenation and hydrolysis of  triacylglycerols, and, given the reactants, predict the products.

Reactions:  

Hydrogenation of unsaturated fatty acid acyl chains;  can produce trans FA as by-product  

○ Hydrolysis with base to release free FA  

What are sterols?

Be able to recognize sterols and their derivatives, generally  describe their structures and roles. Describe some of the  functions of cholesterol.

Steroids  

○ Core structure is a fused planar ring  

Cholesterol

○ "sterol"

○ Contains an -OH

○ Modulates fluidity of mammalian cell membranes  ○ Precursor of steroid hormones and bile salts  ○ Less flexible than most other lipids (fused rings)  

What are membrane lipids?

Describe the difference between micelles, liposomes and  bilayers. Be able to describe the role of membrane lipids and  how proteins interact with membranes.

What are membrane lipids?

Describe the difference between micelles, liposomes and  bilayers. Be able to describe the role of membrane lipids and  how proteins interact with membranes.

Micelles

Fatty acids are wedge-shaped and tend to form  spherical micelles

Liposomes

Form to minimize interactions between water and  

the hydrophobic "edges" of a bilayer  

Has polar heads in the middle; micelle has tails in  

the middle and heads on the outside  

Bilayers

Forms when cross-section of the head group and  

acyl chains are similar-sized  

Membrane Proteins •

Integral membrane proteins ○

Contain hydrophobic regions embedded in the  

hydrophobic lipid bilayer. Many span the  bilayer completely  

Peripheral membrane proteins ○

Associated with membrane through charge

charge or H-bonding interactions, often with  integral membrane proteins or lipid

Lipid-anchored membrane proteins  ▪

Peripheral membrane proteins ○

Associated with membrane through charge

charge or H-bonding interactions, often with  integral membrane proteins or lipid

Lipid-anchored membrane proteins  

▪ Tethered to the membrane by a covalent bond  

Role of Membrane Lipids  •

Lipids are amphipathic and aggregate to minimize  

hydrophobic surface area that interacts with water  

What is the nature of a cell membrane?

Be able to describe the general organization of a cell  membrane and identify some of its common components. •

What are eicosanoids?

Be able to recognize eicosanoids.

Eicosanoids  

Oxygenated derivatives of C20 polyunsaturated  fatty acids  

Fall 16

Chapter 18 Proteins Learning Objectives

What are the structural features of amino acids? Classify amino acid side chains if given a structure (nonpolar,  uncharged polar, etc). Describe how ionic charges on an amino  acid vary with pH.

Nonpolar side chains  •

○ ○

Glycine ▪

Alanine ▪

Valine  ▪

○ ○ ○

Leucine

Isoleucine ▪

Methionine  ▪

○ ○

Proline  

Phenylalanine ▪

Tryptophan  ▪

Uncharged polar side chains  •

○ ○

Serine

Threonine  

 

○ ○

 

Asparagine  ▪

Glutamine  ▪

Tyrosine

○ ○

Tyrosine ▪

Cysteine  ▪

Charged Basic Polar side chains  •

○ ○

Lysine ▪

Arginine

Histidine ▪

Charged Acidic Polar side chains •

○ ○

Aspartic acid ▪

Glutamic acid  ▪

At physiological pH the alpha-amino acids are  

zwitterions (dipolar ions)

○ Amino group = -NH3+

○ Carboxyl group = -COO-

What are the properties of amino acids?

Describe the types of interactions mediated by the amino acid  side chains

Interactions between Amino Acids

○ Maintaining protein structure  

○ Binding small molecules

○ Facilitating interactions with other proteins  ○ Forming catalytic "active" sites in enzymes  ○ Regulating enzyme activity  

1. Van der Waals Interactions

2. The Hydrophobic Effect

3. Hydrogen Bonding

4. Charge-Charge Interactions

5. Ring Stacking

6. Cation-Ring Interaction

7. Disulfide Bonds  

How are amino acids linked to form peptides and  polypeptides?

Describe how a peptide bond is formed and basic features of a  peptide bond.

Peptide bond

Linkage between amino acids is a secondary amide  bond

Formed by condensation of the alpha-carboxyl of  one amino acid with the alpha-amino group of  another (with loss of water)  

one amno ac wt te apa-amno group o  another (with loss of water)  

What is the primary structure of a protein and what  conventions are used for drawing and naming primary  structures?

Be able to define protein primary structure and explain how  primary structures are represented,

• Amino acid sequence  

Shorthand sequences are written from the N-terminus to  

the C-terminus  

What types of interactions determine the overall shapes of  proteins?

Describe and recognize disulfide bonds and noncovalent  interactions such as hydrogen bonding, etc. between amino  acid side chains in proteins.

1.

Van der Waals Interactions

a.

Weak non-valent interaction between any two  atoms in close proximity

2.

b. Temporary dipoles The Hydrophobic Effect

a.

Nonpolar molecules and nonpolar regions of  molecules tend to associate with each other to  exclude polar water molecules

3.

b. Stabilizing interaction Hydrogen Bonding

a. Dipole-dipole interation

b.

Formed between the H and a second electronegative  atom (F, O, N, S)

4.

Charge-Charge Interactions

3.

b. Stabilizing interaction Hydrogen Bonding

a. Dipole-dipole interation

b.

Formed between the H and a second electronegative  atom (F, O, N, S)

4.

Charge-Charge Interactions

a.

Oppositely charged amino acids participate in  electrostatic attractions  

b.

Interaction between similarly charged amino acids  in strongly repulsive

5.

Ring Stacking

a.

Dipole-dipole interaction between two aromatic  groups  

6.

Cation-Ring Interaction

a.

An ion-dipole interaction between an aromatic  group and a neighboring cation

7.

Disulfide Bonds  

a. A covalent "interaction"

b. Commonly found in proteins c. Protein stability  

What are the secondary and tertiary structures of  proteins?

Describe these structures and the attractive forces that  determine their characteristics; describe the α-helix and β sheet. Describe distinguishing features of globular and fibrous  proteins.

Secondary structures •

A peptide bond has characteristics of a partial  double bond  

○ Peptide bonds are planar  

○ Free rotation around the C-N bond does not occur

Alpha-helix

Stabilized by H-bonds within the helix  backbone

H-bonds are parallel to the long axis of the  helix

▪ R-groups protrude outward from the helix ○

Beta-Strand and Beta-Sheet

A more extended conformation of the  polypeptide chain is the beta-strand  ▪

Beta-strands form H-bonds between the  peptide bond C=O on one strand and  amide H on another

 

   

A more extended conformation of the  polypeptide chain is the beta-strand  Beta-strands form H-bonds between the  peptide bond C=O on one strand and  amide H on another

▪ Strands appear as pleats

Adjacent R groups in B-strand protrude from  the sheet in opposite directions  

Tertiary structures  •

Overall arrangement of the atoms of a protein in 3- D space

Globular proteins

Atoms are packed closely together; compact  overall structure

Hydrophobic residues in the interior,  hydrophilic on surface  

Fibrous proteins

▪ More extended, elongated structures  ▪ Generally provide structural support  

Poor water solubility allows for use as  structural support  

What is quaternary protein structure?

Be able to define quaternary structure and identify the forces  responsible for quaternary structure.

• Protein's subunit structure  

Subunits held together by noncovalent interactions or by  

disulfide bonds

Two or more polypeptide chains which may be identical  

or different  

What factors affect the stability of a protein? Describe how extremes of pH and heat affect a protein and  why.

Denaturation  

Most proteins are sensitive to pH and temperature  changes and their structures may "unfold"  

Renaturation  

Process by which a denatured protein refolds into  its original or "native" conformation  

Hydrolysis

Breakdown of a protein into its constituent amino  acids using either acid or an enzyme  

 

 

Process by which a denatured protein refolds into  its original or "native" conformation  

Hydrolysis

Breakdown of a protein into its constituent amino  acids using either acid or an enzyme  

What are some examples of a small peptide hormone,  globular protein and fibrous protein?

Describe the properties of insulin; compare and contrast the  structures and functions of myoglobin and hemoglobin;  describe general structural features of collagen.

Insulin

○ Contains 2 chains linked by disulfide bonds  ○ Synthesized in the pancreas

Regulates cellular uptake, utilization, and storage of  glucose, amino acids, and fatty acids  

Myoglobin  

A single-chain protein that facilitates the diffusion  of oxygen in tissue

Hemoglobin  

A multi-subunit protein that transports oxygen in  blood  

○ 2 alpha and 2 beta subunits  Collagen

Triple helix composed of 3 tightly wrapped helical  alpha-chains each about 1000 amino acids in  length  

Each alpha-chain is composed of repeating  tripeptide sequence Gly-X-Y where X if often Pro  and Y is often 4-hydroxyPro  

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