CHEM 504 – LESSON PLAN ASSIGNMENT #1 – …wwalsh/Walsh Protein Lesson.pdfCHEM 504 – LESSON PLAN ASSIGNMENT #1 – PROTEIN STRUCTURE STUDENT: Kate Walsh MCEP Cohort 6 DATE: July

CHEM 504 – LESSON PLAN ASSIGNMENT #1 – PROTEIN STRUCTURE STUDENT: Kate Walsh MCEP Cohort 6 DATE: July 3, 2007 TARGET AUDIENCE: AP Chemistry Students MOTIVATION: As a part of the required AP Chemistry curriculum, a certain amount of organic chemistry must be covered. What follows is a quotation from the College Board’s Acorn Book for AP Chemistry which describes the organic chemistry requirements: “3. Introduction to organic chemistry: hydrocarbons and functional groups (structure, nomenclature, chemical properties)” Thus the topic of protein structure would fit into the course quite well as a part of the organic chemistry unit. I typically take a tri-faceted approach to the organic chemistry unit: functional groups and naming, structures including isomerization, and reactions unique/common to organics. I have always felt challenged in that the organic chemistry unit seems disjointed and out of flow with the rest of the course. It seems ideal to use the student’s previous knowledge of amino acids and peptides from biology to help give some relevance to the otherwise seemingly out of flow organic chemistry unit. Amino acids are something with which they should be familiar from biology, although they very likely did not realize they are a hybrid of amines and carboxylic acids. Furthermore, they were introduced to peptide bonds as a part of their study of proteins in biology, again without any discussion of dehydration reactions which is a crucial organic reaction type covered in the AP Chemistry course. Another essential organic reaction type covered in AP Chemistry involves the formation of polymers. The AP Chemistry students were certainly introduced to the concept of a polypeptide or protein in biology but likely did not learn about them in the wider context of polymers and polymerization reactions. I am also interested in using 2o protein structure as an example of hydrogen bonding which is a part of one of the most enduring concepts in the AP Chemistry course, intermolecular forces. I am always looking for ways to reinforce and exemplify this very important type of interaction. A reference back to their study of proteins in biology should provide just such an opportunity. I will incorporate this as a part of an extension (PIM-like) follow-up to the POGIL which is part of my lesson. PLACEMENT IN THE COURSE : These lessons would be presented as a part coverage of organic chemistry. It would also follow the course’s coverage of hydrogen bonding as a part of the inter-/intramolecular forces unit.

LESSON FOCUS: Proteins are polymers formed through a dehydration mechanism. PRE-REQUISITE KNOWLEDGE

• Understanding of amino acids/amino acid structure- This is covered in the biology course which is a pre-requisite for AP Chemistry as well as in the organic section of the AP Chemistry course itself.

• Understanding of peptide bonds – This is covered in the pre-requisite biology course.

• Understanding of proteins (polypeptides) – This is covered in the pre-requisite biology course.

PRE-CLASS ASSIGNMENT

• Handout entitled “Organic Chemistry” is typically distributed to students prior to a long weekend, school vacation, or one of 3 annual junior class retreats in which several students will miss 3 or more days of class. (In order to cover the required AP Chemistry curriculum, I typically asks students to do the majority of the organic chemistry background work on their own and hence the placement at a time when I will not be seeing them for a long stretch.)

• Students are asked to complete the examples and questions in the packet of notes prior to returning to class.

IN-CLASS ACTIVITIES (70 minute AP Chemistry period)

• DO-NOW EXERCISE – “Functional Groups Identification Quick Quiz” (5 mins) • Review “Functional Groups Identification Quick Quiz” and field student questions.

(10 mins) • Instructor leads the completion of questions 1-4 on the “Organic Nomenclature”

worksheet. (5 minutes) • Instructor cold calls on students until the entire “Nomenclature Worksheet” is

completed. (10 minutes) • Students will likely run into trouble when they reach the final two questions. A

classwide discussion will be necessary to deal with this confusion. (15 minutes) - The instructor should ask the students to think about where they might

have seen a compound like this before. - Instructor asks each student to do their best to name the second to last

compound. - Instructor circulates and reports all unique names on the board. - The instructor then asks students to try to discuss and come to a

consensus on one of the chosen names or a revised name as necessary. The instructor should remind students to think about where they might have seen these compounds before! (Additional hints might include, think biology, what functional groups are present, etc.)

- The desired connection is that students realized they saw these as amino acids in biology.

• Students complete “POGIL-Proteins” exercise in randomly assigned groups. (I draw names from a prepared “hat” whenever we do POGIL exercises. See POGIL PROCEDUCRES for an explanation of how the POGIL was developed. (25 minutes)

FOLLOW-UP ACTIVITY • Students are to individually complete the exercises and problems from “POGIL-

Proteins” before the next class meeting.

Organic Chemistry Key Terms: Hydrocarbon = a compound consisting of hydrogen and carbon Saturated hydrocarbons = hydrocarbons containing only single bonds Unsaturated hydrocarbons = hydrocarbons containing multiple bonds Cyclic compounds = compounds in which the bonds form a ring. Aromatic hydrocarbons = a special class of unsaturated cyclic hydrocarbons, i.e. benzene

Carbonyl group = a carbon atom double bonded to an oxygen atom.

C O

Polymers = large chain like molecules which consist of repeating monomer units.

Functional Groups

Class

Functional

Group

General Formula

Suffix

Alkanes

CCH

H

H

C

H

H

H

H

H

R R

-ane

Alkenes

CCH

H

C

H

H

H

H

R R

-ene

Alkynes C C C HH

H

H

R R

-yne

Halohydrocarbons

X

XR

(prefix) -chloro, bromo, etc.

Alcohols

OH

OHR

-ol

Ethers

O

R O R'

Ether

Aldehydes C H

O

R C H

O

-al

Ketones C

O

R C R'

O

-one

Carboxylic Acids C OH

O

R C OH

O

-oic acid

Esters C O

O

R C O

O

R'

ester

Amines

NH2

NH2R

amine

* R= a hydrocarbon group

Naming:

1. Find the longest carbon chain. Assign it the appropriate prefix from the list below and the appropriate suffix from the list above.

# Carbons Prefix

1 Meth- 2 Eth- 3 Prop- 4 But- 5 Pent- 6 Hexa- 7 Hept- 8 Oct- 9 Non- 10 Dec-

2. Number the carbons in the chain starting at the end closest to

the first substituent. (substituent = a group bonded to the carbon chain)

3. Describe each substituent using the number of the carbon to

which it is attached. (There is no need to use a number for a substituent bonded to carbon #1.)

*when a hydrocarbon branch behaves as a substituent name it as an –yl group, i.e. methyl-, propyl-, etc.

Some examples:

H3CH2C

H2C

H2C C CH3

5 4 362-hexanol

OH

2 1

H3CH2C C CH3

3 24 1

O

2-butanone

H3CH2C C H

2 13

O

propanal

H3CH2C C OH

2 13

O

propanoic acid H3C N

CH3

CH3

trimethyl amine

HN

CH3

H2C

ethyl methyl amine

CH3

Primary (1°) : Bonded to one carbon Secondary (2°) : Bonded to two carbons (described as sec-) Tertiary (3°): Bonded to three carbons (described as tert-)

H3CH2C

HC CH3

CH3

3o2o1o 1o

1o

CHH3C

CH2CH3

sec-butyl cyclohexane Cyclic Compounds Simply start with cyclo- Use the same numbering and naming system. Number the ring with one at the carbon of the primary substituent. If there are double or triple bonds these are the primary substituents.

cyclohexene

OH

3-cyclohexenol

One important special case is benzene (systematic name: 1,3,5-cyclohexene.)

Isomers – compounds with the same molecular formula but different arrangements of atoms. Structural Isomers – simple isomerism, just differing by arrangement of atoms. 3 isomers of pentane:

H3CH2C

H2C

H2C CH3

H3CH2C

HC CH3

CH3

H3C C CH3

CH3

CH3

pentane

2-butane

iso-pentane2,2-dimethylpropane

2 isomers of propanol:

H2C

H2C OH

H3C CH

CH3

OH2-propanol

H3C 1-propanol

H2C

H2C CH3HO

not a new isomeralso 1-propanol

*You can tell if two structures are isomers by 1) do they have the same formula (numbers and types of atoms) and then naming them and making sure they’d have different names.

Cis-trans isomers – isomers which differ by the arrangement of substituents around a double bond. When the substituents are on the same side of the double bond they are called cis- and on opposite sides they are called trans-.

C C

H

Br Br

H

C C

H

Br H

Br

cis-dibromoethene trans-dibromoethane

Organic Reactions Addition reactions = a carbon-carbon pi bond is broken freeing each carbon atom to bond to another atom.

C C

H3C

H3C CH3

CH3

+ H2 H3C C

H

CH3

C

H

CH3

CH3

HC CH + Br2 C C

H

Br Br

H

Polymerization = generally formed by connecting long repeating chains of monomers. Condensation polymerization, involves polymerization in which water is released as the monomers are joined.

C C

F

F F

F

* C

F

F

C

F

F

*n

tetrafluoroethylene teflon

NH2C N6

H

H

H

HC

H2C

O

O

H

C

O

O

H

4 H2NH2C N C

H2C C

O

OH

H O

6 4

+ H2O

Cracking – larger compounds are broken down into smaller compounds. Generally at very, very high temperatures. n-C30H62 CH3(CH2)5CH CH2 CH3(CH2)10CH3 CH3(CH2)7CH CH2

+ + Oxidation (aka. Combustion) – a hydrocarbon reacts with oxygen to form water and carbon dioxide. Fermentation – an organic compound reacting in the absence of oxygen to form an alcohol and carbon dioxide. (i.e. wine or beer production.

C6H12O6 2 CH3CH2OH + 2 CO2

glucose ethanol carbon dioxide

Esterification – In esterification, an organic acid reacts with an alcohol to produce an ester and water.

CH3C

O

OH H OCH2CH3 CH3C

O

OCH2CH3 + H2O

Properties of Organic Compounds Boiling and Melting Points

Increase with increasing molecular weight i.e. bp of decane is higher than that of methane Increase with increasing degree of hydrogen bonding. i.e. bp of methanol is higher than that of methane

bp of a diol (two alcohol groups) is higher than that of a standard alcohol.

Functional Group Identification Quick Quiz

Name__________________________________________________________________ For each of the following molecules, circle any functional groups of interest and classify each one.

H3C

H2C

CH2

H2C

CH2

CH3

H3C

H2C

CH2

CH2

CH3C

O

CH3

CH3

H2C

CH2

HC

O

H3C

H2C

CH2

CHCH3

H2C

CH

H3C

H3CCH2

CCH

CH3

H3C

H3CCH2

H2C

NH2

H3C

H2C

CH2

H2C OH

C

O

Functional Group Identification Quick Quiz KEY

Name_____________________________KEY_______________________________ For each of the following molecules, circle any functional groups of interest and classify each one.

H3C

H2C

CH2

H2C

CH2

CH3

NO INTERESTING GROUPS

H3C

H2C

CH2

CH2

CH3C

O

KEYTONE

CH3

BENZENE METHYL

CH3

H2C

CH2

HC

O

ALDEHYDE

H3C

H2C

CH2

CHCH3

O

CH

H3C

METHYL ETHER

H3CCH2

CCH

CH3

H3C

PENTENE METHYL

H3CCH2

H2C

NH2

AMINE

H3C

H2C

CH2

H2C OH

C

O

CARBOXYLLIC ACID

Organic Nomenclature Worksheet

Name __________________________________________________________________ Fill in the correct IUPAC name for each of the following organic molecules in the space provided below each structure.

H3C

H2C

CH2

H2C

CH2

CH3

H3CCH

CH

H2C

CH3

CH3

H3C

H3C

H2C

CH2

CHCH3

CH2

H2C

CH3

H3C

H2C

CH2

H2C

NH2

H3C

H2C

OC

CH3

O

HC

H2C

CH3

O

H H

O

H3C

H2C

OH

H3CO CH3

C

O

H3CCH

CH

H2C

CH3

OH

CH3

Organic Nomenclature Worksheet

H3CO

CH2

H2C

CH2

CH3

OH

O

H3C CH2

CH3C

O

H3CCH2

CCH

H2C

CH3

CH3

H3CCH3

H3CC

CCH3

H3C

H2C

CH2

OHC

O

Cl

HN

Cl H2CC

CH

HC

CH3

H3C

H3C

CHO CH3

H2C

CH3

C

O

H2C

CH2

CH3

HONH2

O

NH2

CH

C

H2C

OH

O

C NH2

O

Organic Nomenclature Worksheet KEY

Name _______________________________KEY_____________________________ Fill in the correct IUPAC name for each of the following organic molecules in the space provided below each structure.

H3C

H2C

CH2

H2C

CH2

CH3

H3CCH

CH

H2C

CH3

CH3

H3C

Hexane 2,3-dimethylhexane

H3C

H2C

CH2

CHCH3

CH2

H2C

CH3

H3C

H2C

CH2

H2C

NH2

4-methylheptane butylamine

H3C

H2C

OC

CH3

O

HC

H2C

CH3

O Methyl ethylester Ethylaldehyde (ethanal)

H H

O

H3C

H2C

OH

Methylaldehyde (methanal, formaldehyde)

Ethanol

H3CO CH3

C

O

H3CCH

CH

H2C

CH3

OH

CH3 Dimethylester 3-methyl-2-hexanol

Organic Nomenclature Worksheet KEY

H3CO

CH2

H2C

CH2

CH3

OH

O

Methyl, butylether ethanoic acid

H3C CH2

CH3C

O

H3CCH2

CCH

H2C

CH3

CH3

H3CCH3

Methyl, ethylketone 3,3,4-trimethylhexane

H3CC

CCH3

H3C

H2C

CH2

OHC

O

2-butyne Propanoic acid

Cl

HN

Cl H2CC

CH

HC

CH3

H3C

Dichloroamine 2-methyl-1,3-pentadiene

H3C

CHO CH3

H2C

CH3

C

O

H2C

CH2

CH3

Methyl secbuytl ester Propylbenzene

HONH2

O

NH2

CH

C

H2C

OH

O

C NH2

O

Aminoethanoic acid 1-amino-2-ethylamidyl-ethanoic acid???

POGIL PLANNING TEMPLATE

Adapted from David Hanson’s, “Designing Process-Oriented Guided-Inquiry Activities” in Faculty Guidebook- A Comprehensive Tool for Improving Faculty Performance, edited by S.W. Beyerlein and D.K. Apple (Pacific Crest, 2nd edition, 2005.) Title Proteins Why?

A. What will the student learn? B. Why is it relevant to the subject? C. Why is it relevant to the learner?

A. Proteins are polypeptides form via a condensation polymerization mechanism.

B. It is a very important example of both organic function groups as well as of polymers and condensation polymerization.

C. Proteins form the building blocks of life.

Learning Objectives -Proteins are amino acids joined by peptide bonds. -Peptide bonds produce water as a byproduct. -Proteins are polymers, specifically polypeptides.

Success Criteria -Identify peptide bonds and amino acids. -Demonstrate condensation as a result of peptide bond formation. -Identify monomer units. -Describe (symbolically) polypeptides formed from given peptide monomers.

Prerequisites -Understanding of amino acids. -Understanding of synthesis reactions.

Resources -Organic Chemistry Notes -Functional Group ID Quiz -Organic Nomenclature WS

Vocabulary Amino acid Peptide Condensation mechanism Monomer Polymer Protein (student definition)

Information Vocabulary


Plan and/or Tasks 1. Define amino acid. 2. Identify amino acids from a set of

organic molecular structures. 3. Define peptide bond. 4. Identify potential sites of peptide

linkage. 5. Identify what is lost in peptide

formation. 6. Define condensation

reaction/mechanism. 7. Define polymer/monomer with

example. 8. Identify monomers within polymer

structures. 9. Form a polymer from specific

monomers. 10. Develop definition of protein,

polypeptide. Model 1. Amino acid structure

2. Monomer units 3. Polymer structures 4. Protein structure

Key Questions 1. Circle the structures which represent amino acids. Explain your choices.

2. Connect each pair of amino acids with a line between atoms in each which could form a peptide bond.

3. Is there more than one possibility? Why or why not?

4. If there is more than one possibility does it matter which way they bond? Why or why not?

5. Identify the monomer in the following polymers.

6. Do all group members answers agree? Do they need to? Why or why not?

7. Form a 5 monomer segment of a polymer by linking these two amino acids using a peptide linkage. Show all products.

8. Do all group members get the same result? Must they?

9. The polymer you just created is an example of a protein. In your own words, using grammatically correct English sentences, define protein.


Skill Exercises A. Circle the peptide linkages in a set of structures.

B. Identify monomer units. C. Identify amino acids which could

have been used to form proteins. D. Identify number of waters produced

in the formation of a particular protein.

E. Construct specific proteins. Problems A. Identify hybridization of specific

atoms within a protein and predict geometry about each atom. Make predictions about planarity, etc.

B. Describe side groups as polar or non-polar.

Research Connect to H-bonding, alpha-helices and beta-sheets from Bio.

Validation Whole class reporting on Key Questions. Reflection on Learning Check-in following homework de-brief on

the following day.

PROTEINS – A POGIL ACTIVITY

WHY? • Proteins form the building blocks of life. • Proteins bring together the topics of organic functional groups,

polymerization, and condensation reactions.

An amino acid is an organic molecule which consists of an amino group, a carboxyl group, and a hydrocarbon side chain (R-group, circled) all bonded to the same carbon.

H2NOH

HO

R group = hydrocarbon side chain

H2NOH

HO

O

KEY QUESTIONS

OH

H2N

O

HN

C

OH

O

H2N CH C

CH2

H

O

CH CH3

CH3

H3C CH C

CH2

OH

O

HN

H2N CH C

CH

OH

O

OH

CH3

NH2

CH

C

H2C

OH

O

H2C

H2C NH C NH2

NH

1. Circle the structures above which represent amino acids. Explain your choices.

A peptide bond is a linkage between the amino group of one amino acid and the carboxyl group of another amino acid. When a peptide bond forms water is lost. This is known as condensation.

H2N CH C

CH3

OH

ON CH C

CH2

OH

O

SH

H

H

H2N CH C

CH3

O

N CH C

CH2

OH

O

SH

H

+ H2O

peptide bond

2. Connect each pair of amino acids with a line between atoms in each which could

form a peptide bond. Pair A

OH

H2N

O

H2N CH C

CH

OH

O

OH

CH3 Pair B

HN

C

OH

O

H2N CH C

CH2

H

O

CH CH3

CH3 Pair C

H3C CH C

CH2

OH

O

HN

NH2

CH

C

H2C

OH

O

H2C

H2C NH C NH2

NH



A polymer is a large molecule comprised of repeating units called monomers. A polymer generally contains 10+ monomer units. Polymer = Poly-2-chloropropane

Cl

Cl

Cl

Cl

Cl

Cl

Cl

Cl

Cl

Cl

Cl

Cl

Cl

11 units of 2-chlorpropane

Monomer = 2-chloropropane

Cl 2-chlorpropane

We use the following short hand conventions when describing polymers.

Cl

Cl

Cl

x

or

Cl

Cl

Cl

20

5. Circle the basic monomer unit in the following polymers.

O

O

O

O

O

NH CH C

CH3

O

NH CH C

CH

O

OH

CH3

HN CH C

CH3

O

NH CH C

CH

O

OH

CH3

H2N CH C

CH3

O

NH CH C

CH

O

OH

CH3

NH CH C

CH3

O

NH CH C

CH

OH

O

OH

CH3

HN CH C

CH3

O

NH CH C

CH

O

OH

CH3

HN CH C

CH3

O

NH CH C

CH

O

OH

CH3

6. Do all group members answers agree? Do they need to? Why or why not?

7. Draw a 5 monomer segment of a polymer by linking these two amino acids using a peptide linkage. Show all products.

H2N CH C

CH2

OH

O

NH2

CH

C

H2C

OH

O

H2C S CH3

8. Do all group members get the same result? Must they? 9. How many waters were formed as the 5 monomer segment was assembled? 10. The polymer you just created is an example of a protein. In your own words, using

grammatically correct English sentences, define protein.

Exercises 1. Circle the peptide linkage(s) in each of the following structures.

H2N CH C

CH

O

OH

CH3

H2N CH C

CH2

O

NH

CH

C

CH

O

CH3

H2C CH3

HN

CH

C

H2C

O

NHN CH C

H

OH

O

H2N CH C

CH2

O

OH

HN CH C

CH2

OH

O

CH2

CH2

NH

C

NH2

NH

2. For each of the proteins shown below, circle one monomer unit, give the number of amino acids which comprise the monomer, draw the structure of the individual amino acids, and indicate the number of waters which would condense in the formation of the polymer.

H2N CH C

CH3

O

NH CH C

CH2

O

CH2

S

CH3

NH

CH C

CH2

O

NH CH CH

CH2

O

CH2

S

CH3

H2N CH C

CH3

O

NH CH C

CH2

O

CH2

S

CH3

NH

CH C

CH2

O

NH CH CH

CH2

O

CH2

S

CH3

H2N CH C

CH3

O

NH CH C

CH2

O

CH2

S

CH3

NH

CH C

CH2

O

NH CH C

CH2

O

CH2

S

CH3

OH

Number of Amino Acids per Monomer

Amino Acid Structures

Number of H2Os produced

H2N CH C

CH2

O

CH2

C

NH2

O

N

C

O

HN CH C

CH3

O

NH CH C

CH2

O

CH2

C

NH2

O

NH CH C

CH2

O

CH2

C

NH2

O

N

C

O

HN CH C

CH3

O

NH CH C

CH2

O

CH2

C

NH2

O

NH

CH C

CH2

O

CH2

C

NH2

O

N

C

O

HN CH C

CH3

O

NH CH C

CH2

O

CH2

C

NH2

O

OH




3. Draw a structure for the protein composed of 4 monomers containing the

three amino acids shown below. The each monomer is constructed by linking the amino acids in ACABA order.

A

H2N CH C

CH2

OH

O

SH

B

H2N CH C

CH2

OH

O

C

H2N CH C

CH

OH

O

CH3

CH3

Problems

1. Examine the protein below. a) Give the hybridization at each atom in the main chain. b) Give the geometry at each of these atoms. c) Circle any of the regions of the protein you expect to be planar. d) Describe the R-groups as polar or non-polar.

H2N CH C

CH3

O

NH CH C

CH

O

CH3

CH2

CH3

NH CH C

CH2

O

CH2

S

CH3

HN CH C

CH3

O

NH CH C

CH

O

CH3

CH2

CH3

NH CH C

CH2

O

CH2

S

CH3

HN CH C

CH3

O

NH CH C

CH

O

CH3

CH2

CH3

NH CH C

CH2

O

CH2

S

CH3

OH

Extension

1. Do you think consecutive planar sections of the protein with be co-planar with each other? Why or why not?

2. Can you suggest what effect the polarity or non-polarity of the R-groups would

have?

PROTEINS – A POGIL ACTIVITY - KEY

WHY? • Proteins form the building blocks of life. • Proteins bring together the topics of organic functional groups,

polymerization, and condensation reactions.

An amino acid is an organic molecule which consists of an amino group, a carboxyl group, and a hydrocarbon side chain (R-group, circled) all bonded to the same carbon.

H2NOH

HO

R group = hydrocarbon side chain

H2NOH

HO

O

KEY QUESTIONS

OH

H2N

O

HN

C

OH

O

H2N CH C

CH2

H

O

CH CH3

CH3

H3C CH C

CH2

OH

O

HN

H2N CH C

CH

OH

O

OH

CH3

NH2

CH

C

H2C

OH

O

H2C

H2C NH C NH2

NH

1. Circle the structures above which represent amino acids. Explain your choices.

• #2,5,6 – all contain amine and carboxyl groups bonded to the SAME carbon (shown with a star)

A peptide bond is a linkage between the amino group of one amino acid and the carboxyl group of another amino acid. When a peptide bond forms water is lost. This is known as condensation.

H2N CH C

CH3

OH

ON CH C

CH2

OH

O

SH

H

H

H2N CH C

CH3

O

N CH C

CH2

OH

O

SH

H

+ H2O

peptide bond

2. Connect each pair of amino acids with a line between atoms in each which could

form a peptide bond. Pair A

OH

H2N

O

H2N CH C

CH

OH

O

OH

CH3 Pair B

HN

C

OH

O

H2N CH C

CH2

OH

O

CH CH3

CH3

Pair C

H2N CH C

CH2

OH

O

HN

NH2

CH

C

H2C

OH

O

H2C

H2C NH C NH2

NH


Yes, because the –OH can bond to the amine or the amine to the –OH.


Students will likely say yes because they will think this forms two different compounds. Later they will see this makes essentially the same polymer excluding the end termini.

A polymer is a large molecule comprised of repeating units called monomers. A polymer generally contains 10+ monomer units. Polymer = Poly-2-chloropropane

Cl

Cl

Cl

Cl

Cl

Cl

Cl

Cl

Cl

Cl

Cl

Cl

Cl

11 units of 2-chlorpropane

Monomer = 2-chloropropane

Cl 2-chlorpropane

We use the following short hand conventions when describing polymers.

Cl

Cl

Cl

x

or

Cl

Cl

Cl

20

5. Circle the basic monomer unit in the following polymers.

O

O

O

O

O

NH CH C

CH3

O

NH CH C

CH

O

OH

CH3

HN CH C

CH3

O

NH CH C

CH

O

OH

CH3

H2N CH C

CH3

O

NH CH C

CH

O

OH

CH3

NH CH C

CH3

O

NH CH C

CH

OH

O

OH

CH3

HN CH C

CH3

O

NH CH C

CH

O

OH

CH3

HN CH C

CH3

O

NH CH C

CH

O

OH

CH3

6. Do all group members answers agree? Do they need to? Why or why not? All group members answers should agree. There is only one possible monomer which repeapts to form a polymer. This monomer might be comprised of more than one amino acid.

7. Draw a 5 monomer segment of a polymer by linking these two amino acids using a peptide linkage. Show all products.

H2N CH C

CH2

OH

O

NH2

CH

C

H2C

OH

O

H2C S CH3

H2N CH C

CH2

O

HN CH C

CH2

OH

O

CH2

S

CH3

This is one monomer

H2N CH C

CH2

OHN CH C

CH2

O

CH2

S

CH3

HN CH C

CH2

OHN CH C

CH2

O

CH2

S

CH3

HN CH C

CH2

OHN CH C

CH2

O

CH2

S

CH3

HN CH C

CH2

OHN CH C

CH2

O

CH2

S

CH3

HN CH C

CH2

OHN CH C

CH2

OH

O

CH2

S

CH3

H2O H2OH2O H2OH2O H2OH2OH2OH2O

8. Do all group members get the same result? Must they? They should all get the same answer although some may have done it from left to right and others from right to left. 9. How many waters were formed as the 5 monomer segment was assembled? 9 H2O molecules 10. The polymer you just created is an example of a protein. In your own words, using

grammatically correct English sentences, define protein. A protein is a polymer consisting of a series amino acids joined by peptide bonds forming monomers which repeat to form the polypeptide or PROTEIN.

Exercises 1. Circle the peptide linkage(s) in each of the following structures.

H2N CH C

CH

O

OH

CH3

H2N CH C

CH2

O

NH

CH

C

CH

O

CH3

H2C CH3

HN

CH

C

H2C

O

NHN CH C

H

OH

O

H2N CH C

CH2

O

OH

HN CH C

CH2

OH

O

CH2

CH2

NH

C

NH2

NH

2. For each of the proteins shown below, circle one monomer unit, give the number of amino acids which comprise the monomer, draw the structure of the individual amino acids, and indicate the number of waters which would condense in the formation of the polymer.

H2N CH C

CH3

O

NH CH C

CH2

O

CH2

S

CH3

NH

CH C

CH2

O

NH CH C

CH2

O

CH2

S

CH3

NH

CH C

CH3

O

NH CH C

CH2

O

CH2

S

CH3

NH

CH C

CH2

O

NH CH C

CH2

O

CH2

S

CH3

NH

CH C

CH3

O

NH CH C

CH2

O

CH2

S

CH3

NH

CH C

CH2

O

NH CH C

CH2

O

CH2

S

CH3

OH


3



11

H2N CH C

CH3

O

OH

H2N CH C

CH2

O

CH2

S

CH3

OH

H2N CH C

CH2

O

OH

H2N CH C

CH2

O

CH2

C

NH2

O

N

C

O

HN CH C

CH3

O

NH CH C

CH2

O

CH2

C

NH2

O

NH CH C

CH2

O

CH2

C

NH2

O

N

C

O

HN CH C

CH3

O

NH CH C

CH2

O

CH2

C

NH2

O

NH

CH C

CH2

O

CH2

C

NH2

O

N

C

O

HN CH C

CH3

O

NH CH C

CH2

O

CH2

C

NH2

O

OH


3



11

H2N CH C

CH2

OH

O

CH2

C

OH

OHN

C OH

O

H2N CH C

CH3

OH

O

3. Draw a structure for the protein composed of 4 monomers containing the three amino acids shown below. The each monomer is constructed by linking the amino acids in ACABA order.

A

H2N CH C

CH2

OH

O

SH

B

H2N CH C

CH2

OH

O

C

H2N CH C

CH

OH

O

CH3

CH3

H2N CH C

CH2

O

SH

HN CH C

CH2

O

NH CH C

CH2

O

SH

HN CH C

CH2

O

SH

HN CH C

CH

O

CH3

CH3

HN CH C

CH2

O

SH

HN CH C

CH2

O

NH CH C

CH2

O

SH

HN CH C

CH2

O

SH

HN CH C

CH

O

CH3

CH3

HN CH C

CH2

O

SH

HN CH C

CH2

O

NH CH C

CH2

O

SH

HN CH C

CH2

O

SH

HN CH C

CH

O

CH3

CH3

HN CH C

CH2

O

SH

HN CH C

CH2

O

NH CH C

CH2

O

SH

HN CH C

CH2

O

SH

HN CH C

CH

O

CH3

CH3

continued on line 2

OH

Problems

1. Examine the protein below. e) Give the hybridization at each atom in the main chain. f) Give the geometry at each of these atoms. g) Circle any of the regions of the protein you expect to be planar. h) Describe the R-groups as polar or non-polar.

H2N CH C

CH3

O

NH CH C

CH

O

CH3

CH2

CH3

NH CH C

CH2

O

CH2

S

CH3

HN CH C

CH3

O

NH CH C

CH

O

CH3

CH2

CH3

NH CH C

CH2

O

CH2

S

CH3

HN CH C

CH3

O

NH CH C

CH

O

CH3

CH2

CH3

NH CH C

CH2

O

CH2

S

CH3

OHsp3

sp2

sp3sp3 sp3 sp3sp3

sp2sp2

sp2

sp2sp2 sp2 sp2 sp2 sp2

sp2

sp2

sp2

sp2sp2 sp2

sp3 sp3 sp3sp2

sp2 = trigonal planar sp3 =tetrahedryl

sp3

polar

non-polar

non-polar

non-polar

non-polar

non-polar

non-polar

polarpolar

Extension

3. Do you think consecutive planar sections of the protein with be co-planar with each other? Why or why not?

4. Can you suggest what effect the polarity or non-polarity of the R-groups would

have?

Documents

CHEM 504 – LESSON PLAN ASSIGNMENT #1 – …wwalsh/Walsh Protein Lesson.pdfCHEM 504 – LESSON PLAN ASSIGNMENT #1 – PROTEIN STRUCTURE STUDENT: Kate Walsh MCEP Cohort 6 DATE: July