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LESSON PLAN ASSIGNMENT #1 – PROTEIN STRUCTURE ..., Slides of Chemistry

Karel De Grote HogeschoolChemistry

Thus the topic of protein structure would fit into the course ... Students complete “POGIL-Proteins” exercise in randomly assigned groups.

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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.
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Download LESSON PLAN ASSIGNMENT #1 – PROTEIN STRUCTURE ... and more Slides Chemistry in PDF only on Docsity!

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.

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 H C C

H

H C

H

H

H

H

H R R -ane

Alkenes H C C

H

C

H H

H

H R R -ene

Alkynes

H C C C H

H

H

R R (^) -yne

Halohydrocarbons (^) X R X

(prefix) -chloro, bromo, etc.

Alcohols OH^ R^ OH -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 NH 2 R NH 2 amine

  • R= a hydrocarbon group

Some examples:

H 3 C

H 2

C

H 2

C

H 2

C C CH 3

2-hexanol

OH

H 3 C

H 2

C C^ CH 3

O

2-butanone

H 3 C

H 2

C C H

O

propanal

H 3 C

H 2

C C OH

O

propanoic acid

H 3 C N

CH 3

CH 3

trimethyl amine

HN

CH 3

H 2

C

ethyl methyl amine

CH 3

Primary (1°) : Bonded to one carbon

Secondary (2°) : Bonded to two carbons (described as sec-)

Tertiary (3°): Bonded to three carbons (described as tert-)

H 3 C

H 2

C

H

C CH 3

CH 3

2 3 o

1 o^ o

1 o

1 o

CH

H 3 C

CH 2

CH 3

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.)

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

H 3 C

H 3 C CH 3

CH 3

+ H 2 H 3 C C

H

CH 3

C

H

CH 3

CH 3

HC CH + Br 2 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

N

H 2 C 6 N

H

H

H

H

C

H 2 C O

O

H

C O

O

H

4 H^2 N

H 2 C N C

H 2 C C

O

OH

H (^) O

+ H 2 O

Cracking – larger compounds are broken down into smaller

compounds. Generally at very, very high temperatures.

n-C 30 H 62 CH 3 (CH 2 ) 5 CH CH 2 CH 3 (CH 2 ) 10 CH 3 CH

3 (CH^2 ) 7 CH^ CH^2

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.

C 6 H 12 O 6 2 CH^3 CH^2 OH^ +^ 2 CO^2

glucose ethanol^ carbon dioxide

Functional Group Identification Quick Quiz

Name__________________________________________________________________

For each of the following molecules, circle any functional groups of interest and

classify each one.

H 3 C

H 2

C

C

H 2

H 2

C

C

H 2

CH 3

H 3 C

H 2

C

C

H 2

C

H 2

C CH 3

O

CH 3

CH 3

H 2

C

C

H 2

H

C

O

H 3 C

H 2

C

C

H 2

CH

CH 3

H 2 C

CH

H 3 C

H 3 C

C

H 2

C

C

H

CH 3

H 3 C

H 3 C

C

H 2

H 2

C

NH 2 H 3

C

H 2

C

C

H 2

H 2

C 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.

H 3 C

H 2

C

C

H 2

H 2

C

C

H 2

CH 3

NO INTERESTING GROUPS

H 3 C

H 2

C

C

H 2

C

H 2

C CH 3

O

KEYTONE

CH 3

BENZENE

METHYL

CH 3

H 2

C

C

H 2

H

C

O

ALDEHYDE

H 3 C

H 2 C C H 2

CH CH 3

O

CH

H 3 C

METHYL

ETHER

H 3 C

C

H 2

C

C

H

CH 3

H 3 C

PENTENE

METHYL

H 3 C

C

H 2

H 2

C

NH 2

AMINE

H 3

C

H 2

C

C

H 2

H 2

C OH

C

O

CARBOXYLLIC ACID

Organic Nomenclature Worksheet

H 3 C

O

C

H 2

H 2

C

C

H 2

CH 3

OH

O

H 3 C C

H 2

C CH 3

O

H 3 C

C

H 2

C

CH

H 2

C

CH 3

CH 3

H 3 C

CH 3

H 3 C

C

C

CH 3

H 3 C

H 2

C

C

H 2

OH

C

O

Cl

H

N

Cl H 2 C

C

C

H

H

C

CH 3

H 3 C

H 3 C

CH

O CH^3

H 2 C

CH 3

C

O

H 2

C

C

H 2

CH 3

HO

NH 2

O

NH 2

CH

C H 2 C

OH

O

C NH 2

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.

H 3 C

H 2

C

C

H 2

H 2

C

C

H 2

CH 3

H 3 C

CH

CH

H 2

C

CH 3

CH 3

H 3 C

Hexane 2,3-dimethylhexane

H 3 C

H (^2) C C H 2

CH CH 3

CH 2

H 2 C

CH 3

H 3 C

H 2

C

C

H 2

H 2

C

NH 2

4-methylheptane butylamine

H 3 C

H 2

C

O

C

CH 3

O

H

C

H 2

C

CH 3

O

Methyl ethylester Ethylaldehyde (ethanal)

H H

O

H 3 C

H 2

C

OH

Methylaldehyde (methanal,

formaldehyde)

Ethanol

H 3 C

O CH 3

C

O

H 3 C

CH

CH

H 2

C

CH 3

OH

CH 3

Dimethylester 3-methyl-2-hexanol

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

POGIL PLANNING TEMPLATE

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.