CHEM 504 – LESSON PLAN ASSIGNMENT #1 – …wwalsh/Walsh Protein Lesson.pdfCHEM 504 – LESSON...
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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.
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
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.
POGIL PLANNING TEMPLATE
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
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?
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
Number of Amino Acids per Monomer
Amino Acid Structures
Number of H2Os produced
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
3. Is there more than one possibility? Why or why not?
Yes, because the –OH can bond to the amine or the amine to the –OH.
4. If there is more than one possibility does it matter which way they bond? Why or why not?
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
Number of Amino Acids per Monomer
3
Amino Acid Structures
Number of H2Os produced
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
Number of Amino Acids per Monomer
3
Amino Acid Structures
Number of H2Os produced
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?