sense-able smells making organic structures accessible for high school andro rios and gerald french...
TRANSCRIPT
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Sense-able SmellsSense-able SmellsMaking Organic Structures Accessible for High Making Organic Structures Accessible for High
SchoolSchool
Andro Rios and Gerald FrenchAdapted from Bio-Bridge Pilot Training
SessionCopyrighted All Rights Reserved
CH3
H3C CH2
H3C O
O
CH3
CH3O
O
OH
CH3
CH3
H3C CH3
OH
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2004 Nobel Prize in Physiology 2004 Nobel Prize in Physiology or Medicineor Medicine
“ for their discoveries in odorant receptors and the organization of the olfactory system”
Linda BuckFred Hutchinson Cancer Research
Center Seattle, WA, USA
Richard Axel Columbia University New York, NY, USA
Our Sense of Our Sense of Smell Smell
http://nobelprize.org/nobel_prizes/medicine/laureates/2004/illpres/
Nobel Prize 2004 Website
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How do we How do we Smell?Smell?CH3
H3C CH3
OH
H3CO
O
CH3
CH3
CH3
H3C CH2
http://nobelprize.org/nobel_prizes/medicine/laureates/2004/illpres/
Odorant molecules Odorant molecules can serve as can serve as sources of sources of
engagement!!engagement!!
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Why introduce bond Why introduce bond line organic line organic structures?structures?
They highlight only the important parts of a molecule
They are easier to use for discovering patterns
To directly address the “intimidation factor”
Scientists use this language, why not students of science?
N
NN
N
O
O
H3C
CH3
H
N
NN
N
O
O
CH3
CH3
H3C
Compare and Compare and ContrastContrast
N
NN
N
O
O
H
HH
N
NN
N
O
NH2
GH2O
H
H
http://well.blogs.nytimes.com/2012/03/26/the-chocolate-diet/?_r=0
bayfieldcoffeecompany.com/
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What is the unifying pattern in What is the unifying pattern in amino acids?amino acids?
Consider two structural versionsConsider two structural versions
H2NOH
O
OHH3C
H2NOH
O
H2NOH
O
CH3
H2NOH
O
NH2
H2NOH
O
HNN
HN
N C C
C
OH
OH
N C C
C
OH
O
OH
C
H
HH
H
HHH
H
HN C C
C
OH
O
CN
C N
C
HH
H
H
H
HH
N C C
C
OH
O
CC
N C
C
C C
CC
H
HH
H
H
Threonine
HH
H
N C C
C
OH
O
C
C
C
N
HH
HHH
HH
HH
HH
HH
Histidine Alanine Tryptophan Lysine
H
H
HH
H
HH
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Activity ObjectivesActivity Objectives
1. To demonstrate the everyday role of organic molecules.
2. To make molecular structures less intimidating.
3. To provide students with the opportunity to make their own observations and conclusions.
4. To empower students with the skills to engage in other activities relating to bio-molecules.
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Are you hypersensitive to common odors or fragrances?
While these odors are considered pleasant and safe, there are many people who suffer severe irritation
even from the most common and mild odors/aromas. If you are one of these individuals,
you should not participate in this activity.
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Before you begin….……..Before you begin….……..For each sample, first try wafting, because some odors are stronger than others.
If you still can’t smell anything, bring the sample closer to your nose.
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Part A. Aldehydes
Molecular Structure
Description and association of odor
Odor identification
H
O
O
HO
H3C
H
O
H
O
Part A. Fill out this table as you go about wafting the odors from the three samples
Odor 1
Odor 2
Odor 3
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Aldehydes Part A. Compare and Contrast:
All aldehydes seem to have this in common:
H
O
O
HO
H3C H
O
H
O
Odor 1 Odor 2
Odor 3
H
O
H3C
Molecule 4
H
O
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The Aldehyde OdorsThe Aldehyde OdorsOdor 1
Vanilla
Odor 2
Cinnamon
Odor 3
Almonds
or Cherries
Images: http://en.wikipedia.org/wiki/Vanilla_(genus)http://www.outsideonline.com/fitness/bodywork/fitness-coach/The-Best-Anti-Inflammatory-Spices-Cinnamon-20120530.htmlhttp://www.waterfordnut.com/facts.html http://www.rawsmoothierecipes.com/green-smoothies-with-cherries/
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Part B. Esters
Molecular Structure
Description and association of odor
Odor identification
Part A. Fill out this table as you go about wafting the odors from the three samples
Odor 4
Odor 5
Odor 6
O
O
OH
CH3
H3C O
O
CH3
H3CO
O
CH3
CH3
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Esters Part B. Compare and Contrast again
All esters seem to have this in common:
Odor 4 Odor 5
Odor 6
O
O
O
O
OH
CH3
H3C O
O
CH3H3C
O
O
CH3
CH3
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Esters Part B.Esters Part B.
O
O
OH
C
CC
C
CC C
O
O
O
H
H
H
H
C
H
H
H
H
CH3 =
Odor 4Short-hand version
Odor 4Full atom version1. How many carbon and hydrogen atoms do you see in the short-hand
version of Odor 4? one C atom and two H atoms
2. How many carbon and hydrogen atoms do you see in the full atom
version?
eight C atoms and eight H atoms
• In comparing the short hand and full atom version, what does the number 3 on the H3 refer to in the short-hand version?
Indicates there are three hydrogen atoms
4. Oxygen atoms are easy to spot since they are always shown in both the short-hand and full atom versions. How many oxygen atoms are in Odor 4? __3__
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H3C O
O
CH3 CC
CC
OC
O
CH
HH
H
H
H
H
H
H
HH
HOdor 5
Short-hand verisonOdor 5
Full atom verison
=
Esters Part B. Slide 2Esters Part B. Slide 2
5. Using the Full atom version circle the parts on it that are visible in the short hand version.
6. Using the short-hand version, fill in the missing atoms on it that are shown in the full atom version.
4. Oxygen atoms are easy to spot since they are always shown in both the short-hand and full atom versions. How many oxygen atoms are in Odor 4?
three O atomsCompare the two versions of Odor 5 then answer these related questions:
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Esters Part B. slide 3Esters Part B. slide 3
8. How many carbon atoms are in odor 6 total?
Now look at the Odor 6 molecule (shown below). Draw in the symbol for carbon for the missing carbons atoms on the molecule.
H3CO
O
CH3
CH3
Odor 6Short-hand verison
seven C atoms
7. Describe and illustrate how you think the missing carbon atoms are represented in the short-hand version:
At the points where lines meet(a vertex), or other joining of multiple lines, is where the missing carbon atoms are found.
H3CC
CC
CO
O
CH3
CH3
Odor 6Short-hand verison
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The Ester OdorsThe Ester Odors
Odor 4
Wintergreen
Odor 5
Pineapple
Odor 6
Banana
Images:https://www.gardenerdirect.com/buy-plants-online/630/Perennials-for-Groundcover-or-Crevices/Gaultheria-procumbens-Spreading-Wintergreen http://www.babyfood101.com/pineapple_baby_food_recipes/ http://www.myrtlebeachproduce.com/fruits-veggies/attachment/banana/
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Part C. Terpenes
Molecular Structure
Description and association of odor
Odor identification
Part A. Fill out this table as you go about wafting the odors from the three samples
Odor 7
Odor 8
Odor 9
CH3
H3C CH2
CH3
H3C CH2
CH3
H3CCH3
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Terpenes Part C. Compare and Contrast
All terpenes seem to have this in common:
Odor 7 Odor 8
Odor 9
CH3
H3C CH2
CH3
H3C CH2
CH3
H3CCH3
CH3
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1. Did you observe that two of the terpene odors smelled similar?
2. Can you provide a reason based on the molecular structures shown below as to why two of them smelled similar?
CH3
H3C CH2
CH3
H3C CH2
Odor 7 Odor 8
Terpenes Part C. slide 2Terpenes Part C. slide 2
CH3
H3CCH3
Odor 9
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CH3
H3C CH2
CH3
H3CCH3
Odor 7 Odor 9
Can you find all 10 of the carbon atoms in Odor 7 and Odor 9 (shown below)? Three of them are easy to find, but can you find the other seven which are the not drawn in on the short-hand version. Circle all 10 carbon atoms for each molecule.
Terpenes Part C. slide 3Terpenes Part C. slide 3
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The Terpene OdorsThe Terpene Odors
Odor 7
Orange
Odor 8
Lemon
Odor 9
Pine / Pine needles
Images:http://commons.wikimedia.org/wiki/File:Oranges_in_the_tree.JPG http://commons.wikimedia.org/wiki/Citrus_%C3%97_limon#mediaviewer/File:Lemon_tree_Berkeley_closeup2.jpghttp://commons.wikimedia.org/wiki/File:Pine_cone_on_pine_tree.jpg
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Part D. Alcohols
Molecular Structure
Description and association of odor
Odor identification
Part A. Fill out this table as you go about wafting the odors from the three samples
Odor 10
Odor 11
Odor 12
H3C OH
CH3 CH3
OH
CH3
CH3H3C
CH3
H3C CH3
OH
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OH
CH3
CH3H3C
CH3
H3C CH3
OH
Alcohols Part D. Compare and Contrast
All alcohols seem to have this in common:
Odor 10
Odor 11 Odor 12
OH
H3C OH
CH3 CH3
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Alcohols Part D. slide 2 Alcohols Part D. slide 2
5. No matter which carbon atom you look at in the Full atom version, how many lines are connected to it?
6. If the letters (C, H and O) in Odor 10, or any molecule you have smelled today, represent atoms in a molecule, what might the lines connecting the letters represent?
The short-hand and full atom version of Odor 10 is shown below. Answer the following questions relating to the structures.
Always four lines.
H3C OH
CH3 CH3
CC
CC
CC
CC
O
C CHH
H
H
HH
HH
H
H
H
H
H
H H
H
H
H=
Odor 10Short-hand version
Odor 10Full atom version
They represent the chemical bonds between atoms in a molecule.
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H3C OH
CH3 CH3=
Odor 10Short-hand version
H3C OH
CH3 CH3
Odor 10Short-hand with hydrogen atoms
included
H
H
H
H H
H
HH
Alcohols Part D. slide 3 Alcohols Part D. slide 3
Hypothesis:
Shown below are two short-hand versions of Odor 10, the one on the right includes all of the hydrogen atoms. Look at the arrows pointing at two different carbon atoms in the representation on the left. Observe in the representation on the right that each of those carbon atoms has a different amount of hydrogen atoms bonded to it. Look for a pattern and provide a reason why you think this happens?
Each vertex needs four lines. If there are less than four linesat a vertex, then lines with an ‘H ’ are added until the vertexhas a total of four lines.
Hint: Question 1 provides a strong clue……
Each carbon atom needs four bonds. If there are less than four bonds at a carbon atom, then hydrogens are added until the carbon atoms has four bonds.
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AlcoholsAlcohols
Odor 10
Rose
Odor 11
Thyme
Odor 12
Peppermint
Images:http://commons.wikimedia.org/wiki/Rosa_Hybrid_Tea#mediaviewer/File:Rosa_%27Mrs_Aaron_Ward%27.jpghttp://wellandgood.com/2012/04/06/thyme-may-be-more-effective-against-acne-than-benzoyl-peroxide/http://hips.seas.harvard.edu/recent-news
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Part E. Ketones
Molecular Structure
Description and association of odor
Odor identification
Part A. Fill out this table as you go about wafting the odors from the three samples
Odor 13
Odor 14
Odor 15
O
HO
CH3
O
H3C
CH3
O
H3C CH2
CH3
O
H3C CH2
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CH3
O
H3C CH2
CH3
O
H3C CH2
Ketones Part E. Compare and Contrast
Odor 13
Odor 14 Odor 15
O
HO
CH3
O
H3C
All ketones seem to have this in common:
O
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O
HO
CH3
O
H3C
Ketones Part E.Ketones Part E.
2. How many carbon atoms does it have?
3. How many oxygen atoms does it have?
4. How many hydrogen atoms does it have?
Odor 13
1. Circle all of the carbon atoms in Odor 13
Eleven C atoms
three O atoms
fourteen H atoms
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Ketones Part E. slide 3Ketones Part E. slide 3
5. Draw the full-atom version of odor 13 in the box below
Full atom version of Odor 13
C
CC
C
CC C
CO
O
CC
O
CH
HH
H
H
H
H
H
H
HH
H
H
H
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CH3
O
H3C CH2
Circle carbon atoms on here
CH3
O
H3C CH2
Draw in the missing hydrogen atoms here
H
H
H
H
H
H
Ketones Part E. slide 4Ketones Part E. slide 4
6. Circle in all of the carbon atoms in odor 14 shown below on the left. Then determine which carbon atoms need hydrogen atoms and draw them in on the structure on the right.
CH3
O
H3C CH2
Circle carbon atoms on here
CH3
O
H3C CH2
Draw in the missing hydrogen atoms here
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KetonesKetonesOdor 13
Ginger
Odor 14
Spearmint
Odor 15
Caraway
Images:http://macabido.com/natural-ingredients/macabido-womens-formula/ginger/http://www.dandycloud.fr/produit/flavour-art-spearmint-10-ml/http://www.swallowtailgardenseeds.com/herbs/caraway.html#gsc.tab=0