Sense-able Smells Making Organic Structures Accessible for High School Andro Rios and Gerald French...

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

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

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!!

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/

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

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.

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.

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.

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

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

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/

Part B. Esters

Molecular Structure


Odor identification


Odor 4

Odor 5

Odor 6

O

O

OH

CH3

H3C O

O

CH3

H3CO

O

CH3

CH3

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

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__

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:

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

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/

Part C. Terpenes

Molecular Structure


Odor identification


Odor 7

Odor 8

Odor 9

CH3

H3C CH2

CH3

H3C CH2

CH3

H3CCH3

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

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

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

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

Part D. Alcohols

Molecular Structure


Odor identification


Odor 10

Odor 11

Odor 12

H3C OH

CH3 CH3

OH

CH3

CH3H3C

CH3

H3C CH3

OH

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

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 10Full atom version

They represent the chemical bonds between atoms in a molecule.

H3C OH

CH3 CH3=


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.

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

Part E. Ketones

Molecular Structure


Odor identification


Odor 13

Odor 14

Odor 15

O

HO

CH3

O

H3C

CH3

O

H3C CH2

CH3

O

H3C CH2

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

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

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

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

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

Sense-able Smells Making Organic Structures Accessible for High School Andro Rios and Gerald French...

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Transcript of Sense-able Smells Making Organic Structures Accessible for High School Andro Rios and Gerald French...