Category Archives: Chemistry

Semester 2 Launch

Welcome to second semester!  A new semester brings fresh start and a new unit.  Before we dive in, we will roll out a new seating chart, welcome new faces to our classroom, review the class Syllabus and Safety Contract and hold a class discussion around expectations this semester.

Next, students will receive back their graded Unit 2 exams.  We will discuss any questions students have about the exam.  Students who took the Unit 1 exam will also receive it back graded.  Two groups of students took the exam:

  • Students with an A after the unit 2 exam was graded had the option of taking the Unit 1 exam.  The exam score does not affect the semester 1 grade.  However, students who earn a 70% or better on the exam will receive an Honors designation on their transcript for 1st semester chemistry.
  • Students who did not turn in the Unit 1 Project had the option of taking the Unit 1 exam.  The exam score (up to 60% max) will replace the missing score from the project.

Finally, we will wrap up 1st semester with an Exit Task designed to help them reflect on their successes and consider opportunities to grow during 2nd semester.  After the Exit Task, students should confirm access to the class textbook (full student gmail address and HighlineMM/DD where MM/DD are birth month and day) and the class Newsela account.

Unit 2 Review

Friday, January 17, 2020: For the entry task, students are assigned the job of accessing the Swart Chemistry Unit 2 Review Google Doc designed to facilitate the unit 2 review process.  Each student is responsible for:

  1. Selecting one question from the Unit 2 Review section of the textbook (pages 252-256) and writing both the question (including all multiple choice answers), highlighting the correct answer using bold text, and then explaining why the correct answer is correct along with including a page citation from the textbook.
  2. Selecting at least three exercise questions from Lessons 28-48 in the textbook.  The questions are found at the end of each lesson.  Follow the same steps as above.
  3. Note: If all Unit 2 Review questions have been addressed, verify one answer (include your name as the verifier) and then answer at least four questions from Lessons 28-48 in the text.

Tuesday, January 21, 2020: For our first day of review for the Unit 2 Exam taking place on Thursday, we briefly reviewed the vocabulary of chiral, achiral, and dehydration synthesis reactions (encountered in Lesson 34) by visualizing the reaction in the context of amino acids.  Class notes are shown below:

Unit 2 Review Picture 1

Unit 2 Review Picture 2

Next, students played a Kahoot! designed to test their understanding and retention of material they had the opportunity to study over the three-day weekend.  After the Kahoot!, students had the remainder of the class period to answer or verify answers on the class Google Doc started last Friday.  All students received a copy of a practice test to complete in class or as homework.  In addition, students were reminded to prepare one 8.5″ x 11″ page of notes (front and back) to use on the exam.

Wednesday, January 22, 2020: For our final day of review before the Unit 2 Exam, we began with reviewing question 18 from the multiple choice portion of the unit 2 review.  Next, students received the answer key to the practice quiz they received yesterday and had the opportunity to ask questions about any points of confusion.  Students had the remainder of the class period to ask questions, share ideas, add to or review the Google Doc, and add to notes that can be used on the exam tomorrow.  Areas of focused study should include:

  • Connection between molecule name, molecular formula, functional group, and smell
  • Larger molecule shapes and smells
  • HONC 1234 Rule
  • Connection between molecule size, polarity, and smell
  • Lewis dot diagrams (lone pairs, bonded pairs)
  • Molecule shape
  • Advantages and disadvantages of types of molecular models
  • Receptor-site theory
  • Electronegativity: calculations, partial charges, dipole, symmetry
  • Mirror-image isomers (chiral molecules)
  • Amino acids: how are they similar? different? R group polarity

Notes from the white board (click arrows to move through slide show):

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Amino Acids and Proteins

The final lesson of Unit 2 explores how amino acids connect to make proteins.  The Lesson 48 PowerPoint includes the vocabulary terms of amino acid and protein.  Lesson 48 connects with Lesson 47, as amino acids are chiral molecules.  Notably, all of the 20 different amino acids in human proteins are “left-handed” (as opposed to the mirror-image “right-handed” isomers), meaning they all have the L conformation (L for laevus, Latin for “left”) rather than the D conformation (D for dexter, Latin for “right”).  Students will work in pairs to complete the Lesson 48 Worksheet, learning about the properties of amino acids and how they bind together to form proteins.  For more on the D and L convention, click on the picture below.

As noted previously, there are 20 different amino acids.  All amino acids share the same base structure of a central carbon atom bound to a carboxylic acid (-COOH), an amino group (-NH2), and a hydrogen (H).  The central carbon is also bound to an R group, with R indicating any one of the 20 different amino acid structures.  The structures each have different physical properties.  When individual amino acids link together, a polypeptide chain is formed (and a molecule of water is removed as each new amino acid is linked to the chain).  The polypeptide chain, composed of a string of amino acids, folds into a particular shape determined by the interactions of all of the amino acids.  The shape of a protein determines its function in the body.  Mr. Anderson of Bozeman Science has a fantastic video explaining the nature of proteins:

For students looking for a good review of Central Dogma (DNA > RNA > Protein > Trait), the Crash Course Biology video DNA, Hot Pockets, & The Longest Word Ever is a good resource:

Finally, for students with access to a home computer, the Fold.It website will have you folding proteins in no time!


  • Read Lesson 48 in the textbook.  Login via and enter your username and password.
  • Write notes for Lesson 48 and work through the practice problems at the end of Lesson 48
  • Please ask questions about anything from Lesson 48 you do not yet fully understand.

Mirror-Image Isomers

Yesterday, students were introduced to the concept of mirror-image isomers, chiral objects (an object that is not equal to its superimposed reflection), and achiral objects (an object that is equal to its superimposed reflection).  We applied the terms chiral and achiral to real-world 3-dimensional objects all students are familiar with like hands, springs, and barbells:

Lesson 47 Picture 1

We then watched a video to more fully understand how to apply those terms to central carbon atoms with less than 4 different groups (achiral carbons) and 4 different groups (chiral carbons):

After the video, we applied drew molecules with a central carbon atom and increasing numbers of attached groups.  Students had the opportunity to build the molecules and their mirror-images using molecular modeling kits in order to better visualize superimposability.

Lesson 47 Picture 2

Next, we applied the concept of chirality to molecular smell.  Students smelled extracts containing one of two different mirror-image isomers containing a chiral carbon, finding one to smell like mint and the other like pickles.  This evidence supports the concept of receptor-site theory, where molecules with highly specific shapes are recognized by distinct receptors in the olfactory system, resulting in the perception of distinct smells.

Students then received the Lesson 47 Worksheet, working in pairs to model the compounds using the class set of molecular modeling kits.

Day 2: We will begin class today with an extension of the concept of chirality.  Prior to 1961, scientists did not fully appreciate the profound biological importance of chirality as it relates to medicine.  The tragic story of thalidomide illuminated scientists to a level of chemical complexity not previously appreciated as biologically relevant:

Keep Learning!

Want more?  Check out the blog post Perhaps looking-glass milk isn’t good to drink for an overview of Lewis Carroll, looking-glass milk, and L- and D-carvone.  Want more?  Joanna Shawn Brigid O’Leary from Rice University published an even more extensive investigation of how Lewis Carroll (author of Alice in Wonderland and Through the Looking Glass) weaved biochemistry into his fiction.  Her paper (available as a PDF), WHERE ‘THINGS GO THE OTHER WAY’: THE STEREOCHEMISTRY OF LEWIS CARROLL’S LOOKING-GLASS WORLD is well worth the read.  Perhaps it will even inspire students to read the book before the movie is released in theaters on May 27!


  • Read Lesson 47 in the textbook.  Login via and enter your username and password.
  • Write notes for Lesson 47 and work through the practice problems at the end of Lesson 47
  • Please ask questions about anything from Lesson 47 you do not yet fully understand.

Phase, Size, Polarity, and Smell

Chapter 8 concluded with the Lesson 46 PowerPoint and Lesson 46 Worksheet.  Lesson 46 brought together the various concepts needed to understand how molecules with certain properties can be detected by our noses, with our brain recognizing those molecules as having a specific smell.  The entry task (ChemCatalyst) asks students to model why perfume molecules can be smelled from across a room, but paper cannot (both placed near a sunny window).

Students also received a copy of the Chapter 8 Study Guide to use in preparation for the quiz on Tuesday.  Work through the quiz questions on your own, then compare your answers to the key.

Notes from class (January 10):

Lesson 46 Picture 1

Lesson 46 Picture 2

Notes from class (January 13):

Lesson 46 Day 2 Picture 1

Lesson 46 Day 2 Picture 2

Keep Learning!

Wondering how to determine whether a molecule is symmetrical or asymmetrical?  Work through the slide deck from Dr. Fred Omega Garces and focus in on slide 15.  Look familiar?  Students received a copy of this flow chart in class today.


  • Read Lesson 46 in the textbook.  Login via the Sapling website and enter your username and password.
  • Write notes for Lesson 46 and work through the practice problems at the end of Lesson 46
  • Please ask questions about anything from Lesson 46 you do not yet fully understand.

Polar Molecules and Smell

We continued our study of polarity, this time exploring how the polarity of molecules might impact our ability to smell the molecule.  Through the Lesson 45 PowerPoint, students learned that polar molecules are more likely to be detected by the nose as something with a scent although there are still polar molecules (like water) that do not smell.  We also visualized several molecules using a Java-based Molecule Polarity PhET simulation to give students a better sense of the concepts of electron density, bond dipoles, and molecule dipoles.  Emphasis was placed on the connection between bond electronegativity and overall molecule geometry.  During student work time, students cut out the molecules in the molecules handout and used the molecules to complete the Lesson 45 Worksheet.


  • Read Lesson 45 in the textbook.  Login via the Sapling website and enter your username and password.
  • Write notes for Lesson 45 and work through the practice problems at the end of Lesson 45
  • Please ask questions about anything from Lesson 45 you do not yet fully understand.

Electronegativity Scale

After learning about the concepts of electronegativity and polarity in yesterday’s lesson, students learned that scientist Linus Pauling assigned electronegativity values to individual atoms as a measure of how strongly an atom attracts electrons (click here for a deeper dive into how he calculated electronegativity).  Although not used in class, the Lesson 44 PowerPoint is provided here as a resource and includes a copy of the periodic table with electronegativity values for each element.  It also explains the difference in electronegativity between covalent bonds (0.5 and less), polar covalent bonds (between 0.5-2.1), and ionic bonds (greater than 2.1).

After practicing how to calculate bond differences as a class, students worked through the Lesson 44 Worksheet using the Electronegativity Scale and Bonding Continuum handout.

Students who finish the work early had time to complete yesterday’s Lesson 43 worksheet and Monday’s Polarity and Intermolecular Forces Gizmo.  Students who are fully caught up have the opportunity to investigate vectors and may earn bonus credit for completing one or both vector-related Gizmos.

Notes from class:

Lesson 44 Picture 1

Lesson 44 Picture 2

Keep Learning!

Want more information about dipoles from yesterday’s lesson?  Read about how dipole moments are calculated.

Wondering how scientists measure the electronegativity of atoms?  One new technique involves atomic force microscopy.  Read more:  Electronegativity of a single atom scrutinized under the microscope.

The Pauling scale of electronegativity was updated in a paper published a year ago (January 2019, Journal of the American Chemical Society).  Read a summary of the work: New scale for electronegativity rewrites the chemistry textbook.  Want more?  Take a look at the supporting data for the journal article.


  • Read Lesson 44 in the textbook.  Login via the Sapling website and enter your username and password.
  • Write notes for Lesson 44 and work through the practice problems at the end of Lesson 44
  • Please ask questions about anything from Lesson 44 you do not yet fully understand.