Blog

Streak Plate

Microbiologists have a technique called "Streak Plating" where you successively dilute your bacteria until eventually you get single isolated colonies. These single colonies are used to obtain a pure culture (single strain of bacteria). Dr. Gary Kaiser of the Community College of Baltimore County, Catonsville Campus has a very nice computer animation showing how this is actually done in a practical sense.

Link to Dr. Kaiser's Streak Plate Animation: https://cwoer.ccbcmd.edu/science/microbiology/Lab%20Manual/lab2/3_streak.swf.html

Link to this other animations: https://cwoer.ccbcmd.edu/science/microbiology/animations/lab.html

Kirby Bauer Page from Dr. Kaiser: https://cwoer.ccbcmd.edu/science/microbiology/Lab%20Manual/lab18/lab18.html

Nice efficient video from Reddit by showing streak plate being done: https://www.reddit.com/r/microbiology/comments/1dkw1zi/serratia_marcescens_on_macconkey_agar/

SMC's New Biotechnology Program

Check out this news article about SMC's new Biotechnology Program! The SMC Biotech pathway leads to jobs in biotech companies in Southern California! These industries are struggling to find highly skilled technicians to supports its rapid growth. This program leads to stackable certificates that could lead to careers as a:

Biotechnology/Life Sciences laboratory Assistant
Biotechnology and cell Science Laboratory Technician
or possibly link to a Bachelor's Degree in in Biomanufacturing at one of three California Community Colleges: Solano, MiraCosta, and Moorpark (see Biotechnology website for more specifics)

More information:

SMC Biotech Program: https://www.smc.edu/academics/areas-of-interest/stem/life-sciences/biotechnology.php
Biotech Association Club (student-led group with lots of useful info on the Biotech program) https://smcbiotechassociat.wixsite.com/biotech-association/biotechnology-program

Kirby-Bauer Test (Disc Diffusion Test)

This Spring 2024 semester, I am on sabbatical at Loyola Marymount University (Lum Lab) learning how to incorporate microbiology techniques into my Organic Chemistry classes. Here is an example showing how the Kirby-Bauer assay is used to determine whether a particular antibiotic will be effective against clearing a particular type of infection. In the Kirby-Bauer Test, the drug compound diffuses out of the disc and into the surrounding media, interacting with the bacteria that is growing on the media. You can measure the diameter of the zone of inhibition to get a sense of the effectiveness of the antibacterial properties of each compound. I used six standard discs here and tested them against a lawn of E. coli incubated overnight at 37 oC. Using the reference table, which antibiotics is this E. coli bacteria susceptible to? Which antibiotics is this E. coli resistant to? E. coli happens to be a Gram-negative bacterium. When I tried this experiment with S. epidermidis (a common Gram-positive bacteria found on the skin), I found that S. epidermidis was susceptible to ALL six of these antibiotics! The point here is that different antibiotics are good/bad against different strains of bacteria. Penicillin, which apparently has no effect on E. coli is terrific against S. epidermidis. It makes sense why there are so many different antibiotics out there (because there are so many different strains of bacteria!). Not to mention, that a particular strain of bacteria can rapidly develop resistance to an antibiotic too so that an antibiotic that works today on that strain might not work later on an evolved descendant of that same bacteria! We need scientists to think about and work on problems like these. Consider joining the Science 10 Drug Discovery Lab course to get hands-on experience and learn more!

Penicillium fungus inhibits growth of bacteria (real-life Disk Diffusion Assay)

The image above was taken from the Wolfe Lab at Tuft's University. Their website publishes photos of their research to help inform the public on the type of research taking place inside the laboratory! Below is the caption from their webpage (source: https://sites.tufts.edu/wolfelab/open-lab/ Entry from 11/23/2020)

"November 23rd: Students in Ben’s course Microbiome Research Lab are exploring how fungi in cheese rinds produce antibiotic compounds. Here is a plate showing some [Penicillium] fungi with strong antibacterial activity! The orange “lawn” is a bacterium spread across a Petri dish containing nutrients. Each circle on the plate is a “plug” of either fungi (top left and bottom plugs) or a control plug with just media (top right). The areas around the fungi where the bacterium is not growing are due to something the fungi secrete into the medium that can kill bacteria. We are excited to work with chemistry collaborators to better understand what those compounds might be!"

This image is very reminiscent of the classic image of Penicillium fungus inhibiting growth on a bacterial lawn from Alexander Fleming's original report describing a potent antimicrobial compound (later discovered to be Penicillin). Image source: https://digital.nls.uk/scientists/biographies/alexander-fleming/index.html

More info on this "agar plug" method: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8570476/

Did you know Alexander Fleming also "painted" portraits using bacteria? Check out Alexander Fleming's Germ Paintings! https://www.smithsonianmag.com/science-nature/painting-with-penicillin-alexander-flemings-germ-art-1761496/

Sodium acetate recrystallization

Cool demonstration by Phil Reedy involving spontaneous crystallization of sodium acetate: https://www.youtube.com/watch?v=nrmQBdYp5tU

Another video of the same recrystallization process: https://www.reddit.com/r/Damnthatsinteresting/comments/p4rvtw/hot_ice_sodium_acetate_incredibly_beautiful/

SMC Physical Sciences Dept Flex Day

Our Fall 2023 Flex Day was held at SMC's new Malibu Campus. We did an activity the that the Engineering/Physics professors use in their engineering class - build your own self-propelled race cars! https://www.youtube.com/watch?v=6_Glw0-xnSE

Illustrations with Artificial Intelligence

12-19-2023 I used Bing's DALL-E 3 program today with the following prompt as my first foray into using AI for creating illustrations:

charizard doing organic chemistry in the lab

Looks like the program recognizes that Personal Protective Equipment (goggles, lab coat, gloves) are part of working in the organic lab! (They forgot about closed toe shoes and long pants, however...) . Some of these Charizard images look more like orange Pikachu or orange Eevee... They got the flaming tail part right. It's intersitng how one image also has a flaming bunsen burner while another has a flaming microscope (?!?). Let's not look too closely at the organic structures written in the background....

I also have a teaching mnemonic for sugar chemistry "Birds above and Ants below" for remembering that when the anomeric OH points up (toward where the birds live) it is the beta anomer and when the OH points down (toward where the ants live) it is the alpha anomer. I gave the AI the prompt Birds above and Ants below and got this image.

IR simulation website

This website lets you draw a structure and simulate the resulting appearance of the IR spectra: https://ir.cheminfo.org/

NMR Practice Site (www.nmr-challenge.com)

www.nmr-challenge.com

(actual site: https://nmr-challenge.uochb.cas.cz/)

NMR practice site that gives you Molecular Formula and NMR (1H and sometimes 13C data). You draw the structure in the box below and it tells you if you got the problem right! It also gives some hints if you've made some minor errors (wrong molecular formula, etc.)

https://pubs.acs.org/doi/10.1021/acs.jchemed.2c01067

ChemDraw Prime (Chem Draw 21) Shortcuts and Hotkeys

Magic Hotkeys Cheat Sheet (available from within ChemDraw via Help --> Shortcuts and Hotkeys)

ChemDraw 21 manual: https://drive.google.com/file/d/1HgOS7TSgF3B-WhuqW93V0vnCMmZhHcDg/view?usp=drive_link

New discoveries: First example of oxygen as a chiral center!

https://www.nature.com/articles/s41586-023-05719-z

Significant Figures are no joke

AlphaFold accelerates artificial intelligence powered drug discovery: efficient discovery of a novel CDK20 small molecule inhibitor

Amazing proof of concept from the University of Toronto using AI (PandaOmics) to identify a protein target to inhibit a type of liver cancer cell known as hepatocellular carcinoma, then using AI (AlphaFold) to determine the structure of the protein target from its amino acid sequence, then finding potential "weaknesses" (druggable sites) in the protein target and then finding potential chemical structures that might bind effectively to those "weaknesses" also using AI (Chemistry42), and then finally synthesizing the candidate structures (done by humans), and testing it on the hepatocellular carcinoma cells (done by humans). And all in the span of one month.

News article: https://www.thestar.com/amp/news/canada/2023/01/19/u-of-t-researchers-used-ai-to-discover-a-potential-new-cancer-drug-in-less-than-a-month.html

Scientific paper from Chemical Science (Open Source): https://pubs.rsc.org/en/Content/ArticleLanding/2023/SC/D2SC05709C

Real Organic Chemistry.org

Prof. Dennis D. Cao at Macalester College has developed a compilation of literature/patent organic chemistry reactions titled "RealOrganicChemistry.org: A Collection of Introductory-Appropriate Organic Chemistry Reactions"

www.realorganicchemistry.org

https://pubs.acs.org/doi/10.1021/acs.jchemed.2c00424

Copy and Pasting the abstract of this 2022 J Chem Ed article below: For most students, completing practice problems is an essential prerequisite for success in organic chemistry courses. Practice work, however, is sometimes perceived to be easier than or even not related to the types of chemistry that students see in assessments and “real-world” science. This negative view may contribute to a reduced level of engagement with course content and scientific learning practices. To combat this perception, a collection of introductory level-appropriate organic reactions bearing literature citations has been assembled and made available at RealOrganicChemistry.org. Portions of this collection were crowdsourced by introductory organic chemistry students through a three-part literature assignment intended for students reading the chemical literature for the first time. For students, RealOrganicChemistry.org is intended to provide a wealth of practice opportunities to complement conventional learning resources. For instructors, RealOrganicChemistry.org hosts a simple-to-complex range of reaction examples that are useful for literature-backed teaching efforts.

It's all a matter of perspective - Newman Projections!

Found this image in a facebook group and this should somehow relate to Newman Projections right? For an introduction to Newman Projections, see link and video below from Master Organic Chemistry.

https://www.masterorganicchemistry.com/2020/03/27/conformational-isomers-of-propane/

Compare and Contrast these two images: the Hubbell Space Telescope (launched ~30 years ago) to the James Webb Space Telescope (brand new and this year!)

Image and Text Source: https://bigthink.com/starts-with-a-bang/webb-first-science/?fbclid=IwAR3XWhd3sRyXaFpYRUN9nldkjH6L-b5XzaqP92EY0WlosuZiJMC3mvpydsc

Caption taken from the website above: This composite blinker image was constructed by rotating our first view from the White House release of JWST’s first science image and pasting it atop the previous Hubble image. The number of new features revealed are spectacular.

Resources for visualizing DNA and other biological macromolecules

Left side animation: https://proteopedia.org/wiki/index.php/DNA
Right side graphic: https://biomodel.uah.es/en/model4/dna/dnapairs.htm
Both sites offer computer models that can be easily manipulated/rotated/zoomed in, etc.
Additional very useful sites
- Top 5 "easy-to-learn" techniques/tutorials: https://www.umass.edu/microbio/chime/top5.htm
- Other structures/animations: https://www.umass.edu/microbio/chime/

Do Not Mix!

Very helpful reminder and lots of chemistry to be thinking about.

ChemDraw tips and tricks for drawing basic mechanisms

Things I learned from this video:

Using 3 anchor points when using the free draw tool makes for drawing beautiful mechanism arrows (I didn't even know there was a anchor points tool!)
Use the expand label so that things like H2SO4 become automatically drawn
Use the chemical formula tool to automatically fill in the subscript positions for things like H2SO4

Things I learned from this video for drawing catalytic cycles:

For an arrow that is curved, if you highlight the end of the arrow and drag it out, ChemDraw will automatically draw the rest of the curve out (to create a complete circle or a complete ellipse)
You can copy and paste the curved arrow, overlay it exactly in the same position, resize it, all to get a "perfect" circle/ellipse for your catalytic cycle mechanism

2021 Nobel Prize in Chemistry - Prof. Benjamin List and Prof. David Macmillan

https://www.youtube.com/watch?v=IW4zgOHhefc

Illustration of Chair Flips

A nice animated gif image of chair flips. Notice how during the chair flip, axial/equatorial relationships switch, while up/down relationships stay the same. Example: The Bromine is axial down in one chair, while it becomes equatorial down in another chair.

** Note that the actual ring flip actually proceeds through a "twist-boat" conformation (instead of a coplanar arrangement). Nonetheless, this animation does a very nice job of conveying how the starting chair and the ending chair are related. Thank you to Prof. Ezra Depperman of the University of New Mexico for making this available to chemistry instructors!

Pfizer unveils its oral SARS-CoV-2 inhibitor

The antiviral candidate is the first orally administered compound to enter clinical trials that targets the virus’s main protease

by Bethany Halford

APRIL 7, 2021 | APPEARED IN VOLUME 99, ISSUE 13

Link to article: https://cen.acs.org/acs-news/acs-meeting-news/Pfizer-unveils-oral-SARS-CoV/99/i13?utm_source=mostread&utm_medium=mostread&utm_campaign=CEN

Lectures on Pd-catalyzed Cross Coupling Reactions by Prof. Oliver Reiser (Universitat Regensburg)

https://www.youtube.com/watch?v=r_OVI-ZCyo0

Sonogashira Coupling reaction video

Nice youtube video of the Sonogashira Coupling reaction from CSIR North East Institute of Science and Technology, Jorhat, India including reaction setup, workup, column chromatography, and NMR analysis https://www.youtube.com/watch?v=fSDnXUIt4VI

COVID update 1-21-21

The current Winter 2021 session is online and the upcoming Spring 2021 session will also be online. SMC announced on 1-21-21 that the Summer 2021 session will also be online, with a decision regarding Fall 2021 to be forthcoming in the next few weeks. More info about SMC COVID-19 updates are available here: https://www.smc.edu/news/coronavirus/index.php

Regioselectivity of enamine formation

Basically, whether you get the more substituted or less substituted enamine really depends on the nature of the substituents on the amine... (so it's complicated). In Chem 22, we typically convert symmetrical ketones to enamines (effectively skirting the regioselectivity issue), but there is a regioselectivity component when using asymmetrical ketones.

Source: Baran group meeting link: https://www.scripps.edu/baran/images/grpmtgpdf/Lockner_Nov_07.pdf

COVID update 9-9-20

(graphic below prepared by the LA Times using their Coronavirus tracker by county)

As of Wed 9-9-20, SMC (and the rest of LA County) is in Tier 1 (Widespread). Of the four tiers, being in Tier 1 is the bottom of the scale (the worst). Tier 1 is coded in purple in the map below. Hopefully we will work our way up one rung at a time.... In Tier 1, most nonessential indoor business operations are closed. SMC is currently in Week 2 of the Fall 2020 semester and we are teaching classes online.

Legend