Friday, April 28, 2017

Musical Alleles

Scott Woody, a friend and fellow science educator, asked me a few years ago to do some illustrations for a manuscript for American Biology Teacher.  That article featured a really nice analogy Scott came up with to help students understand what makes alleles dominant or recessive (Woody and Himelblau, 2013. Understanding & Teaching Genetics Using AnalogiesThe American Biology Teacher, Vol. 75, No. 9, pages 664–669. ISSN 0002-7685, electronic ISSN 1938-4211).  It has some good stuff for teaching genetics including a nice analogy for homologous chromosomes.

The thing in the paper I've used the most in my own teaching is the series of drawings about 'musical alleles' or 'musical mutations'.  The drawings here are slightly different than the ones in the paper.
Here we see two musicians playing a lovely melody.  In this analogy, the music you hear while sitting in the audience is the phenotype.  The musical score (shown above their heads) is the genotype...it contains the information for how the music should be played.  In this case the both have the correct sheet music, analogous to the wildtype (WT) allele.  There are two musicians representing the two alleles of each gene found in a diploid.
In this drawing we see that a mistake happened at the sheet music printer.  One musician's sheet music is messed up forcing him to stop playing.  In genetics we would refer to this as a loss of function allele.  This image helps to show why a loss of function allele is typically recessive to wildtype...even though one musician has to stop playing the performance can continue since one musician has the correct (WT) sheet music.  In genetics we would say that the gene is in a heterozygous state (two different alleles with the dominant allele determining the phenotype).
Now we see that both copies of the sheet music are unreadable.  In this case (homozygous for the recessive loss-of-function allele) the performance has to stop.  In an organism, being homozygous for a loss-of-function allele can lead to disease or death.
In the final image we see that, yet again, the sheet music printer has made a mistake. However, the nature of the mistake is different than in the previous two examples.  Our musician is frantically trying to play all the extra notes this misprint has created.  If you were in the audience for this performance, what would you hear?  Would you hear the musician playing the correct (wildtype) part?  No!  You would hear the musician working frantically to play all those extra notes.  In this case the mistake has created a gain-of-function allele.  Gain-of-function alleles tend to be dominant to wildtype and this illustration helps to establish why that is.  (One note: students often hear "gain" and think "better"...it should be clear from these illustrations that, compared to wildtype, both loss-of-function and gain-of-function mutation have negative consequences.)

Monday, March 27, 2017

Chromosome Counting with Corn

Download the images and worksheet associated with this post.


I like to give my students different ways to practice chromosome counting.  Below is a micrograph taken by a former undergraduate student in my lab, Maya Benavides.  To take this picture, Zea mays (corn) seeds were germinated and the root tips were removed.  The root tip is where most of the mitosis is occurring in the root and, since we wanted to capture condensed chromosomes, using a tissue with many mitotic cells was important.  After digesting the cell walls and squashing the tissue on a slide it was possible to find nice chromosome spreads like the one shown below.

Maya Benavides, Cal Poly, 2008

The circled shape is a pair of sister chromatids.  I give my students this picture along with the following questions as a way to reinforce their understanding of chromosome numbers during mitosis and meiosis.  (Get this as a worksheet from the download page.)

1) How many pairs of sister chromatids are shown in the picture?
Answer...20.  Question 1 is straightforward...you just need to count how many "blobs" there are in the picture.  Sometimes students overthink this step and say 40.  The number of chromatids is 40 but the question is asking for the number of sister chromatid pairs.  (I usually interrupt the students after they have been working for a minute or two and make sure that they have the correct answer for question 1...if they get off track here they will miss most of the remaining questions.)

2) A diploid corn cell has _____ total chromosomes.
Answer...20.  Each of the pairs of sisters is a single chromosome despite the fact that each pair of sisters is actually composed of two double-stranded DNA molecules (see my previous post on chromosomes and chromatids).  There were 20 chromosomes in this cell before DNA replication and there are 20 chromosomes in the cell now (at the start of mitosis).  DNA replication doesn't change chromosome number.

3) A diploid corn cell has _____ homologous pairs of chromosomes.
Answer...10  Corn is diploid meaning that it has homologous chromosomes.  For each chromosome in the picture there is another chromosome with similar length, centromere position, and gene content.  (An expert could look at this picture and match all the homologs up.)  These homologs are not be identical...they have the same genes in the same order, but, they can have different alleles of those genes.

4) If a Z. mays cell were to undergo meiosis, _____ bivalents would be visible in metaphase of meiosis I.
Answer...10.  In meiosis I homologous chromosomes pair up to form a bivalent (also known as a 'tetrad', see picture below).  Since there are 20 total chromosomes, 10 bivalents form when the homologs come together.
Bivalent.png


"Bivalent" by internet - http://110.138.206.53/bahan-ajar/modul_online/biologi/meiosis/glossary/glossary_frameset.htm. Licensed under CC BY-SA 2.5 via Wikimedia Commons.

5) A Z. mays gamete will have _____ total chromosomes.
Answer...10.  A gamete is a haploid cell produced by meiosis.  If one corn cell was to undergo meiosis the result would be four haploid cells.  During meiosis I the homologous chromosomes separate into different cells...each of those cells has 10 total chromosomes and no homologous pairs.  (Even though there are 10 chromosomes in the cell at this point each chromosome is still represented by a pair of sister chromatids.)  During meiosis II the sister chromatids separate and go into different cells.  Meiosis II doesn't reduce the number of chromosomes (again, this is just the weird way geneticists count chromosomes.)

Thanks for checking this out.  Please submit questions or suggestions in the comment area below.

Thursday, March 9, 2017

March

You know what they say, March comes in like a......(what was it again?)
Can you think of any animals that start with 'L' that I left off this cartoon?  Please comment and let me know.

Wednesday, December 14, 2016

Erlenmeyer's Early Experiments

Two minutes of web searching revealed the amazing fact that Emil Erlenmeyer and Robert Bunsen, two giants of lab equipment, worked in the same laboratory in the 1850s.  During that time Erlenmeyer converted his backyard shed into a lab so he could mentor students (something not allowed in the Bunsen Laboratory).

Sunday, October 23, 2016

Human Chromosome vs. Human Nucleus (Part II)

I previously posted an image I made of a human cheek cell compared to the length of chromosome 21...the smallest chromosome.  Here's a new version of that image featuring the largest piece of DNA in the nucleus, chromosome 1.  (Click on the image below to see a full-sized image.)


Pretty impressive!  The small blue shape in the center of the image is a human cheek cell.  The nucleus is visible as a small, dark blue spot at the center.  The thin line looping around the cell represents the length of chromosome 1.  Chromosome 1 is about 248 mega basepairs (mbp, 248,000,000 base pairs).  To see how I calculated the length of the chromosome line see my previous post about chromosome 21.

I added some additional features to this image.  The thicker grey line represents the centromere of chromosome 1 which is approximately 7 mbp...about 3% of the total length of the chromosome.  The small green tick marks on the upper left of the chromosome line represents the exons of the largest gene on chromosome 1.  The gene is AGBL4 and it stretches across about 1.5 mbp.  The product of AGBL4 is involved in chemical modification of proteins and mutations in AGBL4 are associated with age-related macular degeneration.  Notice that most of the DNA base pairs in the AGBL4 region of the chromosome are non-coding introns.

Bottom line...chromosome 1 is big!  Two copies of chromosome 1 fold up to fit inside the nucleus of every human cell.  And there are 44 other chromosomes folded up in there too!

Saturday, August 27, 2016

A Stir Bar Love Story

Here's a clip from a talk I gave for the @ScienceAfterDarkSLO.  (I really do enjoy working with undergraduates in the lab...).  You can see another clip from this talk in an earlier post.


In addition to the stir plate and stir bar, I also show the micro centrifuge in the cartoon.  Here are some centrifuge cartoons.


The character on the right with the striped shirt appears in another of my centrifuge-related cartoon.



Friday, August 12, 2016

Olympics of Molecular Biology

In honor of the Games in Rio, here are some cartoons I drew in 2000 (Sydney Olympics).



Tuesday, July 26, 2016

Spaghetti Cell

What is it like inside a cell?  In my experience students come to my Introductory Cell Biology course picturing a cell as a bag of water with things floating around inside.  Maybe that isn't surprising since many of the structures inside cells (especially the cytoskeleton) aren't visible in a light microscope.

To help students develop a more accurate conception of what it's like inside a (eukaryotic) cell I started asking them to imagine a plate of spaghetti and meatballs stuffed into a small plastic bag.  There would be no empty space and nothing would be 'floating around' in there.

After using this analogy for a while I decided...why not do it as a demo.  Here's a video from lecture:


I always use a clean bag and gloves so I can eat the spaghetti for lunch later.  The meatballs represent organelles while the noodles taking up most of the space in the bag represent cytoskeleton.  I do this demo before covering motor proteins.  The spaghetti bag helps students understand the role of motor proteins...when large structures move inside a cell they are being dragged through a dense matrix.