Buster Bear Goes Fishing

For Animal Stories for Kids

Buster Bear was having a lazy day.  But as the sun reached higher into the sky, his fur started to get hot and his stomach was starting to growl. 

“All right” he said to himself.  “Time to get a move on.”

Slowly and methodically, Buster Bear started to head downhill to the Laughing Brook.  The movement felt good to his well-rested muscles and the water ahead looked inviting. 

As he approached the Laughing Brook, Buster noticed that he wasn’t the only one that had thought about having fish as a mid-morning snack.  Once he was close, he realized that it was Little Joe Otter.  He also came to realize that the otter had been successful.  Little Joe Otter had a nice big trout in his mouth!

Buster Bear crept up to the unsuspecting otter and snarled.  As you can imagine, poor Little Joe Otter panicked at the sound, dropped the fish, and dove into the nearby water. 

“Just as I had hoped!” Buster Bear thought as he pounced on the trout before it flip-flopped its way down the stream bank.

Little Joe Otter popped his head out of the water of the water and stared coldly at Buster Bear’s mouth. 

Buster Bear stubbornly stood there and eventually said, “If you would like the fish back, just come get it.”

This did nothing to get Little Joe Otter to stop his unblinking gaze, so Buster Bear repeated his half-hearted offer.  “Come get your fish if you want it.”

Furious, Little Joe Otter dove under the water and slipped downstream until he met Billy Mink.  It didn’t take long to tell Billy about his encounter with Buster Bear.  Billy Mink listened to Little Joe’s tale and nodded sympathetically.  However, being a practical sort of animal, Billy Mink could only say, “There’s not much you can do about it, is there?”

Stewing in his anger, Little Joe Otter thought over his options until a plot for revenge took root in his mind.  Without a word, Little Joe Otter took to the water again and made his way upstream until he spotted Buster Bear.

It was clear that one fish did not satisfy the lazy bear’s appetite, so Buster Bear was progressing from one deep pool to the next.  Little Joe Otter picked up on Buster’s plan and moved quickly into action.  He first went to the pool Buster Bear was going to next.  Once there, he swam at a frantic pace in circles to scare away the fish in the pool and disturb the mud to make the water murky.

Buster Bear fished unsuccessfully there for a while and, discouraged, moved on to the next pool only to find the conditions to be similar.  All day long, Little Joe Otter sabotaged the lazy bear’s fishing.  Buster Bear’s stomach continued to growl and Little Joe Otter’s stomach joined in the chorus. 

Biology connection: Food resources, like fish, are prized by many different types of animals.  The battle for food is called competition.  The population size of one type of animal is often limited not only by the amount of food in an area but also by whether other types of animals eat that food, too.

Re-write of “Thornton Burgess Bedtime Stories” chapter 1.

Central Dogma of Biology

For Conversational Biology series – topic POLS

To learn a topic, it is nice to have a central framework upon which to build your “mind map”.  When it comes to biology, my central framework is called “The Central Dogma of Biology”.  To get us started learning about biology, I think it is appropriate to provide this concept for you to use when building your mind map of biology.

If we go back in time to 1956, we would find that Francis Crick was an important figure in biology, particularly molecular biology.  Just a few years earlier, he had looked at Rosalind Franklin’s data and, along with James Watson, had described the structure of deoxyribonucleic acid (DNA).  This was a big deal because biologist were beginning to come to grips with the idea that DNA is the molecule (a type of macromolecule under the umbrella of “nucleic acids”) that stores genetic information.  Prior to this, protein was the top dog in the minds of most scientists.  DNA was considered “boring” and proteins (another type of macromolecule) were considered to be more interesting, so it stood to reason that proteins would have been suspected to be the storage molecule for molecular biology. 

Anyway, back to the central dogma of biology (aka the central dogma of molecular biology).  This concept was proposed by Francis Crick.  His framework can be overly simplified to “DNA is transcribed to RNA and RNA is translated to protein” or, even more simply, “DNA à RNA à protein”, where the arrows are steps that read information of one molecule to create the next molecule in the progression.

Let’s back up a step again.  What’s RNA?  It, like DNA, belongs to the nucleic acid macromolecule class.  It looks a lot like DNA, but it is one oxygen molecule short, so RNA (ribonucleic acid) has a similar name to DNA (deoxyribonucleic acid).  Notice that the difference in the names is “deoxy”, which is a scientific way of saying “lacks an oxygen”.

Francis Crick had one more arrow in his “DNA à RNA à protein” framework and that was a reverse arrow between DNA and RNA (DNA ß RNA).  This left open the possibility that information in the form of RNA could be used to create a new molecule of DNA.  This turns out to be true, so this process is called “reverse transcription” since the process of DNA à RNA is called transcription.

One final point, Crick wisely avoided drawing an arrow from protein back to RNA (RNA ß protein).  When we get to the topic of the genetic code, we will see why “reverse translation” isn’t a thing.

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Plasmid basics

I found that the blog post about plasmids that I had outlined in my head had been written already on a website called Addgene.  The beginning of the Addgene post echoes many of the points that I made in the “Why work with Escherichia coli (E. coli)?” post.

E._coli_Bacteria_(16598492368).jpg

Image: Escherichia coli – scanning electron micrograph from Wikimedia Commons

Here, I will paraphrase and throw in my two cents for the “plasmid elements” table:

  1. Origin of Replication (ORI) – Genetic element with low melting temperature (high percentage of adenine-thymine base pairs that use only two hydrogen bonds).  When the bacterial DNA replication machinery gets recruited to this element, the strands can be separated and replication forks will proceed in one or both directions from the ORI.
  2. Antibiotic Resistance Gene – During the bacterial transformation process, not all bacteria will take up the plasmid DNA you mix them with.  How do you separate the bacteria that successfully take up DNA versus those that don’t?  The inclusion of an antibiotic resistance gene in the plasmid DNA will make the successfully-transformed bacteria capable of growing in the presence of an antibiotic.
  3. Multiple Cloning Site (MCS) – The MCS is an area of the plasmid that is loaded with restriction enzyme recognition sites.  Most, if not all, of these restriction sites are “unique”.  That is, these unique restriction sites are only found once in the entire sequence of that plasmid.
  4. Insert – As plasmids are constructed, the new piece of DNA is called the insert, whereas the original plasmid DNA is called the vector.  Inserts may add new functional DNA to a plasmid to create ever-increasing complex plasmids.  However, in day-to-day molecular biology work the insert is often a gene from another organism that the scientist wants the model organism to “express”, where expression typically means that the model organism reads the DNA and makes a protein from it.
  5. Selectable Marker – Often in the form of resistance to an antibiotic, the selectable marker allows the cell(s) that take up the DNA to live in conditions that would otherwise cause it to die.  The protein encoded by the selectable marker could alternatively provide a way for the organism to live by providing an enzyme in a metabolic pathway such as for an essential amino acid.  The antibiotic resistance gene is common in plasmids that are taken up by bacteria such as E. coli.  In contrast, the genes encoding metabolic enzymes are often used in yeast such as bakers’ yeast, Sacchromyces cerevisiae.

Saccharomyces_cerevisiae_SEM.jpg

Image: Sacchromyces cerevisiae (a type of budding yeast also known as bakers yeast)- scanning electron micrograph from Wikimedia Commons

The Big World of RNAs

Biotechnology Chapter 5 Day 1 Questions

  1. What is a ribozyme? What does the hammerhead ribozyme do and where did it get its name?  How does our definition of ribozyme get violated by hammerhead’s activity?  Name a ribozyme that doesn’t violate our ribozyme definition.
  2. Piwi-interacting RNAs are highly expressed in testes. Given the textbook’s description of these small RNAs, why might this make sense from an evolutionary perspective?
  3. The book doesn’t talk about CRISPR much, so watch these two videos to learn more:

****Sorry about the image**************

 

  1. If a DNA oligonucleotide binds to an RNA target, what might happen? What enzyme (that we been talking about over the past couple of weeks) would do this?
  2. MicroRNAs regulate gene expression “in trans”. What does this mean?  What is the other category of regulation?
  3. Draw a diagram to show how to create an antisense transcript from a plasmid construct. How could you make a plasmid that makes two RNAs that form a double-stranded RNA?