Monthly Archives: May 2015

Genetic Goofs

Yet another geneticist’s pick-up line: If I had to choose between RNA and DNA, I’d choose RNA – because RNA has U in it.

Buckle in, folks, because we’re diving once again into the murky molecular world of genetics.  We’ll be focusing our attention on DNA (DeoxyriboNucleic Acid) and RNA (RiboNucleic Acid), two indispensable molecules that make us – and by us I mean all living organisms on Earth – what we are.

We’ve discussed DNA before.  DNA is the molecule that contains the instructions for building a living thing.  Every one of your cells – except mature red blood cells – stores a complete blueprint for making you.  That blueprint is encoded in DNA.

The beautiful thing about this genetic code is its simplicity.  Everything in your genes is spelled out using just four letters: A, T, C, and G.  These are the initials of four molecules called adeninethyminecytosine, and guanine.  DNA, you may recall, is shaped like a twisted ladder.  The rungs of this ladder are made of two of these molecules in complementary pairs.  For example, adenine and thymine – A and T – always pair up together in a rung, and so do cytosine and guanine – C and G.

DNA base pairs

At the risk of digressing from the main topic, that seems pretty incredible!  How can just four letters make a you?  After all, you’re way more complex than that, right?

The letters tend to work in triplets called codons.  So for example, one side of a DNA molecule might read:


And its complementary strand would read, in the same direction:


Each triplet codes for a particular amino acid, and the sequence of amino acids makes up a protein, which is a major structural and functional component of living cells.  Working proteins handle every other function the cell needs to live, from manufacturing molecules to digesting nutrients.

Here’s an analogy; if the cell were a city, then DNA would be blueprints for important facilities and machines to build the city.  Each machine is fine-tuned for an important function, so it’s important that its blueprints are stored, interpreted, and copied as accurately as possible.

Human cells keep DNA in the nucleus – the membrane-bound central region of the cell.  The nucleus is like a vault.  It is vital to the safety of these all-important blueprints that DNA never leaves the relative safety of the nucleus.  How, then, do the genetic instructions get to the cellular machinery and infrastructure that interpret them?

That’s where RNA comes in.  RNA is built in the cellular nucleus, transcribed directly from DNA.  DNA unzips, and complementary bases are laid in along the exposed bases.  After transcription, RNA is shipped outside the nucleus, where it dictates the instructions for building proteins to special protein-building units called ribosomes.

DNA Transcription

As you can see, RNA is single-stranded, unlike double-stranded DNA.  But that’s not the only difference.

RNA does not contain thymine.  When the DNA-to-RNA transcribing machinery encounters an adenine base on the parent DNA molecule, it adds a different base, uracil, U, to the growing RNA strand.  So if a DNA strand reads:


The complementary RNA strand reads:


Now here’s the big question: Why?  Why does RNA have U in it?

The better question, as we shall see, is why doesn’t DNA have U in it?

As with all of life’s problems, the answer has to do with chemistry.  All of your cell’s important molecules are bathed in a soup of chemicals with varying degrees of reactivity.  Plus, we amble about in an environment awash in radiation; ultraviolet, gamma rays, X rays – you’re sure to absorb a few hits from ionizing radiation in your day-to-day activities.  It’s just common sense that your DNA is going to take a beating.

For example, the base cytosine, C, is easily converted to uracil, U.  Left unchecked, this simple substitution could wreak havoc on your genetic code.  Fortunately, all of your cells have a repair mechanism to hunt down and correct errors just like this one.  Your cells “know” that uracil doesn’t belong in DNA, so they convert it back to cytosine whenever they find it.

This is no small problem, by the way.  It happens about 100 times per day, per cell.  The enzyme that handles this repair, Uracil-DNA glycosylase, or UDG*, has its work cut out for it.

So DNA cannot contain uracil as one of its bases, because if it did, then UDG would have no way of knowing which uracils to keep and which to replace with cytosine.  That repair pathway would not work.

But hold on, the savvy reader will ask: if U isn’t good enough for DNA, why is it good enough for RNA?  Can’t cytosine get converted to uracil in RNA just as it is in DNA?

Yes, but RNA isn’t meant to exist for very long; just long enough to transfer the genetic code from the nucleus to the ribosomes, where proteins are assembled.  See, DNA gets copied and transcribed over and over; its code has to be durable.  A persistent error in DNA can kill the cell, or worse, lead to cancer.  But RNA is a short-lived throw-away molecule. If an RNA molecule suffers a cytosine-to-uracil mutation, the worst that happens is a couple of proteins don’t get made correctly.  It doesn’t matter in the long run; there will be hundreds or thousands of RNA molecules that don’t get mutated.  Business will carry on as usual.

So we know why thymine is preferable to uracil in DNA, but we haven’t discussed why uracil is preferable in RNA.

It’s because uracil is energetically “cheaper” than thymine.  It costs less energy and resources to manufacture and use uracil than it does for thymine.  So thymine is only used in DNA, whose accuracy is tantamount to the cell’s – maybe even the entire organism’s – survival.  And cheap, easy uracil is used in cheap, disposable RNA.  It’s true what they say: you really do get what you pay for.

Now that we know how DNA and RNA use thymine and uracil, respectively, is this really an effective pick-up line?  If the intended recipient of your woo knows anything about genetics, probably not.  In essence, you’re telling him/her that they are cheap and easily replaced.  These are not the words of a lover.

*UDG is notable as an initialism in that one of its letters stands for another initialism.  Which is a shame, because I think it would be fun to talk about UDNAG.

A Furry Friction Funny

Q. Two cats are sitting on a roof.  Which one slides off first?

A. The one with the smaller mu!

Of course this joke assumes that the cat in question is totally complacent to slide off the roof, making no effort to maintain his position.  Strange cat.

Anyway, “mu” is pronounced like “mew“, as in the sound made by a cat.  It is a Greek letter, usually represented by the following symbol: µ.  Mu must be the favorite Greek letter of mathematicians and scientists; it pops up in fields as diverse as computer science, number theory, physics, orbital mechanics, chemistry, and pharmacology.  In this joke, µ is meant to represent the coefficient of friction, about which more in a moment.

What is friction?  To greatly oversimplify things, friction is a force that resists relative motion between two surfaces, or between a surface and a fluid.  When you experience resistance while pushing a refrigerator across a tile floor, you’re working against friction.  When you rub your hands together to warm them up, friction is your friend.  Friction is an even greater friend to the skydiver; when she opens her parachute, fluid friction against the atmosphere reduces her speed from a spine-shattering 120 miles per hour to a totally survivable 10 miles per hour.)

Here’s an interesting side note about friction; scientists used to think that the friction was caused by microscopic grooves and bumps that tended to lock surfaces together, requiring extra force to break their grip and get the surfaces sliding past each other.  Now, scientists think that friction is caused by chemical bonds forming between the atoms in the adjacent surfaces.  That’s a strange thought; merely by touching something, you bond with it.  In a way, you become a part of it and it becomes a part of you.  Deep, man.  Deep.

But I digress.  Mathematically, the friction between two surfaces – such as, say, a roof and a cat’s butt – can be expressed using the following formula:

Ff = µ * m * g * cosθ

Ff represents friction, which is measured in units of force called newtons.  The letter m represents the mass of the cat in kilograms, g is the acceleration due to gravity (On Earth, that’s about 9.8 m/s/s) and cosθ is cosine of angle theta, where theta (another Greek letter strongly favored by the academic elite) is the angle that the roof makes with the ground.

Just to have some numbers to play with, let us assume that the cat’s mass is 3 kilograms, giving her an Earthly weight of about 6.6 pounds.  Now let us assume that the roof has a pitch of, say, 30º.  To find the friction between the cat’s derriere and the rooftop, we would substitute and multiply:

Ff = µ * m * g * cosθ

Ff = µ * 3 kg * 9.8 m/s/s * cos(30º)

Ff = µ * 25.5 newtons

I have not yet specified the roof-feline coefficient of friction, because frankly, I don’t know what it is.  My search of the literature has been fruitless.  For the sake of argument, let’s assign a completely arbitrary value of 0.6 to µ, and see what that gets us.

Ff = 0.6 * 25.5 newtons

Ff = 15.3 newtons (about equal to 3.4 pounds of force)

So there you go; there are 15.3 newtons of friction preventing the cat from sliding down the roof.  Whether the cat actually slides or not depends on whether the gravitational component pulling the cat down the roof is greater than the friction holding the cat in place.

But let us assume that the coefficient of friction between the cat and the hot tin roof were smaller, perhaps because the cat had just finished grooming and her fur was unusually even and smooth.  Instead of 0.6, let’s say the coefficient of friction were only 0.3, giving the cat a static friction of only about 7.7 newtons.  Naturally, with a smaller coefficient of friction – a smaller mu – the cat would be less able to hold its position on the roof and more likely to start sliding downward.

So there you have it: the cat with the smaller mu is the one that starts sliding first.  Next time somebody tells you this joke, they’ll be met with less friction, because you’ll understand it purr-fectly.

Okay, I’ll go now.