Archives: Biology

Gene Regulation and Expression

To get an idea of how gene regulation and expression work in your cells, imagine someone went through your house and turned on all your electrical components at full-blast. The radio and the TV would be blaring, the fridge would turn into a freezer, and your home heating system would melt you into a puddle of sweat. It’d be chaos!

To get things back to normal, you’d need to go through and turn off the things you didn’t need on or adjust the volume and settings so you’re getting the proper amount of sound, heating, cooling, etc. Your home is a precisely-tuned system when you think about it!

Your cells work the same way. Each one of your 37.2 trillion cells has a complete copy of all of the genes within your DNA, but they’re not all turned on at the same time. The cells that make your toenail, for example, still have the genes that a heart muscle cell or a bone cell uses to make heart and bone-specific proteins. So what distinguishes the toenail-making cell from the bone-making cell and the heart muscle-making cell if they all have the same genes?

It’s all in how each cell expresses them! The toenail-making cell, for example, does have the gene to make myoglobin (a protein found in muscle cell), but it has disabled the gene for that particular protein (could you imagine if it did? Your toenails would turn red and could absorb oxygen!).

Instead, the toenail-making cell creates keratin (a protein found in your nails), while the heart muscle-making cell disables this gene.

How do they do it?

Each cell in your body has ways to turn genes on and off, just like you going through your house and flipping the on/off switches. Cells can also adjust the “volume” of each gene and control how many proteins are produced.

This process is called gene regulation and expression, and there are many ways that cells can do it. In fact, we haven’t even discovered them all yet! In this article, we’ll go over some of the most common ways that cells can regulate and express genes.

The Big Picture: What’s happening in the cell, and where can we control it?

There are a lot of steps that happen in the process that starts with a cell’s DNA and ends with a protein. Genes can be regulated at each one of these steps, so it’ll be helpful to go over them what they are.

There are two major cellular processes that produce proteins: transcription and translation. In transcription, the goal is to produce an mRNA (messenger RNA) copy of an entire gene from its DNA template. This mRNA template is then translated into an actual protein.

First, DNA is transcribed into an mRNA template when RNA polymerase (the gene copying machine) attaches to a gene on the DNA strand. The RNA polymerase slides down the DNA and spits out and exact mRNA copy of the gene.

Our little mRNA template then floats peacefully out of the nucleus and into the cytoplasm (the rest of the liquidy goop that makes up the inside of the cell), where a ribosome attaches to it. The ribosome then slides down the mRNA template, reads the code, and assembles a chain of amino acids based on whatever the code says. At the end, the ribosome falls off and the chain is finished—except now the amino acid chain is called a protein.

Transcription: The First Regulation Point

Transcription is the start of everything, so it’s easiest to regulate which genes are used or not at this point. That way, your cell isn’t wasting time with stuff it’s already built further down the road.

It’s a bit like cancelling an unwanted order before it’s shipped to you. Otherwise, you’d have to wait for it to get to you and then decide you don’t need it anymore. Your time and money will have been wasted.

Similarly, if you need to boost production of a certain protein, it’s also fairly easy to regulate at this point as well. If you need more proteins, just place an order for more!

DNA Methylation

There are several ways that the cell manages to up-regulate or down-regulate its mRNA levels. Perhaps one of the coolest is by turning particular genes off through a process called DNA methylation.

Each gene is outlined by two separate DNA sequences in the genome—a promoter sequence (the start of the gene), and a terminator sequence (the end of the gene). They are like the front and back cover of a book; they serve to denote the beginning and the end of the information contained within.

There is also a molecule called a methyl group, which is made up of one carbon atom and three hydrogen atoms. This methyl group can bind to lots of things—it’s kind of like a sticky note! When a methyl group binds to a promoter sequence of a particular gene, it makes it virtually “invisible” to the RNA polymerase. If it can’t find the promoter sequence of the gene anymore, it can’t start translation. It masks the gene and turns it off!

One of the really cool things about DNA methylation is that these methyl groups are even reproduced along with the DNA in DNA replication. For example, if a metabolism gene is methylated (turned off) and that cell splits in two, the new DNA will also have a methyl tag on that same gene.

This can even apply to genes that are passed down when you reproduce. Based on how you live and which genes your body turns on or off, your kids might inherit genes that are physically present, but not turned on!

Enhancer Sequences

What if you need to turn up the volume for a particular protein? That’s where enhancer sequences come in. They work just like promoter sequences in a gene, except that if a particular protein binds to an enhancer sequence, it ramps up mRNA production even further. It’s as if there was a giant neon sign erected over the gene that says, “Hey, RNA polymerase! Come transcribe this gene! It’s really important!”

Translation: The Second Regulation Point

mRNA transcripts are pretty powerful little pieces of code. They can be read many times per minute, and each transcript has a half-life of about seven hours. That means every seven hours, the number of mRNA transcripts made at a certain time point will be cut in half. When you look at it that way, one single mRNA transcript can be used to make hundreds of proteins!

Seven hours is a long time to be hanging out around the cell. Sometimes, the cell needs to adjust gene regulation right away—not seven hours from now. It doesn’t have time to wait for those mRNA transcripts to dissipate on their own.

For example, let’s say you’re going for a hike and you surprise a bear in the bushes. You’ll get a sudden jolt of adrenaline (and hopefully you don’t mess your pants!), and your cells will instantly try to boost metabolism-related genes so that they can burn energy faster and be prepared for the flight-or-fight response. To do that, it needs to get all of the genes related to storing fat out of the way (now’s no time to store fats—you need to burn them for energy!).

One of the ways the cell can do this is by boosting production of proteins that break down mRNA strands faster. That way, the ribosomes will be unoccupied and free to make more of the metabolism-related proteins to burn fuel faster and get you out of there.

Post-Translational Modification: How To Alter What’s Already Been Made

If the cells in your body need to change their function, they may also need to change the proteins that are already floating around in the cell. There are two main ways that the cell can do this:

Protein Phosphorylation

Some proteins come with a built-in on/off switch in the form of a phosphate group—a molecule composed of one phosphorus atom bound with four oxygen atoms. It works just like the DNA methyl groups: if a phosphate group is added onto a protein, it can change the function of the protein.

Each protein reacts differently to being phosphorylated. Sometimes the phosphate group can turn the protein on, and with other proteins, the phosphate group turns the protein off.

Protein phosphorylation is especially important for many metabolic processes. For example, hormone-sensitive lipase is a protein that is turned on when phosphorylated. It breaks down fat stored in your cells so that it can be used as fuel when you exercise.

Glycogen synthase, on the other hand, is a protein that creates glycogen to be used as a short-term energy source. It turns off when phosphorylated.

Ubiquitin

What if a protein is no longer needed at all? You would need to find some way to go through and mark each individual protein for removal, similar to foresters marking certain trees for removal followed by a team to harvest these marked trees.

The cell does this on a microscopic level. If a cell knows that it’ll no longer need a certain protein, it’ll attach another protein—ubiquitin—to it. Once a protein is “tagged” with ubiquitin, it’s marked for removal.

Ubiquitin-marked proteins make their way to an area of the cell called the proteasome, which is like a cellular recycling center. When a protein goes into the proteasome, it’s chopped up into its component parts—amino acids. These free amino acids float out of the proteasome and can be reused in another protein.

Why study gene regulation and expression?

If we understand how genes are expressed and regulated in organisms, we might be able to manipulate them to make people (or other organisms) healthier. It’s a lot of work to put new genes into an organism. If we could just use the genes that are already there, it would be far easier!

For example, people’s metabolism changes as they get older. Usually people are thin and athletic when young, but as they age they begin putting on more weight. When you’re older, those genes that kept you slim and trim when young are still there, they’re just turned off.

But, what if we could turn those genes back on again? We could make people slim again just like when they were younger!

So far, we only know of a handful of ways that genes can be regulated and expressed, but it’s very likely that there are many more. Who knows—maybe you can be the one to discover a new regulation or expression method, or crack the code in how to turn individual genes on or off!

Chromosome Genetics

A chromosome must have been a scary thing to see for the first few people who peeped into a microscope. They wouldn’t have had any idea what they were, aside from squiggly, wiggling little X-shaped bundles that appeared when cells were about to divide and then “dissolved” as soon as the cells were separate.

chromosome genetics

Chromosomes were discovered around the same time that Mendel was doing his genetic experiments on peas, but because Mendel didn’t do a great job at publicizing his results, no one really made the connection until scientists rediscovered his work decades later.

Mendel thought that some sort of inheritance factor must be controlling how different traits end up in pea plants across the generations; those inheritance factors (now called alleles) turned out to be located on the chromosomes!

We now know that chromosomes are a key feature in genetics because they actually are the units responsible for transmitting genes from one generation to the next. We’ve learned a ton about how chromosomes work since first discovering them, but we also have a long way to go.

What are chromosomes, exactly?

Chromosomes are basically bundles of protein and DNA with a special job: they get all the DNA within your nucleus from one cell into another. They form whenever a cell divides, whether it be in a skin cell in your big toe or a cell that later becomes another person (if you have kids). Chromosomes are how you got all of your genetic information from your parents!

To accomplish this monumental task, chromosomes rely on some pretty precise organization. Whenever a cell divides, it needs to wrangle up all of its DNA into discrete little packages, just like how you pack everything up into boxes when you move from one home to another. To form the chromosomes, the DNA is carefully wound around proteins called histones, just like how you wind up fishing line on a fishing reel.

The DNA-covered histones create a mass of strands called chromatin, which can actually be seen as a tangled clump when stained and viewed under a light microscope. The chromatin, in turn, arranges itself into a chromatid: one single, complete strand of DNA all wound up and arranged into a stick-like package. Each chromatid has a sticky button-like center called a centromere, which allows it to attach to another completely identical sister chromatid (you have two copies of your DNA, remember).

You have two complete sets of genetic information distributed among 46 chromosomes in each cell in your body. In genetics lingo, having two sets of DNA is called 2n. Your gametes (sperm or eggs), on the other hand, have one complete copy of DNA distributed among 23 chromosomes (this is called 1n).

The reason your gametes have just one set of DNA is important. When two 1n gametes combine, the resulting offspring will have two complete sets of DNA (2n)—one complete set from the mom and one complete set from the dad. Otherwise, each generation would double the amount of DNA we get, and we’d all eventually be swamped underneath living DNA blob monsters!

Not All Chromosomes Are the Same…

Humans may have a standard set of 46 chromosomes within their nuclei, but some organisms do things their own way—this pond protist, for example, sets the record with 15,600 chromosomes!

Most living things also have stick-shaped chromosomes, but bacteria are the odd ones out: they possess circular chromosomes!

Even within humans, our mitochondria have their own chromosomes that reproduce independently of our nuclear chromosomes. Plants have similar organelle-specific chromosomes within their chloroplasts, too!

Nondisjunction: When Cell Division Goes Wrong

Chromosomes are precisely organized packages that have to undergo precisely timed movements during the cell division cycle. There’s a lot that can go wrong, and it’s one of the reasons why many genetic diseases are caused by errors in cell replication.

To see how this works, we’ll look at a specific error that can affect chromosomes during cell replication called nondisjunction. Here’s how it works, one step at a time:

Nondisjunction

In Step A, an egg cell is just getting ready to complete its final division through a process called meiosis that produces 1n egg or sperm cells. This egg cell has only two chromosomes (way simpler than your own cells which have 46 chromosomes) which are lined up along the center of the cell.

In Step B, the chromosomes are pulled apart to opposite ends of the cell by spindle fibers. The blue chromosome gets split in half correctly so that each identical sister chromatid ends up in the final, divided cell. The red chromosome, on the other hand, does not split like it should. Oh no!

In Step C, the cell has finished dividing in two. Each cell has the correct amount of blue DNA (one chromatid), but one cell has twice the amount of red DNA (two chromatids), while the other cell is missing the red DNA!

In Step D, each egg cell is fertilized by a sperm cell, which has the correct amount of red and blue DNA (one chromatid each).

In Step E, each fertilized embryo has an incorrect amount of red DNA distributed among its chromosomes. The top cell has just one red chromatid, while the bottom cell has three red chromatids—one too many. The blue chromatids are correctly distributed, however—two per cell, bundled together into one chromosome each.

In humans, this can happen with any one of our 46 chromosomes. Because chromosomes contain such a large amount of DNA in them, though, it’s rare for a fetus with an incorrect number of chromosomes to survive. You might be able to survive a mutation in a single gene, but a nondisjunction error affects thousands of genes in one fell swoop.

There are a few exceptions, though. People with Down syndrome have an extra 21st chromosome, and people with Klinefelter syndrome have an extra X chromosome. These diseases still affect people with adverse symptoms like mental retardation and infertility, but they’re still able to survive with the extra DNA.

It’s easy to diagnose cases of nondisjunction with a special tool called a karyotype, a picture that allows doctors to see which chromosomes—and how many—are present.

Chromosomes and Crossover

These days, everyone is up in arms about whether genetically-modified organisms are safe. But, what would you say if I told you that you yourself were a genetically-modified organism? It’s true!

During cell replication, the parent cell produces two sets of chromosomes that will get distributed equally to each of the two daughter cells. When the cell gets ready to divide in half, each chromosome finds its identical copy (called a homologous chromosome) and aligns next to it in an intricate dance (sort of like the Macarena, but on a smaller scale).

Once the two homologous chromosomes are aligned, they’ll sometimes swap large chunks of the same DNA with each other like this:

Chromosomal Crossover

These swapped DNA pieces contain the same genes, but they might have different alleles—i.e., versions of the same gene. So, for example, the red and the blue chromosomes might both have genes for hair color, but one chromosome might code for red hair while the other codes for black hair.

Crossover is one of the major ways that genes get reshuffled across generations and allows new combinations to form. It keeps us fresh!

Gene Linkage—When Close Friends Just Can’t Let Go

Scientists discovered how crossing over occurs after they noticed an odd thing happening in the lab.

Thomas Hunt Morgan was a geneticist who specialized in breeding fruit flies (one leg up from Mendel’s pea plants). In one experiment, he tried breeding fruit flies with two different traits: body color (black or yellow), and wing shape (tiny or big).

The law of independent assortment gives very specific predictions about what percentage of offspring will have which traits, but he found something very different: some variations of the traits were more likely to be associated with each other than others.

For example, he predicted that only 6% of baby flies would have tiny wings with a black body, whereas 22% of baby flies actually had this trait combination! What could be causing these unexpected results?

It turns out that the genes for body color and wing shape occur on the same chromosome. This means whichever two alleles a parent fly has, they pass it on as a package deal to their offspring, and they aren’t reshuffled. This is why you sometimes see certain traits that occur together in nature. For example, certain coat colors in domestic animals are linked to congenital deafness.

Genes can also differ in how closely linked they are. If they are far apart, there are a lot of opportunities for crossing over to occur in between them. If they’re close together, there are fewer opportunities for crossing over to occur, like this:

Gene Linkage

The closer two genes are to each other, the more likely they’ll always occur together. In one study, 25% of dogs with two copies of the Merle coat color allele showed some form of deafness. This is evidence that these two genes—coat color and deafness—occur very close together on the same chromosome.

Why study chromosomes?

Chromosomes are important to study for many reasons. They’re the main vehicles that get DNA from one cell into another and keep life as we know it flowing along. Otherwise, all life would eventually die out because there’d be no way for the blueprints of life to get from one cell to the next!

Understanding how chromosomes work is also important for a wide range of fields, including ecology, conservation, epidemiology, population biology, medicine, and virtually every other field of biology. You can’t be a good biologist without a basic understanding of how chromosomes work!

One area that requires an especially good understanding of how chromosomes work is genetic engineering. Scientists can engineer microorganisms to be tiny manufacturing plants, getting them to crank out all kinds of useful stuff like medicines or industrial chemicals. Scientists at NYU recently created an entirely new chromosome, for example, that may take the field into the future.

If you’re looking for a cool future career path, this is definitely one to explore further!

Non-Mendelian Genetics

When scientists discovered Gregor Mendel’s work on the basics of genetics, it was hailed as a major breakthrough. For the first time, scientists could reliably predict and describe what was happening when two organisms with known traits were bred to produce offspring.

Things were going great until scientists noticed something funny happening—not all the traits that they predicted in test crosses panned out as expected. What could possibly be the explanation? Was Mendel wrong? Did they need to go back to the drawing board?

We know now that Mendel was correct in his ideas—but the big picture of genetics is a lot more complicated. Mendel described the first simple part of a huge, shifting puzzle. He gave us the tools to understand the basics of how genetics work, but scientists had to figure out what else was happening.

What are non-Mendelian genetics?

Non-Mendelian genetics are basically any inheritance patterns that don’t follow one or more laws of Mendelian genetics. Let’s review those laws quickly:

  • Mendel’s First Law (Law of Segregation) – A parent who has two alleles for a gene can only pass on one allele or the other to each offspring.
  • Mendel’s Second Law (Law of Independent Assortment) – Two or more traits are inherited separately from each other; they don’t always occur together.
  • Mendel’s Third Law (Law of Dominance) – One dominant allele will take charge over a recessive allele and “mask” it. The only way recessive alleles can be seen is if an individual possesses two copies of the recessive allele.

These are the basic rules of Mendelian genetics, but as scientists began exploring more and more test crosses, they found tons of traits that didn’t match up nicely with what these laws predicted.

Some traits exhibited a kind of blending, where the offspring of organisms with two different traits didn’t have one or the other form from the parents—they had something that was sort of in the middle. This implies that certain alleles aren’t dominant over the other ones. Rather, they share roles like harmonious friends.

Some traits seemed to be controlled by complex inheritance patterns. We know now that traits can be controlled by more than one gene, or genetic material may pass down from parent to offspring in different ways than what Mendel predicted with his Law of Segregation.

Finally, non-Mendelian inheritance patterns might just be caused by mistakes in reproduction. There are a ton of different processes all happening together, like a coordinated dance, and all it takes is one thing to trip or mess up and the whole thing goes haywire. There’s so many things that could go wrong that frankly it’s a wonder that we all end up here in one piece!

Let’s take an in-depth look at some of the different types of non-Mendelian genetic inheritance patterns.

Sex-Linked Traits

Did you know that your chromosomes determine whether or not you’re male or female? Everyone has two sex chromosomes, and your gender is determined by which two you possess. Females have two copies of the X chromosome (XX), while males have one copy of the X chromosome and one copy of the Y chromosome (XY).

Because males only have one X chromosome, any genes that are on it will be present. This is because there isn’t a backup copy of the gene on another X chromosome to mask it if it’s recessive, like women have. Men also have their own special Y chromosome that women don’t possess.

But don’t go celebrating about your own special chromosome just yet, dudes: the Y chromosome is much, much smaller than the X chromosome, so technically women have more DNA! And, since any gene on the X or Y chromosome will be expressed regardless of if it’s dominant or recessive, men are far more likely to get sex-linked genetic diseases than women.

Some common sex-linked genetic diseases in men include things like male pattern baldness and red-green color blindness. These disorders are carried on the X chromosome and can only be passed on to males through their moms. Let’s look at a Punnett square to see why:

In this case, the mom is a carrier of the sex-linked trait. She does not have the diseases because her other, normal X chromosome masks it. Half of her kids will get the normal chromosome and be totally fine, but the other half of her kids will get the diseased chromosome.

Whether or not her kids with the diseased allele actually develop the disease is now up to the dad: if he passes on an X chromosome, the child will be a daughter and be safe, although she can still pass on the disease to any of her offspring.

If the dad passes on a Y chromosome, the child will be a son and has a 50/50 chance of having the disease because he has no backup X chromosome.

Codominance

Codominance is a direct violation of the Law of Dominance—thank goodness there’s no gene police to tell it that, though!

When the alleles for a particular trait are codominant, they are both expressed equally rather than a dominant allele taking complete control over a recessive allele. This means that when an organism has two different alleles (i.e., is a heterozygote), it’ll express both at the same time.

Have you ever seen speckled flowers? This is a common case of codominance, where the plant breeder has bred two different colors of flower together, resulting in a speckled hybrid that has patches of color from both parents.

One really good example of this in humans is blood type. The most important blood type is the ABO system, because if you get a blood transfusion with the wrong type of blood, you could develop a severe allergic reaction and die!

The A and B blood types are codominant. Thus, if two people with AA and BB blood type alleles have children, it’ll look like this:

In this case, every single child (male or female) from this couple will be heterozygotes. Both alleles will be expressed equally, meaning that every blood cell in their little bodies will have both A antigens and B antigens present. One allele is not dominant over the other in this case.

Incomplete Dominance

With codominant alleles, both traits are expressed at the same time. With incomplete dominance, the same thing occurs—but the traits are blended together just like paint mixed together, rather than occurring in discrete patches like the speckled flowers.

Going back to our flower example, if flower color shows incomplete dominance then two different flowers crossed together will produce a hybrid that’s in between both of the parents. So, for example, if you cross a white flower with a red flower, you would get a pink flower if the two alleles showed incomplete dominance.

Polygenic Inheritance

Up until this point we’ve been talking about traits that are controlled by alleles from one gene and fit neatly into our Punnett square. But, some traits are controlled by many genes. Scientists estimate that your height is controlled by more than 400 different genes, for example!

The reason human height is controlled by so many different genes is because height isn’t a simple on/off, yes/no-type trait. We’re actually pretty complex critters for some types of traits!

There’s a lot of things that have to happen to make people tall—blood vessels, muscles, nerves, and bones have to grow and elongate; more blood has to be produced to accommodate the extra tissue; the brain needs to send out hormones to coordinate everything, etc. It’s a big job and it’s no wonder there are a lot of genes that come into play!

Many other human traits are controlled through polygenic inheritance, such as IQ, skin color, eye color, etc. Can you think of some of the things that might need to happen to produce these traits?

Gene Linkage

If the above examples are in direct conflict with the Law of Dominance, then gene linkage is in direct conflict with the Law of Independent Assortment!

When Mendel broke ground with his pea experiments, he was looking at traits that just happened to be located on different chromosomes. Thus, when he looked at two traits, they were inherited separately because they were on different chromosomes. Green peas were equally likely to occur on short plants as they were on tall plants, and wrinkled peas were equally likely to be green or yellow, for example.

But, each chromosome can have hundreds or thousands of genes on it. You have upwards of 2,000 different genes on Chromosome 1 alone, for example. That’s a lot of genes! And because they’re all on the same chromosome, they’re inherited pretty much as a package deal.

Many experiments have been done on gene linkage in fruit flies (hopefully the scientists didn’t have too much rotten fruit in their offices!). For example, some combinations of wing shape and body color are inherited together. Fruit flies that have brown bodies are more likely to have normal wings, while fruit flies that have black bodies are more likely to have itty-bitty wings, in one example.

Gene Swapping

Did you know that some organisms don’t even need to reproduce to pass on their genetic material? It sounds strange but it’s true! Some types of bacteria can pass on their genetic material directly to their neighbors, sort of like trading baseball or Pokemon cards.

This obviously makes it very hard to predict genetics of some bacteria, because they can do whatever they want with their genetic material! It’s also one reason why bacteria can evolve very quickly—rather than waiting for a whole new generation, bacteria can pass on their chromosomes to their comrades instantaneously and evolve within a single generation.

Extranuclear Inheritance

Your nuclear DNA lives inside the nucleus in your cells, but did you know you also have other DNA outside your nucleus? It’s true—it lives in your mitochondria, and it’s called mitochondrial DNA. Plants even have their own version too, that lives in their chloroplasts.

Because mitochondria and chloroplasts have their own DNA and reproduce on their own inside each cell, they’re thought to be ancient bacteria that eventually evolved to live inside our cells and provide power. Animals and plants might actually be an amalgamation of several different species!

Mitochondrial DNA is passed down from a mother to her offspring because the mitochondria in sperm cells don’t make it into the egg. Thus, all of the mitochondrial DNA in your body—whether you’re male or female—originally came from your mom!

Mitochondrial diseases are rare, but when they do happen any children that a woman has will also have the disease too, because her mitochondria are passed on unchanged from mother to offspring.

This has given rise to a new phenomenon: three-person babies. If a mother has a mitochondrial disorder and doesn’t want to pass it on to her kids, she can conceive a baby using some pretty amazing science.

First, doctors take a donor egg from a healthy woman and remove the nucleus—leaving behind an empty shell with plenty of healthy mitochondria inside. Next, they take the nucleus out of one of the biological mom’s eggs and implant it in the empty shell egg.

That way, the new egg has healthy mitochondrial DNA from the donor mom, plus all the nuclear DNA that actually makes up a person from its biological mom. The egg can then be fertilized, implanted, and carried to term just like any other test-tube baby.

Why study non-Mendelian inheritance?

As we’ve seen here, some cases of genetic inheritance can be far more complex than simple Mendelian inheritance. Both types of inheritance are equally important to unlocking the clues hidden away in our own DNA.

Because non-Mendelian inheritance patterns are so complex, there’s plenty of room for new geneticists in the field—maybe you could be the one to discover how an important gene is inherited?

Mendelian Genetics

Think about the last time you went to the produce section in your grocery store. It’s chock full of all kinds of plants, and even bacteria and fungi. Now, think about the last time you saw a dog show on TV: each dog breed was bred for a purpose, just like each of the foods in the grocery store.

All of these organisms required careful breeding to get them to where they are today, and we’re still constantly changing and tinkering with domesticated organisms. In order to breed organisms for their desired traits, we need to know how to reliably predict what’ll happen when you breed two things.

This brings up a huge problem: how exactly do you predict which crosses will yield desirable traits? It’s a problem that scientists have been working to solve for a long, long time. Scientists originally thought that all traits were a blend between the mother and the father, like making chocolate milk by mixing chocolate powder and milk together.

The blending hypothesis seemed to explain most of it, but every so often something weird would happen: a trait would skip a generation. Maybe a couple with freckles would have a clear-skinned daughter, who would in turn give birth to another freckled child. Or perhaps a wrinkly-kernelled corn plant produces a smooth-kernelled corn plant, which in turn produces another wrinkly-kernelled plant.

These weird cases defied explanation until the year 1900, when a few botanists came across a secret written decades before.

Gregor Mendel: The Father Of Genetics

A small garden in a Czechoslovakian monastery doesn’t seem a likely birthplace for the field of genetics. But in the 1850s it was exactly the right place for exactly the right person: Gregor Mendel, an Austrian monk.

Mendel had been puzzling about how to predict what offspring from different parents will look like. He knew that the blending hypothesis explained some, but not all of the results he saw from various crosses.

Mendel decided to get to the root of the problem by breeding peas. They were a perfect choice: they had a lot of clear-cut discrete traits that didn’t seem to blend, such as pea color, pea shape, plant height, etc. The peas either expressed one form of a trait or another; there was no in-between.

Peas also have short generation times, so he didn’t need to wait long to see the results of his test crosses. They were prolific: one pea plant can produce many individual peas to collect data from. Plus, fresh garden peas are a tasty research subject!

How Mendel Discovered Genetics

Over the years, Mendel bred thousands of peas. He tried crossing plants with green peas and plants with yellow peas. He crossed tall plants with short plants. He crossed plants with wrinkly peas and plants with smooth peas. Then, he crossed their offspring.

Let’s take a look at how one of these crosses worked. Mendel started out with two parent plants: one with green peas and one with yellow peas. If you crossed them you might expect to come out with yellowish-green peas. Instead, something surprising happened: he ended up with all yellow peas!

The peas resulting from a cross between parents with two different traits is known as an F1 hybrid, for Filial 1. If you cross the F1 hybrids with each other, they become F2 hybrids, and so on.

Mendel was intrigued by these weird results and tried something new: he bred the F1 peas together to see what would happen. All the F1 peas were yellow, but instead of ending up again with all yellow peas again, he got another surprise. The new F2 hybrid peas varied: 75% of the peas were again yellow, but 25% of the peas were green!

What on earth could be happening? It seemed like pea color is inherited in a helter-skelter manner. But, Mendel persisted and tried out these results in many other pea traits such as seed shape and plant height.

No matter which trait he tracked, the F1 pea generation always resulted in peas with only one trait. The F2 pea generation always resulted in a 3:1 ratio between the main trait and peas with the previously-hidden trait.

Alleles: The Intergenerational Messengers

Mendel was the first person to ever describe the pattern of how these unique traits are inherited over generations. He didn’t know about DNA or genes yet, but he speculated that these patterns were caused by inheritance factors—what we now call alleles.

Alleles are simply different forms of a gene. Pea color is controlled by a gene and there are two alleles: green and yellow. Similarly, pea shape is a controlled by a gene that has two alleles: smooth and wrinkled.

Mendel’s First Law: The Law of Segregation

Through his experiments, Mendel learned that each plant has two alleles, one from the mom and one from the dad. They can either be two of the same alleles (called homozygous), or two different alleles (called heterozygous). If we symbolize the two alleles by upper or lower-case letters for pea color, it looks like this:

yy

Each possible combination of alleles is referred to as a genotype: its genetic makeup. Each genotype leads to a phenotype, the trait we actually end up seeing.

Whatever the combination of alleles that a pea has, each allele becomes segregated from the other one during egg or sperm production, and therefore it can only transmit one allele or the other to its offspring. This is known as the law of segregation, or Mendel’s First Law:

law-of-segregation

How Punnett Squares Let Us Predict Results From Crosses

Long after Mendel a simple tool came along called a Punnett Square. This tool uses Mendel’s law of segregation to predict what might happen when you cross two individuals.

To create a Punnett square, draw a square and divide it into quarters. Along the left edge, write a possible allele from one of the parents. Along the top edge, write another possible allele from the other parent. It looks like this:

punnett-setup

Now let’s find out what might happen if you cross these two parents. Fill in each box with its possible allele combination from its parent:

filled-punnett-square

You can see from this cross between a plant with green peas and a plant with yellow peas how each offspring ended up with the exact same genetic combination: Yy. This is why the entire F1 generation had yellow peas.

Mendel’s Second Law: The Law of Independent Assortment

This works well for one trait, but in reality organisms have thousands if not millions of genes! Mendel also wondered about this. How do different traits work together? He decided to track two traits at once.

In the language of alleles, one individual with two genes might look like this: YYBB, YYBb, YYbb, YyBB, YyBb, Yybb, yyBB, yyBb, or yybb. Again, each letter represents a different gene, and each uppercase or lowercase letter represents one version of each allele.

Mendel found that when each trait was tracked with another trait, it behaved as he had predicted for a single trait. For example, wrinkled peas were equally likely to occur with green peas as yellow peas, and smooth peas were also equally likely to occur with green peas as yellow peas.

In other words, each trait was independent of the other trait; no two traits were linked together. This is known as the law of independent assortment.

Mendel’s Third Law: The Law of Dominance

Let’s go back to Mendel’s F1 hybrid crosses between plants with green peas and plants with yellow peas. As we saw above with the law of segregation, each one of those baby pea plants had the genotype Yy.

Mendel had crossed each one of these Yy F1 hybrids with each other and got some surprising results: 75% of pea plants had yellow peas, while 25% of pea plants had green peas. Here’s what the Punnett square for that cross looks like:

law-of-dominance

Not all alleles are created equal for Mendelian traits. One allele is always dominant and takes charge over the other recessive allele.  We usually symbolize the dominant allele with an uppercase letter, while the recessive allele is symbolized with a lowercase letter.

If an individual has one or two dominant alleles (Yy or YY), they will always express that trait. The only way that an individual can express a recessive trait is if they have two copies of the recessive allele (yy)—because then there isn’t a dominant allele present to bully it around!

We can see this happening in the Punnett square above. Three quarters of the possible combinations have the dominant allele, while one quarter of the possible combinations has two recessive alleles. This matches up with what we see in reality: three quarters of these F2 hybrid peas have yellow peas, while one quarter of these F2 hybrid peas have green peas.

This is known as the law of dominance, and it’s one of the hallmarks of Mendelian inheritance.

These are the basics of Mendelian inheritance. Now that we know how it works, let’s look at a real-life example in something other than peas!

Case Study: Human Rh Factor

You might have heard of the ABO blood group, but did you know there are more than two dozen different types of blood groups identified so far? Aside from the ABO blood group, you might have heard of the Rh factor. You sometimes see this after someone’s ABO blood type, listed either as a + or a —.

There are two possible alleles for the Rh factor: a dominant allele which encodes for a D antigen protein on red blood cells, and a recessive allele which does not encode for a D antigen, leaving the cell comparatively naked. If someone has a DD or Dd genotype, they have the D antigens and are Rh+. If someone has a dd genotype, they do not have D antigens and are Rh-.

D antigens are highly immunogenic, meaning that if a Rh- person comes into contact with Rh+ blood, they’ll have an immune reaction. This is why it’s very important for people with Rh- blood type to receive blood transfusions only from Rh- people.

Curiously enough, it’s even possible for a Rh- mother to develop an allergy to her own baby in some circumstances. To see how this works, let’s see what happens if a Rh- mother has a baby with a Rh+ father:

rh

If the baby’s father was homozygous dominant, there’s a 100% chance the baby will be Rh+. (Bonus points: if the father was heterozygous, what would be the chance that the baby would be Rh+? Scroll to the end of this section for the answer)

There won’t be any problems for the woman’s Rh+ baby. But, when she’s giving birth she’s likely to come across some blood from her baby. Just like when you are exposed to an allergen and develop an allergy, the mother might develop an allergy to Rh+ babies.

If the mother gets pregnant with another Rh+ baby, her body might actually mount an immune reaction against her fetus. To prevent this, she must get a shot of a medicine called RhoGAM during her first pregnancy in order to prevent any problems with future pregnancies.

The crucial piece is knowing whether or not the medicine is needed—and that’s why it’s important to know both the mother’s and the father’s blood types. (Answer to bonus question: There’s a 50% chance that the baby would be Dd and be Rh+, and a 50% chance that the baby would be dd and be Rh-)

Genetics Since Mendel

Mendelian inheritance is one of the first things we understood about how genetics work. Many traits work outside of these basic inheritance rules, but millions more traits still abide by these laws—which is why they’re essential to know.

Knowing how Mendelian traits work allows us to make better sense of our world. We can use these rules to predict the risk of many genetic diseases, identify parentage, understand evolution and how genes spread through populations and the world, create better approaches for conservation, and countless other things…like whether to buy green or yellow peas in the produce section!

Genetic Diseases

Imagine you spelled a single word wrong in an instruction manual. Then, that manual was sent out and used in a manufacturing plant. The plant went on to make faulty products based on the error in the instruction manual. Those faulty products, in turn, were sent out all over the world where they wreaked havoc—all because of your one spelling mistake. That’s essentially what happens with genetic diseases.

A single error in the DNA code can cause your body to make the wrong types of proteins. Those proteins go out into your body. Depending on the type of protein, what its job is, and how widespread it is in your body, it might not have any effect at all or could cause widespread chaos.

While it’s possible to take medicine to cure common illnesses like the flu or bronchitis, genetic diseases are generally incurable. They’re literally written into the code of your body.

But there’s also good news: scientists are working hard as we speak to develop completely new technology that may one day permanently cure genetic diseases once and for all.

What causes genetic diseases?

Genetic diseases are all caused by one or more errors in the parts of DNA that make proteins. If you have the genes that produce a genetic disease, it’s as much a part of you as your hair color or how many fingers you have.

There are many different ways that genetic diseases can get passed down through generations. Here are some of the more common ways that genetic diseases can be inherited:

Recessive Genetic Disorders

You inherit two alleles (a copy of a gene) from your parents—one from your mom, and one from your dad.

Some genetic diseases are passed down as autosomal recessive alleles. Autosomal simply refers to the fact that these genes “live” in autosomes (non-sex chromosomes) and can affect anyone regardless of gender. Recessive alleles will be ignored by your body if the other allele is normal; but if you have two recessive alleles, you will have the disease. Your body won’t have a backup normal allele to read the code from.

People who have one normal copy of the allele and one disease-causing allele are called carriers. They will only know that they have the disease-causing allele if they get tested for it, yet they still “carry” the disease in the population. If they have children with another carrier, their kids will have a 25% chance of having the disease.

On the flip side, if you inherit two copies of the disease-causing allele, you will have the disease. This is because the body doesn’t have a normal gene to reference. The only thing it “knows” is how to make the incorrect protein.

Have a look at this Punnett square. Can you predict what percent of a couple’s children will be normal, carriers, or have the disease if 1) the parents both have the disease, 2) one parent has the disease and the other is normal, or 3) one parent is a carrier while the other parent is normal?

recessive-punnett-square

Most genetic diseases are recessive disorders. Some common ones you may have heard of include cystic fibrosis, Tay-Sachs disease, and sickle-cell anemia.

Dominant Genetic Disorders

Genetic disorders are sometimes passed down as dominant alleles. These diseases are a bit scarier because you only need a single copy of the disease-causing allele in order to have the disease. It’s not possible to be only a carrier because if you have the disease-causing allele at all, you have the disease.

Fortunately, these diseases are much more rare than other types of genetic diseases due to the lack of carriers. It’s easier for recessive genetic diseases to “hide out” in a population inside of carriers. With dominant genetic diseases, they’re out in the open for all to see, for better or for worse. It’s certainly not fun for the person who has the disease, but if the disease makes a person less able to reproduce because of it, the disease will naturally be weeded out of the population.

Marfan syndrome and Huntington’s disease are two examples of dominant genetic disorders.

Sex-Linked Genetic Disorders

Do you know any balding men? If so, they may be suffering from male pattern baldness—a sex-linked genetic disease that’s probably the most common of any genetic disorder

Sex-linked genetic disorders affect men more often than women. To see how this works, we need to briefly review how chromosomes differ between men and women.

Women possess two sex chromosomes, X and X, which they got from their mother and father. If a woman has a child, she will only be able to pass on an X chromosome to her offspring, since that’s the only type of chromosome she has to give.

Men, on the other hand, have two different sex chromosomes—X and Y. Males get their X chromosome from their mothers (since that’s the only type of chromosome they can give), and their Y chromosomes come from their fathers.

Women have an advantage because if one allele on the X chromosome is defective, they’ve got a backup copy on the other X chromosome. Men have no such advantage—if they have a defective allele on the X chromosome, they have no backup copy. They will have the disease.

This Punnett square describes how this works. Can you think of a situation in which a female might have a sex-linked disease?

sex-linked-punnett-square

One of the most fateful cases of sex-linked inheritance occurred in the Romanov family, the last dynastic rulers of Russia. Tsarina Alexandra inherited one copy of the gene for the blood-clotting deficiency called hemophilia on her X chromosome from her grandmother, Queen Victoria. She was a carrier for the disease, but did not have it herself.

Tsarina Alexandra married Tsar Nicholas II and began having children. Her first four children were daughters who were totally healthy. The kids may have been carriers for the disease if they received one of Alexandra’s disease-causing alleles, but they were safe because they also received a backup copy of the normal allele from their dad’s X chromosome.

Then Alexandra gave birth to a son—finally—but he was unlucky enough to receive a copy of Alexandra’s disease-causing allele. He had no second X chromosome to protect him, so he got the disease. Small bruises and cuts became life-threatening situations because he could have bled to death.

In a desperate attempt to protect him, Alexandra fell into the bad company of Rasputin, a mystic who promised to save her son but instead took advantage of a position of power. This ultimately contributed to the demise and murder of the entire family by Russian revolutionaries.

Chromosomal Disorders

Some genetic diseases aren’t caused by one allele at all, but rather abnormalities in entire chromosomes. It is possible to have either too much or not enough genetic material.

A person can have too much genetic material through a process called nondisjunction. When a parent’s cells are forming either eggs or sperm, they halve their number of chromosomes from 46 (what’s in their own body cells) to 23 (what’s in their sperm or egg cells). That way, a person’s children will have the normal number of chromosomes when their DNA is combined with the other parent’s DNA.

When nondisjunction happens, an extra copy of a chromosome accidently gets put into a sperm or egg cell. That child will have three copies of a chromosome—one more than they should have.

Down’s syndrome is the most famous example of this disorder. Usually, a mother’s egg cell will accidentally end up with two copies of the 21st chromosome. When that egg cell combines with a sperm cell carrying one copy of that chromosome, the resulting child will have three copies of the 21st chromosome—hence the disease’s alternate name, Trisomy 21.

Chromosomal disorders can also happen through deletions—when a portion of an entire chromosome is accidentally broken off. In cri-du-chat (cry-of-the-cat) syndrome, a short portion of the 5th chromosome is completely missing, resulting in its hallmark symptom: an odd cat-like cry from infants.

You may notice that the chromosomal abnormalities resulting in diseases are pretty specific. There’s a good reason: people with these specific chromosome abnormalities can typically still survive with the genetic material they have.

There are many more possible chromosomal abnormalities, but it’s pretty rare for people to survive them. Chromosomal abnormalities, unlike errors in the DNA of a single gene, can affect hundreds or thousands of genes in one fell swoop. Most of the time, when chromosomal abnormalities happen, they affect a critical gene that a person can’t live without, and the embryo may die in the womb before it even starts forming.

Why do genetic diseases stay in the population?

By now, you’ve learned that genetic diseases can cause anything from minor annoyances like male pattern baldness to embryo death before a person even really starts to develop at all.

If genetic diseases have such harmful potential, you might wonder why they are even still around at all? Wouldn’t people with genetic diseases be unable or less likely to pass on those disease-causing genes to offspring? Wouldn’t the diseases gradually fade out of a population on their own?

There are many reasons why genetic diseases continue in our populations. Here are a few:

One of the biggest reasons that genetic diseases stay in populations is because new disease-causing mutations are always happening. The hemophilia-causing allele that led to the downfall of the entire Romanov dynasty was likely the result of one single mutation in Queen Victoria herself.

Genetic diseases may also stay in a population if carriers are more likely to be fit—i.e., to survive and have more children. It sounds strange, but it’s true: sometimes, having one copy of the disease-causing allele can actually be beneficial.

For example, people with one normal allele and one sickle-cell-anemia-causing allele are actually more resistant to malaria, believe it or not! In tropical places where malaria is common, people who are carriers for sickle-cell anemia are more likely to avoid malaria and have more children. The population as a whole benefits from increased fitness, unfortunately at the expense of the unlucky individuals who inherit two disease-causing alleles and go on to develop sickle-cell anemia.

In some cases, a genetic disease can persist in a population because the disease doesn’t manifest itself until after a person’s already had children (and passed on their disease-causing alleles).

Huntington’s disease is an example. People with Huntington’s disease generally don’t start showing symptoms until as late as 50. By that time, they’ve usually had children, and so the disease-causing allele has already perpetuated to the next generation.

Can scientists cure genetic diseases?

Every cell in your body—all 37.2 trillion of them—has the same DNA. If you’ve got a genetic disorder, that’s at least 37.2 trillion errors.

Your genes are also immutable. Up until recently, that is…

One of the fastest-growing areas of science today is genetic engineering. Scientists can now go into the DNA of an entire organism and change it.

Scientists usually start out with single embryonic stem cell or a single-celled organism like bacteria and insert desirable genes (it’s a lot easier to edit the DNA of just one cell versus trillions). They can implant insulin-producing genes into bacteria to produce insulin for diabetics, for example, or implant vitamin-producing genes into an agricultural crop to make it more nutritious.

Scientists have been honing their genetic engineering skills on commercial products since about the 1970s. In the 1990s they realized the power of this technology and decided to try it on humans to cure genetic diseases.

Gene therapy has been a mixed success so far. Some patients have died as a result of gene therapy, which is probably one reason why these techniques aren’t more widespread. Researchers are tirelessly working to improve the technology and make it safer for patients.

Gene therapy holds tremendous promise. To date, there have been hundreds of clinical trials, some of which have successfully treated or even cured diseases from Severe Combined Immunodeficiency Disorder (“bubble boy” disease) to congenital blindness. Some scientists are even using gene therapy techniques to cure certain kinds of cancer.

Scientists still have a long way to go before they perfect gene therapy techniques and make them safe, affordable, and effective for the remaining untreatable diseases. But the initial successes they’ve had are encouraging: for the first time in human history, we’ve been able to edit our own DNA to make us healthier.

Molecular Genetics

Have you ever noticed how well things are organized at your local library? Imagine you wanted to find a certain book among the thousands. You’d need to find its call number, head to the right bookshelf, then scan along the rows of books to find the precise book you’re looking for.

Imagine how long it would take to find your book if all the books were scattered around in disorganized piles—forever! But thanks to the careful and precise organization of the information, you’re able to quickly get the information you need, find the book, read it, and then take that knowledge out of the library and into the world.

Did you know that you have your own little libraries that work in a similar fashion but on a smaller scale: inside every single cell in your body?

We’re going to explain how your own mini-libraries works. See the list at right for other in-depth articles on genetics!

Major Genetics Molecules

Libraries contain a lot more than just books. They have CDs, DVDs, periodicals, classes, etc. Your own body is the same. Your genetic information is contained in several different types of materials.

DNA

Much like most information in libraries is contained in books, the master copy of all your genetic information is contained in your DNA. DNA is famous for its unique shape—imagine if you had a small bendable ladder and twisted it around your finger. Scientists call it a double helix.

DNA is really cool because it actually stores information within its structure. The “rungs” of the ladder are actually a code, believe it or not! There are four “letters” in the code, called nucleotides. The order of the nucleotides translates into building instructions for your body, just like the letters in the word “dog” translate into a furry, lovable creature.

Scientists work hard at understanding the DNA code because if we know the code and what it produces, theoretically we can engineer organisms similar to the ways we engineer machines. We might even be able to bring back extinct organisms, like the wooly mammoth:

RNA

Have you ever noticed how some books in the library are too important or rare to be checked out? If you want to take that information out of the library, you have to make a copy of the parts you’re interested in.

It works the same way in your body. If DNA is the master copy of your body’s blueprints, then RNA serves as the temporary copies that can be taken elsewhere in the cell so the master copy can stay safe in the nucleus (the cell’s version of a vault).

RNA is very similar in structure to DNA, with a few differences. It’s copied directly from a DNA molecule, so it maintains the original order of the code, with one difference: it replaces one specific nucleotide, thymine, with another RNA-specific nucleotide, uracil. It’s also single-stranded, rather than double-stranded.

Your body uses RNA for a lot of things. It’s mostly used as temporary blueprint copies that get taken out into the construction area (the cytoplasm, or jelly-like material inside the cell), so the originals can stay in the vault (the nucleus) and not get damaged. RNA is also used to make up the structure of the cellular construction machines (the ribosomes) that actually translate the code into a real product to build your body.

Chromosomes

Sometimes, libraries need to move to a new location. To make sure they don’t lose track of their books, they have an orderly system of packing books into boxes, transporting the books to their new location, and then unpacking them back onto their new shelves. It’s a big job!

Your body does the same thing. Sometimes your cells divide, and each new cell needs to get the same “books”. Your body carefully packages the DNA (the “books”) into chromosomes (the “boxes”) which get transported to the new cells before being unpacked again.

DNA poses some unique packing challenges, though. You have a ton of DNA—enough that if all of it were stretched end-to-end, it would reach from the Earth to the sun and back 300 times! In order to wrangle up all of that DNA, it’s carefully wound around proteins called histones, similar to line on a fishing reel.

Those histones are organized even further and crammed together to form a long, hot-dog-shaped bundle of DNA called a chromatid. Finally, two chromatids are bound together at the middle with a centromere to create the final chromosome.

Each cell in your body has 46 chromosomes. They’re actually large enough that when they form, it’s possible to see them under a microscope. Some genetic diseases are caused by abnormalities within the chromosomes. If this is suspected, scientists can make a karyotype—a picture of each of the 46 chromosomes—to check if the chromosomes are normal or not.

Proteins

Your body goes through a lot of fuss dealing with DNA, RNA, and chromosomes. It’s all to produce one thing—proteins!

You might see “protein” and picture your food’s nutritional labels, but there is a much wider definition to consider. No one knows exactly how many proteins there are, but the worldwide Protein Data Bank lists information for 114,983 proteins as of October 2016.

Proteins are like Legos. They serve as the building blocks for your body, doing everything from making up the structure of your muscles (composed of the two proteins myosin and actin) to bringing oxygen to your muscles via the protein called hemoglobin. Every protein has at least one job, and there’s a lot of things they do to build you up and keep you alive!

Amino Acids

If proteins are like Legos, then amino acids are the plastic and dyes that make the Legos. Proteins are actually just long chains of amino acids hooked together. The order of the amino acids is what determines what kind of protein it is.

Your body uses 20 different amino acids to produce proteins. Your body can make most of them on its own, but nine of them you actually need to get from your diet. These are called essential amino acids.

Your body can’t make all the proteins it needs without these essential amino acids. This is why some people on specialized diets (such as gluten-free) need to work with a dietician to make sure they’re getting a balanced diet; otherwise they could become malnourished.

What does your body do with this genetic information?

Now that you know the molecular major players in the game, let’s take a dive into how they all interact to produce you.

Let’s say you’ve gone on a long hike with your family one weekend. The next day, you’re super sore. A tiny amount of your leg muscles have actually broken down and need to be replaced (don’t worry—you’ll be stronger afterwards!). Let’s look at how this process gets started.

Transcription

First, we need to get the blueprints to make more actin and myosin—the two types of muscle proteins.

The blueprint for each protein is called a gene. A gene is a specific sequence of code written somewhere in your DNA. It begins with a promoter sequence (a line of code that says, “Hey! This gene starts here!”), has the code for the protein in the middle, and ends with a terminator sequence (a line of code that says, “Hey! This is the end of the gene!”).

The molecular copy machine for each gene is an enzyme called RNA polymerase. It finds the promoter sequence of the correct gene and attaches to it on the DNA strand. Then, it splits that section of the DNA in half. It scans down the DNA, unzipping as it goes and re-zipping it back up after it passes through as it builds a single-stranded RNA copy from the DNA molecule.

Finally, when it hits the terminator sequence, it drops off of the DNA (perhaps with an evil cry of “I’ll be back.”). The end result is an intact piece of DNA, a free-floating RNA polymerase molecule, and a new piece of RNA.

This piece of RNA travels outside of the nucleus and now acts as a messenger template for proteins to be made, so scientists refer to it as messenger RNA, or mRNA.

Here’s a cool video of it in action:

Translation

What good are the blueprints for new muscle proteins if we can’t read them? We need to find a translator to read the RNA code and turn it into a protein that we can use. This is where the process of translation comes in.

By now, our little mRNA strand has made its way outside of the nucleus. It hooks up with a ribosome, a tiny cellular machine that has all the equipment in it to translate the mRNA into a protein. The ribosome has a special tool hidden up its sleeve: transfer RNA, or tRNA.

tRNA is actually another piece of RNA (confusing, I know), but it has one job: translate the mRNA code into a series of amino acids that can be hooked together into a chain that makes the protein.

tRNA does this by reading the code in 3-letter sequences called codons. In fact, the entire piece of DNA is a code that specifies the order of amino acids when broken up into 3-letter chunks. It works by starting out with an RNA strand full of nucleotides like this:

AUGAUCGAUCAAUAUUAU……UAG

tRNA reads it like this:

AUG   AUC   GAU   CAA   UAU   UAU……UAG

Next, tRNA finds the appropriate amino acid that each codon calls for, and hooks them together like this:

Methionine-Isoleucine-Aspartate-Glutamine-Tyrosine-Tyrosine….Stop

Methionine is always the amino acid that starts the chain. There isn’t an amino acid that ends the chain; rather, when the tRNA reads that code, it simply falls off and leaves a complete amino acid chain. To see the full list of how the code specifies each amino acid, click here.

Here’s another cool video showing how the mRNA is translated into a protein:

By the end, we have a fully-stitched-together chain of amino acids, now known as a protein. It’ll float on further in the cell for any post-translation processing. After that, the protein will be incorporated into muscle tissue so that the next time you go on a long hike (or take a long walk through the library), you’ll have a little more muscle and be a little less sore!

Sneaker Males

Two fish compete to be the baby daddy for the female ocellated wrasse, a colorful Mediterranean fish. It’s up to her ovarian fluid to decide who wins.

With skills like building nests from algae and nurturing young, the “nesting male” is the preferred choice. They grow faster, live longer, and pass on better genes. The “sneaker male” is smaller but carries a much larger load. The fast, clever, and virile sneaker waits by the nest for his opportunity. Once the female lays her eggs, he dashes in to release a cloud of sperm, and the swims away.

wrasse-sneaker-male-2

To counter the sneakiness, the female wrasse uses what ecologists call “cryptic female choice.” Her ovarian fluid favors the nesting male’s sperm, enhancing their speed and making them more likely to reach the eggs first. “It makes sense that you would see these kind of effects in the reproductive tract, but that it’s happening in the water is pretty amazing,” said evolutionary biologist Suzanne Alonzo of UC Santa Cruz in a news release.

This strategy isn’t a guarantee; sneaker males succeed in fertilizing about one-third of the eggs. So, who stays to care for those young? The gallant nesting males, of course.

Article by Teressa Carey

How do caterpillars turn into butterflies and moths through metamorphosis?

When I was a kid, I once found an alien in a forest. It was very small and hiding in a shiny green case about the size of a thumb. It dangled from a branch and was completely still. I reached out to touch it, and it cracked and started leaking pink goo all over my fingers.

Horrified, I ran back to my parents. They told me to leave them alone; the green alien cases were actually baby butterflies. I was very confused—how the heck did the green aliens turn into butterflies? And why was there gross pink goo inside of them?

looking-at-caterpillar

Now I’m a bit older, but I’ve always remembered that experience. What was really going on inside that case? I wanted to learn exactly how all that goo turned into the butterflies we see peacefully floating around during the warmer months of the year.

How Butterflies and Moths Start Life

First, a male butterfly meets a really cute female butterfly, and they mate. After the eggs are laid, they start developing into wee caterpillars.

Instead of developing like most other animals do, caterpillars have something very special inside of them: imaginal disks. These “disks” are just small clusters of cells that match up with the structures they’ll need as adults. There’s one imaginal disk for every adult body part—wing, eye, leg, etc. Remember these imaginal disks; we’ll see them again.

After caterpillars hatch from eggs, they turn into greedy little eating machines. All they want to do is eat, eat, eat (remember The Very Hungry Caterpillar book?). They eat so much that they grow too large for their own bodies, and they need to shed, or molt, their skin, just like a snake. Some caterpillars have tiny bristles or hairs to defend themselves against predators, either as a sort of armor or to inject venom.

The caterpillars repeat this eat-shed-eat process a few times until they reach a size where they’re large enough to undergo metamorphosis.

How do butterflies and moths go through metamorphosis?

Once a caterpillar has eaten its fill, it finds a nice little nook on a branch somewhere (hopefully out of reach of curious children). It hangs itself upside down from the branch and does one of two things, depending on the species. It’ll either wrap itself tight in a silky cocoon, or molt one final time into a hard, sparkling chrysalis (note: these are not actually alien cases).

Here’s a cool video showing how a Monarch butterfly starts the metamorphosis process:

When the larva is tucked neatly away in its cocoon or chrysalis, that’s when the magic starts. Enzymes are released and literally dissolve almost the entire larva into a nutrient soup (the pink goo so vivid from my childhood experience). Only a few other things remain: the nervous system, the breathing tubes, and the imaginal disks (remember them?).

Now that the imaginal disks are free, they start to rebuild the bug. The disks move to the correct positions (no one wants a leg where an eye is supposed to be), and the cells in the disks start to absorb the nutrient soup to grow and multiply.

Very slowly, the new insect starts to take shape. If you ever wanted to see what a caterpillar looks like while undergoing metamorphosis, check out the pictures on this website.

metamorphosis

Interestingly enough, even though the entire bug goes through this whole process, some things do stay the same. For example, some scientists have done an experiment to prove that moths can remember things from way back when they were just caterpillars! This shows that even though the body is rearranged, most (if not all) of the nervous system remains intact.

Wrapping Up the Transformation

By the time the transformation is complete, the new butterfly or moth is fully-formed within its cocoon or chrysalis. It then hatches for the second time in its life. The new bug will pause to get its bearings and test its new body; its wings and antenna unfurl and harden. Then, it’s off into the air to start its new life!

The Scientific Method

What do you think about when you hear the words, “the scientific method?” Do you picture a bunch of dusty old men in lab coats, fiddling with beakers?

Those scientists might be using the scientific method, but so are lots of other scientists doing all kinds of interesting, lively things. In fact, you yourself even use parts of the scientific method every day to make decisions.

At its heart, the scientific method is just a process that scientists use to verify new facts. It’s sort of like a checklist, and by going through it one step at a time, you can be sure that you’re coming up with the right facts. No one wants to discover the cure for cancer only to find that they skipped a step and the “cure” actually doesn’t do anything.

Although the scientific method is one of the most important things that humans have ever invented (it’s how we know anything with certainty!), it’s not entirely formalized. As a result, the steps you see in the process might vary from place to place.

As we dive in, you can follow along, too! At each step we’ll give an example, but you can also think of something that you would do if you were studying a scientific problem.

Here we go:

Steps in the Scientific Method

1 – Make an Observation

You can’t study what you don’t know is there. This is why scientists are so curious—they’re always looking for patterns, trends, questions, and problems that we don’t understand. Once a scientist finds a really interesting pattern that they want to know more about, they move onto the next step.

For example, let’s say that you notice a lot of people are drinking alkaline water because they think it’s healthier for them, but you’re not sure if it actually is or not.

Your turn: What’s something that you find very interesting that you wish you knew more about?

2 – Ask a Question

Once a scientist finds an interesting thing to study, they need to ask a question that hopefully they can answer.

A question that you could ask about alkaline water might be, “Does alkaline water actually make people healthier?”

Your turn: What is a question you’d like the answer to regarding the interesting thing from step one?

3 – Do Background Research

To find out the answer to your question, you need to know what potential answers are. That’s where background research comes in, remembering that not everything you read online is true. Use reliable sources, like Google Scholar…and untamedscience.com!

In our alkaline water example, you could search online for articles or published scientific papers showing how people change when they drink alkaline water. You could look at overall health, or specific thinks like lung function, blood pH, etc…

Your turn: Spend a minute or two searching online for some possible answers to your question from step two.

4 – Form a Hypothesis

A hypothesis is a statement of what you think the answer to your question is. It’s different from the question you formed because it’s answering the question you developed with a specific prediction that you’ll go on to test. A good hypothesis should be falsifiable, meaning that it’s possible to prove it wrong.

Let’s say that your background research showed there wasn’t much of an effect on overall health. A hypothesis for this might be: “Drinking alkaline water has no effect on how well people feel.”

Your turn: What is a potential hypothesis that you might have for your question?

5 – Conduct an Experiment

How do you find an answer to your hypothesis? You conduct an experiment to test it! Depending on what a scientist is studying, an experiment can be very quick or take years—some experiments have even been going on for hundreds of years!

Designing a good experiment is a whole industry that some scientists spend their whole careers working on. But any good science experiment must always serve its one main function: to prove or disprove a hypothesis.

To develop an experiment for the alkaline water example, you’d need a creative way to get people to drink normal and alkaline water, and ask them to rank how well they feel after drinking each.

Your turn: What is a good experiment that you could set up to test your hypothesis?

6 – Analyze Results and Draw a Conclusion

This is what we’ve all been waiting for—what is the answer to the question? In this step, scientists take a step back, look at the data, and decide whether to accept or reject the hypothesis. Sometimes the conclusion is pretty straightforward, but scientists always do statistical tests just to make sure they’re reading the results correctly.

Now that you’ve collected your data from the alkaline water experiment, let’s say that there is no real difference in how well people feel based on what type of water they drink. In this case, you’d accept (or, fail to reject) your original hypothesis. Alkaline water would just be a scam that didn’t really affect how well people feel.

Your turn: What would make you think that your hypothesis is correct or incorrect?

7 – Report Your Results

You’ve just tested an important piece of information. It’s something that nobody else in the world knows. What good is that knowledge if you keep it to yourself? The final step of the scientific process is to report your results. Scientists generally report their results in scientific journals, where each report has been checked over and verified by other scientists in a process called peer review.

If your alkaline water study were real, then you’d need to find a relevant journal and submit your article to them for publication.

How do scientists use the scientific method in real life?

Although the process above sounds pretty rigid, it’s actually quite fluid and adaptable. Some scientists never really conduct true “experiments” and focus on other things instead. Taxonomists, for example, focus on how to best classify organisms. They don’t go through the whole process of hypothesis testing and data analysis for what is very important for writing research papers and term papers often assigned to college and university students. Only professional academic writers who work for research paper writing services use scientific method in writing.

Without the scientific method, people might make up random explanations to problems with no real data to back it up. Thanks to the scientific method, the sum of human knowledge has grown tremendously and hopefully will continue to improve our lives.

Trophic Cascade

The term “trophic cascade” refers to changes in a food web where energy is passed from one organism to others in that community. Famous wildlife ecologist Aldo Leopold first noted early in the 19th century that predators maintain a balance within an ecosystem. Marine ecologist Robert Paine coined the term ‘trophic cascade’  in 1980 to describe this phenomenon. Since then, our understanding of trophic cascades has expanded.

Top-Down Effect

By regulating the populations of other organisms, predators keep a balance in a food web and increase species richness. The most well-known terrestrial example of a top-down effect is what happened in Yellowstone National Park when grey wolves were reintroduced after being absent for 80 years. When the wolves were eradicated, the populations of herbivores erupted. The plains were overgrazed, saplings were consumed, and waterways dried up. Dozens of other species that relied on those microhabitats, such as songbirds, amphibians, reptiles, and insects, disappeared as well. You can learn more about Yellowstone’s wolves here.

wolf-and-caribou-sketch-art

Pisaster Disaster!

One of the first examples of an ecosystem that was completely changed through a trophic cascade was from an experiment conducted by Robert Paine in Mukkaw Bay, California. Paine observed a carnivorous sea star, Pisaster ochraceus, prey on mussels; he was inspired to study the effects if the sea stars were removed.

In the experiment, Paine created a control plot in which he did nothing, and a plot where he removed sea stars gradually over a year. After a year, he noticed an extreme difference between the plots. For the control plot, where Pisaster was left alone, vegetation flourished. However, in the plot without the sea stars, mussels overcrowded the rock surfaces and pushed out other species. Vegetation had been devoured.

trophic-cascade-pisaster

A Killer Problem

Around the Aleutian Islands, in an area of 1500 miles of Arctic waters, another major ecological transformation occurred between 1980 and 2000. Where 100,000 sea otters once thrived among thick kelp forests teaming with fish, crabs, and shrimp, there became barren zones with heavy populations of sea urchins. Why?

Marine ecologist, Jim Estes, who has studied this phenomenon for 30 years, discovered the reason. As certain fisheries have been established—boosting cod, tuna, and salmon for human consumption—smaller fish such as smelt have decreased or disappeared. The smaller fish were the prey source for seals and sea lions. Orcas preyed on the seals and sea lions for centuries, but when those animals disappeared from the ecosystem, the orcas had to find another food source: sea otters.

In order to make up for the calories orcas would have gotten from seals and sea lions, they needed to eat a lot of sea otters. Estes figured out that in just 5 years, 3 orcas had consumed around 40,000 otters! The drop in otter numbers resulted in an increase of the otter food source: sea urchins. The urchins destroyed the kelp through over-grazing. No kelp forest meant no habitat for other species. The ecosystem was totally changed.

Thankfully, conservation efforts have been underway since then, including the establishment of protected areas and tighter fisheries regulations.

orca-sea-otter-sm-pic-by-katey-duffy

Ecology of Fear

Some indirect effects can also occur simply through the threat of predation, which changes behavior in prey species. A trophic cascade can be in action from the mere presence of a predator, such as a tiger, when the fear of being preyed on keeps herbivores on the move. This prevents overgrazing.

trophic-cascade-katy-duffy

In areas with no risk of predation due to lethal predator control methods, livestock have lost the instinct to fear predation, so they tend to stay in the same range until vegetation is no longer sustainable. On the other hand, ranchers who practice predator coexistence husbandry have livestock that do fear predation. Their pastureland remains healthier overall with higher biodiversity. This ecological relationship, combined with nonlethal predator management for livestock husbandry, can be used to help protect wilderness, while allowing people to continue their way of life.

wildabeast-and-crocodile sketch

Bottom-Up Effect

While the focus of a top-down effect is on the importance of predators, bottom-up effects center on the primary producers of an ecosystem. In other words, it’s all about the plants. Many plants, such as aspen and birch trees, are highly sensitive to environmental impacts like climate change and pollution. A decline in certain species can be a sign that something is wrong. When keystone vegetation species decline, the rest of a food web will collapse just as dramatically as when keystone predators are removed.

Here is a short middle-school level video we made early on in our filmmaking careers that explain an up-side down pyramid, or a bottom-up effect food web.

snow-leopard-and-ibix