Basics of Genetics

In trying to solve the puzzling results he found in his experiment, Mendel developed a hypothesis that explains what genes do on chromosomes when they are transmitted, even though he had no idea what genes or chromosomes were. We can divide Mendel’s hypothesis into four related ideas. First, Mendel argued that the different versions of what he called “heritable factors” must be responsible for producing the different traits. A “heritable factor” was responsible for the purple flower, and a different one was responsible for white flowers. What Mendel called heritable factors are what we now call genes. The different versions of the genes are what we call alleles. For example, the gene responsible for flower color in peas has two alleles, one for purple flowers and the other for white flowers.

Mendel’s second idea was to conclude that each individual had not one but two different particles for each character. In other words, each individual has two alleles for each gene. Mendel made this conclusion knowing nothing about chromosomes, but microbiologists confirmed this by showing that each offspring has two copies of every gene.

Mendel’s third suggestion was that one allele of the two that an individual possesses might actually be dominant over the other one. In other words, one allele is expressed even if the other allele is present. We say that one allele would be dominant, and the one that is not expressed we call recessive.

Let’s go back to Mendel’s experiment to clarify this. He started with true breeding lines of purple and white flowers. He argued that these true breeding lines, that produce only one or the other flower color, must always have two of the same kind of allele. The purple flower plant has two purple alleles and the white plant has two white alleles.

The offspring of this cross must receive one allele from each parent, and thus have one purple allele from one parent and one allele from the other parent. Because all of the offspring in the F1 generation had purple flowers, Mendel argued that the purple form must be dominant over the recessive white form.

Mendel’s forth idea was that when a parent produces gametes in preparation for sexual reproduction; each gamete only gets one of the two alleles that that parent possesses for a particular gene. If we are talking about flower color, if a parent possesses two of the same kind of allele, when it produces gametes, all of the gametes would have only that kind of allele. For example, purple plants from Mendel’s parental generation would only make gametes that have purple flower alleles. The same would be true of the parental white plants.

Here’s the kicker. When we have individuals that have two different kinds of alleles, for example individuals in the F1 generation, can produce two kinds of alleles. They have both a purple allele and a white allele, so they can produce gametes that have either purple or white alleles. In fact, they do so in a 50:50 ratio. It is equally likely that their gametes would have one or the other allele.

The original parental plants Mendel started had two alleles for the same color. We call individuals that posses two of the same kind of allele “homozygous”. The parental plants were homozygous. By contrast, when an individual possesses two different kinds of alleles for the same gene, we say that it is heterozygous. Individuals in the F1 generation were heterozygous.

We give some labels to the alleles. We’re going to give the purple flower allele the capital letter P, and the white flower allele the lowercase p. Giving the uppercase and the lowercase versions of the same letter is one common way that geneticists designate different alleles for a gene.

Because the original in Mendel’s cross were homozygous, they could produce only one kind of gamete. We’ve already said why their offspring should have all purple flowers. If the purple allele is dominant to the white allele, the F1 offspring all have one big P and one little p. Because they all have a big P, which is dominant, they’ll all be purple, regardless of the fact that they have the little p too.


Now I want to introduce two new terms: phenotype and genotype. An organism’s phenotype refers to what it looks like. It refers to the traits that organism expresses. For example, we would say of a purple plant that it has the purple phenotype. The genotype of an organism represents its genetic makeup. The genetic makeup of an organism clearly would have something to do with the traits that the organism expresses. It is important to keep in mind, though, that a given phenotype might be produced by different genotypes.

Let’s go back to our pea plants. Because the purple allele is dominant over the white allele, there are two possible genotypes that could give rise to the purple flower phenotype. Individuals having two big P alleles clearly would have the purple phenotype. So would individuals having one P and one p allele. Both the PP and the Pp genotypes yield the purple flower phenotype. That’s because the purple allele is dominant over the white allele.

On the other hand, the only way we could get the white flower phenotype is if we have a genotype that has both p alleles. This helps us explain the surprising findings from Mendel’s first cross. The white flower phenotype had disappeared completely in the F1 generation, but not the white allele, which was hidden in the heterozygous genotypes of those individuals.

Let’s look at what Mendel found when he crossed these heterozygous F1 individuals together. He found that the offspring in the F2 generation produced both purple and white phenotypes in the ratio 3:1. To understand that 3:1 ratio, let’s consider again the kinds of gametes and the proportions of gametes that those F1 individuals could produce. Because these individuals were all heterozygous, they could produce two kinds of gametes, either a purple allele or a white one. Indeed, each individual would produce equal numbers of both types of gametes.

This makes an intuitive sense. This is very like flipping coins. We’ve got two possibilities; we could come up with a heads or a tails. The key question to ask is what proportion of individuals in the F2 generation would have the possible genotypes that could be formed by joining the gametes that the F1 individuals produced.

An easy way to think about this is to use a convention that we call a Punnett square. Along the top of the square we have one column that has big P on top of it and one column that has little p. Along the side, we have one big P and one little p.

The point of making this grid is that it helps us think about how these different gametes can combine to form genotypes in the offspring. If you fill out the grid by connecting the two alleles possible for each cell, you’ll see that you’ll get three different genotypes. We have PP, Pp and pp individuals. What you also see is that both PP and Pp have the dominant allele, which is the represented in the phenotype. Looking at this you’ll expect to see three purple individuals for every one individual.

With this we can explain why Mendel found a 3:1 ratio in his experiment in the F2 generation. Mendel’s brilliant insight was to put all of this together without knowing anything about genes or the physical basis of chromosomes.

We now refer to this key idea of the existence of two different alleles in each individual as “Mendel’s Law of Segregation”. This law is significant for a number of reasons. First, it completely refuted the blending hypothesis and demonstrated that heritable factors must be particulate. Second, what Mendel did was to provide a framework for looking at more complicated patterns of how traits are transmitted between parents and offspring, which allow us a more complete understanding of the genetic basis of inheritance.

Mendel: The Father of Genetics

Mendel grew up on a small farm in Austria, so he got an intuitive understanding of plant and animal breeding. Mendel wasn’t an ordinary monk. In the 1850’s, his order sent him to study at the University of Vienna, one of the leading universities of Europe. He was taught by many outstanding scientists there, most notably the physicist Christian Doppler. When he returned to the monastery, he began to study heredity in garden peas.

At the time of Mendel’s work, chromosomes hadn’t been described, let alone mitosis and meiosis. Nothing was known about the physical basis of inheritance. It was obvious, though, as it had been for many thousands of years, that offspring tend to resemble their parents. It also was obvious that different combinations of traits in parents would appear to be mixed in different ways in their offspring, sometimes surprisingly so.

At that time, the dominant theory about how inheritance worked suggested that some material from the two parents was blended together when offspring were produced. You can think of this like mixing paint. What scientists thought was that when offspring were produced, paint from the two parental buckets would simply be poured together into the offspring’s bucket, and the result would be some mixture of the two. If for example an animal with light colored fur mated with a dark colored one, the result would be an intermediate color. Indeed, sometimes that is observed.

The blending hypothesis didn’t account for many other observations made by plant and animal breeders, though. Specifically, the blending hypothesis predicts that over time, all variation within a species should vanish. Think of blending buckets of paint. If we start with a whole bunch of colors in different buckets, and as those buckets are mixed together, over time we’ll just have buckets with the same color.

In the real world, however, plant and animal breeders realized that even when individuals in a population mated randomly for a very long period of time, there always remained variation among individuals. Also, sometimes traits would appear in offspring that weren’t present in either of the parents.

These were the problems Mendel was trying to address when he began his work on pea plants. To understand Mendel’s work, let’s see the very first experiment he did: the monohybrid cross.

Mendel’s most famous experiment involved looking at the inheritance of flower colors. In these pea plants, flower colors occur in only one of two forms: purple or white. We call this kind of character a “dichotomous character”. It’s one thing or the other. Pea plants have many such dichotomous characters, not only flower color, but also seed color, the shape of the seed and the height of the plant.

Mendel understood that the existence of this kind of dichotomous traits couldn’t be reconciled easily with the blending hypothesis, so he decided to investigate how these traits were transmitted across generations.

Mendel began his first experiment with parents that came from what we call true breeding lines. These were pea plants that would produce only one form of the trait. For example, one plant that produced only white flowers, or only purple flowers. He then crossed a white flower plant with a purple flower plant. This is called a monohybrid cross because he is hybridizing two varieties that differ in only a single character.

When Mendel performed this cross, he found a very surprising result. Remember, one parent was purple and the other white. When he crossed them, all of the offspring were purple.


We started with a parental generation, one purple and one white. The offspring of this parental generation are called the F1 generation. The result that Mendel got was surprising because it completely contradicted the blending hypothesis. The blending hypothesis predicted that he’ll get an intermediate color, like a light purple. But no, all of the offspring were purple flowered. The white flower color seemed to be completely lost.

Even more surprising was what happened when he crossed these F1 individuals. What he found in the so called F2 generation was that the white flower color reemerged. He would have some purple flower individuals and some with white flower individuals. Furthermore, these individuals would always occur in approximately the same ratio. There always would be about 3 purple individuals for every one white individual.


Mendel did this kind of cross with a number of other dichotomous traits, like seed color and seed shape, and he always got the same result. One trait would disappear in the F1. Then it would reappear in the F2 in the ratio of 3 to 1. What could account for this pattern of inheritance? How could you have one trait lost completely and then have it again?

In trying to solve this puzzle, Mendel developed a hypothesis that explains what genes do on chromosomes when they are transmitted, even though he had no idea what genes or chromosomes were. In so doing, he essentially established modern genetics. In the next article we’ll see the hypothesis Mendel developed to explain the surprising and exciting results he got.

Pea Images Source: Wikimedia Commons. Here and here.

The Genetic Code, Part I

You may be familiar with the cryptic code puzzles that appear on the comic sections of newspapers. They involve some famous or amusing quote that has all of the letters in it substituted for other letters. For example, all the A’s may be substituted with W’s, all the V’s with P’s, etc. The substitutions are always consistent, and the puzzle is solved simply by figuring out the correspondence of letters. This code is very simple, because it just involves finding the equivalents of single symbols, which are both in the same alphabet. Unfortunately, the code needed to direct protein synthesis has to be more complex than that.

The first reason our code needs to be more complex is that DNA and proteins are very different kinds of molecules. Even if we could imagine a code that establishes a relationship between the bases in the nucleic acid and amino-acids, how could this correspondence work on a molecular level? Is there some molecular mechanism that could predict an interaction between a particular amino-acid, and one or more particular nucleic acid bases?

The fact that proteins and nucleic acids have different biochemical properties suggests that a direct molecular correspondence is unlikely to occur. What we need is to have nucleic acids and proteins communicated through a translator, who speaks the language of both. Francis Crick was the first to propose this solution.

Crick suggested that there must be a molecule with two functionally different ends. On the one end there must be a mechanism for attaching a specific amino-acid, and at the other end, there must be a mechanism for interacting with a specific sequence of nucleotide bases. Crick was correct indeed. There are such molecules. These are small, highly specialized, strings of RNA, called “transfer RNA” (tRNA).

Three-Letters Words

The second reason the genetic code needs to be more complex than newspaper puzzles is that there are 20 kinds of amino-acids, but only four kinds of bases in nucleic acids. We have A, G, T and C, and that’s it. If we had a simple substitution that was one for one, we could only have a code that was specific for four different amino-acids. We have 20 of them to account for, however.

What that suggests is that sequences of more than one nucleotide must be used to code for a single amino-acid. This would be like having the bases of a nucleic acid combined together to form code-words, where each base is a single letter. How many letters long must each word be?

Imagine that we had code-words that were made up of two letters each. That would not be sufficient to code for all the amino-acids. This is simple math. If we have four things, and we combine these four things in pairs, then we can make 4 squared combinations. That’s sixteen combinations. However, if we make combinations of three things, we would have 4 cubed combinations, that’s 64, more than enough. Actually, a three letter code suggests that the code has some sort of redundancy.

The logic in support for having a three letter code seems pretty obvious, but it simply suggests a testable hypothesis which then had to be demonstrated. Once again, it was Francis Crick along with colleagues who demonstrated experimentally that the genetic code must involve sequences of three bases. Crick used a technique in which they could cause a very particular kind of mutation in the DNA of a virus. This involved the elimination of just one base-pair from a DNA double helix. Alternatively, the mutation involved the addition of just one base-pair. If they applied this treatment in the appropriate fashion, they could be assured that either one base pair, or one was added.

Consider the simple sentence: “Old men are fun”, but without the spacing. Consider it as a string of characters. That sentence is composed of four words, each specified by three letters. If we delete the first letter, and try to read it, we’ve got: “ldmenarefun”. If we deleted two letters, we’d have: “dmenarefun”. Neither of these strings of characters makes any sense because we have shifted the place we start reading by one or two positions. The resulting remainder of the string becomes nonsensical.

Now, if we delete three letters, the words make sense again: “menarefun”. It’s not the same sentence as we’ve started with, but that’s not the point. The point is that the words in that sentence, comprised of three letters, only make sense if we take out three letters. We could do the opposite. If we add three letters, part of the string would make sense.

Crick used the same kind of logic, deleting or adding just one base-pair from a viral DNA, to show that there must a three letter code. If they induced one mutation in a gene, then all of the amino-acids coded by that gene would get changed. If they eliminated two base-pairs, they’d have the same results. If they deleted three base-pairs, however, they found that the remaining portion of that gen would make sense, in the sense that most amino-acid sequences would be intact.

It was pretty clear that the genetic code had to be made of three bases each. Many experiments since that have used a variety of techniques to verify the existence of this three letter code. The three-base sequences that serve as fundamental units for the code have come to be known as codons. Each codon corresponds to a unique amino-acid.

The next step was to establish what the correspondence is between particular codons and particular amino-acids. I will leave that for next time.

A History Of DNA, Part III: The Code is in DNA

In my last post we saw how Avery and his colleagues demonstrated (but not conclusively to the scientific community) that the molecule which holds the genetic material in living things is DNA. Now I want to look at a very interesting experiment that really changed the minds of biologist in the matter. In the early 1950’s, Hershey and Chase took a novel approach in trying to found out what the genetic material might be made of, by looking at how a particular kind of virus worked.

Let me give you some background. Viruses are not true cells. They are made of an outer coat of protein with an inner core of nucleic acid. Viruses are made of just two things. The way a virus makes its living is by attaching to a cell, say a bacteria cell, injecting something into that cell and taking over the machinery of the cell. Here is a great introduction to viruses by Salman Khan(Sal), I really recomend you to watch it to understand viruses better.



Hershey and Chase were working with a particular kind of virus, called the T2 phage. This is a bacteria-eating virus, which makes its living by taking over a bacteria and using the protein-synthesizing machinery of the bacteria to make more viruses. Viruses can’t replicate themselves, they have to take over another cell. Clearly, then, what a virus must be doing, is injecting some information. It’s the information that would cause the cell to be taken over. What Hershey and Chase set out to do was to ask, what is it that these T2 viruses are actually putting inside the bacteria? There were only two candidates, proteins and nucleic acids.

The trick was to figure out how to determine which part was being injected. It is a very simple experiment to propose conceptually, but like many experiments in science, the devil is in the details. Hershey and Chase developed a very clever way to figure that out. They did this by radioactively labeling the proteins and the DNA that the virus was made of. In proteins, sulfur is a fairly common element. There is a radioactive form of sulfur (S-35). So, they could grow some T2 viruses in a medium that had a lot of this radioactive sulfur in it. What would happen is that as the viruses reproduce, they would incorporate sulfur into their protein codes. That meant that you could ask not where did the protein go, but where did the radioactivity go.

Alternatively, they could label the DNA. They could grow the same kind of virus in a medium that had radioactive phosphorus (P-32). Phosphorus is not found in proteins, but it is a major chemical constituent of DNA.

So, they grew viruses in a medium that either had radioactive sulfur or radioactive phosphorus. This resulted in some viruses having their proteins radioactively labeled, and others their DNA radioactively labeled.

In separate experiments, they added either the radioactively labeled sulfur viruses (with the radioactive protein), or the radioactively labeled phosphorus viruses (with the radioactively labeled DNA). In both cases they would give these viruses just a couple of minutes. Enough time for them to attach to bacteria and inject whatever they are injecting. Then they would stop the whole process. They were given enough time to inject but not enough time to take over the cell and cause it to build more viruses.

They gave the viruses just 20 minutes, and then they would put the solution in a blender. Then they put this solution in a centrifuge, which spins it around. Because of the action of the centrifuge, the heavier stuff would go down to the bottom of the tube. This would be the relatively large bacterial cell bodies. The lighter stuff, which would be the outer coats of the tiny viruses, would remain up in the solution. If you centrifuge them just right, you’ll get a little lump of stuff at the bottom of the tube, that’s going to be all the bacteria. Then you’ll have the rest of the fluid in the tube, which would include the viral coats.

They then would ask, where is the radioactivity? Is the radioactivity at the bottom, or at the rest of the fluid? What they found was that if they radioactively labeled the sulfur, marking the proteins, the radioactivity was found in the fluid, where the viral coats were. If you radioactively labeled the DNA with phosphorus, the radioactivity was found at the bottom, where the bacteria were. This was a very simple result but took the world by storm, because it showed incontrovertibly that what these viruses were injecting in the bacteria (and happened to be the genetic material), was DNA.

Hershey and Chase published these results in 1952, and it really caused a lot of interest. Biologists began to take a closer look at nucleic acids. That is what I want to do in my next post, look at the structure of DNA.

A History Of DNA, Part I: Before the Discovery

Proteins are the biological molecules that make things work in living systems. We could say that they are involved in every process in the cell. They are controllers of biochemical reactions, structural elements that hold parts of the cell together, motors that make things move, signals, and so forth. The function of a protein depends almost entirely on its shape. Its three dimensional shape determines its physical and chemical properties, which in turn allow the protein to serve its unique function. The three dimensional shape of a protein, in turn, depends almost entirely on the linear sequence of the building blocks of life, the amino-acids.

There are 20 kinds of amino-acids. An average protein might have a few hundred amino-acids. So, proteins are the work horses, and their function is determined by its chemical sequence of amino-acids. Now, how do we get a protein of a particular sequence built? To answer this question we need to address two things. First, what is the blueprint that is used to build proteins? Second, how does that molecule actually work?

It is the first question that I want to talk about today. Before we can understand how the code works, we need to understand what the code is made of. I think that we all know the answer today: DNA. Interestingly, though, that was one of the questions that defined molecular biology in the 20th century.

At the very beginning of the 20th century, it was already known to scientist that the code was in genes, which in turn resided in chromosomes. This was known from the work of early cell biologists, Walter Sutton and Theodor Boveri being the most important, who discovered that the particular movement of chromosomes that occurs when cells divide corresponded to patterns of transmission of traits between parents and their offspring. These patters of trait transmission had actually been discovered earlier by the Austrian monk Gregor Mendel.

Cell biologists knew about Mendel’s work, how chromosomes moved, and they developed what now is called the chromosomal theory of inheritance. This theory basically says that the way chromosomes move is somehow related to the way that inheritance occurs, therefore, chromosomes are related to information in cells.

We today know that chromosomes are made of DNA, but how that became a known fact? We must begin by going back to the earlier part of the 20th century, to the work of an English physician named Frederick Griffith. This experiment that I am about to describe really provided the first insight into the chemical nature of genetic information.

Griffith’s Experiment

Griffith was a physician and he wasn’t interested in the molecular basis of inheritance. Instead, he was working on a much more applied problem. He was studying Streptococcus pneumoniae, which is a bacteria that causes pneumonia in humans. What Griffith wanted to do was to develop a vaccine against this particular organism, because the pneumonia caused by it often proved fatal. This was before the advent of antibiotics, of course.

As often it is the case for disease-causing bacteria, there were different strains that varied in their virulence. They varied in how likely they were to induce the disease and cause death. Griffith was working with two strains of Streptococcus pneumoniae. He was working with what we call the S strain on the one hand. This was a very virulent strain. It is called S because if you grow it in a colony, it actually looks kind of shiny and smooth. He had another strain, which he called the R strain, which was non-virulent. If you got the R strain, you might be a little sick but you wouldn’t die. It is called the R strain because the bacteria look kind of rough on the surface.

The important thing to note is that these strains did breed true. In other words, as they reproduced, their offspring had the same properties. S strain bacteria gave rise to more S strain bacteria and so on. It is inferred from that, that the difference between the S strain and the R strain bacteria somehow must be genetically encoded.

What did Griffith do? Griffith was using the approach pioneered by Louis Pasteur, which was to take the organism that you want to develop a vaccine for and kill it. This organism could no longer harm you, but nonetheless, would perhaps induce some sort of immune response if injected in a subject. The idea was to take S strain bacteria, kill them by heating them up, and then take these dead S strain bacteria and inject them into a laboratory mouse, and see if that mouse develops immunity. The mouse wouldn’t die if you injected dead S strain bacteria, but the parts of the bacteria that are injected might nonetheless induce an immune response.

This is a great idea, but it didn’t work. It often doesn’t work. There wasn’t enough left of these dead S strain bacteria to induce an immune response. If you injected these in a mouse, and then injected live S strain bacteria, the mouse would die.

Another common technique that was used then and now to develop vaccines was to eject not only the dead offending organism, but some related organism that was less virulent. In this case, we are talking about the R strain bacteria. The idea is that the live R strain bacteria, because they are alive, would induce the organism to develop a full immune response. That development of a full immune response would somehow pickup some immunity to the dead S strain bacteria. This is a common technique and it often works.

What Griffith did then? He killed some S strain bacteria and injected them in with living R strain bacteria. What he hoped would happen is that the mouse would develop immunity to the S strain, but what happened instead was unexpected, and unfortunate for the mouse, the mouse died. This is a surprising result. What’s being injected into the mouse are dead S strain bacteria, that wouldn’t kill the mouse; and live R strain bacteria, that wouldn’t kill the mouse neither. Nothing was injected in the mouse that should kill it, and yet the mouse died.

What Griffith found out when he dissected the poor dead mouse was that inside it were living S strain bacteria. He injected dead S strain, and when he took the mouse apart, he found living S strain. What Griffith concluded from this work, and correctly, was that somehow the living R strain bacteria had taken up something from the dead S strain bacteria, and incorporated it into them. That somehow transformed the R strain into the S strain.

Griffith later showed that he didn’t need the mouse. You can do this in a beaker. If you put dead S strain and live R strain bacteria in a beaker, some of the live R strain would become transformed into live S strain.

What’s really interesting from this experiment, in my opinion, is that the material that they incorporated must somehow be genetic material. It must somehow have information in it. How else could the R strain bacteria now become virulent like an S strain bacteria? The difference between S and R had to have something to do with genetically transmitted information. What Griffith did was he left it there. It was only 1929 when he was doing this work. He said that he had discovered what he called the transforming principle.

Our interest in this, and of scientist interested in genetics, is that somehow this transforming stuff must involve genetic material. In my next post we will see how this experiment helped in discovering that DNA is the molecule that holds genetic material in living things.