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Table of Contents
Alleles - Versions of a Gene
Alleles - Versions of a Gene
Reviewing Genes
Reviewing Genes
Before we dive into the depths of basic genetics, it is important that we orient ourselves as to what the subject entails. Recall that a gene is a section of DNA that codes for a protein. Proteins, as you will remember, are the "doers" of all cells - if something needs doing, a protein will do it. So genes code for proteins, and proteins allow you to do things, look the way you do, etc.
What are Alleles?
What are Alleles?
Alleles are those things that you used to write in those Punnett squares that everyone remembers and loves (because they were easy to fill in!) from middle school. But we will worry about crossing in Punnett squares after we truly understand what alleles are. For a given gene, alleles represent different options. So, if there was a protein for flower color, as shown, each different allele codes for a different color. Each allele is represented by a letter, in this case B and b. B is the purple allele, so it codes for purple petals. b is the white allele - it codes for white petals.
Genotypes vs. Phenotypes
Genotypes vs. Phenotypes
Now recall that organisms we will work with are diploid. So they have two copies of every chromosome. So there is a chromosome, say chromosome number 1, for this plant that has a gene that codes for petal color. Simple enough, right? Well, remember that being diploid means that it has two copies of chromosome 1... meaning it has two alleles - one on each chromosome copy. In this example, there are two different alleles - A or a. So, if you have two copies and there are two different options, you can have 2 A's, 2 a's, or 1 of each. Now the math behind this will come in the next section, so for now I just want you to be comfortable with the fact that organisms will have two alleles for each gene.
Your combination of alleles is referred to as your genotype. So if an individual has 2 A alleles, then their genotype would be AA. Other genotype options in this example are Aa and aa. Your genotype determines your phenotype, or the physical attributes for that gene (so purple petals or white petals).
Homozygous vs. Heterozygous
Homozygous vs. Heterozygous
Your genotype can be classified as either homozygous or heterozygous. Recall that 'homo' means same and 'hetero' means different. So, if your alleles are the same (i.e. AA or aa), then you are considered to be homozygous. If your alleles are different (i.e. Aa), then you are considered to be heterozygous. Getting comfortable using this terminology is going to be crucial in this unit, so make sure you practice now.
Heterozygotes are also referred to as carriers because they carry the recessive allele (a), but do not show it in their phenotype. So they can pass it on to their children and they might not even know that they have the allele!
Dominant vs. Recessive Alleles
Dominant vs. Recessive Alleles
Not all alleles are created equal - some are 'stronger' than others. When you are a heterozygote (meaning you are Aa in our example), it is pretty easy to tell which allele is 'stronger'. Just take a look at the phenotype of the heterozygote. In this case, if you have a genotype of Aa, your phenotype shows purple petals. So even though this individual has a white allele (a), it is not expressed, or shown, in its phenotype.
So in a heterozygote for a gene such as this petal color, one allele is expressed (purple, or A) and the other is masked, or covered up (white, or a). You wouldn't know that individual had a white allele unless you knew its genotype somehow. So we would call this individual (and any heterozygote) a carrier for the hidden allele. The allele for purple color, A, is the dominant allele because it covers up the other allele and is expressed even if the individual only has one copy of it. The allele for white color, a, is the recessive allele because you only express that phenotype if you have all recessive alleles. So in order to have white petals, you'd have to have a genotype of aa. If there is even a single dominant allele (A), you will not have white petals.
It's important to keep in mind that the letters we assign to alleles are arbitrary. It could've been any letter. What does matter, however, is that the dominant allele is represented as a capital letter and the recessive allele as a lowercase letter. Later, when our genes get more complicated, we will see some other representations, but this is a good way to start doing genetic crosses (those nice and easy Punnett squares you all love!).
Gregor Mendel and His Pea Plants
Gregor Mendel and His Pea Plants
Gregor Mendel, an Austrian monk, is known as the father of genetics. He worked extensively with pea plants and found that some of their characteristics were sometimes passed on to their offspring in predictable fashions. The traits he focused on are shown here.
Mendel crossed thousands of pea plants and made meticulous observations that formed the foundation of modern genetics. While he did not understand everything about genetics (we still do not, of course), without his discoveries genetics would have evolved very differently.
His key discoveries led to the establish of two 'laws'. Now, like all of biology, laws are rarely resolute - there are exceptions to these laws as we delve deeper into more complex questions, but these are absolutely necessary for you to know and understand moving forward.
These laws are known as Mendel's law of segregation and Mendel's law of independent assortment.
A. Mendel's Law of Segregation
A. Mendel's Law of Segregation
Recall that meiosis results in haploid gametes. Each gamete contains half of the chromosomes (each with one allele of each gene). When two gametes fuse via fertilization, they form a zygote which will grow and develop into an adult organism.
When those gametes were formed, the two alleles (from the parent) for each gene segregate into different daughter nuclei. This means that the combination of alleles across all chromosomes in a gamete is random. This increases the genetic variation of the gametes each parent makes. Track each allele within the diagram below as the gametes are formed.
This is Mendel's law of segregation - it states that each gamete gets only one copy of each chromosome (thus one allele from each parent) and that copy is assigned randomly. Each allele has a 50% chance of being placed into a given sperm or egg cell. If this law was untrue, a single sperm or egg cell may get two R alleles or two Y alleles, for example.
B. Mendel's Law of Independent Assortment
B. Mendel's Law of Independent Assortment
Mendel's second law, the law of independent assortment, states that the alleles of different genes are assigned independently of one another (hence, independent assortment). In other words, receiving one allele does not guarantee that a gamete will receive another. So just because a sperm cell was given an allele for blonde hair does not mean that the sperm cell will definitely get an allele for blue eyes. They are each assigned independently and randomly. Please keep in mind that complex traits like hair and eye color are not determined by a single gene - I simply used that as a demonstrative example. Also keep in mind that this is a simplification - it worked for the traits that Mendel observed, but we have since discovered more complex phenomena such as linked genes (we don't need to cover this here).
Genetic Crosses - Makin' Babies!
Genetic Crosses - Makin' Babies!
Now that we have established some terminology for basic genetics and have discovered how gametes are made, we can investigate how gametes are fused to form zygotes. When two individuals mate and we are looking at their genetics, we call it a genetic cross. Genetic crosses are ways to predict and represent what offspring between two parents may 'look like' (meaning what their genotype will be).
A. Punnett Squares - What They Really Represent
A. Punnett Squares - What They Really Represent
I don't think I need to tell you how to fill in a Punnett square - almost every high schooler loves them because they're easy to fill in. You simply bring the alleles from the corresponding column and row to the center of the square.
What is more important, however, is what it represents. A Punnett square is a simple statistical tool that allows us to investigate probability. Each allele has a 50% chance of being passed on to offspring. So if a heterozygote (Rr) is making gametes, there is an equal chance (50%) that each gamete will get an R allele or an r allele.
That accounts for one parent's gametes. So those possibilities are placed on the top row. But in sexual reproduction, we obviously have two parents. So we have to do the same for parent #2. In this example, parent #2 is also a heterozygote (Rr). So, there is a 50% chance for parent #2 to pass a R and a 50% chance to pass a r.
So what about what's in the middle? Well, the middle represents possible offspring. More than that, however, each square represents an equal probability of each offspring. So, in this Punnett square for petal color, there is a 25% chance that an offspring's genotype will be BB because there are 4 squares and only one of them is BB.
But let's investigate why 25% is the correct chance for BB using math. In order for an offspring to have a genotype of BB, they had to get a B from one parent AND a B from the other parent. If both of these conditions must be met, then you have to multiply the probabilities. So the chances that the male parent passes a B is 50%, or 1/2. The chances that the female parent passes a B is also 50%, or 1/2. So, if you multiply the probabilities, you get (1/2)(1/2) = (1/4) = 25%
Let's try that again, but this time let's make it a little more difficult. Let's calculate the probability that the offspring will be a heterozygote. A heterozygote in this example has a genotype of Bb. This means that they had to get a B from one parent and a b from the other. The male parent could pass a b allele and the female parent could pass a B allele. This result is represented by the top-right box of the Punnett square (25% as well). HOWEVER, there is another way the individual could be a heterozygote: the male parent could have passed a B and the female parent could have passed a b allele. This would also happen about 25% of the time because (1/2)(1/2) = 25%. This result is represented by the bottom-left box.
So what are the chances that an offspring is a heterozygote for this petal color gene? Well, if there are two probabilities, but either of them would be acceptable, you simply add the probabilities. Think about a coin. What are the chances that a coin flip will land on head OR tails? 50% chance for heads, 50% chance for tails. 50% + 50% = 100%. So, the chances of an offspring being a heterozygote can be calculated as:
(Chance that dad passes a B and mom passes a b) + (Chance that dad passes a b and mom passes a B) =
25% + 25% = 50%. Thus, the chances are 50% that the offspring will be a heterozygote. Obviously you could just count the squares. 2 of the 4 squares are heterozygotes and 2/4 is 50%. But it is crucial that you understand what a Punnett square REPRESENTS.
B. Genotypic vs. Phenotypic Ratios
B. Genotypic vs. Phenotypic Ratios
Now that we've learned how to perform a genetic cross and calculate the chances offspring will have particular genotypes, we can start to discuss genotype and phenotype ratios. Ratios are basically just representing the probabilities another way. For this example, T is dominant to t. T is an allele for a tall plant and t is the allele for a short plant.
Phenotypic ratios basically represent how likely each phenotype is. So, we need to determine the phenotype for the possible offspring. T is dominant to t, so if an individual has a T allele, they will be tall. So the offspring have a 3/4, or 75%, chance to be tall. There is a 25%, or 1/4 chance for the offspring to be short. So if this cross happened a million times, there'd likely be 3 tall plants for every 1 short plant. So, the phenotypic ratio is 3 tall:1 short.
Genotypic ratios basically represent how likely each genotype is. For this example, the possible genotypes are TT, Tt, and tt. 1 box is TT, 2 are Tt, and 1 is tt. So, the genotypic ratio for this cross is 1 TT: 2 Tt: 1 tt. So, for every 1 tt, we would expect 2 Tt individuals and one TT individual. Are these ratios guaranteed? No, of course not. Parents have a 50% chance to have a male child and a 50% chance to have a female. Does that mean that if you have two kids, you will definitely have both a male and a female? No, of course not. Similarly, you could have 5 kids and that all be TT - that's how chance works! These are all just predictions.
This particular cross in which two heterozygotes are crossed is very common (we will discuss some terminology for this crossing in the next little section). As a result, you need to be aware of these ratios (3:1 for phenotype and 1:2:1 for genotype) when two heterozygotes are crossed. Another example is shown here for petal color.
Please note that you would not be able to know for sure what the genotype of an individual is if they had purple petals. That could mean that they are PP or Pp. Pp is more likely but it is not guaranteed. The recessive trait, white petals, only occurs if the individual is homozygous recessive, however. So if an individual has white petals, you immediately know its genotype will be pp. This will be VERY important when we get to pedigrees next so keep it in mind moving forward.
C. P, F1, and F2 Generations
C. P, F1, and F2 Generations
The experiment shown here introduces some terminology that you should be familiar with. This experiment involves 3 generations of plants that Mendel worked with in his experiments involving petal color. the first general, labeled the P generation (P is for parental) is a cross between two true-breeding parents.
True-breeding just means that they will always pass a particular allele. So the purple parent will always pass a purple allele and the white parent will always pass a white allele. Can you imagine a situation in which a parent will always pass a given allele? That's right - it is a homozygote. If an individual is a homozygote for an allele, they are true-breeding for that allele.
So the P generation crosses and forms the F1 generation. The F1 generation will have received a purple allele, P from one parent and a white allele, p from the other. So all individuals in F1 are heterozygotes (Pp). If those F1 individuals are crossed with one another, they will produce the F2 generation.
This cross is just like the heterozygote crosses we saw before. We would expect a 3:1 phenotypic ratio. And if we look at Mendel's data, he found 705 purple and 224 white flowers. This is roughly a 3:1 ratio, so this sample holds up to our predictions. Please note that if a smaller sample size is used, the predictions may not be as consistent with the actual results due to sampling error.
D. Monohybrid Crosses
D. Monohybrid Crosses
All of the crosses we have looked at so far are focusing on one trait, so are considered monohybrid crosses. 'Mono-' means one, so we are tracking one trait (one gene). This is the simplest situation, and that is why we started with it. Unfortunately, however, things get a bit more complex...
E. Dihybrid Crosses
E. Dihybrid Crosses
A dihybrid cross is exactly what you'd expect - a cross tracking two traits (two genes). However, this becomes much more complicated when it is time to actually create a Punnett square.
To investigate dihybrid crosses, let's take a look at those annoying pea plants again. This time, we will be looking at two traits, of course: seed color and seed shape. Seed color can be either green (G) or yellow (g). Seed shape can be either round (R) or wrinkled (r).
The most complicated dihybrid cross would be between two individuals that are heterozygous for BOTH genes. So, their genotype would be GgRr. Thus, their phenotype would be green, round seeds because green is dominant to yellow and round is dominant to wrinkled.
But, remember, each gene is passed independently (thanks, Mendel!). So, if a green allele (G) is passed, it could be passed alongside either a round (R) allele or a wrinkled (r) allele. So, the possible gamete genotypes for a parent that is GgRr would be: GR, Gr, gR, or gr.
Since there are 4 possible gametes from the parent, we have to make 4 boxes across. But the other parent also has a genotype of GgRr, so has the same possible gametes. So a Punnett square for a dihybrid cross can have 16 squares within it!
Because of the two genes, there are 4 possible phenotypes:
green & round seeds
green & wrinkled seeds
yellow & round seeds
yellow & wrinkled seeds
So, the phenotypic ratio for a dihybrid cross is 9:3:3:1. Be sure that you understand how this ratio is confirmed using this Punnett square. Remember that each box has an equal chance (1/16) of being 'chosen'. Really no genotype is chosen, the boxes just represent the likelihood a given offspring will have that genotype.
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