Crash Course: Biology

Genetics: Mendelian Genetics

What the eff is Mendelian Genetics?

To sum it up in two words, Punnet Squares.
(Actually, it's a bit more complicated than that. Out of all genetics, this is likely the most mathematical).

So, who's Mendel?

He was a monk (boring, I know). Who did experiments with pea plants. Apparently, he also came up with a bunch of laws:

1. Mendel's First Law: The Principle of Segregation: members of a gene pair will seperate during gamete formation.
Why? If genes that determine traits exist in pairs (e.g RR or Rr or rr), then there must be a mechanism that prevents the genes from being doubled in the next generation (e.g RRRR, RRRr, etc.). To prevent this, each gamete can only contain one member of the gene pair (e.g R or r) which combines with another gamete to give the offspring two members of the gene pair (egg + sperm = child)

2. Mendel's Second Law: The Principle of Independent Assortment: genes for different traits can segregate independently during gamete formation
Isn't that just rephrasing his first law? Well, no. In this case, the genes for different traits segregate independently. For example, if someone's genotype was RrBb, their gametes could be RB, rB, Rb, or rb. 

3. Mendel's Third Law: The Principle of Dominance: some alleles are dominant while others are recessive; an organism with at least one dominant allele will display the effect of the dominant allele.
This is the only 'law' that isn't completely true. 
More on that in a second.

Calculating dihybrid, trihybrid, tetrahybrid crosses, or even more: the Fork Line Method

I was going to go out on a limb and assume that everyone already knew how to use a punnett square, but I'll include a little diagram on the side. See how it's all color coded? They're pretty easy.

Next, the dihybrid cross. You could draw out all sixteen squares and do it the same way you do a monohybrid cross, sure.

But if the question was, say, In a cross between a RRSS and a rrss, what is the phenotypic ratio of the F2 generation if the F1 is allowed to self pollinate?

The first thing you would recognize is that the entire first filial (F1) generation is RrSs. Instead of drawing out sixteen boxes to realize that, just knowing was easier, right?

But still, you should really just know that the F2 phenotypic ratio of a classic dihybrid cross (RrSs x RrSs) is 9:3:3:1. And while we're at it, the classic genotypic ratio is 1:2:1:2:4:2:1:2:1.

But okay, we'll make it harder. What about... trihybrid crosses? You could be dedicated and draw out 128 boxes and figure out the ratio from that, but... only dedicated people have time for that when they have to do ten of these problems.

So, what is the probability of having a aabbcc genotype in a cross between AabbCc and AaBbcc? 

First thing to recognize? Not a classic cross.

Second thing? SO MANY LETTERS.

But it's okay. We'll take it step by step.

First thing to do: a monohybrid cross on the As. So Aa x Aa. If you actually do a punnett square for that, you'll find that you have a 1/4 chance of having AA, 2/4 of Aa, and 1/4 of aa.

Since we don't care about AA or Aa, we'll just keep the aa.
1/4. Don't forget it. Write it down.

Next, the cross on the Bs. bb x Bb.
That's 2/4 Bb and 2/4 bb. Keep the 2/4 bb. Don't lose it.

After that, the Cs. Cc x cc.
That's 2/4 Cc and 2/4 cc.

Now, multiply all the ratios. Since we want the probability of aabbcc, we multiply 1/4 * 2/4 * 2/4 to get a 4/64 chance of having the genotype aabbcc.

In the same cross, AabbCc x AaBbcc, if you wanted the probability of having a phenotype equivalent to AabbCc (meaning that AAbbCc would also count), then this is what you do:

Find the probability of AabbCc. It's 8/64.

Then, find the probability of AAbbCc. It's 4/64.

Then, add them together for your final answer: 12/64.

I put a diagram on the side of how you would actually write this out. (it's for a dihybrid, but same principles apply for the trihybrid, you just have an extra fork).

Testing the Experimentals: the Chi-Square Probability Analysis

too lazy to explain this right now, remind me later.

Exceptions to the Rule of Dominance

1. Codominance: when both traits share the dominance. For example, ABO blood typing, where you can be type A, type B, type O, or type AB. A and B are codominant, producing the AB type.

2. Incomplete Dominance: when one trait is dominate over the other, but it's not completely dominant. For example, in cats, you can have no white spots (ee), some white spots (Ee) or extensive white spots (EE). White spots are kind of dominant, but you need two copies of the dominant allele (EE) to have extensive white spotting; an Ee genotype produces some white spots.

3. Epistasis: when one gene covers another. For an example, the agouti gene. If the agouti gene dictates no tabby striping, then it doesn't matter if the genotype says the tabby striping is blotched or mackerel; the color of the cat is solid with no tabby striping.

4. Lethal Alleles: cause an organism to die when homozygous. In cats, we'll consider Manx cats, which have no tails. If, in the womb, the child carries the genotype MM, it will spontaneously abort. Mm produces a manx cat, and mm produces a normal cat with a tail.

Obviously, there are more exceptions, but I think I've covered the main ones.

Genes vs. Chromosomes

Genes occur in pairs (alleles), and so do chromosomes (homologues).

Members of a gene pair seperate during meiosis, and members of a homologous pair seperate during meiosis.

Members of one gene pair independently assort from other gene pairs during meiosis, and members of one chromosome pair independently assort from other chromosome pairs during meiosis.

See the connection?

Yes- *gasp* genes are on chromosomes. So, say you have brown eyes, which are dominant over blue eyes? Your DNA, which transcribes to RNA, which codes to a protein, says that your eyes are brown, while the RNA produces the proteins necessary to create brown eyes. And that, is what the Central Dogma of Molecular Biology is.