30th Jul 2014

oh my god that’s it, we’re done, the previous post was officially the last in the Bio 101 series

I’ll compile all the posts and upload them in some fashion over the comings weeks

but in the meantime, I’m going to take a few days off, and then this blog will be back to regular cool science shit

any suggestions for articles, drop them in. if not, your science education is in my hands, so buckle up friends

30th Jul 2014

The Plot Thickens

The two main principles that Mendel discovered—the law of segregation and the lat of independent assortment—were the foundation for our modern understanding of genetics. But what Mendel didn’t realise was that there are exceptions to these “laws”, and that inheritance is a whole lot more complicated than that.

It turns out, Mendel’s pea plants had relatively simple genes, always completely dominant or completely recessive. But some alleles can exhibit different degrees of dominance and recessiveness. In some genes, neither allele is completely dominant—this is called incomplete dominance. In some plants, like in snapdragons, the F1 generation produced from crossing a red with a white can actually have pink petals—because the flowers have less red pigment.

We have to be careful here, because it seems to provide evidence for “blending” genes, but it’s actually not. If the blending hypothesis were true, we wouldn’t be able to “recover” the original red or white trait from the pink plant, but we can. When F1 hybrids produce F2 offspring, they can actually be red, white or pink. This tells us that the alleles maintain their identity and aren’t mixed up.

Alleles can also be co-dominant, which means they affect the phenotype in separate and unique ways. For example, there are several alleles for human blood groups, commonly known as A, B, and O. But the A and B alleles are codominant, so when they appear on adjacent loci in an offspring, that offspring doesn’t have A blood type of B blood type—they have AB blood type.

Body image sourced from Wikimedia Commons

29th Jul 2014

Probability in Genetics

So far we’ve been talking about simple ratios, but how can we mathematically figure out the probability or the percentage that an organism will inherit a trait?

Consider a cross between YyRr and YyRr. Using a Punnett square, we can deduce that for colour, ½ the offspring will be Yy, ¼ yy, and ¼ YY. The same probabilites apply for shape: ½ Rr, ¼ rr, and ¼ RR. (Remember Y=yellow, y=green, R=round, r=wrinkled.) But how do we then figure out how many will be round and yellow, or green and wrinkled?

The rules of probability, of course.

We can determine the probabilities of the genotypes by just multiplying the traits we want to know about together. For example, what’s the probability of the pea ending up yellow and wrinkled? Well, we know that ¾ of our offspring will be yellow, and ¼ will be wrinkled. ¾ x ¼ = 0.1875. So about 18.75% of our offspring will be both yellow and wrinkled. (If you don’t like fractions, just use 0.75x0.25.)

What about green and wrinkled? ¼ x ¼ = 0.0625. So 6.25% will be green and wrinkled. We can do the same for the others:

Yellow and round: ¾ x ¾ = 0.5625 = 56.25%

Green and round: ¼ x ¾ = 0.1275 = 18.75%

Adding all of these up gets you 100%, of course. It also gives us our ratio that we’ve talked about—9:3:3:1.

Further resources: Probability in Genetics: Multiplication and Addition Rules video

28th Jul 2014

The Law of Independent Assortment

But all of the above only describe what happens when we follow one particular gene through the cross. Mendel also observed the ratios of different characters as they were crossed together—such as following colour and shape, knowing that round peas are dominant (R) and wrinkly peas are recessive (r). He wanted to know whether certain genes stayed together and were more commonly found with each other, generation after generation, or whether they went their own way—whether they’re inherited independently.

To figure this out, Mendel performed a dihybrid cross, crossing YYRR with yyrr. He found that in the F1 generation, all plants are YyRr, so they’re all yellow and round. But in the F2 generation, after self-pollination, you end up with a ratio of 9:3:3:1—9 parts yellow and round, three parts yellow and wrinkled, three parts green and round, one part green and wrinkled.

(Image Source)

If the colour and shape were inherited together, you’d end up with a 3:1 ratio, 3 parts yellow and round, one part green and wrinkled. But because Mendel ended up with the other, more complicated ratio, he realised that the alleles couldn’t be inherited together—they were independently passed down, paying no attention to any of the other alleles. This is called Mendel’s Law of Independent Assortment.

Note that this law only applies to genes on different chromosomes—those on the same chromosome tend to be inherited along with nearby genes (remember it’s more probably that far-away genes are crossed over). Their inheritance are more complex than this law can predict.

Further resources: Educationportal Video

28th Jul 2014

Ratios and Punnett Squares

One way to easily illustrate and predict the patterns of inheritance is using a Punnett square. Usually, we use a capital letter to indicate a dominant allele and a lowercase letter to indicate a recessive allele. For example, Yy would be a pea plant with one dominant yellow allele and one recessive green allele.

If an organism has two identical alleles for a particular gene (like, a pea with two yellow alleles), then they are called homozygous for that gene (i.e. YY). If they have two different alleles, they are called heterozygous for that gene (i.e. Yy). When you cross two organisms that are both homozygous for the same gene, then their offspring will always be homozygous for that gene too. This is called purebreeding, or breeding true.

When we cross organisms that are heterozygous for that gene, we get:

When we cross organisms that are homozygous but have different alleles like yellow true bred peas and green true bred peas, we get:

Let’s say we have a plant that has a yellow phenotype, but we don’t know what its genotype is—since yellow is dominant, it could be YY or Yy. How can we figure it out? We can perform what’s called a test cross: cross is with a plant that is homozygous but only recessive, like yy. The allele contributed by the yellow plant will therefore always determine the appearance of the offspring—and if all the offspring are yellow, we know the original plant had dominant YY alleles.

If the offspring are half yellow and half green, we know the original plant had Yy alleles.

Further resources: A Beginner’s Guide to Punnett Squares

27th Jul 2014

Anonymous said: Do you have any posts explaining sodium-potassium pumps?

Hey bud, I don’t have a specific post about it, but I do have an article where I discussed active transport. When I was studying, I also found this Khan Academy video useful, as well as this animation

27th Jul 2014

Anonymous said: Quick, possibly dumb, question: how was Mendel sure that the P generation peas were pure-bred?

Nope, not dumb at all. Mendel knew the P generation was true-breeding because he bred it himself. Basically, he allowed a certain variety of pea plant to self-pollinate (which is what peas ordinarily do) for several generations until they were homozygous for a given trait.

He could test this—say he had a yellow pea and allowed it to self-pollinate. If it’s homozygous, it could only ever produce yellow offspring, not the ratios we’ll see later on.

27th Jul 2014

Mendel’s Gene Ideas

In the 19th century, a European monk called Gregor Mendel performed experiments in the garden of his abbey that would forever change the course of biology. Until that point, farmers and agriculturalists had been attempting to grow hybrids of plants with mixed success, because they didn’t really know what laws dictated how genetic information is passed on. Though Mendel had never looked through a microscope and had no idea what the actual process of DNA replication and meiosis was, he still was able to determine four fundamental rules of genetics through the power of his well-designed experiments.

Mendel’s experimental subjects were peas (Pisum sativum). Not very exciting, but perfect for what he wanted: they had short generation times, a large number of offspring, can both self-pollinate or pollinate with others, and they were available in lots of varieties. Their physical characteristics like colour and shape were also very obvious, allowing him to visually track the changes through the generations. Remember that the expression of a gene is called a character, like pea colour, and the expression of an allele is called a trait, like green or yellow pea colour.

Mendel selected pure-bred pea plants with particular traits and cross-bred them in order to see what phenotypes they expressed in different generations. Using carefully planned experiments, he figured out patterns of inheritance.

In a typical experiment, Mendel would take two very different pure-bred plants and cross them together. For example, he crossed a pure-bred yellow pea plant with a pure-bred green pea plant. This mating is called hybridisation. Note: we call the first generation the P generation (for parent), the second generation the F1 generation, and the third generation the F2 generation, usually given by self-pollination.

In completing this yellow and green pea cross, Mendel found this relationship:

(Image Source)

In the F1 generation, all plants produced yellow peas. Even though the parents were green and yellow, the F1 generation didn’t mix the colours to be greeny-yellow—they were just yellow.

Then, when Mendel crossed the F1 gen with the F1 gen (through self-pollination), he found that only three quarters of the plants had yellow peas, and one quarter mysteriously were green. This 3:1 ratio is recurring—remember it.

This happened every single time Mendel crosses plants in this way. He realised that this regularity must be the key to some underlying mechanism of inheritance.

(Image Source)

If crossing two different genes plants could blend the genes, then we’d expect the F1 generation to be a greeny-yellow colour. However, this isn’t the case. So what happened to the green in the F1 generation? Obviously it hasn’t disappeared completely, because it crops up again in F2. Mendel reasoned that it was hidden from view, and termed the yellow colour as a dominant trait and the green colour as a recessive trait. We now know that there are dominant alleles and recessive alleles, and only one is expressed in the phenotype.

In order to come up with the law of segregation, Mendel noted four related concepts.

  1. Offspring have different physical characteristics because genes have different “versions”, called alleles. These account for variation.
  2. For each gene, an offspring inherits one allele from each parent.
  3. If two alleles at a locus are different, then the dominant allele will determine what the organism looks like. The recessive allele will have no observable effect.
  4. The two alleles for a gene of one parent separate when gametes are formed. They end up in different gametes, so the egg or sperm only get one of the two alleles present in the somatic cells of the organism. For example, if the gene has a dominant and a recessive allele—this separation means that 50% of gametes will end up with the dominant allele, and 50% will end up with the recessive one. This is called the Law of Segregation.

27th Jul 2014

The Origin of Genetic Variation

Mutations in the nucleotide sequences are the original source of genetic variation, causing different versions of alleles to exist. Once we have these differences, alleles can then be reshuffled, like a pack of cards, in order to produce the variation that makes each individual organism have its own unique combination of characteristics.

In sexually-reproducing organisms, most variation arises from processes that happen during meiosis and fertilisation.

Independent Assortment of Chromosomes:

  • When homologous pairs (with one maternal and one paternal chromosomes) line up at the metaphase plate in meiosis I, their orientation is random—there’s a 50% chance that the daughter cell will be given the maternal or the paternal chromosome of any given homologous pair.
  • In addition, each homologous pair orients itself independent of whatever any other chromosome is doing, i.e. independent assortment.
  • The daughter cells are therefore just one of many possible combinations of maternal and paternal chromosomes. Because humans have 23 chromosomes, the number of possible combinations is 2^23, or about 8.4 million.

(Image Source)

Crossing Over:

  • Also known as recombination
  • Each individual gamete does not have only one paternal or one maternal chromosome. Rather, it actually ends up with a mix of them. This is due to recombinant chromosomes.

  • As we saw in our discussion of meiosis, in prophase I homologous pairs join up along their lengths, precisely aligning with corresponding alleles next to each other. Then, they essentially swap out alleles, exchanging them along their lengths—like swapping arms.
  • The further away alleles are from each other, the more likely they’ll be swapped. Alleles that are located close to each other are therefore more likely to be inherited together.
  • What results is a pair of homologous chromosomes that have been randomly mixed up.
  • This is incredibly important, because mutations are happening all the time. They can actually destroy the function of genes, so if no crossing over ever occurred to increase diversity, mutations would just accumulate and eventually all genes would be destroyed. Instead, crossing over helps non-mutated chromosomes to reform.

Random Fertilisation:

  • Basically, a sperm cell randomly chooses an egg cell. Because each one is already one of 8.4 million combinations, the random fusion of sperm and egg produces a zygote of 70 trillion possible combinations (2^23 x 2^23).

Body images sourced from Wikimedia Commons

Further resources: Genetic variation video

26th Jul 2014

Meiosis

All somatic cells are produced through mitosis, which is the process of cell division that we’ve already talked about. But sex cells, or gametes, do not replicate and divide this way—they go through a similar but distinct process called meiosis. This is because they have to remain haploid, otherwise the next generation would have two sets of 43 chromosomes, and the next generation would have double that, and overall it would be an enormous disaster.

Meiosis only occurs in the ovaries and testes, and many of its steps are similar to mitosis. You might want to go quickly brush up on my cell division post before we go on, so you remember how it’s done for somatic cells.

Like mitosis, meiosis is preceded by chromosomes replicating, but the actual process is split into two parts—meiosis I and meiosis II, each with their own version of prophase, metaphase, anaphase, and telophase and cytokinesis. Meiosis starts with one diploid cell and results in four haploid daughter cells, as opposed to the two diploid cells that mitosis creates. The point of mitosis is to preserve identity and copy the cells’ DNA faithfully, while the purpose of meiosis is to create gametes with maximum diversity.

image

Interphase

In this initial stage, the homologous chromosomes in the diploid parent cell replicate, forming sister chromatids. It goes from two sets of chromsomes to four sets of chromosomes (represented as 2n to 4n).

Meiosis I

In this stage, the parent cell (4n) divides, forming two haploid cells with the replicated chromosomes (2n).

  • Prophase I: Chromosomes condense and form homologous pairs (i.e. composed of one paternal and one maternal chromosomes). These pairs are lined up gene for gene, so the loci for different genes are aligned. A special protein structure physically connects them along their lengths—this process is called synapsis. While they’re connected, crossing over is completed (we’ll talk about that later—basically it’s a process to boost diversity). Then, the spindle forms, the nuclear envelope breaks down, and the homologous pairs move towards the metaphase plate.
  • Metaphase I: The homologous pairs are aligned on the metaphase plate.
  • Anaphase I: Homologous pairs are allowed to separate and they move towards opposite poles, as guided by the spindle apparatus. At this point sister chromatids are still attached to each other and move together.
  • Telophase I & Cytokinesis I: Each half of the cell has a complete haploid set of chromosomes, each composed of two sister chromatids. Cytokinesis occurs, forming two haploid daughter cells.

Meiosis II

Then, the two haploid cells replicate and divide again, forming four haploid daughter cells (1n).

  • Prophase II: Spindle apparatus forms. Chromosomes move towards metaphase plate.
  • Metaphase II: Chromosomes align, and because of crossing over, the sister chromatids aren’t identical.
  • Anaphase II: Sister chromatids are separated and more to opposite poles are individual chromosomes.
  • Telophase II & Cytokinesis II: The nuclei form and the chromosomes decondense. Cytokinesis splits the cells, producing four haploid daughter cells in total. Each is genetically distinct from BOTH each other and from the parent cell.

Body images sourced from Wikimedia Commons

Further resources: Crash Course video and Khan Academy video