Tag Archives: alleles

The first hand : Mendel in Wonderland

In wonderland, much depends upon the suit and rank of a card. In the time of Alice, the Hearts held power, but since then, the Queen of Hearts has been imprisoned and the Kind of Spades now rules the land.

Families now strive to have children of high suits in order to give them the best chance at a good life.

Suit values are as follows:

Clubs < Diamonds < Hearts < Spades


Conveniently, the inheritance of the suits follows the same order. That is Spades are dominant over all suits, Hearts are dominant over Diamonds and Clubs, and Diamonds are dominant over Clubs.

SC < SD < SH < SS

Two cards come into your clinic to get genetic counseling. They want to know what chance they have of having a Hearts or Spades baby.

Mom is the Three of Hearts

Dad is the Five of Diamonds

They already have three children: a Two of Hearts, a Seven of Clubs, and a Jack of Clubs.


From the information provided above, what do you know?

Is it possible that they can have a Hearts Baby?


Posted by on November 7, 2014 in Uncategorized


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I love having a blackboard in my home office

In class this week we are discussing genes alleles homologous genes between species and pseudogenes. In order to organize my thoughts (to the extent that I can), I sketched out this diagram to model the flow of information from DNA into proteins and tie this together with the idea that DNA undergoes mutations from time to time and that these mutations are the source of new alleles in the population.


 1.Recall the central dogma

DNA –> RNA –> Protein

Information flows from the DNA out of the nucleus giving rise to proteins that make up the body and do its work. For EVERY gene, you have two alleles, one from mom, one from dad. We tend to only talk about the ones that give us distinct traits that we can see from the outside, but every gene these.

2. Mutations are altered forms leading to altered function

All genes are subject to mutations. Mutations may change the protein that the gene encodes or not. In cases when it does change the protein, we may see a change in function (Form dictates Function). Once we have two different versions of a gene that remain for any period of time, we call these forms alleles of the gene.

3. Interaction of Alleles

Mutations result in these new alleles that may function differently. This may manifest in a form of dominance. If one allele codes for a protein and a second suffered a mutation such that no protein is made, we may look for the protein and say that the form that makes the protein is dominant because one copy should be sufficient to get it made.

4. How can Alleles become Pseudogenes?

Sometimes, genes mutate into a nonfunctional allele that has no impact on the organism (e.g. vitamin C synthesis is not required when the animal eats sufficient vitamin C) in this case, there will be no selective pressure against the non-functional allele resulting in more mutations occurring without consequence. Over time, these alleles can be made completely non-functional.  Pseudogenes are the remnants of these old genes that we can find in the DNA, but that are no longer functional due to an accumulation of mutations. (Only if both copies are mutated and there is no functional copy of the gene in the population do we can this a pseudogene).

5. Speciation and Relationships

As time passes, and speciation occurs, we can still see similarities between the genes of the descendent species, whether these are functional, or sometimes even when they are non-functional. My analyzing the similarities between shared genes, it is possible to infer some relationships between species and even quantitate these relationships in a way that can be used to construct a phylogenetic tree.



Posted by on February 14, 2014 in Uncategorized


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A first look at Heredity

Oh Boy! Clarification is definitely in order. In this week’s lecture we outlined what it is that we will be covering in Unit II and then started in on a look at inheritance.

What does it mean to inherit something?

What is it that we are inheriting?

How can we understand the principles in operation in such a way that we can even make predictions about what certain crosses will result in?

There are a lot of different ways to approach these questions. The traditional method is to imagine that we are living in the 18th century and don’t know anything about Recombinant DNA Technology or Human Genome Projects or anything about modern science. Have an open mind and just look at what we can see before us.

(material below is modified from an iBook on Inheritance to be released in 2013 from DownHouseSoftware)

For many hundreds, or even thousands, of years inheritance was something that people had an intuitive understanding of, but could not really state in a set of rules how the process operated. There were always surprises that didn’t seem to fit the pattern.

On the positive side people were wise enough to breed the big animals with good temperaments while they slaughtered the others for meat. Similarly, the seeds of larger, tastier fruit and more productive trees were replanted, while those from less desirable plants were not. With time, these guidelines resulted in improved crops and farm animals and allowed for a transition from a hunter-gatherer culture to one that was more settled and agricultural.

As the world opened up to commerce between nations, it became more important for each nation to remain competitive, which meant that they would have to work out the rules of inheritance so that they could produce the highest quality animals and crops and textiles and distilled beverages.

This was the world that Mendel was entering. One in which a man who did not seem to fit into the standard societal roles could utilize his talents in the confines of a monastery in Brno and unravel one of the most basic riddles of life. What are the rules of inheritance?

Mendel eventually chose to work with pea plants that he could exert complete control over and carry out his experiments in a slow, methodical manner and document them with copious notes and definitions that explained his work clearly.

How do you work out something like the rules of life? Put yourself in Mendel’s place. Where do you start?

What this did tell him was that there was something about pink that over-rode the instruction to make white flowers. He called this phenomenon ‘Dominance,’ and came up with a rule that whenever two true breeding strains expressing different phenotypes of the same trait are bred together, and 100% of the offspring express just one of the parents’ phenotypes, that one is Dominant. The other is Recessive.

These results would have come as a shock to an earlier naturalist, Kolreuter, who assumed that the traits of the parents are blended in the offspring. Mendel’s experiments refuted this blending theory of inheritance by demonstrating that the F1 generation (that produced from the crossing of the True breeding parentals) would all express only the dominant parent’s form of a trait. Further, when this F1 was crossed to itself, the two parental forms were produced again.

The units of heredity are particles – not a liquid that is blended!

But there is more to it! These data, and more like it, demonstrated an interesting pattern in the offspring that gave Mendel a mathematical clue. No matter what trait he followed in his flowers, the same ratio of trait expressions in the offspring appeared – always 3:1. Whatever the number of what he called the recessive trait, he always say three times that number of the dominant trait.

He reasoned that this result was due to the particles of inheritance, which he called factors. From these data he proposed his Law of Segregation:


  1. Each individual has two factors for each trait
  2. Factors separate during formation of the gametes
  3. Each gamete has only one factor for each trait
  4. Fertilization gives the new individual two factors for each trait (one from each parent)

Instead of flowers, let us imagine a human couple. Both have brown eyes, but the man is carrying two factors from brown eyes while the woman has one factor for brown eyes and one for blue. Her eyes appear brown though because the brown factor is dominant.

Let B = the Brown eye factor

b = the blue eye factor

From Law of Segregation Part 1: Each individual has two factors for each trait

The man has two factors, they are the same: ‘B’ and ‘B’.

The woman has two factors, ‘B’ and ‘b’.

Because each of them has at least one copy of the dominant factor, that is what they express – brown eyes.

From Law of Segregation Parts 2 and 3: Factors separate during formation of the gametes – and – Each gamete has only one factor for each trait

The man makes sperm that contain one of his factors. Because he has two ‘B’s, all his sperm carry the ‘B’ factor.

The woman makes eggs that contain one of her factors. Because her factors are different, some eggs have ‘B’ and some eggs have ‘b’

From Law of Segregation Part 4: Fertilization gives the new individual two factors for each trait (one from each parent)


The offspring get one factor from each parent (carried in the sex cells) resulting in new individuals with two factors. The expression of the trait depends on what factors they get.

In this example, the man always contributes a ‘B’, while the woman may contribute a ‘B’ , like she does to her son. Or a ‘b’, like she does to her daughter.  However, in either case, all the children will have at least one ‘B’, so they will all have brown eyes.

Years later, at Cambridge, Reginald Punnett devised a much simpler way to depict these interactions visually in what is called a Punnett Square.

As this post is getting long, I think I’ll lay off here. This covers the main elements of what we discussed in class this week and I’d rather start another post later to continue.

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Posted by on November 8, 2012 in Uncategorized


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