Day 14: DNA and Chapter 6

In class we went over the structure of DNA and things like how Guanine (G) is always bonded with Cytosine (C) and how adenine (A) is always bonded with thymine (T). The bonds between  C and G and A and T are intermolecular hydrogen bonds. Double class rings such as guanine and adenine form are classified as purines. Pyrmides are referring to the single ring class such as thymine and cystosine.

For Homework we read chapter 6 of The Survival of the Sickest.

I learned that Edward Jenner from England was the first person to create a vaccine. He noticed that in milkmaids that have cowpox they can be resistant to the disease small pox. He scraped a bit of the infection of cowpox and used it as a vaccine applied to resist small box. Less harmful viruses the body won't notice and it will stimulate immune systems to produce antibodies so when we are exposed to diseases we can defend ourselves. 3 billion pairs of nucleotides are also in zygotes to be able to construct humans. However, scientists discovered that 97% of DNA isn't actually building anything, they called this DNA "junk DNA." They thought that this DNA didn't do anything and was idle this was proved wrong and now we call this DNA "noncoding". It is critical for evolution but it doesn't actually build anything. 1/3 of our DNA can actually be a virus. We defined mutations primarily as a random shift in the sequencing when DNA was getting copied or mutations when there was radiation or powerful chemicals. We discovered that single genes actually do multiple jobs and if we kill off one then another will step in it's place. Barbara McClintock suggested that parts of the genome could actively trigger much larger shifts. DNA can be cut and pasted and mixed into a new sequence. These are called "jumping genes." DNA can be stressed to make changes by a challenge of survival. E coli is a good example of this because in an experiment  scientist starved the lactose intolerant bacteria of nothing but milk. In order for it to survive it went thru a genetic shift and mutated to be tolerant and survive. This is a hypermutation that is a increase in the mutation rate so the bacteria can produce faster. The Germ-Plasma theory is the division of all the cells in the body into two divisions. Germ Cells, which are cells that contain information that is inherited and Somatic Cells which is everything other than germ cells like red-blood cells. Mutations could never be passed thru somatic cells was a common vies, however some viruses are fond to be able to pass thru somatic to germ cells. Immune systems have antibody production which has a behavior of jumping genes. Once your body develops antibodies you will always have them. Like the antibodies that prevent you from catching measles a second time.

Day 13: Genetics

Homework Questions:
1) Gregor Mendel was important because he added to Darwin's theory of natural selection by providing more evidence. Darwin knew what happened and what was the result of a species that evolved with a trait but not how. Mendel by using his pea plants was able to display the laws of inheritance.

2)

3)  The first example of variation is point mutation. This occurs when one singe base pair changes. An example of this is when the mutation inactivates the gene for signaling the muscle to begin growing like in a smaller dog. The second example of variation is insertion. Sometimes a base pair inserts itself into the genes causing a change. An example of this is in wrinkled peas, wrinkled peas are caused by an 800 base pair insertion that changes the phenotype and genetic make up. The third example of this is a gene copy number. This is when each gene copies due to a division error. An example of this chimpanzees because they only eat green plants they contain only one gene for starch digestion but somewhere along the line of evolution we now can have up to 10 of these genes. The fourth example of variation is duplication. Duplication is when the sequences for the same base-pair genes are repeated up to 8 times or more.  An example of duplication is pigs and their colouring. The colouring of pigs with dark spots are a result of copying mistakes when sequences were duplicated and lost a base as a result. The fifth and last example of variation is regulatory changes. Regulatory changes are mutations that controls when and where genes are activated. This can shift a whole organism by altering the formation of entire body parts in the early developmental stages. An example of this is the drastic evolution from the teosinte plant to the modern corn stalk.

4) Evo-devo is the study in biology which is specific to changes in important developmental genes and their effect in evolution.

5)  The migration of humans relates to the the development of being lactose tolerant because that mutation probably occurred on the path out of Africa. The mutation probably arose in the middle east when our ancestors first settled there because they depended on milk-producing animals as their herd. This mutation led them to produce lactase and could continue drinking milk.

Notes:
The other stuff we learned from the Journey of man video was that the Y chromosome is the best place to look for genetic markers. This is because it is easier to spot mutations that don't change, unlike the X- chromosomes that tend to change a lot. Our ancestors also most likely left Africa in the middle of an ice age because this ice age caused the climate to be dry and they most likely suffered in a large drought so they had to move to places with water. Populations also developed lighter skin to absorb the essential uv radiation in cold places where they are less exposed and need to synthesize vitamin D. In reverse other people have darker skin to protect them from the harsh uv radiation in those areas. Central Asian DNA is also important to the study of races because in central asia the major population shift took place so that some people migrated to Europe and East asia. The modern day Chuchki tribe are the living survivors of generations that migrated from central asia to america, yet some stayed in eastern siberia. Bergmann's and Allen's rule is when there is a very cold climate and humans have adapted to have a smaller surface area and be short to preserve as much heat as possible and so that it won't be lost. They along with this adaption have to keep a very active life so they don't freeze. These gives answers to why are ancestors could be successful in cold climates. The first americans also arrived 15,000 years ago through land exposed due to the ice age in eastern siberia.

Day 17: The Migration of Humans Part 1

In the video called "Journey of Man" we learned that a "time machine" is essentially DNA that can help us look back into history. All of our ancestors originated in Africa around 50,000 years ago and then migrated. The tribe that is still present today that is the most genetically similar to our ancestors is the San tribe men in the Kalahari Desert. They display many of the phenotypes that races today have. A genetic marker is a mutation in chromosomes and DNA that took place in one individual and was passed down and inherited. This shows us where all our ancestors split and started having really different mutations. After starting the migration from Africa, the next place we found evidence of our ancestors being present was Australia. This is a problem because this would have been a huge distance to cover and we think that our ancestors walked along the coast to reach Australia. The problem is that there was a lot more land back then due to the ice caps being large and still very frozen. So the route they took is now underwater. Essentially though we are all descendants of early Africans. This poses the question of: Does race really exist? If we were all related to each other 50,000 years ago and our pretty genetically similar than how did race develop? The answer is in the genes of races. Scientists decided to collect data from alus. Alus are short pieces of DNA that are similar in sequence to one another. This is a class of polymorphisms. Polymorphisms are in genetics the presence of variation in a population upon which natural selection can operate. Aluses once they replicate, they can spilt and then reinsert itself into a chromosome, and once inserted those alus will become permanent for a very long time and be inherited. These alus can be analyzed and provide information for people sharing a common ancestor. Scientists took a bunch of alus data from different races and then blindly, without knowing what race corresponded to what organized them into four groups. When they “applied” the labels and discovered what sample was from what race then they saw that they sorted them by similarities and most were from the same area of the world. This has been conducted several times, all yielding similar results that we can sort data into five major groups. These groups are; Sub-Saharan Africans, Northern Africans/ Europeans, West of the Himalayas Asians, East Asians, and Native Americans.  It is easier to distinguish between people from isolated and very separated parts of the world than analysis of people in a population of one country. The one country population in comparison would be very muddled. Natural selection in evolution sets up our standards of what race is. We usually distinguish race based on pigmentation of skin that has been caused by natural selection. Africans and Aborigines in Australia may have the same pigmentation of the skin because it protects them better from the harsh sun in those areas but their alus polymorphisms are very different.. The questions this brings to light is that in society should we change things like the race questions on standardized tests to be more scientifically correct and only state 5 clear races? Should we then change the norm for referring to races based on something other than phenotypes? Polymorphisms also can have beneficial aspects such as how people with one copy of a sickle cell in the Mediterranean area can be resistant to malaria. If such things are possible can we genetically engineer to make all individuals contain beneficial polymorphisms in their genes? 

We will continue watching this video next class time.

Day 16: Unit Test 2

We took a test today, the test was on:

• the modern theory of evolution 
• homologous structures
• analogous structures
• DNA frequency evidence for evolution
• fossil evidence for evolution
• cladograms and species from a common ancestor
• the Hardy- Weinberg equilibrium 
• molecular biology evidence
• natural selection
• mutations and adaptions 

It was also on some Unit 1 questions like diffusion and macromolecules.

Day 15: Hardy-Weinberg Problems

Hardy and Weinberg came up with an idea for genetic equilibrium. In order for there to be an equilibrium in an ecosystem then there must be five present conditions.
These conditions are:

• The population must be large
• Their mating must be random
• No natural selection
• No mutations
• No immigration or emigration

After learning these things. We walked around class with a set of 2 dominant alleles and 2 recessive alleles cards. When a song stopped we had to randomly "mate" (exchange cards) with the person next to us. Then we recorded if we had homozygotes genotypes and heterozygotes for recessive or dominant or both. After recording this we proceeded to calculate the percentages of the dominant alleles and the recessive ones. After finding this out we could solve for things we didn't know using these formulas.

p + q  = 1

p^2 + 2pq + q^2 = 1

The p represents the dominant allele like an A and the q represents the recessive allele an a. Therefore the 2pq is 2 times the heterogenous genotype.

This is important because we can determine the genotypes in a population if we know some minor information about the alleles.

Day 14: Parents Day and Natural Selection in Humans

Today we discussed with our parents natural selection in humans. There has been many studies done about what is preferred in the looks of women and men. What has been scientifically discovered is that women prefer men that have more feminine features because it makes them appear "friendlier" and as a "good parent." They will more likely marry them because they supposedly will be a good parent. Men also prefer women with more feminine features because they feel less threatened in masculinity and the women appear also as "better parents." Thus women naturally selected the stronger better mates to have children with. Males also feel that looking at other males with more feminine features more agreeable because they don't threaten their masculinity.

Here are composite faces that were created out of average faces. Pay attention to the physical characteristics of these people.

Day 13: The Brine Shrimp and Evolution

We started our brine shrimp lab today and talked about evolution and natural selection.

Adaptation: Is a helpful trait that a species has developed over generations.

If a species has an adaptation it is more likely to survive because it has strong traits and the weaker ones will die off. Thus this creates natural selection, the strong species that remain can only breed with each other and therefore survive keeping a "helpful" mutation.

Brine shrimps have adaptations that are different from the other species of shrimp and branchiopods.

We had "dormant" freezer brine shrimp eggs and put them in different solutions of NaCl and de-chlorinated water (0%,.5%,1.0%,1.5%,2.0%). Putting them in the water activates them to hatch under certain conditions. We put a lot of eggs in all the solutions but I predict that they won't all hatch. I also don't think that any of them will hatch in the 0% because there is not enough nutrients in that water for the shrimp.

We have to check on them in 24 hours to see which ones have hatched.

Day 12: Favism

Today we talked about Favism and how it is a specific genetic mutation.

Favism is a modern medical disease. It was first noticed after the Korean war when soldiers were taking a drug called primaquine to not risk catching malaria and this caused them to die suddenly. This is because some of the soldiers had Favism which is a deficiency mutation on the X chromosome. This is more common in men because they only have one X chromosome unlike women who have two X chromosomes so it is less likely to affect them. The deficiency mutation is when the cells lack an important enzyme called G6PD which acts like a "bouncer" for all the free radicals that seek red blood cells and attack them. If you don't have enough G6PD then free radicals can attack your blood cells and make them burst. Eating fava beans releases  free radicals in the form of covicine and vicine  that attack the cells that don't have enough G6PD and the person can die. G6PD deficiency occurs a lot in the places were fava beans are part of the staple diet which is where they are grown in the Mediterranean area. Malaria parasites do not like G6PD deficient cells so they won't attack them. So it is favored to eat fava beans for anti-malaria protection. That is why the malaria medicine also has a lot of free radicals.

Other Plants like fava beans release chemicals sometimes that serves as a defense. For example in the cassava plant if you eat it raw you will die from the cyanide produced in the skin. It produces cyanide to be protected from being predated upon a lot. Cassava will also produce a lot of cyanide in drought because it wants to survive till the next rain. In chili peppers their defense is the spicy capascin that discourages animals to eat it. The animals can't handle the taste so they won't eat the chili peppers. The peppers don't want to be eaten by the mammals because their stomach is a bad condition for their seeds to survive and get excreted and "planted" in another area. Birds on the other hand don't taste this capascin so they are "allowed" to eat the chili so they can carry their seeds in their weak digestive system.