Chapter 6- Embryology

All embryos start from a single parent cell pairing, which becomes a blastocyst, which then attaches to (hopefully) the right place in a mother's uterus, and a flat disk with two layers forms. The disk rolls into a double tube, and three layers of tissue differentiate. The top layer forms the ectoderm, the middle the mesoderm, and the inner the endoderm. The inner tube becomes our guts and inner organs, the outer tube becomes our skin and nervous system, and the middle layer becomes our skeleton and muscles. At one point, there exists a region of tissue can Organize cells into all three layers. Hilde Mangold was responsible for grafting a piece of such tissue onto a newt embryo, creating a twin out of the graft. Organizers from animals can be placed into different species and function properly.

Sex linked and pedigree

Some genes are sex linked, which means that they occur on an X chromosome such that only when there is no other x chromosome, the trait will show. Which means males are more likely to show the trait than females.
when doing problems on sex linked genetics, always label whether the genes are on an X chromosome, and whether the individual has a y chromosome.

this is useful in pedigrees because we can easily see all the genders and genetic identities of individuals. We can then find whether the trait is dominant, recessive, sex linked, or not.

More Complexity

You can have two or three traits going on at the same time. 

all you need to do is either create gametes and do a big chart

or cross the two traits separately and multiply each combination. 

both ways work, but I personally prefer separating traits and multiplying because it's fast and you can choose to only determine a couple of phenotypes. for the big chart it's necessary to finish the chart, which sometimes gives you excess information.

Genetics Problems

Step 1: Write down the information you have. What is the dominate allele, and what is the recessive allele? Who exhibits dominant traits? Is their genotype heterozygous (different alleles) or homozygous (having all the same alleles)? etc
ex. A is dominant, a is recessive
Step 2: write down the genotypes of the parents, mother first
Step 3: write down the gametes- separate each allele
Step 4: draw a Punnet Square and multiply each gamete against the other gametes.
ex. AA x Aa = AA, AA, AA, Aa
Step 5: rewrite your results as ratios
P : 4 dominant, 0 recessive
G: 3 AA: 1Aa: 0aa

the types of ratios possible

AA x AA
P:4dom:0 rec
G:4AA:0:0

AAxAa
P : 4 dominant, 0 recessive
G: 3 AA: 1Aa: 0aa

AA x aa
P: 4 dom, 0 rec
G:0:4Aa:0

Aa x Aa
AA Aa Aa aa
P: 3 dom :1 rec
G: 1 AA: 2 Aa: 1 aa

aa x Aa
Aa Aa aa aa
P: 2 dom: 2 rec
G: 0:2Aa:2aa

aa x aa
P: 0 dom: 4 rec
G: 0:0:4aa

Mutation

Survival of the Sickest Chp 6: Mutations occur during cell reproduction, and this morning glory is a mutated specimen. The rate of mutation creation speeds up during times of stress- special jumping genes pick up and start inserting themselves into other gene sequences to prompt mutation. This flower may or may not have become a seed at a time of stress and change for its parent plant. 

From Chp 3 of Your Inner Fish: If a piece of tissue called the ZPA from the pinky side of a hand moves to the other side during gestation, a mirror image set of fingers grows on the new transplanted side. The ZPA contains special genes, called Sonic Hedgehog genes. If a concentration of Vitamin A is injected into an embryo during the right stage of development, a hedgehog mutation occurs. What happened to the child was either a malfunctioning ZPA or a mutation in the Sonic Hedgehog gene.  

DNA replication

 It starts with HELICASE- which finds the point of origin and unzips the nucleotides from each other in a 3'-5' direction. 

then RNA PRIMASE comes and deposits RNA at the point of origin to tag the location with an OH- so that DNA POLYMERASE III can start adding nucleotides to the OH- ended RNA fragment. It does so also from a 3'-5 direction. BUT the point of origin is in the middle of the gene, and we've only replicated half of the sequence. So RNA primes creates a lagging strand which DNA polymerase III can find and add DNA nucleotides to. After all the nucleotides have been copied with one form of genetic material or another (RNA, DNA) DNA POLYMERASE I comes and substitutes the RNA for DNA. LIGASE then attaches all the unconnected sequences of genetic material made at different times, called Okazaki fragments, and the gene is a complete complimentary copy.   

PGLO

By adding a glowing gene to E-coli bacteria, we can make glow under UV light bacteria strains. 

Our hypothesis: 

1.  We prepare two different solutions, one with pGlo genes and one without. we add a culture of e-coli bacteria to each sample, then flash heat and freeze to encourage the polo dna to enter the e-coli cell membrane. because e coli is a eukaryotic animal, there are no cell nuclei to enter, it's relatively simple to get the foreign pGLO into the cell where it will be integrated during protein synthesis. 

2. we have four petri dishes

+/amp/ara, +/amp, -/amp, -/nothing else.

the sample bacteria cultures with pGLO added are placed in the + dishes. 

3. after incubating, we find that the dish containing arabinose grew bacteria that glowed, and the dish with ampicillin containing non-glowed/ ampicillin R bacteria didn't grow. the other two dishes grew to varying degrees. 

From the results we can see that the pGLO gene is activated by the presence of arabinose, because the only pGLO petri dish that glowed contained arabinose. 

quick chap 6 recap!

Natural selection picks the mutated organisms that are best adapted for survival. But the mutations are not the result of purely random mistakes during gene replication. Darwin postulated that mutations are the result of cell reproduction errors, but an alternate theory, set forth in recent times by Barbara McClintock, that holds more water is that we have perhaps evolved to actively mutate our genes when the environment changes, so as to give our offspring a better chance for survival.

Viruses exhibit this behavior, when antigenic drift causes original mutations in a disease. After a solar flare-up in 1917, two deadly smallpox outbreaks killed millions of people. It is possible that the virus strains mutated when they were irradiated. Antigenic shift, when a virus gets new genes from a similar strain of virus, is also a form of survival enhancing mutation. Viruses also have genes that jump around and either copy and paste or cut and paste new sequences around. Scientists are really interested in these jumping genes, and have taken to giving them punny names like Jordan and Evelknievel. We also have “jumping genes.” Scientists think these are former viruses that we have swallowed into our DNA. 97% of our DNA is used for mutational purposes.We are programmed to mutate if we need to. Our DNA is like a smart computer program that seeks input, not just a simple string of commands that occasionally fail at replication. 

From Atoms to Traits

1. Explain the significance of Mendel. 
Darwin originally thought that traits mixed in offspring, but Mendel's pea plant experiments showed that traits are passed down in discreet units. He called them genetic factors, and his results fixed some of the errors in Darwin's hypothesis.  

2. Draw the structure of DNA and who discovered this structure. 

 

top to bottom: Rosalind Franklin, James Watson, Francis Crick. Franklin thought of doing X-ray microscopy, and WC interpreted the results. WC got the Nobel. 

3. Explain each of the five examples of variations that occur to DNA and give an example of each. 
Point Mutation: A base-pair change that can change the functionality of a gene sequence, like whippet dogs with two mutations who grow extra muscle when the gene itself should code for not growing muscle.
Insertion: when a sequence is added to a gene, like when a mutated extra sequence causes peas to grow with less starch and sugar and become wrinkled instead of smooth.
Gene Copy Number: extra copies of genes are created and passed on, like the starch gene was made 10 times in humans but only once in chimps.
Duplication: when the same base pair appears more than 8 times in a row it is very likely to be copied incorrectly during cell reproduction. Homopolymers like the C-G pair in pigs cause light colored vs spotted coats when copied incorrectly.
Regulation error: when the part of the gene that codes for when each part of the sequence kicks in is copied incorrectly, examples include the teosinte plant versus the modern day corn plant.

4. What is evo-devo? 
The specialized study of the way genes and mutations affects evolution.

5. Make a connection between human migration and the mutation of lactose intolerance.
Lactose intolerance is default for populations who only feed milk to their babies, not their adults. the mutation of lactose tolerance developed when humans migrated with their hunting sources but settled down to become agricultural societies in China, Europe, and the Middle East and needed to digest milk products from their domesticated prey.  

Human History is Written in Genes

Though we consider our species incredibly advanced, 99% of our gene sequence is identical to the gene sequence of chimpanzees. And though we consider our species incredibly diverse, even going as far as to attack fellows of our species on account of their phenotypes, we are genetically even less different from other human beings than from chimpanzees- less than 1% to be precise. In context of the scientific, genetic explanation for human diversity, our previous hypotheses about our origin and the distinction between races seem outdated.

            For one thing, it’s highly likely that all the humans on earth are descended from a single mother, a “mitochondrial eve”(Shreeve, 62)*. We know this because mitochondrial DNA is passed down directly from mother to child with all the previous mutations preserved, and the earliest and most ubiquitous mutation originated in Africa. Scientists deduce that a group of people in Africa decided to migrate out because the genetic markers of those people still appear all around the world. This means that everyone alive today is descended from those people who lived in Africa. Scientists have isolated the most common and thus the earliest genetic markers, and the San bush people of southern Africa, the Biaka Pygmies of central Africa, and tribes in eastern Africa seem to be the source of those genetic markers. Scientist Spencer Wells met with the San people, and they exhibit various phenotypes present in other groups of people. The scientific explanation for the population of the earth- that humans are the ones who did the traveling and the creating, not creator gods- chafes with traditional origin stories. For example, Wells received a flat-out denial of his research from an Aboriginal man who chose to support the origin stories of his own culture. Nevertheless, evidence indicates all humans are distant relatives from Africa.

             Race as defined by skin color is also a social construct that genetics refutes. Skin color varies from light to dark as an adaptation to millennia of sun exposure, and doesn’t exclusively indicate genetic similarity. People from Africa may have the same skin tone as Aboriginal Australians, and still be genetically distinct in almost every other way. It is true that different evolutionary populations have common polymorphisms- Alus and short tandem repeats are two types of gene sequences that are inheritable. Scientists can group people based on the amount of common Alus or short tandem repeats they have, but with varying degrees of accuracy. There is debate over whether it’s even useful to group populations based on gene sequences that don’t inherently code for anything vital to survival. But there is research that indicates some populations have adaptive traits from long ago that are medically relevant to disease treatment and prevention today. If people can be categorized into their genetic groupings, doctors can better search for genetic traits that may influence their diagnoses and treatments. Despite the potential benefits of grouping people genetically, it is still too close to the practice of racial profiling for many scientists’ comforts.  

            Gene sequencing supports the theory of evolution by demonstrating the similarities between humans and other primates. It also shows the process of random mutation and natural selection over time. The human population is one of the best sources of raw data on evolution. We have populations with very little immigration, we have populations who have emigrated to other climates, we have populations who have mixed in one region, and we have populations who have mixed in many locales. Though genetic sequencing hits some controversial nerves on origin and race, disrupting social constructs may be exactly what we need to progress as a species.  

*Shreeve, James. "The Greatest Journey Ever Told." National Geographic. March 2006. pages 62-69.

Hardy-Weinberg

Evolution will not occur if
1. the sample size is large and thus everything is more evenly random
2. mating is random- there is no particularly attractive trait
3. DNA does not mutate
4. There is no differential migration, where new genes are introduced
5. phenotypes do not influence survival

p*p + 2pq + q*q = 1
p+q=1
these equations detail the rates of occurrence of alleles and genotypes.
dominant alleles are p and recessive alleles are q.

If the entire population is allowed to breed randomly, then an equilibrium will remain in the sample. 0.5 vs 0.5 dominant and recessive alleles. But if the population is separated, the final occurrence of dominant and recessive alleles will not be 0.5 vs 0.5.

Natural Selection

Genotype- the gene sequence that an organism inherits from its parents.
Phenotype- the characteristics an organism shows as a result of their genes.

There is a dominant and a recessive allele. The dominant allele will determine the phenotype whenever it appears. The recessive allele will show if it is the only allele in the genotype.

In the case of Bengal Tigers, a recessive phenotype means no fur. And no fur means death in the winters. So we did an experiment on natural selection's effects on a gene pool. We used colored beads to represent alleles, and picked them two at a time randomly out of a bag.
Each time we got a recessive phenotype, those bead alleles were eliminated. Eventually after about 6 generations of random breeding, the recessive phenotype stopped occurring, thought the recessive alleles remained in the gene pool.

Natural selection is the process of eliminating those traits that do not help survival. Evolution operates on populations over time, not individuals. Individuals just die and fail to pass on their genes.

Brine Shrimp

We hatched Brine Shrimp!
Brine Shrimp have evolved a mechanism that allows them to stay in egg stage until the time is right to hatch. Their criteria involve a particular solution of salt- no more, no less.
We placed varying concentrations of salt water (% by mass) into petri dishes, then placed glass slides covered with around 20 brine shrimp into solution. We waited 24 hours, took stock of how many shrimp were swimming, then took a second set of measurements at 48 hours.
Our class data was off because we committed some human errors.
We may have miscounted the shrimp.
or
mixed up the saline solution labels.

Our class graph indicated the optimum salinity for brine shrimp to be 0.5% NaCl.

Fava Beans

Fava beans are known commonly as broad beans. 

They look every inch a healthy food, and would be except that for many people they are actually toxic. If your ancestors hailed from a region suspect to malaria back in the day, you would inherit a trait that made you lack enzyme G6 PD. Favism would cause an allergic reaction in your body, the symptoms of which include diarrhea, hemolytic anemia (breakdown of your blood cells), and thus extreme fatigue.This affects mostly people from the Mediterranean and Africa. This evolved as a way of preventing the carrier of the G6 PD deficiency from Malaria, because the disease could not infect those with Favism.

Quiz

1. The four animals show changes in limb shape and size over time, indicating that the Basilosaurus evolved from a Mesonychid.
2. Australia
3.Dragonflies, birds, bats are examples of convergent evolution. The three animals all have wings, but the underlying structure of those wings are completely different. The feature just evolved out of necessity for all animals.
4. DNA sequences reveal the amount of genetic coding different animals have in common with each other. Primates and humans only differ in genetic makeup by a 0.5 -1.0% difference.
5. Homology refers to similarities between animals. For example, horses and donkeys have genetic coding for cytochrome C so similar that they are homologous for all but 1 amino acid in the selection we examined in class. Whales and other mammals have homologous limb structures, just that taaktalik the fish with feet had homologous structures with humans and other wrist-ed creatures.

Common Descent

We are descendants of fish.

Many other animals are also descended from fish.
Which is to say, we have a common ancestor with many animals.

The process of determining common descent consists of examining differences in amino acid sequences . For example, we examined a section of Cytochrome C protein's amino acid code. We compared the sequences of different animals, and counted the number of differences. If there are many discrepancies, then the two animals are less related. Horses and donkeys only have 1 difference, whereas horses and yeast have 44 differences. Horses and yeast have 44 differences as well, but yeast and wheat have 47 differences.
Based on our data, we can construct a cladogram.
The closer a branch is to the original animal on the cladogram, the more closely the two are related.

Osmosis Lab

For the past two days we've been learning about diffusion and osmosis.
Osmosis is a particular type of diffusion that involves water.
Diffusion is essentially the dispersion of a substance from a place with high concentration of itself to a place with low concentration. In the case of osmosis water is moving from a place of high concentration  of water (pure H20 or low molarity of solute) to a place with low concentration of water (high molarity of solute) through a semi permeable membrane.

A solution on one side of the membrane is hypertonic if has more solute particles than the other solution. The other solution would be hypotonic because it has less solute particles. To reach equilibrium/ homeostasis/ be isotonic, the hypotonic solution would send water to the hypertonic solution so that their solute concentrations average out. Water continues to move from side to side, but at the same rate so that the isotonic/ equal solute concentrations remain constant. 

Water potential describes the likelihood that water will enter a solution. the lower/ more negative it is, the higher the chance that it will be flooded. Water potential is equal to the pressure potential of the cell (so for plants it would be the cell wall pressure) plus the solute potential, which is 0 for pure water and goes increasingly negative as solute is added. Water potential is measured in bars, which are the same value as atms.

Our bodies contain water, so osmosis plays many integral roles in our organs. Our blood cells, for example, will burst if our blood contains too much water- the interiors of the blood cells become hypertonic to the blood and plasma, and because animal cells don't have cell walls to exert back pressure, the water will continue to enter the blood cell until the cell membrane rips open. The shards of burst cell could travel and lodge in bad places, or the cells could all pile up somewhere and cause an aneurysm. The opposite will happen if you are de-hydrated. Instead of bursting, your cells will shrivel up as all the water leaves the cell for the bloodstream. And the cells wouldn't be able to cary oxygen around as successfully.

We did a series of experiments on osmosis: pictures in next post

Cabbage Juice Indicator

Cabbage juice contains anthocyanidin, which is a sugar molecule attached to a cyanin molecule.
Cyanidin acts as a pH indicator because it changes color when it gains or loses H+ ions.

Color change is based on the wavelength of light that a molecule will absorb.
When the electrons of a compound are confined to one position, the wavelengths of light needed to jump energy levels are high energy. When there are many resonance structures that give the elrctrons options, then the wavelengths don’t need to be so high energy. Blue light absorption is associated with confined electrons and red light absorption with free movement.

If the cyanidin is in acidic solution and takes up the H+ ions, the wavelength absorbed by the compound will be blue, and as a result the color refracted, which we observe, will be red. If the cyanidin is in basic solution, and the H+ ions are taken from the cyanidin compound, the color we observe will be blue.

If there were to be acid rain on a red cabbage patch, the cabbage would become more red. 

WATER!

Dihydrogen Monoxide is responsible for many facts of life that we take for granted.

The beach is typically cooler than the inland regions.

The ocean is cold even when the temperature on the beach is hot.

Small bugs can walk on water.

You can slightly overfill a glass with water, and it won’t overflow.

Dry porous materials draw up water.

Ice floats.

We sweat to cool down.

It feels hotter on a hot, humid day than on a hot, dry day.

The explanations for all these things comes down to the unique molecule that is water. Water is made of two hydrogen atoms and one oxygen atom. When they bond, the oxygen atom is more electronegative (ie electron hungry) than the hydrogen atoms, so the electrons of both Hydrogens tend to spend their time around the Oxygen atom. This results in a slight positive charge on each of the hydrogens that isn’t quite a proper charge, but a positive dipole. The oxygen likewise has two negative dipoles.

So on each water molecule there are four dipoles- and because the elements in question are hydrogen and oxygen, the intermolecular bonds that are formed between the positive dipole of Hydrogen and the negative dipole of Oxygen are H-bonds.

Because of the ease with which water can break and form weak intermolecular bonds, it has a heat capacity of 4.184 joules/ gram Celsius. This means that to heat one gram of water up one degree Celsius, it takes 4.184 joules.

So:

The beach is typically cooler than the inland regions because the ocean and the water vapor from the ocean take won’t heat up as easily.

The ocean is cold even when the temperature on the beach is hot because the sand has a lower heat capacity than water does.

Small bugs walk on water because h-bonds allow for cohesion of water molecules and thus a surface tension that, when treaded upon with the fuzzy feet of small bugs, can hold the bug’s weight.

You can slightly overfill a glass with water, and it won’t overflow because water has such strong cohesive properties that it can sit on top of itself when there is no surface to adhere to. The same property can be observed on a wet penny.

You can also place a toothpick on an overfilled penny and observe the strength of water’s surface tension, which makes it easier to visualize how water bugs walk on water.

Dry porous materials draw up water because some water is attracted to the stronger bonds of the material (adhesion), and the rest of the water tags along because the water molecules are cohesive due to their h-bonds.

Ice floats because water freezes in a hexagonal lattice shape that is less dense than the h-bonded liquid structure.

We sweat to cool down because the heat that allows sweat to evaporate comes from our body.

It feels hotter on a hot, humid day than on a hot, dry day because if there is water vapor pressure in the air, it is harder for your sweat to evaporate (think boiling water in high atmospheric pressures), no matter how much body heat you have. You literally can’t cool down as efficiently. On a hot humid day, drinking water can sub in for the cooling effects of sweating.

-D