Microevolution:changes in population

Part 1: Evolution 101

1. How do the authors of this page define microevolution? Microevolution is evolution on a small scale — within a single population. That means narrowing our focus to one branch of the tree of life.

2. How do they define a population? For animals, it's fairly easy to decide what a population is. It is a group of organisms that interbreed with each other — that is, they all share a gene pool. So for our species of beetle, that might be a group of individuals that all live on a particular mountaintop and are potential mates for one another.

--Read the section “Mechanisms of Microevolution”

3. Summarize each of the 4 mechanisms of microevolutionary change that are discussed.

Mutation: a rare process of change when a species gives birth

Migration (or genetic flow): some species who mate with a different type of specie like if some certain type of beetle mates with another type of beetle

Genetic Drift: one non mutated specie mating with a non mutated specie. One mutated specie mates with a mutated specie. one mutated and another mutated specie mate.

Natural selection: Depending on the environment a specie will mutate to survive the change in the environment.

4.  Summarize the 3 examples of microevolution that they present.

The size of the sparrow: It depends on the environment so the sparrow will have to change to survive.

coping with global warming: depending on the temperature the specie will either move to a warmer place or the offsprings will have more feathers or be much bigger.

Building resistance: for example if you were to have an infection and will have to take medication for the certain amount of days and you take it once and miss a couple days then the infection will do what ever it takes to survive so it will build resistance to that medication.

Part 2

1. Why do some guppies tend to be drabber than others? So they can hide away from predators

2. Why do some guppies tend to be more colorful? so they can mate

3. What role does color play in guppy survival? if they are a dark color it makes it easer for them to survive and if they are colorful they will have offsprings

4. Explain the push and pull that the environment (including predators) has on the

coloration of guppies in Endler’s pools. 

If the environment is dark and there is a dark guppies they they can hid from predators and if the predators are dark in a dark environment the guppies can be caught by the predators because the guppies will not be able to see the predators but if the guppies are colorful in a dark environment they are less likely to survive because they are easier to be seen by predators and if the predators are colorful in a dark environment they probably won't survive very long because they won't be able to catch any guppies because they will have already seen the predator and they get away. vice versa if they lived in a brighter more colorful environment

Results of your pairwise alignment comparing the beta globin gene in humans and in chimps

1. Data about the alignment can be found below the blue/black alignment chart. How many base pairs (bp) are

there in the beta globin gene for:

a. The chimp? 600 basepair or bp

b. The human? 626 bp

2. A blue asterisk indicates that the nucleotides (bp) in both sequences are the same, we say they are conserved. What percentage of the beta globin sequence is conserved in chimps and humans? (Don’t include the insertion at the beginning of the human gene). This percentage is often reported as a similarity “score” below the alignment.
99% similarity score

3. Would you expect the protein structure to be highly similar or markedly different in the chimp and the human?Explain.
I would expect the protein structure would be highly similar in the chimp and humans because of the 99% similarity score

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Results of your pairwise alignment comparing the beta globin gene in humans and in chickens:

1. What is the percentage of sequence conservation between the beta globin gene in chickens and humans?  57%

2. Looking at the two pairwise alignments you have performed, would you expect the beta globin protein found in humans to be more similar to that found in chickens or that found in chimps? Explain.

The beta goblin protein found in humans would be more similar in chimps than in chickens because of the alignment similarity

3. Do the results achieved by running these alignments support the results on evolutionary relationships determined by scientists using anatomical homology (similarities)? Explain.

since it shows such a similarly comparison to a chimp I do believe that this can be evidence on evolutionary relationships.

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Results of your multiple sequence alignment comparing the beta globin gene in a variety of animal species:

1. Examine the Unrooted Tree produced.

Record the species at the end of each branch on the unrooted tree shown below.

2. Based on the information in the unrooted tree:

a. Which two species appear to be most closely related to each other? Explain your choice.

Human and Chimp the reason for this is we have thumbs and on the unrooted tree the chimp and human are really close together.

b. Which two species seem to be the least closely related to each other? Explain your choice.

Chicken and the mouse because mice have fur while chickens have feathers, chickens have a beak while a mouse has a snout.

3. Comparative evolutionary distance between species is indicated by the length of the clades they are on. Give

the comparative evolutionary distance (by percentage similarity “score”) between:

a. The mouse and human 79%

b. The wallaby and the human 75%

c. The chimp and the human 99%

Comment on the significance of these results given your knowledge of mammalian groups.

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Results of your Rooted Phylogenetic Tree:
1. Examine your Rooted Phylogenetic Tree and record the species at the end of each branch.

2. Based on this tree diagram, which species is/are most closely related to:

a. The goldfish: chicken

b. The mouse: human

3. Homology is a term used to refer to a feature in two or more species that is similar because of descent; it evolved from the same feature in the last common ancestor of the species. Hence, similarity in DNA or protein sequences between individuals of the same species or among different species is referred to as sequence homology.  Which two species in the tree above share greatest homology with respect to the beta globin gene?

The two species that share the greatest homology with respect to the beta global gene is the chimp and the human

4. A node is a branch point representing a divergence event from a common ancestor. Which two species have the most ancestral nodes (divergence events) in the tree above? Explain your answer giving the number of nodes leading to these species.

chimp, mouse, and human 3 ancestral nodes

5. Looking at the phylogenetic tree above, which two organisms:

a. Diverged from their common ancestor most recently? chimp and human

b. Diverged from their common ancestor least recently? chimp and mouse

6. Draw a modified phylogenetic tree to show how the tree above might change if the beta globin gene for a kangaroo was added to the multiple sequence alignment.


7. It is important to understand that the phylogenetic trees you generated using bioinformatics tools are based on sequence data alone. While sequence relatedness can be very powerful as a predictor of the relatedness of species, other methods must be used in addition to sequence homology, to determine evolutionary relationships. Briefly describe 3 other methods that you think might be used to determine evolutionary relationships.
● how they look

● bone structure

●what they eat

DNA fingerprinting: Using DNA for identification

Part 1:

1. In your opinion, what role (if any) did newspaper stories and editorials have in the outcome of the original trial of Dr. Sam Sheppard? it was kind of misleading because they were just bashing on sheppard because he was the husband
   
   

Go back to the Killer’s Trail homepage and select ”Create a DNA Fingerprint.”

Read about the crime and the suspects then go on to part 2. Answer the following questions about the technique as you go through the simulation:

2. What is the function of the restriction enzymes in DNA fingerprinting? to cut the DNA into different sections of the DNA to figure out the code

3. What is the function of  the agarose gel electrophoresis step? Act as a molecular strainer allowing smaller pieces of DNA to move through more easily than larger pieces

4. Why is a nylon membrane used to blot the DNA? To make it easier to work with the agarose gel

5. What does a dark spot on the X-ray film indicate? nylon membranes

Part 2: 

1. What evidence was initially used to convict Cotton? They sketched the man in how Jennifer saw him

2. What did the DNA evidence show? The DNA evidences showed that there was no match to cotton but showed a match to an inmate that confessed to the crime

3. How could DNA fingerprinting be used to prevent a false conviction if a case like this was being tried today? DNA can not lie

4. What percentage of convicts are unjustly convicted of sexual assault cases, according to Neufeld and Scheck? 25 percent

5. The O.J. Simpson trial was one of the most visible trials that attempted to use DNA evidence.  In the end, the DNA evidence was not satisfying to the jury, who acquitted Simpson.  What do Neufeld and Scheck believe about the impact of the O.J. Simpson trial on the use of DNA evidence? the way they used to gather the evidence is by swiping the blood around the murder scene but the evidence team didn't swipe the glove entirely there was also lack of a knife.

Personalized genomics: Do you want to know?

As of now scientists are able to read your entire genetic code knowing this you are able to know what kind of diseases you could develop. 

Knowing this would you pay to see your entire genetic code to see what kind of diseases you could have in the future even if it is a diseases that you can not stop from developing like Huntington disease or Alzheimers? 

This can also revolutionize medicine because the genetic code shows us how it develops and by seeing this chance we can prevent the gene and prevent it from changing.

not only can this be a very useful tool but it can run insurance companies out of business because we can get paid for a disease we don't really have yet and their is a slight possibility of not having the disease because as of know we can't tell the exact time it is going to develop.

but also seeing your genetic code can change the way you treat yourself for something like cancer and this can also lead a person to live in fear because of the possibility that you could get the disease, if it is a disease that runs in the family you will have a choice to have kids or not knowing that they have a chance to get the disease.

this can also ruin peoples lives because their can be people who steal your DNA from just a sample of saliva you leave by drinking or eating anything at a restaurant and if you decide to run for anything  political they can use any deficiency that you may have in the future.

knowing all this information I ask this again would you really want to know your genetic code?

Bacterial ID lab

1. As the medical technician in charge of this investigation, what are you trying to determine about the tissue sample provided to you?

I am trying to determine the sequence and the identity of the tissue sample

2. How did you prepare the DNA to be used in this investigation?

Extract the bacterial colony, use a small pipette and transfer it into a micro centrifuge tube, then put it into a heating bath and put it into a centrifuge after that transfer it into a PCR tube.

3. Describe how PCR is used to make copies of DNA sequences. Use the animation and notebook entries in the PCR Amplification step to guide your answer. Note that you may replay the animation as needed.

The heat separates the DNA then it cools it and the DNA makes a copy then it repeats over and over again.

4. Summarize the technique used to purify the PCR product.

Use a buffer solution put it into the column then add PCR, the Other PCR tubes are cooling while you load the column  into the centrifuge for 15 minutes then invert the column into a new column and add more buffer solution into it get rid of the 1st column and the 2nd column will be put into a centrifuge wait 2min then get rid of the column and now the PCR product has been purified.

5. What is produced during the sequencing prep PCR run? Use the animation and notebook as needed in thinking through your answer. 
The DNA pieces in each tube start in the same primer but end with a different nucleotide showing the construction of the DNA.

6. Describe how the automatic sequencer determines the sequences of the PCR products.
Performs gel electrophoresis on the DNA in each tube separating molecules

based on their size

7. What does BLAST stand for? BLAST stands for Basic Local Alignment Search Tool

8. What conclusions did you make using the results of the BLAST search?  Did these conclusions support a clinical diagnosis for the patient (what disease did they have)?
I got a disease called Bartonella Henselae and it did support a clinical diagnosis for the patient.

Bartonella Henselae: Various species of Bartonella that are pathogenic to humans are transmitted via a vector, or directly from an animal reservoir. For example, B. bacilliformis via sandflies causes Oroya fever; B. quintana via body lice causes trench fever; and B. henselae via cats causes cat scratch disease (CSD). CSD typically manifests as swellings of the lymph glands, possibly with skin lesions at the site of inoculation and possibly accompanied by fever, fatigue, and other symptoms. Immunocompromised patients may be particularly susceptible and can develop a different disease, bacillary angiomatosis, as a result of infection by B. henselae or B. quintana.

Human Chromosomes and Genetic Diseases

Part One:
What are the three main parts of a chromosome, as viewed under a microscope?
The three main parts of a chromosome is the p arm (short arm of chromosome) and q arm (long arm of chromosome) and the centromere (center of chromosome)

List at least four human diseases that have been mapped to the X chromosome.
Rett syndrome, Fragile x syndrome, Alport syndrome, Duchenne muscular dystrophy.


Part Two:
What disease did you choose and what gene or genes are associated with this disease?
DiGeorge syndrome
On what chromosome is this gene(s) located?
chromosome 22

• When was the disease first reported in the scientific literature (earliest citation)?

  DiGeorge syndrome was first reported in the scientific literature by an error in recombination at meiosis.

• What are some of the clinical symptoms of this disease?

  Some symptoms of this disease is cardiac problems, speech impediment.

• What lab findings (gene function or biochemical data) are associated with the disease?

  causes by a large deletion in chromosome 22

• What type of inheritance governs this disease?

  The type of inheritance that governs this disease is at birth and can vary greatly between individuals.

Eugenics Project

All this information is from http://www.eugenicsarchive.org/eugenics/

Talents: if you were musically talented or even slightly musically talented they would make a baby and most of the time the kid would be musically talented and some were not and some were slightly musically talented and the reason they did this was because they wanted to see if talents really did come through eugenics and as you see it can be a high possibility if a parent did have a musical talent

The first image #39 the second image #

criminality: Back then scientists say that the reason for crime was because of defective genes even though they did not deny that it may be because of their poor social and cultural background might contribute to crime they just decided to blame it on their biological background.

I found this on the criminality tab and the image #1072 the second image #936

Birth and population control: In the 20th century the rate of population grew even more especially when it came to the poor and as a result they tried reducing the population by making birth control but their was a little debate in making birth control but it eventually happened.

Some pictures as proof of overpopulation in the poor the picture number is #1734

Create a baby Genetics

In this lab we compared our genotype to see what are baby would look like. If one of us had the same trait or different we would flip a coin and we would put the dominate or recessive genotype and it would determine what they would have (For an example if my partner didn't have a dimple and I had a dimple we would flip a coin and see if it would be a dominate genotype or not). After the genotype process we both drew how our baby would look like by just looking at the baby's phenotype which we drew separately without looking at each others paper.

my drawing of what he might look like

My partners drawing of what he might look like but he didn't finish

Harry potter Genetics

 In this lab I learned how to determine genotypes and phenotypes to see their chances of them having this trait from their parents.

Stem cells and Regeneration: Can we regrow body parts?

Should humans be able to regenerate body parts? Why or why not? 
 as of now humans can't regrow body parts but yes we should be able regenerate body parts but we need more stem cells because we just don't have enough cells to keep on regenerating and if we are successful we would need a growth factor but while regenerating a body part we can have a risk of getting cancer because of the continuos cell growing.

Meiosis, Mitosis, and Cloning

Meiosis: A cell that produces 4 daughter nuclei and is only used for sexual reproduction that requires 2 nuclei divisions

Mitosis: A cell that produces 2 daughter nuclei and is only for asexual reproduction and growth that requires only 1 nuclei division

Cloning: Cloning requires only your cell and it copies it exactly

Differences between Meiosis, Mitosis, and Cloning:

Meiosis:

• Requires 2 nuclear divisions, 
• Chromosomes synapse and cross over, 
• Centromeres Survive one anaphase, 
• Halves chromosome number, 
• Producers 4 daughter nuclei, 
• Produces daughter cells genetically different from parent and each other, 
• Used only for sexual reproduction 

Mitosis:

• Requires 1 nuclear division, 
• Chromosomes do not synapse nor cross over, 
• Centromeres dissolve in mitotic anaphase, 
• Preservers chromosome number, 
• Produces 2 daughter nuclei, 
• Produces daughter cells genetically identical from parent and each other,
• Used for asexual reproduction and growth 

Cloning:

• so far we can't clone humans yet, but we have cloned a sheep
• use small pipets to grab the cell and extract the nuclei from the cell and transfer it to another cell 

Genetics

This link is about genetics

https://docs.google.com/drawings/d/1RLK4LBfoO1Acf19Em-hluluSGGhTV8d5cGPu3M8HZYc/edit

Stem cells

Cell-based therapies: Treatment in which stem cells are induced to differentiate into the specific cell type required to repair damaged or destroyed cells or tissues.

Differentiation: The process whereby an unspecialized embryonic cell acquires the features of a specialized cell such as a heart, liver, or muscle cell. Differentiation is controlled by the interaction of a cell's genes with the physical and chemical conditions outside the cell, usually through signaling pathways involving proteins embedded in the cell surface.

Embryonic stem cell line: Embryonic stem cells, which have been cultured under in vitro conditions that allow proliferation without differentiation for months to years.

In Vitro: Latin for "in glass;" in a laboratory dish or test tube; an artificial environment.

Plasticity: the adaptability of an organism to changes in its environment or differences between its various habitats.

Pluripotent: The state of a single cell that is capable of differentiating into all tissues of an organism, but not alone capable of sustaining full organismal development.

Proliferation: Expansion of the number of cells by the continuous division of single cells into two identical daughter cells.

Therapeutic cloning: The process of using somatic cell nuclear transfer (SCNT) to produce cells that exactly match a patient. By combining a patient's somatic cell nucleus and an enucleated egg, a scientist may harvest embryonic stem cells from the resulting embryo that can be used to generate tissues that match a patient's body. This means the tissues created are unlikely to be rejected by the patient's immune system. See also Somatic cell nuclear transfer (SCNT).

1. What are the unique properties of all stem cells?  Explain in your own words what each property means.

The unique properties of all the stem cells is that it can divide and renew themselves over a long period of time.

Stem cells: Cells with a ability to divide and give rise to specialized cells

Proliferate: Expansion of cells by division making a identical sister cell

Long term self renewal: The ability of stem cells to replicate them cells into the same non specialized cells over a long period of time.

Embryonic stem cells: Embryo that is capable of dividing without waiting a long period of time.

Adult stem cells: any body cell other than gametes (egg or sperm)

Cell division: A method where a single cell will divide into two cells

Human embryonic stem cells: A type of pluripotent stem cell derived from the inner cell

Signals: Internal and external that controls the structure and function of the cell.

Genes: A functional unit of DNA that is found on chromosomes

Microenvironment: The nutrients and the growth of the cell

Epigenetic: can turn genes on and off

Cell-Based Therapies: A treatment to repair damaged cells

hematopoietic stem cell: A stem cell that rises white and red blood cells

2. What are the two main kinds of stem cells used by researchers?  What are the major differences between the two types in terms of their sources and usefulness to researchers?  Give examples of possible uses for each type of stem cell.

The two main kinds of stem cells used by researchers are the embryonic stem cells and the adult stem cells.

Embryonic stem cells: forms muscle cells, nerve cells, and many other cell types.

Adult stem cells: Can repair dying cells and regenerate damaged tissues

3. List some of the diseases that scientists think may be treated using stem cell research and suggest how stem cells might be used to treat each disease.

The diseases that scientists think may be treated by using stem cell research is  

spinal cord injury: Inject human adult bone marrow into the spine.

stroke: Inject adult stem cells into the heart wall

4. What are the necessary characteristics that laboratory-manipulated stem cells will need to have in order to be successfully used in cell-based therapies (what will stem cells need to be able to do)?

Stem cells must be able to regenerate the damaged cells or tissues and need to stay healthy.

Cited source: http://stemcells.nih.gov/info/Pages/Default.aspx

Onion root lab

1. What percent of cells were in interphase? 55%

2. What percent were in mitosis (total of every phase except interphase)? 44%

3. Which phase of mitosis (not interphase) takes the longest according to your data? Why do you think that is? 

Prophase would take the longest according to my data because it may take a while for the nucleus to condense and then it will take a while for the Microtubules to become attached to the kinetochores.

4. How can you recognize a cell in interphase? 

The middle of cell is a big black circle

5. How can you recognize a cell in metaphase? 

The spindle fibers are stretching out and attached to the chromosome which the chromosomes will start to form a line.

6. How might you figure out how long (in minutes and/or seconds) each phase of the cell cycle takes based on the data from these onion root cells? Explain your logic and show your calculations and results below. 

Interphase is the longest step in the cell cycle so it may take 20 minutes

Prophase and that would be the second longest step which takes 27.78% of the cell cycle and that may take 5 minutes

Metaphase should take 1 minute because there are few steps and its only 8.33%

Anaphase may take a 30 seconds because the spindle fibers would attach to the chromosomes and it is only 5.56% of the cell cycle.

Telophase is the quickest step so it should take a 10 seconds because the spindle fibers will grab the chromosomes and start to divide the cell and that its only 2.78% of the cell cycle.

7. Produce a pie chart in Create-a-Graph that shows the relative lengths of each stage of the cell cycle in these cells including interphase and each stage of mitosis.

Cell cycle

How do cells determine wether to divide or not to divide? 
The way it determines to divide is by a signal to divide or not to divide.

What are the mechanics of the cell cycle and how is it controlled?
It is controlled by the proteins in the cell.

How does cancer develop? 
it develops when a cell decides to divide on its own without a signal to divide.

What roll do proto-oncogenes and tumor suppresser play in controlling the cell cycle?
The roll proto-oncogenes play is that they stimulate cell division and the accelerator.

How do cancer treatments work and why they are not good for the body?
 cancer treatments use high doses of radiation targeted at the cancer cells. The reason they are not good for the body is because of the radiation.

Why does a multicellular organism need to control and coordinate cell division?  
It needs to control and coordinate cell division because some cells don't need to divide all the time.

What might be the consequences of uncontrolled cell division in a multicellular organism?
The consequences of uncontrolled cell division in a multicellular organism is that it can cause mutation and the cells won't divide.

What does it mean when we say that there are several “checkpoints” that occur during the cell cycle?
it means that cells have to go through a process to be able to divide.

Give an example of an external signal that regulates cell division and explain how it works.
Internal controls: Protein molecules vary concentrations during the cell cycle.

Compare and contrast the functions of proto-oncogenes and tumor suppressor genes.Give an example of each and explain why mutations in these genes can lead to cancer.
Proto-oncogenes: stimulates cell division, go sign for the cell cycle, mutated cells always on.  

Proto-oncogenes can lead to cancer because the mutated genes will still be active and will keep on dividing.

Tumor suppressor genes: Inhibits cell division, the brake peddle of the cell cycle, keeps mutated cells off.

Tumor suppressor genes can lead to cancer because if it does not work properly it can cause it to grow out of control.