Summative 1 Central Dogma and Penguins DNA is stored in the nucleus and mitochondria of the cell

Summative 1
Central Dogma and Penguins
DNA is stored in the nucleus and mitochondria of the cell. A DNA strand contains and a deoxyribose sugar which is connected to the nucleotide bases (A,C,G,T). The base Adenine (A) always links with Thymine (T), and Guanine (G) links with Cytosine (C). The sugar and phosphate make up the 5′-3′ and 3′-5′ structure of the strands, as shown by the image.
In order for the genes to be created into a protein, the “language” must be changed. This is where transcription occurs. A strand of DNA is converted into a strand of RNA, all surrounded by the nuclear envelope. During this conversion, Uracil (U) replaces Thymine (T). mRNA, short for Messenger RNA, takes the converted genes out of the nucleus into the cytoplasm, and to the ribosome in the rough endoplasmic reticulum. Within the cytoplasm, there are also vacuoles, a storage for the cell. Next, the RNA is created into a protein. mRNA is read in triplets, or codons.

Each of those codons represents a specific amino acid. The tRNA carries anticodon, which are the corresponding links of the codons, brings the amino acid based on the codons. The ribosome always starts with the codon AUG (TAC), which would be methionine. It ends with the stop codons, UGA, UAA, UAG. We can use this codon wheel (right) to determine the amino acid created as a product of each codon. A protein is created and the lysosome is responsible for breaking down the protein to do it’s specific “trait”. It’s transported out of the cell membrane by the Golgi Apparatus and the Smooth Endoplasmic Reticulum. The difference between this and the RER is that the RER contains ribosomes on it’s surface. An example is Cytochrome B, a protein that is a part of the electron transport chain and creating ATP.
Mutations can often occur in DNA cells that can change the amino acid and protein. A point mutation or substitution can occur, where a base is replaced by another, or a frameshift, where a nucleotide is added or another is deleted. A point mutation can still result in the same amino acid as a result, which is known as a silent mutation. Viruses can go through the central dogma process by causing a mutation in the DNA sequence. This allows the virus to multiply and make more viruses.

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My animal is the Adelie Penguin (Pygoscelis adeliae), and it’s relatives are the Chinstrap Penguin and the Gentoo Penguin. Their Cytochrome B similarity in DNA are very similar according to the data collected in NCBI. We can see that the Adelie is 98% similar to the Gentoo, and 97% to the Chinstrap. With the Gentoo Penguin, there were a few mutations that occurred. Looking only at the second row of the DNA sequence, there are 3 mutations, all substitutions. A Methionine is substituted for a Threonine, a Valine for a Methionine, and a Phenylalanine for a Leucine. These, in turn, might change the protein that is created, causing the difference in the two animals we see today

(Adelie: Left)
(Gentoo: Right)

Next, the Chinstrap Penguin. The DNA mutations are very similar than the Gentoo Penguin. The only difference in the second row of the sequence an Alanine is substituted for a Threonine. There are ther mutations, however, such as a Leucine for an Isoleucine, and an Isoleucine for a Threonine. Since there are more mutations, it could explain how this looks more distinct from the Adelie Penguin.

Summative 2

We know that in Prokaryotic cells, DNA goes to mRNA to a protein. However, Eukaryotic cells have a slightly longer process. According to the image, RNA has an extra step in developing, known as pre-mRNA. Not all DNA is used to create specific protein. To know which will and which won’t is the operon’s job. The operon contains a promoter and an operator, both used to control the genes becoming proteins. The operator can turn specific genes needed on or off. Promoters include TATA boxes in Eukaryotic cells indicate where genes need to be decoded in a gene sequence.
The genes turned on by the operon are known as exons and the off-genes are known as introns in the gene splicing process. Exons are the genes that will go through transcription and translation and will be crucial in creating the protein. We can use the Expasy Tool that will automatically turn any DNA sequence into RNA and locate which genes are exons and which are introns. The translated DNA sequence of my Adelie Penguin in Expasy highlights the exons in red. Exons will either be coded or non-coded. The difference is that they will have 60% more C and G bases over A and T bases.
These concepts lead to the overall cycle of zygote becoming a full human. As a zygote, all genes in the DNA are turned off. Mitosis occurs 6 times to create 64 totipotent cells. These are stem with a blank sheet and no job to do. Operons turn on specific genes to give totipotent cells a certain type of job (e.g a skin cell), making the cell pluripotent. When more gene splicing occurs and more genes are turned on, the pluripotent cells become multipotent, and have a specific job (skin cell in a certain area of the body). These specialized multipotent cells are somatic as they are for the living organism and not for reproduction. These stem cells are currently being studied to treat different diseases. Recent studies show that stem cell researchers are looking into transplantations for patients with severe scleroderma, a disease that hardens the skin and tissue around the body.

Bibliography
Sullivan, K. M., Goldmuntz, E. A., Keyes-Elstein, L., McSweeney, P. A., Pinckney, A., Welch, B., … & Castina, S. (2018). Myeloablative Autologous Stem-Cell Transplantation for Severe Scleroderma. New England Journal of Medicine, 378(1), 35-47.

Summative 3

Human Karyotype

Adelie Penguin (2n=96)
Arrow – DSG1 for webbed feet (Q arm of 18)

Gene
Location
Purpose
Associated Diseases
Insulin
P-arm of chromosome 11 (15.5)
Help produce hormone- insulin
Diabetes
Lactase
Q-arm of chromosome 2
(21.3)
Help create enzyme – lactase (helps digest lactose)
Lactose Intolerant
MSTN Gene
Q-arm of chromosome 2
(32.2)
Helps create protein – myostatin
Muscle Hypertrophy
SCNN1A gene
P-arm of chromosome 12
(13.31)
Helps create protein – ENaC (channels sodium in to cells
Pseudohypoaldosteronism type 1
RCAN1 gene
Q-arm of chromosome 21 (22.12)
Interacts with calcineurin A
Arthritis
BRCA2
Q-arm of chromosome 13 (13.1)
Tumor suppressor
Cancer

The table above shows genes that create specific proteins for different purposes, and
where on the human karyotype they are located. The second karyotype is the closest representation of the karyotype of the Adelie Penguin. The q-arm of the 18th chromosome contains the gene for their feet. This gene is also in humans and monkeys.
Mitosis vs. Meiosis
The obvious difference between mitosis and meiosis is that mitosis create somatic cells and meiosis creates germline cells. Mitosis also ends up with 2 identical cells while meiosis results in 4 different cells.

Mitosis
Both
Meiosis
Creates Diploids (2n)
Somatic Cells
Cells made are the same
Helps grow and heal
Make daughter cells
Organize/Divide Chromosomes
Copy DNA
Germline Cells
Cells made are different
Genetic Diversity
Crossing over
Mitosis starts off with doubling the DNA from 46 to 92. When the cell splits, each cell will have an even 46 chromosome. These somatic cells are for surviving, the first goal for any organism. 4 stages occur during mitosis: Prophase, Metaphase, Anaphase, Telophase. When the stingy chromatin copy and become chromosomes, they line up and are split. 2 new nucleuses are created. Each pair of chromatids are the exact same as the original. The results are 2 identical cells with the same chromosomes.
Meiosis occurs twice to make 4 different cells. However, when the chromosomes line up during Metaphase, they pair up first as TETRADs. During this, the chromosome pairs crossover. The genes are switched for part of each chromosome. Then they split during Anaphase. This results in 2 different cells, and then meiosis II occurs, and 4 different cells are created. The pairing up, crossing over, and “cut and shuffling” of the chromosome causes genetic variation and results in different sex cells.
Chromosomal Disorder
Incorrect distribution of chromosomes results in disorders such as Down’s Syndrome. Also known as trisomy 21, a baby with Down’s Syndrome had nondisjunction occur in the 21st chromosome. Trisomy is when the 4 chromosomes aren’t separated right, and there are 3 in one cell and 1 in the other. This can occur during meiosis I or meiosis II. During Anaphase, after the chromosomes pair up, they do not separate. When the daughter cells are created, one cell has an extra chromosome. If this happens in meiosis I, there will be two copies with 3 chromosome and two copies with 1. If it happens during meiosis II, there will only be one cell with 3 chromosomes and one with 1 chromosome.

Mitosis in Adelie Penguin
Arrows refer to DSG1 gene
DSG1 gene Q-arm Chromosome 18
(Green: Dad; Pink: Mom)
Prophase: Chromosomes Doubled

Metaphase: Chromosomes line up

Anaphase: Chromosomes split

Telophase: Diploids split

2 identical cells

Summative 4
Restriction enzymes are the big idea of DNA fingerprinting. Restriction enzymes cut DNA into different pieces based on size in base pairs. The restriction enzyme EcoRI cuts where the AATT base pairs meet. This allows the DNA to be read and compared to DNA found at a crime scene. DNA is negatively charged, so it is on the negative side of the gel electrophoresis box with the black lead. It will attract to the positive side, or the red side. The electrical currents make the DNA move from the negative to positive; the bigger DNA pieces with more base pairs will travel a smaller distance, while the smaller pieces travel the farthest. DNA was used to determine if Thomas Schwartz was guilty for first-degree murder, according to the Supreme Court of Minnesota.
https://scholar.google.com/scholar_case?case=1711603818802243408;q=DNA+fingerprinting;hl=en;as_sdt=400006
http://www.nydailynews.com/news/crime/dna-linked-o-simpson-nicole-ron-goldman-murders-article-1.27607
a. Create a list of steps to make the Gel.
Put 50 ml of buffer in beaker
Put ½ g of agrose
Mix
Heat on “4” setting
Stop before boil (bubbles,thermometer)
Mix to cool
Pour into mold
b. Create a list of steps on how to collect AND extract DNA from a cell. http://learn.genetics.utah.edu/content/labs/extraction/
Collect cheek cells into tube (Standard, Crime, Suspect 1, 2, 3)
Add lysis solution in tube
Put into warm water
Add concentrated salt to tube
Place it into centrifuge
Place a tube containing water on the other side to balance the centrifuge
Remove the top liquid (bottom contains protein and debris) and place into clean tube
Add some isopropyl alcohol
Put in centrifuge again with water on other side
c. How to prepare your chamber, add your casting tray and fill the wells with DNA.and from the first link
Pour melted agrose in casting tray
Place comb in and wait for it to cool
Remove to make wells in gel
Pour liquid buffer in GE box
Place the tray into the box
Use a pipette to get some loading buffer and put in DNA sample
Suck some of the DNA sample and put in well of gel
Use DNA size standard and put in next well.
The FBI CODIS is a big database that contains DNA profiles of anyone ever commited for a crime. This is similar to the NCBI database containing DNA profiles of animals. According to Gina Kolata of The New York Times, scientists say that the chance of DNA fingerprinting causing a wrong accusation is extremely low. However Alexandra Ossola states that the different locations that scientists focus on can become weak in the sample, so finding a match in DNA become difficult. These circumstances can end up putting the wrong person in jail. This suggests that DNA always has the chance to screw up. There are also ethical questions about DNA fingerprinting. Some say it could invade someone’s privacy, and also the fairness of taking someone’s DNA is a concern. From my viewpoint, DNA testing in general could be used for reasons that aren’t for justice. Paternity tests are an example of unfair DNA usage.

https://www.popsci.com/dna-evidence-not-foolproof

Summative 5
Law of Dominance
Webbed feet
FF FF

FF
FF
FF
FF
FF
FF

Geno: 4:0
Pheno: 4:0
Penguins have a 100% chance of having webbed feet. This shows no evidence of changing in the future, as the pedigree represents that all the generations are homozygous dominant.

Incomplete Dominance
Color of Webbed Feet
P p

P
PP
Pp
p
Pp
pp

Geno: 1:2:1
Pheno: 1:2:1

This punnett square shows the mix of penguin feet colors with a heterozygote. The pedigree shows the
trait of homozygous dominant and recessive. The different colors of webbed feet could result in even more colors in the future (i.e pinkish feet could be a mix of homozygous dominant (red) and recessive (white)).

Codominance
Fur Color
B b

B
BB
Bb
b
Bb
bb

Geno: 1:2:1
Pheno: 1:2:1

This penguin will have both black and white (dominant and recessive) genes showing. This could mean that in the future, if a homozygous recessive or homozygous dominant gene was passed on, it could result in all-black or white penguins.

Sex-linked traits
Beak color (Red beak female with black beak male)
Homozygous Dominant-Red
Homozygous Recessive-Black
XB XB

Xb
XBXb
XBXb
Y
XBY
XBY

50% – Female with red beak
50% – Male with red beak
Males can get black beaks
https://www.coursehero.com/file/p4fanfm2/In-penguins-red-beak-color-is-a-sex-linked-recessive-trait-The-normal/

Epistasis (albino)
Color
P P

p
Pp
Pp
p
Pp
Pp
Homozygous Dominant- Black belly
Homozygous recessive-Gray belly Heterozygous – Albino (“colorless”)
Geno: 4:0
Pheno: 4:0
http://www.chegg.com/homework-help/questions-and-answers/2-penguins-belly-color-determined-two-genes-labeled-g-two-alleles-allele-allows-production-q5654149

The following are evidence for other types of genetic inheritance that were not found in research of the penguin:

Dihybrid Evidence: Evidence not related to Animal
Human eye shape and nose shape
Mom: AAbb Dad: AaBB
Homozygous Dominant: (A) – Big eyes (B)- Big nose
Homozygous Recessive (a) – Small eyes (b)-Small nose
Heterozygous-Dominant wins
Ab Ab Ab Ab

AB
AABb
AABb
AABb
AABb
aB
AaBb
AaBb
AaBb
AaBb
AB
AABb
AABb
AABb
AABb
aB
AaBb
AaBb
AaBb
AaBb

100% – Big eyes Big nose

Polygenic Inheritance
Skin color
Mom: AAbbCc Dad: AaBBcc
AbC Abc AbC Abc AbC Abc AbC Abc

ABc
AABbCc
AABbcc
AABbCc
AABbcc
AABbCc
AABbcc
AABbCc
AABbcc
ABc
AABbCc
AABbcc
AABbCc
AABbcc
AABbCc
AABbcc
AABbCc
AABbcc
ABc
AABbCc
AABbcc
AABbCc
AABbcc
AABbCc
AABbcc
AABbCc
AABbcc
ABc
AABbCc
AABbcc
AABbCc
AABbcc
AABbCc
AABbcc
AABbCc
AABbcc
aBc
AaBbCc
AaBbcc
AaBbCc
AaBbcc
AaBbCc
AaBbcc
AaBbCc
AaBbcc
aBc
AaBbCc
AaBbcc
AaBbCc
AaBbcc
AaBbCc
AaBbcc
AaBbCc
AaBbcc
aBc
AaBbCc
AaBbcc
AaBbCc
AaBbcc
AaBbCc
AaBbcc
AaBbCc
AaBbcc
aBc
AaBbCc
AaBbcc
AaBbCc
AaBbcc
AaBbCc
AaBbcc
AaBbCc
AaBbcc
Homozygous Dominant: Very Dark Homozygous Recessive: Very Light

Animal Comparison – Adelie Penguin

Evidence of Evolution in Penguins
Penguin’s closest relative in cladogram = alligator

Genetic Drift: Natural or human caused death
Penguins are isolated from alligators, so they reproduce their own genes that are evolved from the cold environment with each other,
According to National Geographic, global warming causes depletions of many of the penguin’s prey, and also shrinks their habitat.
Gene Flow: Migration or Isolation
Most penguins are isolated to the Antarctica, but some live in southern Australia, Africa and South America.
Penguins living in those areas only reproduce with the penguins in their environment.
Carrying Capacity
Adelie Penguins are not endangered yet, but global warming is causing the carrying capacity to decrease over time.

Summative 7
Homology

Penguin Skeleton Bird Brain

The skeletal system are homologous because they are very similar in structure. Their wings are very similar, but birds can fly and penguins can’t which could explain why penguins might need a slightly longer neck while birds can fly to any height.

Penguin Heart Dolphin Heart (90% similarity)

Both are mammals or birds so they have 4 chambered hearts, but penguins swim and walk on land requiring more energy.

Major Differences in Organization
Brain
Penguin Dissected Sheep Human Brain

Penguins have a larger olfactory lobe while sheep have a larger temporal lobe. Both give them advantages in their environment which will be discussed later.

Heart
Penguin Sheep Human

All 3 are mammals, so they have 4 chambered hearts. Oxygenated and deoxygenated blood are kept separate. A 3 chambered heart would have some oxygenated, deoxygenated, and mixed.

Evolution
Brain

Hammerhead Shark (74% similar)

Penguins have a large olfactory lobe and cerebellum that suggests it’s movement capabilities and sense of smell.
The large hammerhead hold the olfactory lobe, which also explains the shark’s reliance on its sense of smell.

Heart 84% similar

The penguin moves a lot more and requires a lot more energy so its aorta is extended to allow blood to flow quicker. Snakes have a smaller aorta because it can move its heart to flow blood throughout its entire body.

Rat: Systems

Digestive System
The dissected rat holds a similar digestive system with some differences. Humans have a gallbladder to store bile; however, rats do not have a gallbladder. This may be because rats have a large diet (in other words, they eat a lot) and so they need bile to quickly digest food so it can go straight to the small intestine, which means there will not be excess bile to store and the gallbladder is not needed.
Penguins
Penguins have a crop: a pouch that can hold food in case the stomach is full or the food needs to be regurgitated. A penguin’s stomach also has 2 parts: a proventriculus–digestion enzymes breaking down food–and a gizzard, where food is grinded to be digested. This system work around the penguin’s diet that composes of mostly crustaceans.

Summative 8
Macroevolution – Billions of Years in the making
Summative 7 proved that penguins were homologous with birds when it comes to their bone structure. According to the timeline below and the ones created, the first bird appeared about 160-200 million years ago, suggesting a common ancestor. They can also date back to fish and water based animals (510 million years ago), being 89% similar in DNA with the manatee (also mostly in bone structure), and reptiles (320 million years ago) such as the snakes and turtles according to summative 6. A huge similarity was found through research from Atlas Obscura by Cara Giaimo, that they have similar movements due to their metabolism. This causes similar angle turns when they move. Gene flow could be a reason that differentiated penguins the most because of their habitats in cold areas. Penguins evolved from the first penguins, but mostly from the bird and other animals
Microevolution – Generations
Penguins are known as flightless birds. The explanation could be that as they slowly became more water based, they relied less on the need to fly and have wings, which could be why the wings in it’s skeleton could be getting smaller due to it possibly becoming a vestigial structure; however, they still have their wings because it helps them swim.
An example of life in general evolving is antibiotic resistance. The antibiotics we used in the lab were not killing the bacteria effectively, which is evidence that bacteria is evolving to become more resistant to antibiotics, hence the name.
Those that are anti-evolutionists say that there is no evidence that explains how life originally started, or how cells were created as prokaryotes, and how they claimed a nucleus. An example of evolution is the Miller Urey Experiment. They found that raw materials could create amino acids, used for creating proteins. These proteins could have been given a job and evolved themselves. For example, proteins able to break down for energy from light or glucose could become photosynthesis and cellular respiration by chlorophylls and the mitochondria. Also, the endosymbiotic theory by Lynn Margulis showed that bacteria and cells can consume other cells and bacteria; ultimately creating eukaryotic cells. These cells began to divide up and create multiple cells; cells were beginning to have different jobs: some managing movement, some managing breaking down for energy, and other systems. Multiple cells will create tissues, and then organs and organ systems to create an organism.

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