Forensics Quiz

Case: A twenty-year old man was found supine on Thompson Creak Trail with a bullet wound. The entrance of the wound was on the left lateral side 1cm above the third rib. The exit wound was 5cm above the belly button in the umbilical region. While tracing the bullet path you notice at the entrance the bullet travels in the frontal plane with a 45-degree downward angle. On inspection of the right side of the rib cage by x-ray you observe the 8th rib fractured. Fragments of the bullets are then traced to the final exit wound.

Hypothetic Situation: The young college student went out for a refreshing walk along Thompson Creak Trail. While he looked normal, he was in fact a heavy gambler, and was thousands of dollars in debt. He couldn't pay back the money he owed to people, and was planning to run away after a few days, but he didn't know that he was being watched by one of the gang members. After confirming that he was going to run away, the gang member, who was a bit taller than the college student, shot him from the left side, and thwarted his plans of running away (and killed him too.)

The leading diagnosis is the internal blood loss resulted from the bullet injuring his heart or possibly the aorta of his heart, since the entrance of the wound was on the left lateral side 1cm above the third rib.

Another possible diagnosis might be that the bullet went through his lung, which resulted in loss of air and blood clogging up his lungs. However, this possibility can be ruled out by inspecting the lungs during an autopsy. More possibilities can be that, as stated in the case, while tracing the bullet path we notice at the entrance the bullet travels in the frontal plane with a 45-degree downward angle, and the exit wound was 5cm above the belly button in the umbilical region. This means the bullet might go through his stomach and damaged his stomach. The harmful acids in his punctured stomach might corrode his other organs and tissues causing damage to his other systems in the body, which might lead to his death. The same, after an autopsy and examination of his stomach, we could rule out this possibility. 

Jell-O-- What's in it?

I've been eating Jell-O since I was a toddler, but I've never wondered what's in it. I mean, it was just colorful and wobbly joy that I used to eat. But what's in Jell-O?
   Jell-O contains gelatin, water, sweetener, artificial colors (oh dear), and flavoring. The key ingredient is the gelatin, which is a processed form of collagen, a protein found in most animals. 
   Lots of people have heard that gelatin comes from cow horns and hooves (which it sometimes does, but not mostly), but most of the collagen used to make gelatin comes from pig and cow skin and bones (I don't think I want to eat Jell-O anymore.) These animal products are ground up and treated with acids or bases to release the collagen. The mixture is boiled and the top layer of gelatin is skimmed off the surface. 
   When you dissolve the gelatin powder in hot water, you break the weak bonds that hold the collagen protein chains together. Each chain is a triple-helix that will float around in the bowl until the gelatin cools and new bonds form between the amino acids in the protein. Flavored and colored water fills in the spaces between the polymer chains, becoming trapped as the bonds become more secure. Jell-O is mostly water, but the liquid is trapped in the chains so Jell-O jiggles when you shake it (which was really fun when I used to eat it.) If you heat the Jell-O, you will break the bonds that hold the protein chains together, liquefying the gelatin again. So after researching about Jell-O a bit, I've decided to lay back on the Jell-O. 

Chapter 6 of "Your Inner Fish"

All tetrapods have one head and four limbs arranged in two pairs (for humans, arms and legs, but for other animals, just their legs), a tail, and a variety of other features. But how and why are animals and humans so similar in the embryo stage? And where did this basic body plan come from? Chapter 6 of "Your Inner Fish" explained most of this strange phenomenon.

1. Embryology:  The study of the development of an embryo from the fertilization of the ovum to the fetus stage. The study focuses on comparing different species at their early stage (for example, shark embryos and human embryos.) By comparing these early life forms, scientists are able to find the common structures of various species, and determine how some species may be related. 

2. Germ layers:  Karl Ernst Von Baer, a Russian biologist and one of the founding fathers of the study of embryos,  discovered that there are three layers in embryos (also known as germ layers). 

a. The endoderm is one of the germ layers formed during animal embryogenesis, the process by which the embryo forms and develops. Cells migrating inward along the archenteron form the inner layer of the gastrula, which develops into the endoderm. Endoderm forms many of the inner structures of our bodies, including digestive tract and numerous glands that are associated with it. 

b. The mesoderm germ layer forms in the embryos of triploblastic animals. During gastrulation, some of the cells migrate inward to contribute to the mesoderm, an additional layer between the endoderm and the ectoderm. The formation of a mesoderm led to the development of a coelom. Organs formed inside a coelom can freely move, grow, and develop independently of the body wall while fluid cushions and protects them from shocks. 

The mesoderm has several components which develop into tissues: intermediate mesoderm, paraxial mesoderm, lateral plate mesoderm, and chorda-mesoderm. The chorda-mesoderm develops into the notochord. The intermediate mesoderm develops into kidneys and gonads. The paraxial mesoderm develops into cartilage, skeletal muscle, and dermis. The lateral plate mesoderm develops into the circulatory system (including the heart and spleen), the wall of the gut, wall of the human body, and forms the tissue in between the skeleton and the muscles. 

c. The ectoderm is the outer layer of the embryo, and it forms from the embryo's epiblast. The ectoderm develops into the surface ectoderm, neural crest, and the neural tube.

The surface ectoderm develops into many parts: epidermis, hair, nails, lens of the eye, sebaceous glands, cornea, tooth enamel, and the epithelium of the mouth and nose.
The neural crest of the ectoderm develops into: peripheral nervous system, adrenal medulla, melanocytes, facial cartilage, and dentin of teeth.
The neural tube of the ectoderm develops into: brain, spinal cord, posterior pituitary, motor neurons, and retina.

More Microscope~

During class, we continued using the microscope to observe either an onion root cell or an animal cell (whitefish). We needed to find the different phases of mitosis when looking at these cells, which we mostly did. We compared the different phases that we found to ones that other groups found. For our group, we observed the onion root cell:

Microscope!!

During class, we learned how to use a microscope! By using this new microscope, we observed a dog flea and a plant cell in different magnification settings. Also, we made our own slides --- cheek cells from our cheeks. With the help of such a pro microscope, we were able to observe the cells' structures closely and could tell differences between each stage of mitosis and meiosis. 

Meiosis and Mitosis

Mitosis is the process by which a cell has previously replicated each of its chromosomes. Separates the chromosomes in its cell nucleus into two identical sets of chromosomes, each set in its own new nucleus. It is generally followed immediately by cytokinesis, which divides the nuclei, cytoplasm, organelles, and cell membrane into two cells containing roughly equal shares of these cellular components.
Mitosis and cytokinesis together define the mitotic (M) phase of the cell cycle—the division of the mother cell into two daughter cells, genetically identical to each other and to their parent cell.

• Mitosis occurs only in eukaryotic cells and the process varies in different species.
• Prokaryotic cells, which lack a nucleus, divide by a process called binary fission.
• The sequence of events is divided into stages corresponding to the completion of one set of activities and the start of the next. These stages are prophase, prometaphase, metaphase, anaphase and telophase.  

Meiosis is a special type of cell division necessary for sexual reproduction in eukaryotes. 

• The cells produced by meiosis are either gametes (the usual case in animals) or otherwise usually spores from which gametes are ultimately produced (the case in land plants). 
• In many organisms, including all animals and land plants, gametes are called sperm in males and egg cells or ova in females.
• Meiotic division occurs in two stages, meiosis I and meiosis II, dividing the cells once at each stage. The first stage begins with a diploid cell that has two copies of each type of chromosome, one from each the mother and father, called homologous chromosomes. All homologous chromosomes pair up and may exchange genetic material with each other in a process called crossing over. 
• In the second stage, each chromosome splits into two, with each half, called a sister chromatid, being separated into two new cells, which are still haploid. This occurs in both of the haploid cells formed in meiosis I. Therefore from each original cell, four genetically distinct haploid cells are produced. These cells can mature into gametes.

Genetics Part 2

Monohybrid:

A monohybrid cross is a mating between individuals who have different alleles at one genetic trait of interest. The character(s) being studied in a monohybrid cross are governed by two alleles for a single trait.

To carry out such a cross, each parent is chosen to be homozygous or true breeding for a given trait. When a cross satisfies the conditions for a monohybrid cross, it is usually detected by a characteristic distribution of second-generation (F2) offspring that is sometimes called the monohybrid ratio.

Monohybrid cross - a cross between parents that differ at a single gene pair (usually AA x aa)

Monohybrid - the offspring of two parents that are homozygous for alternate alleles of a gene pair

Generally, the monohybrid cross is used to determine the F2 generation from a pair of homozygous grandparents (one grandparent dominant, the other recessive), which results in an F1 generation that are all heterozygous. Crossing two heterozygous parents from the F1 generation results in an F2 generation that produces a 75% chance for the appearance of the dominant phenotype, of which two-thirds are heterozygous, and a 25% chance for the appearance of the recessive phenotype.

Dihybrid:

A dihybrid cross is a cross between F1 offspring of two individuals that differ in two traits of particular interest. A dihybrid cross is often used to test for dominant and recessive genes in two separate characteristics.

*Two genes that are heterozygous mix together. When two genes that are heterozygous cross over, the phenotypical ratio is 9:3:1.

Genetics Steps :D

Solving genetics problems:
Step 1: Write down information
Step 2: Parent's genotype
Step 3: Gametes * Law of segregation
Step 4: Lay out information --- make info-squares
Step 5: Calculate ratios (Genotypic and phenotypic ratios)

There are two different ways to do it: 1. Fitz's way, which is short and mathematical, and 2. Quick's way, which is longer but drawn out more clearly.

Fitz's way:

Quick's way: 

I personally like Quick's way more because I like seeing everything written out. If I went with Fitz's way, I'd worry too much about there being mistakes. 

Genetics Part 1

Gregor Johann Mendel (July 20, 1822 – January 6, 1884) was a German-speaking Silesian scientist and priest who gained posthumous fame as the founder of the new science of genetics. Mendel demonstrated that the inheritance of certain traits in pea plants follows particular patterns, now referred to as the laws of Mendelian inheritance. These laws initiated the modern science of genetics.

Law of Segregation: The two alleles for each gene separate during gamete formation. 

Law of Independent Assortment: Alleles of genes on non-homologous chromosomes assort independently during a gamete formation. 

Vocabulary

1. Pure Line - a population that breeds true for a particular trait

2. Phenotype - literally means "the form that is shown"; it is the outward, physical appearance of a particular trait

3. Dominant - the allele that expresses itself at the expense of an alternate allele; the phenotype that is expressed in the F1 generation from the cross of two pure lines

4. Recessive - an allele whose expression is suppressed in the presence of a dominant allele; the phenotype that disappears in the F1 generation from the cross of two pure lines and reappears in the F2 generation

5. Allele - one alternative form of a given allelic pair; tall and dwarf are the alleles for the height of a pea plant; more than two alleles can exist for any specific gene, but only two of them will be found within any individual

6. Allelic pair - the combination of two alleles which comprise the gene pair

7. Homozygote - an individual which contains only one allele at the allelic pair

8. Heterozygote - an individual which contains one of each member of the gene pair

9. Genotype - the specific allelic combination for a certain gene or set of genes

10. F1 - First generation offspring

11. P - Parental generation

12. Backcross - Offspring mating with parents 

* Somatic cell --- Body cell, anything but not sex cell. 

Cell division: meiosis/ 46 in total of chromosomes, 23 pairs

Operon System

Operon system makes sure that there is no energy being wasted. Operon systems only exist in prokaryotes, since eukaryotes use TATA box for the control. There are two types of operon system: 1) repressible and 2) inducible. [Repressible---on to off/ Inducible---off to on] For the pGLO lab we did in class, it was an inducible operon system. Arabinose was brought into the system from an outside source, and it was added in front of the pGLO gene. Then, it produced protein to help it grow. Yet, overtime, the bacteria would not glow anymore due to the fact that the system would create arabinase that digests away the arabinose.

Glow in the dark example! 

Operon system is a genetic regulatory system found in bacteria and their viruses in which genes coding for functionally related proteins are clustered along the DNA. This system allows protein synthesis to be controlled coordinately in response to the needs of the cell. (By providing the means to produce proteins only when and where they are required).

A typical operon consists of a group of structural genes that code for enzymes involved in a metabolic pathway, such as the biosynthesis of an amino acid. These genes are located contiguously on a stretch of DNA and are under the control of one promoter (a short segment of DNA to which the RNA polymerase binds to initiate transcription). A single unit of messenger RNA (mRNA) is transcribed from the operon and is subsequently translated into separate proteins.

The promoter is controlled by various regulatory elements that respond to environmental cues. The regulator protein can either block transcription, in which case it is referred to as a repressor protein; or as an activator protein it can stimulate transcription. Further regulation occurs in some operons: a molecule called an inducer can bind to the repressor, inactivating it; or a repressor may not be able to bind to the operator unless it is bound to another molecule, the corepressor. Some operons are under attenuator control, in which transcription is initiated but is halted before the mRNA is transcribed.

Example of how it works

Protein Synthesis

Protein synthesis has three steps: 1) Transcription from DNA to mRNA, 2) RNA processing happens where introns are cut off. Protective cap/ G-cap and poly-A-tail are added, and 3) Translation of RNA to protein. Translation happens in the ribosome.  

Transcription:

RNA Processing:

Translation: 

DNA Replication

DNA replication is the process of producing two identical copies from one original DNA molecule. This biological process occurs in all living organisms, and is the basis for biological inheritance. DNA is composed of two strands and each strand of the original DNA molecule serves as template for the production of the complementary strand, a process referred to as semiconservative replication. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication.

First of all, helicase unzips the strand and breaks hydrogen bonds. Then, RNA primase lays down RNA at the 3’ end. Afterwards, DNA poly III lays down DNA nucleotides on the leading and lagging strands. Last but not least, DNA poly I replaces the RNA with DNA, and ligase glues the lagging strand (Okazaki fragments) together using polypeptide bonds.

DNA Structure

DNA has a double helix shape, which is like a ladder twisted into a spiral. Each step of the ladder is a pair of nucleotides. Nucleotides are molecules made of deoxyribose, a sugar with 5 carbon atoms, and a phosphate group made of phosphorus and oxygen, and nitrogenous base. There are four types of nucleotide: Adenine (A), Thymine (T), Cytosine (C), and Guanine (G). The DNA ladder is made of two bases, one base coming from each leg. The bases connect in the middle: 'A' only pairs with 'T', and 'C' only pairs with 'G'. The bases are held together by hydrogen bonds. Adenine (A) and thymine (T) can pair up because they make two hydrogen bonds, and cytosine (C) and guanine (G) pair up to make three hydrogen bonds.

DNA Strand

Explanation of the Two Pictures

I. Morning Glory
   As we known, DNA is copied from the “parent” cell to the “daughter” cell. Despite the proofreading process that usually produces accurate copies, errors do occur. When an error does occur, the new combination of DNA sequences is called a mutation.
   DNA can be modified in more ways that only by random mutations. By doing so, “jumping genes” are formed --- the whole sequence of DNA that moves from one place to another over times of environmental stress. Normal morning glory favors the color of blue over the color of white. Yet, due to the different growing environment, helpful mutation occurs that causes DNA retro-transposon happens; therefore, in the picture, the morning glory contains more of the color of white than the color of blue.

Normal Morning Glory

Mutated Morning Glory

II. Handy Genes

   As mentioned in Chapter 3 of Your Inner Fish, “Our limbs exist in three dimensions: They have a top and bottom, a pinkie side and a thumb side, a base and a tip. The bones at the tips, in our fingers, are different from the bones at the shoulder. Like wise, our hands are different from our thumbs.” What DNA actually makes a pinky different from a thumb? How does our body know to develop in this way? In order to find out these answers, Randy Dahn, a researcher in Dr. Shubin’s laboratory did experiments on the embryos of sharks and skates by injecting a form of Vitamin A.

Nevertheless, in the 1950’s and 1960’s a number of biologists did amazingly creative experiments on chicken eggs to understand how the pattern of the skeleton forms. By cutting up embryos and moving around tissues, biologists were able to discover that two little patches of tissue essentially control the development of the pattern of the bones inside limbs.

   On the other hand, Mary Gasseling did another experiment that could explain why the infant’s hand in the picture looks differently. In the picture, the infant has two more extra fingers growing out from the index finger. How so? This is because of ZPA (the zone of polarizing activity, also known as the patch of tissue that control the development of the pattern of the bones inside limbs.) Although ZPA causes fingers to look different, something else inside ZPA controls how fingers form and what they look like, which is Sonic Hedgehog.

    Sonic Hedgehog is active in the ZPA tissue. If Sonic Hedgehog hasn’t turn on properly during the eighth week of one’s own development, then one either would have extra fingers or one’s fingers would look alike. Furthermore, moving a little patch of the ZPA tissue would cause the fingers to duplicate and supplying Vitamin A at the right concentration and at the right stage, fingers would form mirror-image duplication. This is why the infant’s hand looks differently in the picture.

Mutated Hand

Normal Hand

DNA Replication Enzymes

Helicase:

Helicase is a class of enzymes vital to all living organisms. Their main function is to unzip an organism's genes. Helicase is often used to separate strands of a DNA double helix or a self-annealed RNA molecule using the energy from ATP hydrolysis, a process characterized by the breaking of hydrogen bonds between annealed nucleotide bases. 

They also function to remove nucleic acid-associated proteins and catalyse homologous DNA recombination. Metabolic processes of RNA such as translation, transcription, ribosome biogenesis, RNA splicing, RNA transport, RNA editing, and RNA degradation are all facilitated by helicases. Helicase moves incrementally along one nucleic acid strand of the duplex with a directionality and processivity specific to each particular enzyme.

DNA Polymerase III:
Being the primary holoenzyme involved in replication activity, the DNA Polymerase III has proofreading capabilities that correct replication mistakes by means of exonuclease activity working 3'→5'(reads in this direction). DNA Polymerase III is a component of the replisome, which is located at the replication fork.

DNA Polymerase I:
In the replication process, DNA Polymerase I removes the RNA primer (created by Primase) from the lagging strand and fills in the necessary nucleotides between the Okazaki fragments in 5' -> 3' direction, proofreading the strand as it goes.

It is a template-dependent enzyme - it only adds nucleotides that correctly base pair with an existing DNA strand acting as a template.

RNA Primase:
RNA Primase is a type of RNA polymerase, which creates an RNA primer. DNA polymerase uses the RNA primer to replicate ssDNA.
Primase catalyses the synthesis of a short RNA segment called a primer complementary to a ssDNA template. Primase is of key importance in DNA replication because no known DNA polymerases can initiate the synthesis of a DNA strand without an initial RNA primer.  
The RNA segments are first elongated by DNA polymerase and then synthesized by primase.

Ligase:
Ligase is an enzyme that can catalyse the joining of two large molecules by forming a new chemical bond, usually with accompanying hydrolysis of a small chemical group dependent to one of the larger molecules or the enzyme catalysing the linking together of two compounds, such as enzymes.