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.

Chapter 6--Survival of the Sickest

Edward Jenner, a country doctor in Gloucestershine, England, created the first vaccine in the end of the 18th century. He discovered that milk maids who had cowpox were immune to smallpox. Thus, he tested out his assumption by giving a harmless version of cowpox to a group of young boys. It turns out that they all were able to produce antibodies to protect themselves from smallpox. The first vaccine was then created.
   By creating the first vaccine, bioscientists found that genes could change. Each human beings starts off with exactly the same number of cells as the simplest form of bacteria, one single cell --- zygote. Inside of zygote has every single genetic instruction. These instructions carry 3 billion pairs of nucleotides (DNA base pairs) that have 30,000 genes. The genes of a person are organized in 23 pairs of chromosomes. One set of chromosomes comes from the mother, and the other set comes from the father. Yet, less than 3% of DNA contains instructions for building cells. The rest of DNA (about 97%) are noncoding DNA. Scientists changed the name of "Junk DNA" into noncoding DNA because the 97% of DNA are not directly involved in creating protein doesn't necessarily mean that it is junk, or non-usable. Later the author mentioned mitochondria, the microscopic workhorses. They function as powering plants, producing energy (called ATP) to run cells. They were mostly likely once independent, parasitic bacteria that evolved mutually beneficial relationship with some of pre-mammal evolutionary predecessors. They have their own inheritable DNA, mtDNA. Back to the point that genes could change, genetic changes are the product of accidental mutations caused by random and rare errors. Mutation happened when an error gets through and forms a new combination of DNA sequences( rearranging DNA). Mutations also occur when organisms are exposed to radiation or powerful chemicals. Outbreaks and pandemics are caused by either antigenic drift, which is when mutations occur in DNA of a virus, or antigenic shift, which is when a virus acquires new genes from a related strain.
    Last but not least, the author covered another topic, the "Jumping genes". In recent years, scientists have discovered that DNA can be modified in more ways that only by random mutations. In 1950's, Barbara McClintock discovered "jumping genes" --- whole sequence of DNA that moved from one place to another over times of environmental stress. She discovered this by observing the genetic of corn, in which the plants seemed to be undergoes a kind of intentional mutation. There are two types of "jumping genes"(transposons). The first one is DNA transposons, which perform a cut-and-paste process. The second one is DNA retrotransposons, which perform a copy-and-paste process. Moreover, large portions of our noncoding DNA/ Junk DNA are made of jumping genes. On the other hand, retroviruses are made of RNA, and can be written into DNA. 

Hardy-Weinberg

In class, we learned about the Hardy-Weinberg law of genetic equilibrium and studied the relationship between evolution and changes in allele frequency by using our own class to represent a sample population. 

During this lab, we used the class as a population, the allele frequency of a gene controlling the ability to taste the chemical PTC could be estimated. If the person could taste the bitterness, then it is evident that the person has the presence of a dominant allele in either the homozygous condition (AA)  or the heterzygous condition (Aa). If the person could not taste the chemical, then the person has evidence of the presence of homozygous recessive alleles (aa).

p= the frequency of the dominant allele in the population

q= the frequency of the recessive allele 

p^2 +2pq+q^2 = 1 

p+q= 1 

p^2= AA

2pq= Aa

q^2= aa   

Hardy and Weinberg states that if 5 conditions are met, the population's allele and genotype frequencies will remain constant from generation to generation, meaning maintaining equilibrium. 

These conditions include: 

1. The breeding population has to be large. The effect of chance on changes in allele frequencies is thereby greatly reduced. 

2. Mating is random. Individuals show no mating preference for a particular phenotype. 

3. There is no mutation of the alleles. No alteration in the DNA sequence of alleles. 

4. No differential migration occurs. No immigration or emigration. 

5. There is no selection. All genotypes have an equal chance of surviving and reproducing. 

Shells in Class!!

For today's class, we chose partners for an activity involving shells. My partner was Linfei, and we were given a bag of shells that were collected from the same beach. We were to separate and group these shells by different characteristics, such as size, color, patterns, etc. We did this a few time. The first time, Linfei and I separated the shells by their patterns, like whether there were stripes or not. The second time, we separated them by whether the lines on the shells were vertical or horizontal, no matter their shape. For the last time, we divided the shells into different groups by size.

Halfway through, we realized that many of these shells had holes in them, mostly on the top. These holes indicated that the animals that had lived inside the shells were attacked by other organisms from outside of the shells, who could use their tongues as drills to dig holes on the shells. The shells were then empty because the outside organism had eaten them. However, difference in shells was not an evidence of evolution, but more as result of mutation. Based on different environment, physical appearances of shells would alter, possibly due to trying to camouflage. Due to the mutations, shells were able to pass down the genes that helped them to survive and reproduce.