Population Dynamics

The “Oh Deer!” activity during Wednesday’s biology class demonstrated the dynamic nature of population within an ecosystem. The activity was designed to simulate the impact on the deer population of a forest under different environmental conditions. The factors that affect the population of a species were broken down into density dependent and density independent factors. Density dependent factors are the factors in which the density of the species plays a significant role in shaping the population size of that species. Population independent factor on the other hand are factors that change the population with no correlation to the density of that particular species.

During the first part of the activity each student was assigned a role in the ecosystem as either a deer or a resource. At first the deer population is very tiny while the resources are abundant; no competition existed amongst the deer. As resources was consumed and more deer were born the resources starts to deplete and competition became increasingly intense. At a certain point the resources in the forest could not support the large population and deer died off and became resources for future deer. An equilibrium was reached where the resources is just enough to maintain the deer population. The competition for limited amount of resources is an example of density dependent factor in population dynamics. A few outside forces was introduced into the ecosystem such as flood, drought and other natural disasters. Each natural disaster was followed by a decline in the deer population. These factors are density independent factors.

In the second part of the activity predators were introduced into the ecosystem and the effect of predation on population was simulated. Similar to the relationship between the deer and forest resources, the wolves had little competition when the wolf population was small compared to the deer’s population and the competition escalated as less deer were available and more competitors entered the hunt.  This phenomenon is once again due to the density dependant factor of intraspecies competition. When the wolf population was not controlled and increased rapidly the deer population in that area was decimated and was eventually driven to extinction. In real life the deer would probably migrate somewhere else to avoid total annihilation, this phenomenon was also evident in our activity when some deer went off the grid to escape the wolves.  

The Study of Metabolism: Biological Thermodynamics

The three Laws of Thermodynamics govern the universe and everything it contains. These three laws are fundamental to our understanding of the universe, and in this particular case they help us to understand the various biological processes.

The First Law states that the total energy of the universe is always constant. Energy could neither be created nor destroyed, it could only be transformed. This is also known as the Law of conservation of energy.

The Second Law states that in any open system the total entropy always increases, in simpler terms the universe is always becoming more chaotic, disorderly.

The Third Law states that at all motion stops at when temperature reaches absolute zero, the entropy would also be zero.

When understanding metabolisms only the first two laws are of interest to us.

 Every metabolic process whether it is hunting for food, cellular respiration, or reproducing offspring requires energy. Since energy could not be created at will according to the First Law, organisms must obtain energy from somewhere. Plants take light energy from the sun and transform it into chemical energy in the form of carbohydrates. Animals take the chemical energy stored in plant and transform it into kinetic energy and heat. The First Law of Thermodynamics explains why I need to eat in order to do anything, but why do I need energy when I am not moving, not thinking, not digesting? This is where the Second Law of Thermodynamics comes in. Every spontaneous event always increases the entropy of the system, which means the entropy level in our body always increases just by existing in the universe. This means our body gets more disorganized, our cells breakdown, and we age. Our body is like a china plate, and time, which could be understood as increase in entropy is like a hammer that breaks the plate. The plate shatters into many pieces as it follows the Second Law of Thermodynamics. We try to glue the pieces back together but no matter how hard we try the plate would not return to its unbroken state. As time goes on and the plate is shattered again and again, it will eventually reach a state beyond repair. Our body is constantly undergoing wear and tear and it is constantly being repaired which of course requires energy and nutrient. Just like the china plate our body will reach its limit one day and then we die. Just as a side note this is also the reason why our universe will end in 500 billion years. But what can you do, it is the way of the universe.

Facts about carbohydrates

-Carbohydrates are simply chemicals compounds composed of carbon, hydrogen, and oxygen

-The formula for carbohydrates follows a ratio of 1 carbon:2 hydrogen:1 oxygen

-Carbohydrates are the primary source of energy for our body and makes up the majority of our diet

-There are three groups of carbohydrates, or saccharides as referred to in biochemistry: monosaccharide, polysaccharide, and oligosaccharide

Monosaccharide

-Monosaccharaides are the simplest of all the carbohydrates, these simple sugars are either aldehydes or ketones with hydroxyl groups; i.e. glucose and fructose

-These simple sugar are the building block for more complex carbohydrates and essential building blocks for nucleic acids

-The monosaccharaides are separated by the number of carbon molecules; a monosaccharide with 5 carbons is called a pentose, and hexose with 6 carbons

Oligosaccharide and Polysaccharide

-The simple sugars could join together to form more complex carbohydrates through the formation of glycosidic bonds

-Condensation is the process of forming glycosidic bonds, in which the hydroxyl group of two sugars join together and splitting out water molecule as by-product

-Hydrolysis is the process in which a complex sugar reacts with water to produce two or more simpler sugars

-Oligosaccharides are carbohydrates formed when a few sugars are joined together, typically between two to ten

-Sucrose is a disaccharide formed by a glucose molecule and a fructose molecule, it is commonly known as table sugar

-Oligosaccharides has many function, including forming glycoproteins and glycolipids

-Oligosaccharides play important role in cell-to-cell recognition

 -Polysaccharides are carbohydrate chains of lots of simple sugars

-Polysaccharides could be linear in shape (i.e. amylose) or branched (i.e. glycogen)

-Polysaccharides act as energy storage units in organisms and provide structural support

-Amylose is a linear glucose polymer found in plants as energy storage; because it is linear it is harder to digest and takes up less space

-Glycogen is a branched glucose polymer found in animals, its structure provides rapid release of glucose which is then transformed into energy

-Cellulose is another linear glucose polymer found in plants, it is the main material for cell walls, and it is very hard to digest in our body and is the major source of our dietary fibre

biotechnology

Restriction Endonucleases

-commonly used tool in molecular biology, aka restriction enzymes

-molecular scissors that can cut double-stranded DNA at a specific base-pair sequence

-each restriction enzyme recognizes characteristic sequence of nucleotides that is known as its recognition site

-recognition sites are usually 4-8 pairs long and are usually a pair of complementary palindromic sequence

-disrupts the phosphodiester bonds with hydrolysis reaction

-there are sticky ends which has unpaired nucleotides, and blunt ends which means all nucleotides are paired

-many restriction enzymes comes from bacteria, and its purpose was to disrupt virus DNA sequence, these enzymes are named after the bacteria of origin

Gel electrophoresis

-a process of isolating desired excised gene fragment from the rest

-DNA is negatively charged and each nucleotide which contain a phosphate group carries a charge of -1

-the charge to mass ratio between nucleotides is relatively consistent

-the DNA fragment travel at different speed through the gel, the shorter it is the faster it moves

-the DNA fragments are dyed and become visible so that the electrical currents can be turned off before they reach the positive terminal

-the DNA fragments are later stained and each set of fragment has a particular banding pattern

Plasmid

-plasmids are used to express a particularly desirable gene such as insulin

-plasmids are small, circular, double-stranded DNA molecules lacking a protein coat

-plasmid’s size ranges from 1000 to 200000 base pairs.

-bacteria benefit from plasmid because plasmid usually contain gene that codes for useful functions such as antibiotic, resistance to heavy metals, and industrious chemicals

-the copy numbers of the plasmid, which is the number of a particular plasmid within a bacteria, the higher the copy number the stronger the expression of that particular gene

Transformation

-the introduction of DNA from another source

-plasmids are used to carry desired genes into a host cell

-if a bacterium readily takes up foreign DNA it is described as a competent cell

-calcium chloride is used to chemically alter the cell membrane, freezing the bacteria physically alters the cell membrane making is easier for bacteria to pick up foreign DNA

-selective plating is used to isolate bacteria with the recombinant DNA, if the bacteria grows in a environment with the specific antibiotics it contains the recombinant DNA

Compare and Contrast: Replication, Transcription, Translation

	Initiation	Elongation	Termination
Replication	Enzymes involved: Helicase unwinds the DNA strands. Single-strand binding proteins (SSBP) keeps the two untwisted strands separate, and protects it from damage. Gyrase releases the tension and cut the DNA. Primase, an enzyme that codes for RNA (primer) kicks starts the elongation process.	DNA polymerase III helps catalyze, and is responsible for the elongation of new DNA strand from 5 prime to 3 prime. Two daughter strands are replicated simultaneously. The leading strand elongates into the fork, the lagging strands grows away from the fork. Each segment on the lagging strand is called an Okazaki fragment.	DNA polymerase I is responsible for proof reading the replicated sequence and replacing RNA with DNA. Ligase acts as the glue at the end of the replication process and joins the fragments of DNA together.
Transcription	The upstream of the template DNA strand contains the promoter, which signals the start of transcription. The promoter region contains transcription factors, which recognizes the TATA box which initiates the transcription process. The transcription factors (TF), TATA box, and RNA polymerase II forms the initiation complex.	RNA polymerase II is responsible for the elongation portion of the transcription process. RNA polymerase II untwist the double helicase of DNA, reads the DNA sequence from the template and transcribe it into a RNA strand with corresponding sequences, and lastly it joins the DNA back together.	Once the RNA polymerase II encounters the TTATT sequence on the antisense DNA strand the transcription will come to an end with the formation of the AAUAA sequence on the RNA transcript. Around 50-250 adenine nucleotides are added to the pre-mRNA, the poly (A) tail. A modified guanine is added to the front of the sequence, called the 5, cap which protects the RNA sequence. A large portion of the RNA transcript is cut from the strand, the introns which have little function. The remaining sequences are called the exons. This process is called RNA splicing.
Translation	At the start of the translation process tRNA or transfer RNA reads the codon from the mRNA and forms the anticodon. Each anticodon consists of three bases. The last base on the anticodon is usually flexible, for example UAC and UAU could code for the same amino acid. This reduces the effect of small errors along the translation process.	The first codon that is recognized and translated is AUG; this is the universal starting codon. After the starting codon is read the ribosome reads the codons 3 bases at once and forms a polypeptide chain with the correct amino acid sequence.	The ribosome will encounter three stop codons, which do not code for amino acids. These three codons are UGA, UAG, and UAA. A protein called the release factor will help with the release of the polypeptide chain once the translation has come to a halt.

Big Names in the Field of Genetics

The study of genetics has brought great scientific advancement to the field of biology. The discovery of DNA as the building block of life in the last century gave scientists keys to unlock the mysteries of life and could potentially answer fundamental questions of our existence. The discipline of genetics was built upon the works of brilliant minds spanning many generations.

Gregor Mendel (1822-1884)

It is impossible to introduce the study of genetics without mentioning Gregor Mendel who many consider as the “Father of Genetics”.  Mendel was born in the Austrian Empire (now the Czech Republic) and studied practical and theoretical philosophy and physics in the University of Olomouc as a young man. After graduation Mendel became a priest and worked in a monastery, and it is during this time that he made his greatest discoveries and kicked start the study of genetics. Mendel conducted studies on the pea plants in the monastery’s garden and noticed interesting phenomenon between the pea plants of successive generations. He noticed that when two pea plants with different traits were cross-bred the second generation pea plants only took one of the two traits. However when the second generation plants were cross-bred the third generation plants exhibits both traits from the first generation plants and the traits existed in a fixed ration. This discovery led to Mendel’s Law of Segregation and Law of Independent Assortment which laid down groundwork for modern genetics. Gregor Mendel published these findings in 1866.

Oswald Avery (1877-1955)

By the early 1900s scientists already know that there is a link between parents and offspring and that some traits and characteristics were passed down from one generation to the next but the exact nature of such a linkage was still a mystery, this is where Oswald Avery comes in. Avery was a Canadian-born American medical researcher who was one of the pioneers in immunochemistry. In 1944 Avery studied strains of bacteria and managed to transfer disease causing material from one strain of bacteria to another previously harmless strain, the material that was moved was the nucleic acid. Avery wrote in his 1944 paper that genes and chromosomes were made of DNA and this is the hereditary material.

Erwin Chargaff (1905-2002)

Erwin Chargaff was an Austrian biochemist who later moved to the United States. Chargaff read Oswald Avery’s work on DNA and was inspired to work out the chemical composition of DNA. At the time it was hypothesized that DNA consists of four bases adenine, thymine, cytosine, and guanine. Chargaff discovered that in any species the ratio of adenine and thymine were roughly equal, so was cytosine and guanine. This was later known as Chargaff’s Rule. He concluded that there exists a complementary relationship between the pairs. Chargaff did not realize the significance of his work; it is based on his work that Francis Crick and James Watson were able to develop the double helix model for DNA.

Rosalind Franklin (1920-1958) 

Rosalind Franklin was a British biophysicist and crystallographer. In 1951 Franklin was appointed to King’s College London to work on the structure of DNA. Franklin was an expert at crystallography; she used X-Ray diffraction to photograph structure of DNA. In the 1940s and 50s Franklin along several other scientist were working on DNA at the college, including Francis Crick, James Watson, and Maurice Wilkins. An x-shaped graph of DNA taken by Franklin was shown to Crick and Watson which helped them to develop the double helix model for DNA. Rosalind Franklin is also known as the “dark lady of DNA” mainly because her work was not recognized and she died an early death from ovarian cancer due to prolonged exposure to X-ray. Maurice Wilkins later took credit for her work and shared a Nobel Prize of Physiology or Medicine with Crick and Watson in 1962. 

Francis Crick (1916-2004) and James Watson (1928- )

By the 1950s scientist were convinced that DNA is the genetic material and a race was on to build the first model of DNA. In the 1953 English molecular biologist Francis Crick and American molecular biologist/geneticist James Watson came up with the double helix model for DNA and unravelled the blueprint of life. Previous ladder model of DNA could not work in real life as it was easily broken by water, it was Watson and Crick that discovered the secret to DNA’s structure was the twist in the ladder. In a paper they published wrote: "It has not escaped our notice that the specific pairing (of purine and pyrimidine bases) that we have postulated immediately suggests a possible copying mechanism for the genetic material."  In 1962 Watson, Crick and Maurice Wilkins shared the noble prize for Physiology or Medicine.