Oh, Deer! Population Study Game

On Thursday we played a game in class called Oh, Deer! that was meant to simulate the effects that various factors have on the population levels of an imaginary population of deer.

In this activity, a portion of the class was assigned to be deer and a portion was assigned to be the resources (food, water, and shelter). At the start of each round, each deer had to randomly pick a resource that they needed for that round, and each person on the resource side of the game had to choose a resource that they would become for that particular round. Then each deer had to rush over to the resource side to pick up the resource that they chose. Upon picking up the resource, the person representing the resource became a deer to signify how the deer reproduced as a result of its needs being satisfied. If a deer was unable to find the resource  it desired, then it "died" and became a resource.

As the game progressed, increased competition for resources over successive rounds caused the deer population levels to reach a maximum and then fluctuate between the maximum level and a lower level. This was an example of density-dependent factors affecting population change.

Also, after a few rounds various scenarios were imposed on the resources, such as a forest fire (no shelter), and drought (no water) to simulate density independent factors affecting population change. Later during the game, individuals were chosen to act as the deer's predators. When a deer was caught by a predator, it became a predator to signify the predators reproducing after eating the deer.

This activity was meant to demonstrate the difference between density-dependent factors and density-independent factors affecting population change.

Density-dependent factors are factors influencing population changes that have a greater impact as population density increases or decreases. Some examples of density-dependent factors include:

• Intraspecific competition for resources. as population density increases, competition for resources also increases. This in turn causes the population density to decrease in subsequent generations.
• Predation. A higher population density of a prey species makes it easier for its predators to find and catch the prey. This keeps the prey population in check, since the higher the prey density, the more prey caught and eaten by predators, and the lower the prey density, the less prey caught and eaten.  
• Disease. A higher population density means that pathogens are able to pass from host to host with greater ease than in a lower population density environment.
• Allee effect. When the density of a population becomes too low, then the individuals in the population may have difficulties finding mates to reproduce with. This can cause the population to die out.

Conversely, density-independent factors are factors that influence population changes regardless of population density. Some exampes of density-independent factors include:

• extreme temperatures and weather conditions
• pesticide use
• natural disasters

This information was found on pages 671-675 of the Nelson Biology 12 textbook.

 

Photosynthesis and Cellular Respiration Poster-Making Activity

Here are two panorama shots of the photosynthesis and cellular respiration poster-making activity that we did last week.

The Krebs Cycle

- Also known as the tricarboxylic acid cycle (TCA cycle), or the citric acid cycle

- Discovered in 1937 by Sir Hans Krebs, a biochemist working at the University of Sheffield in England

- Eight-step process, each step catalyzed by a specific enzyme; cyclic because oxaloacetate is the product of the last step as well as the reactant in the first step

- Overall chemical equation for the Krebs cycle: oxaloacetate + acetyl-CoA + ADP + Pi + 3NAD⁺ + FAD → CoA + ATP + 3NADH + 3H⁺ + FADH2 + 2CO2 + oxaloacetate


- By the end of the Krebs cycle, the original glucose molecule is entirely consumed. The 6 carbon atoms of the original glucose molecule leave the process as 6 low-energy CO2 molecules. The energy of the glucose is preserved and stored in the form of 4 ATP molecules (2 from glycolysis, 2 from Krebs cycle), and 12 reduced coenzymes (2 NADH from glycolysis, 2 NADH from pyruvate oxidation, 6 NADH from the Krebs cycle, and 2 FADH2 from the Krebs cycle). Most of the free energy stored in NADH and FADH2 will eventually be transferred to ATP through processes called electron transport and chemiosmosis.


Steps of the Krebs Cycle:

1. The acetyl group (2-C) of acetyl-CoA condenses with oxaloacetate (4-C) to form citrate (6-C).
2. Citrate (6-C) is rearranged to isocitrate (6-C).
3. Isocitrate (6-C) converted to a-ketoglutarate (5-C) by losing a CO2 and two hydrogen atoms that reduce NAD⁺ to NADH.
4. a-ketoglutarate (5-C) is converted to succinyl-CoA (4-C). A CO2 is removed, coenzyme A is added, and two hydrogen atoms reduce NAD⁺ to NADH.
5. Succinyl CoA (4-C) is converted to succinate (4-C). ATP is formed by substrate level phosphorylation, and coenzyme A is released.
6. Succinate (4-C) is converted to fumarate (4-C). 2 hydrogen atoms reduce FAD to  FADH2.
7. Fumarate (4-C) is converted to malate (4-C) by the addition of H2O.
8. Malate (4-C) is converted to oxaloacetate (4-C). 2 hydrogen atoms reduce NAD⁺ to NADH. The cycle repeats.

Key Features of the Krebs Cycle:

- Since two acetyl-CoA molecules are formed from one glucose molecule, the cycle occurs twice for each molecule of glucose processed.


- In step 1, acetyl-CoA enters the cycle and reacts with a molecule of oxaloacetate (OAA) to produce a molecule of citrate. In this reaction, OAA (4-C) is converted into citrate (6-C) by adding the 2-C acetyl group of acetyl-CoA, releasing CoA, which is recycled. Also, OAA has 2 carboxyl groups and citrate has 3 carboxyl groups.


- Energy is harvested in steps 3, 4, 5, 6, and 8.


- In steps 3, 4, and 8, NAD⁺ is reduced to NADH.


- In step 5, ATP is formed by substrate-level phosphorylation. A phosphate from the mitochondrial matrix displaces CoA from succinyl-CoA. The phosphate is then transferred to guanosine diphosphate (GDP) to form guanosine triphosphate (GTP). Next, phosphate condenses with ADP, forming ATP. Overall, free energy is transferred from succinyl-CoA to ATP.


- Energy is harvested in step 6. However, reaction is not exergonic enough to reduce NAD⁺ to NADH. Instead, free energy is stored by reducing FAD to FADH2, a step closely related to the electron transport chain in mitochondria.


- Last 4 carbon atoms of the original glucose leave as CO2 in steps 3 and 4 (two Krebs cycles to process 1 glucose). The CO2 molecules diffuse out of the mitochondrion and the cell as metabolic waste.

Enzyme Lab Results

Factor tested: temperature

Trial #	Temperature of Substrate (degrees C)	Initial Volume (mL)	Final Volume (mL)	Change in Volume (mL)	Time (seconds)
1	30	105	230	125	40.9
2	22	230	350	120	82.6
3	10	350	480	130	102.6

Metabolism and the Laws of Thermodynamics

The Three Laws of Thermodynamics and how they apply to metabolism are described below:

1. The Conservation of Energy. The amount of energy in the universe is constant. Energy cannot be created or destroyed but may be converted from one form to another. 

The First Law applies to metabolism in the sense that energy is not free. For example, if the body needs to do a certain amount of work - let's say 5 kJ - the body needs to consume 5 kJ of chemical energy in the form of food to do the 5 kJ of work required. Any energy that is released by an exergonic reaction is absorbed by the surroundings. Conversely, any energy that is stored by an endergonic reaction causes a commensurate decrease in energy of the surroundings.

2. The Law of Entropy. The entropy in an isolated system increases with any changes that occur. All spontaneous events act to increase total entropy.

Entropy is a measure of the randomness or disorder in a collection of objects or energy. Everything in the universe favours an increase in entropy. Therefore, reactions that produce an increase in entropy are favoured over reactions that produce a decrease in entropy, and the metabolic processes in living things are no exception. Living organisms obey the Second Law of Thermodynamics. When they use anabolic processes to make complex ordered structures like proteins and DNA, they are creating order out of chaos. However, these processes must be accompanied by an even greater disorder caused by energy-yielding catabolic processes. For example, a child lifting a potato chip to his mouth results in an increase in gravitational potential energy and a decrease in entropy. The child obtains the necessary free energy for this action through the entropy-producing catabolic reactions of digestion and cellular respiration. In the end, the entropy produced by the metabolic processes is greater than the decrease in entropy produced by moving the potato chip to the mouth, resulting in a net increase in the entropy of the universe. In conclusion, "living organisms create order out of chaos in a local area of the universe at the expense of creating a greater amount of disorder in the universe as a whole."

3. Absolute Zero. Absolute zero is the temperature (-273°C) at which all thermal kinetic energy ceases. Nothing can be colder than absolute zero. 

Metabolism is unable to proceed at extremely low temperatures close to absolute zero because of the fact that all molecular motion ceases, making chemical reaction unable to occur. Also, enzymes are unable to function at extremely high and extremely low temperatures. 

20 Things You Should Know About Carbohydrates

- Carbohydrates are compounds containing carbon, hydrogen, and oxygen in the ratio (CH₂O)n

- Carbohydrate is a synonym for sugar

- Monosaccharides: simple sugars with multiple OH groups. Based on # of carbons, a monosaccharide is a triose, tetrose, pentose, or hexose. Disaccharide: 2 monosaccharides covalently linked. Oligosaccharides: a few monosaccharides covalently linked. Polysaccharides: polymer consisting of chains of monosaccharide or disaccharide units.

- A monosaccharide can be a aldose (having an aldehyde group at one end) or a ketose (having a keto group, usually at C2)

- Pentoses and hexoses can form rings as ketone or aldehyde reacts with OH group.

- Special type of bond called glycosidic bond joins two carbohydrate molecules: (R-OH + HO-R' ---> R-O-R' + H₂O)

- Condensation (dehydration synthesis) reactions join together smaller sugar molecules to form larger, more complex sugar molecules by forming a glycosidic bond between the smaller sugar molecules resulting in the release of one water molecule per glycosidic bond formed as a product.

- Hydrolysis reactions split complex sugar molecules by adding a water molecule to each glycosidic bond, causing the bond to break and form hydroxyl groups on both product molecules.

- alpha linkage is shaped like "A" or "V", beta linkage is shaped like " / " or " \ "

- Common disaccharides include: maltose [glucose + glucose with a(1→4) glycosidic bond], lactose [galactose + glucose with B(1→4) bond], sucrose [glucose + fructose with a(1→2) bond]

- Plants store glucose in polymer form as amylose or amylopectin, collectively called starch. Glucose storage in polymer form minimizes osmotic effects.

- Amylose is a glucose polymer with a(1→4) linkages. It adopts a helical structure.

- The end of a polysaccharide with an anomeric C1 not involved in a glycosidic bond is called the reducing end.

- Amylopectin is a glucose polymer with mainly a(1→4) linkages, but also has branches formed by a(1→6) linkages. Branches produce a compact structure and provide multiple chain ends at which enzymatic cleavage can occur.

- Glycogen, the glucose storage polymer in animals, is similar to amylopectin, but it has more a(1→6) branches. The highly branched structure allows the rapid release of glucose. The ability to rapidly mobilize glucose is more important in animals than in plants (ex. during strenuous physical activity).

- Cellulose, the material in plant cell walls, consists of long linear chains of glucose with B(1→4) linkages. In cellulose, every other glucose is flipped over due to beta linkages. This promotes intra-chain and inter-chain H-bonds and Van der Waals interactions that cause cellulose chains to be straight and rigid, and pack with a crystalline arrangement in bundles called microfibrils.

- Multisubunit Cellulose Synthase complexes in the plasma membrane produce very strong microfibrils consisting of 36 parallel, interacting cellulose chains. Cellulose gives strength and rigidity to plant cell walls, making them able to withstand high hydrostatic pressure gradients and prevent osmotic swelling.

- Oligosaccharides are sugars that are often covalently attached to proteins or membrane lipids. May be linear or branched chains.

- Lectins are glycoproteins (proteins that contain oligosaccharide chains covalently bonded to polypeptide side chains) that recognize and bind to specific oligosaccharides.

- Selectins are proteins in the plasma membrane with lectin-like domains that protrude on the outer surface of mammalian cells. They are involved in cell-cell recognition and binding.

Section 6.1 - Biotechnological Tools and Techniques + Section 6.2 - Genetic Engineering (text p.278-294)

These 2 sections in our textbook covered 4 important topics: restriction endonucleases, gel electrophoresis, plasmids, and transformation.

Restriction Endonucleases

• Restriction endonucleases (aka restriction enzymes) - enzymes that are able to cleave double-stranded DNA into fragments at specific sequences, known as recognition sites
• Recognition site - a specific sequence within double-stranded DNA, usually palindromic and consisting of 4 to 8 nucleotides, that a restriction enzyme recognizes and cleaves
• Restriction endonucleases produce DNA fragments with both sticky ends and blunt ends.
• Sticky ends - fragment ends of a DNA molecule with short single-stranded overhangs, resulting from cleavage by a restriction enzyme. These are more useful to molecular biologists, since they can be joined more easily to other sticky-end fragments produced by the same restriction endonuclease.
• Blunt ends - fragment end of a DNA molecule that are fully base paired
• Frequency of cuts of a restriction endonuclease depends on the length of their recognition sites. The more base pairs there are in the recognition site, the lower the frequency of cuts.
• Restriction enzymes are produced from bacteria, who use them to defend against the foreign DNA of viruses.

Gel Electrophoresis

• Gel electrophoresis - separation of charged molecules on the basis of size by sorting through a gel meshwork
• Each nucleotide has the same charge-to-mass ratio. The only difference between fragments of DNA of differing lengths is the number of nucleotides.
• Gel electrophoresis is like a molecular sieve. A shorter fragment will travel through the gel faster because it is able to navigate through the pores of the gel more easily. Longer fragments travel more slowly through the gel because they have a harder time moving through the pores of the gel.
• Solution containing DNA fragments are placed in a well in the gel. Gel consists of a buffer containing electrolytes and agarose, or polyacrylamide. Using direct current, a negative charge is placed at the end of the gel where the wells are, and a positive charge is placed at the opposite end of the gel. DNA will migrate down towards the positively charged electrode, with the shorter fragments migrating faster than the longer ones.
• After process is complete, gel is stained. Most commonly used stain is ethidium bromide, a molecule that fluoresces under UV light. Size of fragments can be determined using a molecular marker as a standard. Desired fragments can also be excised out of the gel for further study.
• Also applied to proteins, using polyacrylamide gels because they have smaller pores and proteins are generally smaller in size than nucleic acids.

Plasmids

• Plasmids are small circular pieces of DNA that can exit and enter bacterial cells. Using bacterial enzymes and ribosomes, DNA contained in plasmids can be replicated and expressed.
• Bacteria benefit from presence of plasmids. Plasmids carry genes for antibiotic resistance, resistance to toxic heavy metals, and the ability to break down certain chemicals. Relationship between bacteria and plasmids is endosymbiotic.
• Plasmids have a copy number - the number of copies of a particular plasmid found in a bacterial cell. More copies of a plasmid lead to more protein being synthesized.
• Artificial plasmids may be engineered to contain a multiple-cloning site - a region in the plasmid that has been engineered to contain recognition sites of a number of restriction endonucleases. Recognition sites are present only once, so only one cut can be made in the DNA.
• If foreign gene was excised using the same restriction enzyme, it will have the same complementary ends as the cut plasmid. When placed together, the sticky fragments will anneal. The foreign gene will permanently become part of the plasmid after the phosphodiester bonds are re-established with DNA ligase. Plasmid is now recombinant DNA. It can be introduced into bacterial cells, where it replicates to form many copies, thereby cloning the gene.

Transformation

• Transformation - introduction of foreign DNA, usually by a plasmid or virus, into a bacterial cell
• Plasmids can be used as vectors - vehicles by which DNA may be introduced into host cells
• Competent cell - a cell that readily takes up foreign DNA. Most bacteria are not naturally competent, but can be chemically induced to become so by being treated with a solution of calcium chloride at 0 degC, adding the plasmids, and then subjecting the solution to a quick heat shock treatment at 42 degC for 90 seconds, creating a draft that sweeps the plasmids into the bacterial cells.
• Selective plating is a method used to isolate cells with recombinant DNA. The plasmid vector also contains an antibiotic-resistance gene. The successfully transformed bacteria will be able to grow on media that contains the antibiotic. To check if the gene exists in the transformed bacteria, colonies are grown until enough plasmid DNA can be extracted. Plasmid DNA is subjected to restriction enzyme digestion to release cloned DNA fragment. DNA is put through gel electrophoresis. If expected pattern of bands appears on the gel, then the colony carries the recombinant DNA plasmid with the desired gene.
• New methods of transformation include electroporators and electrical "gene guns".