Factors Influencing Population Growth

                          Playing "Oh Dear"

Round 1 of the game "oh dear" started off with two deers and habitat component such as: food, water and shelter.  ( Density dependent factors). The deers are placed on one side while the habitat components are on the other side, while the backs are facing each other. The deers decide what resource they want and the habitat components  decide what resource they want to be.  When the two groups face each other, the deers either walk or run (depending on if there is any competition among the dears) towards the resources (habitat components) and mate. Therefore, deer's resource (shelter, food or water) become a deer, because they've been feeding and they are able to reproduce. This process is repeated several times until there are more deers on one side and few amount of resources on the other.  If the deers don't find a resource they die. Then they will decompose and eventually become the resources. 
After the third and fourth round, the deers become nervous, since there are more dears and few resources. Therefore competition builds up between the dears as they compete among each other for resources. Deers run with full speed towards the resources!!!!

Round 2 is similar to round 1. However this time we have independent factors (factors that influence population regardless of density. These include hunters, poor weather and predators). This time the entire class is divided into two groups: deers and resources. In the first round, there are no other resources for dears other than water. So all the other deers (searching for food or shelter died) become resources. The reason for this is, the environment is effected by flood, therefore there is only water left. In the second round, due to forest fire (deforestation) all the deers in search for shelter died because the fire ruined the homes. 
In the third round, due to drought that had occured in the environment, deers in search for water lost their lives. In the fourth round, some of the deers die before even starting the search for resources. So they decompose and became resources. Since there are a fewer amount of deers left competition was less between them. In the next round, two hunters are placed in the middle of the field ready to hunt deers. For every two deers hunted, one deer would become hunters and the other would become resource. If the number of deers caught were odd, one of them would automatically become resource.  


 So what did I learn ?????

• In the end the resources survive
• Density dependent factors include water, food, shelter
• Exponential population works under ideal conditions. When we have  an abundance of resources
•  At  carrying capacity (k), resources become completed and the deers will have nothing to eat, so their population will die
• The reason population populations eventually stop growing is caused by density dependent and density independent factors
• As population density (number of individuals within a certain volume ) increases, birth rate declines ---> less population, and death rate increases---> more competition, less resources
• Negative feed back----> prevents unlimited population growth. When we reach a certain capacity it affects the population so that it decreases, this will reset everything. Decrease in population would increase the amount of resources ----> wave pattern in graph
• Density independent factors (flood, drought, disease, hunting and predators) are unrelated to population density. There is no feed back to slow down population. Here is when we see significant changes. Extinction ---> when we have intervention with no feedback and no regulation, we can loose populations.
• Right now, humans still have enough resources to flourish. However it's only a matter of time for us to reach human carrying capacity. 
• Resource limitation can stop population growth
• Interspecific competition is competition between species.
• Due to predation or insufficient amount of resources, animals will leave their territory
• Everything is in balance. The predators need the prey.  The prey need resources. We can't have too much of something because that will create disorder 

* This game was not only fun, but it also was very helpful in learning the concepts related to factors affecting population growth. It really got the students involved, and helped in building a deep understanding :)

  Photosynthesis and Cellular Respiration

   Enzyme Lab

The Effect of Temperature on Enzyme Activity    

Temperature (oC)	Initial volume (mL)	Final Volume (m)	Change in volume (mL)	Time (s)	Rate of Reaction (mL/s)
10	350	480	130	102.6	1.26
20	301	206	95	90	1.39
22 (control)	230	350	120	82.6	1.45
30	105	230	125	40.9	3.08
40	100	55	45	20	2.25

        Krebs Cycle

• In 1937, Sir Hans Krebs, discovered series of metabolic reactions that became known as Krebs Cycle. He received the Nobel Prize in 1953 for this important discovery 

• Fritz Albert Lipmann shared the Nobel Prize with Krebs for his discovery of coenzyme A and the key role it plays in metabolism

• Krebs cycle is a cyclic series of reactions that transfer energy from organic molecules to ATP, NADH, and FADH2 and removes carbon atoms as CO2
• Krebs cycle is an eight-step process, each step catalyzed by a specific enzyme.

• Krebs cycle is a cyclic process because oxaloacetate, product of step eight is the reactant in step one.
• The overall chemical equation for Krebs cycle is:

oxaloacetate+acetyl-CoA+ADP+Pi+3NAD+FAD---->

CoA+ATP+3NADH+3H+FADH2+CO2

• The Krebs cycle begins as acetyl-CoA condenses with oxaloacetate to form citrate. 

• In glycolysis, glucose is broken down into two pyruvate molecules. 2-carbon fragment of pyruvate is used in making acetyl-CoA. Acetyl-CoA enters the kreb cycle, which takes place in mitochondrion.
• In the process of converting pyruvate into acetyl-CoA, CO2 is produced and a molecule of NADH is formed.
• The acetyl group (2-C) of acetyl-CoA is transferred to a 4-C molecule, which will produce 6-C compound. CoA is released.
• The 6-C molecule is then converted into a 5-C compound by loosing CO2 and 2 H atoms that reduce NAD+ to NADH.
• Oxidation and decarboxylation occurs. NADH and CO2 are produced. ATP is produced as well. As a result of these reactions, 4-C molecule is formed
• 4-C molecule is further oxidized and hydrogens that were removed are used in making NADH and FADH2. These reactions regenerate the 4-C molecule that reacted with acetyl-CoA.
• By the end of Krebs cycle the glucose molecule is entirely consumed. The 6-C atoms leave the process as 6 low energy CO2 molecules, which are released as wastes.
• In one turn of the cycle, the last 2-C atoms of the original glucose molecule are removed as CO2 , and free energy is transferred to ATP, NADH and  FADH2
• All that is preserved of the original glucose molecule is mostof its energy which is stored as: 4 ATP molecules (2 from glycolysis and 2 from Krebs cycle) and 12 reduced coenzymes ( 2 NADH from glycolysis, 2 NADH from pyruvate oxidation, 6 NADH from Krebs cycle and 2 FADH2 from the Krebs cycle)
• Free energy stored in NADH and FADH2 will eventually be transferred to ATP in the last stage of cellular respiration, called the electron transport and chemiosmosis
• The Krebs cycle occurs twice for each molecule of glucose processed, since 2 molecules of acetyl-CoA are formed from one molecule of glucose
• By the end of Krebs cycle, all 6-C atoms of glucose have been oxidized to CO2 and released from the cell as metabolic waste
• The reduced coenzymes, NADH and FADH2 now go on to the next process, electron transport and chemiosmosis, where their free energy will be transferred to ATP

Metabolism and Laws of Thermodynamics

First law of thermodynamics
(conservation of mass, energy), states that energy  cannot be created or destroyed, however it can be transformed or transferred. For example, when we light a match we're not creating energy but we're changing the form of energy. So when the match is burning, potential energy is converted into heat and light energy.

Energy In -- Energy Out = Energy Change 

In the case of human body energy in is the calories from food and energy out is comprised of basal metabolic rate and exercise. Energy change is the accumulation or loss of either fat or muscle. If energy in is greater than energy out, weight is gained. If energy out is greater than energy in, weight is lost.

Second law of thermodynamics
(entropy), explains the phenomenon of irreversibility in nature. This law states that the entropy of universe increases with any  change that occurs. For example, a new package of playing cards is highly ordered. If we throw the cards into the air, the cards get randomly assorted by the time they reach the ground---> entropy gets increases. Entropy is the measure of  randomness in energy or in objects. The universe favours an increase in entropy. In any closed area, the amount of entropy will tend to increase. The metabolism of a cell achieves this by coupling the spontaneous process of catabolism to the non spontaneous process of anabolism. Overall, in thermodynamic terms, metabolism maintains order by creating a disorder. All changes either directly or indirectly result in an increase in the entropy (overall disorder) of the universe.


Third law of thermodynamics
(Absolute Zero) ---> bottom point on the Kelvin temperature scale. The Kelvin scale is absolute, meaning 0 kelvin is mathematically the lowest possible temperature in the universe.This corresponds to about -273.15 Celcius. 

Getting back to normal body temperature from zero temperature would take days and even weeks. At absolute zero, some cells would start up again causing a malfunction in the body system since not all organs or not all cells would be functioning right away after the absolute zero temperature. Getting back to normal body temperature from zero temperature would take days and even weeks. At absolute zero, some cells would start up again causing a malfunction in the body system since not all organs or not all cells would be functioning right away after the absolute zero temperature.

Second Law of Thermodynamics + Metabolic Process

Although living organism's amazing complexity appears to contradict this law, life is possible as all organisms are open systems  that exchange matter as well as energy with their surroundings. Living systems are not in equilibrium, but instead systems maintain their high complexity by causing a larger increasing the entropy of their environment. The anabolic processes in the cell build highly  ordered structures such as proteins and DNA. By coupling free energy yielding catabolic processes with energy requiring anabolic processes, living things building up their bodies and world around them. They do this at the expense of the entropy of the universe as a whole. The entropy in a particular system, such as an organism, may decrease, so long as the total entropy of the system plus its surroundings increases. Thus organisms are islands of low entropy in an increasing random universe. Metabolism enables natural forms to persist in states that are far from equilibrium for extended periods. If the second law of thermodynamics describe the essential tendencies of nature, from largest to smallest  physical systems and spamming organic-inorganic divide the nature's essential activity would be metabolic.
 Living organisms obey the second law of thermodynamics. They create order out of chaos in the local area of universe at the expense of creating a greater amount of disorder in the universe as whole. The evolution of biological order is perfectly consistent with the laws of thermodynamics.

Carbohydrates

Carbohydrates are used by organisms as a source of energy, as building materials, and as cell surface makers for cell-to-cell identification and communication 

• Carbohydrates contain carbon, hydrogen, and oxygen atoms in 1 : 2 : 1 ratio

• Carbohydrates can be classified into: 

 
monosaccharides: simples sugars with many _OH groups 

    

disaccharides: 2 monosaccharides covalently linked

    

polysaccharides: a few monosaccharides

    

oligosaccharides: chains of monosaccharides or disaccharide units

The term saccharide and the suffix -ose both refer to sugars.

• Glycosidic Bond ---> a bond between 2 monosaccharides to form disaccharides

• Condensation---> the process of putting together by removal of water

• Hydrolysis---> opposite of condensation, a large molecule is split into smaller sections by breaking a bond, adding a -H to one section and -OH the other. The products are simpler substances.

Monosaccharides                                                     

• Aldoses---> have aldehyde group at one end (RCHO), and ketoses---> have keto group usually at C2 (RC=OR)

• May be distinguished by the carbonyl group they posses_ aldehyde or ketone, and the number of atoms in their carbon backbone.

• Sugar with 5 carbons is called a pentose, one with 6 carbons a hexose

• Simplest monosaccharides are dihydroxyacetone and glyceraldehyde

• Glucose, galactose and fructose are isomers, they posses the same number and types of atoms but a different arrangement of those atoms

Disaccharides                                                           

• It's formed when two sugars are joined together and a molecule of water is removed. 

• Lactose is made from glucose and galactose 

• Cane sugar, sucrose is made from glucose and fructose

• Maltose is also a disaccharide

Polysaccharides                                                       

• Also known as complex carbohydrates are monosaccharide polymers composed of several hundred to several thousand monosaccharide subunits held together by Glycosidic Linkages.

• Some are in form of straight chains while others are branched 

• Serve 2 important functions in living cells: energy storage and structural support

• Starch and glycogen are storage polysaccharides while cellulose and chitin are structural.

Section of Glycogen

Oligosaccharides                                                 

• Sugars containing 2 or 3 simple sugars attached to one another by covalent bonds known as glycosidic linkages ----> these bonds form by condensation reactions in which the H atom comes from a hydroxyl group on one sugar and _OH group comes from hydroxyl group on another

• Lactose, maltose and sucrose are oligosaccharides consisting 2 simple sugars while raffinose is an oligosaccharide consisting of 3 simple sugars

• They are covalently attached to proteins or membrane lipids and may be linear or branched

• Have many functions; for example they are commonly found on the plasma membrane of animal cells where they play a role in cell-cell recognition

• Selectin is an integral protein that that protrudes on outer surface of mammalian cells

    -----> it participates in cell-cell recognition and binding

Raffinose

Biotechnological Tools and Techniques

Restriction Endonucleases

• Restriction endonucleases, also know as restriction enzymes, are molecular scissors that can cut double-stranded DNA at specific base-pair sequence;
• Each restriction enzyme recognizes a characteristic sequence of nucleotides that is known as its recognition site. Most recognition sites are 4 to 8 bases long and are characterized by complementary palindromic sequence;
• Fragment ends of DNA molecule with short single stranded overhangs, resulting from cleavage by restriction enzyme are called sticky ends;
• Fragment ends of a DNA molecule that are fully base paired, resulting from cleavage by restriction enzymes are known as blunt ends; and
• Restriction enzymes and DNA ligase make recombinant DNA (DNA ligase joins the blunt or sticky ends together).

Gel Electrophoresis

• DNA fragments can be separated using gel electrophoresis. Gel electrophoresis takes advantage of chemical and physical property of DNA;
• DNA is negatively charged. Gel electrophoresis takes advantage of DNA's negative charge. Solution that's containing different size fragments to be separated is placed in a well. A well is depression at one end of the gel;
• The gel is usually a square or rectangle slab and contains a buffer containing an electrolytes and agarose or polyacrylamide;
• Using direct current, negative charge is placed at one end of gel and positive charge is placed in the opposite end of gel;
• The negatively charged DNA will migrate towards the positively charged electrode. Shorter fragments migrate faster than the longer fragments, achieving separation; and 
• Once the gel electrophoresis is complete, the DNA fragments are made visible by staining the gel. Most commonly used stain is ethidium bromide.

Plasmids

• Plasmids are small, circular, double-stranded DNA molecules lacking protein coat that naturally exists in the cytoplasm of many strains of bacteria;
• Plasmids also possess a characteristic known as the copy number. The higher the copy number the higher the number of individual plasmid in ahost bacterial cell;
• Plasmids have the ability to enter and replicate in bacterial cells. Therefore they can be used as a vector to introduce new genes into bacterial cells;
• Region in plasmid that has been engineered to contain recognition sitesd of a nubmber restriction endonucleases is called a multiple cloning site; and
• The combination of the original plasmid DNA and the foreign DNA is known as the recombinant DNA.

Transformation

• Introduction of foreign DNA, usually by plasmid pr virus, into a bacterial cell is called transformation;
• Plasmids can be used as vectors to carry a desired gene into a host cell;
• If a bacterium readily takes up foreign DNA, it is known as a competent cell. Most bacteria are not naturally competent;
• Selective plating is a method that can be used to isolate the cells with recombinant DNA;
• The vectors used for cloning carry an antibiotic-resistance gene. If transformation is successful, the bacteria will grow in the media that contains the antibiotic. No growth ---> bacteria were not transformed and were eliminated by the antibiotic;
• Electroporators - chambers that subject the bacteria to electric shock are also used---> electric shock loosens the structure of cell walls and allows foreign DNA to enter; and
• Modern electrical "gene guns" are used to "shoot" DNA through cell membrane

Comparing and Contrasting Replication, Transcription and Translation

	Replication	Transcription	Translation
Initiation	- Helicase unzips the two complementary parent strands -Single stranded binding proteins anneal to the exposed template strands, preventing them from reannealing -Primase builds RNA primers which will be used as a starting point by DNA pol III	-Transcription factors bind to TATA box -RNA pol II binds to  double helical DNA at the promoter region -DNA strand is unwound exposing the DNA strand - TFs, TATA box and  RNA pol II, together  are called the initiation complex	- The mRNA, a tRNA with the first amino acid and two ribosomal subunits come together. -The ribosomal subunits assemble at the 5'cap of  the mRNA transcript sandwiching the mRNA -Initiation Factors bring the large subunit such that the initiater tRNA occupies the P site. - The first tRNA brought into the P site, is carrying methionine because the start codon is AUG
Elongation	-DNA Pol III adds nucleotides to the free 3' end of the growing strand using template strand as a guide -leading strand, can be used by polymerases as template for a continuous complimentary strand -The lagging strand is copied away from the fork, discontinuously, in short segment known as Okazaki Fragments	RNA pol II begins building the single stranded mRNA in direction of 5' to 3', reading the DNA template in 3' to 5' direction. - The strand of DNA used for transcription is called a template strand. The strand that is not used is known as the coding strand. - This unit is known as the transcription unit.	- consists of three step cycles: - codon recognition: in this stage an elongation factor assists the hydrogen bond between the mRNA under A site with the anticodon of tRNA -Peptide bond formation: In this stage an RNA molecule catalyzes the formation of a peptide bond between the polypeptide in the P site with the amino acid in the A site. This step separates the tRNA at the P site from the growing polypeptide chain -Translocation: in this stage the ribosome moves the tRNA with the attached polypeptide from A site to the P site. Translocation ensures that mRNA is "read" 5' to 3' codon by codon
Termination	-DNA pol I proofreads the new strand, checking for mistakes. It also replaces the RNA primers with DNAnucleotides -DNA Ligase then "glues" the gaps between the Okazaki fragments.	-The mRNA is synthesized till RNA polymerase recognizes the termination sequence at the end of a gene, known as the terminator sequence (AAUAAA) Posttranscriptional Modifications (in eukaryotic cells): - 5' cap is added to the start of the primary transcript -Poly A tail is added to the 3' end - Introns (non-coding parts of the DNA), are taken out by proteins known as spliceosomes ---> Once the primary transcript has been capped and tailed and the intros excised, the process transcript is known as mRNA(messengerRNA) We are now ready to send the mRNA out into the cytoplasm	-Termination occurs when one of the stop codons: UAG UGA UAA reaches the A site - A release factor binds to the stop codon and hydrolyzes the bond between the polypeptide and its tRNA in the P site - Now the polypeptide chain is free and the translation complex disassembles.

Replication

Transcription

Translation