bacterial transformation and transduction

DNA transformation is a process by which DNA can be transferred into bacteria.  Plasmids are DNA that is inputted into the bacteria.  The experiment is to test the different genes (usually foreign genes not native to the bacteria) in the DNA plasmids and whether transformation affect the bacteria.  First, we much examine the molecular form of bacterial transformation.  During rapid growth, the cell membrane of bacteria has pores, called adhesion zones.  The cell membrane is made up of lipid molecules that is negatively charged by phosphates.  The negatively charged membrane is repellent toward the DNA.  Calcium ions are added.  Lowering the temperature allows the negatively-charged phosphates to be stabilized, making them easier to shield.  By having a heat shock, the DNA can sweep through the cell membrane.  DNA must cross the membrane in order to get into the bacteria.(This molecular process is called transduction).  Scientists, Boyer and Cohen, tried to input DNA plasmids into E.coli.  As stated before, the heat shock allows the plasmid to emerge into the bacteria.  The scientists put the bacteria with the plasmids into a petri dish and grow the culture with antibiotics tetracyline and kanamycin.  Only transformed bacteria containing both kinds of resistance genes in the DNA plasmids can survive in the presence of both antibiotics.  This is possible on two conditions: first which the two genes are available on one plasmid or that the genes are present on two set of plasmids.   


       

Shape and Size of Cell vs. Rate of Diffusion

Surface Area	Volume	SA/V	Rate of Diffusion
12.57	4.19	3	1
412.57	4.12	97.91	1
2512.57	4.25	590.97	1
1256.64	4188.79	0.3	0.1
125663.71	4188790.20	0.03	0.01
15.78	4.19	3.77	2.08
30.04	4.19	7.17	4.64

42.61

4.19

10.17

4.64

http://www.mhhe.com/biosci/genbio/biolink/j_explorations/ch02expl.htm

It turns out the highest rate of diffusion I found is 4.64, which can be found with the surface area to volume ratio of 7.17 and 10.17.  Interesting part is that both has the same volume and dimples, but different surface area.  This proves that the volume of a cell and dimples (pores) have more significance on the rate of diffusion than the surface area alone.  However, the surface area does matter.  Through observations, the flat cells tend to have a higher rate of diffusion than the round cells.  This is perhaps because the surface area is much more spread out in a flat cell than a round cell.

The following are screenshots, according to the list in the chart above:

Describe 3 beneficial bacteria include pictures

Acetic Acid Bacteria is vital to the food industry for the production of vinegar products.  It is rod-shaped, Gram-negative, and aerobic.  It often results in yeast fermentation of plant sugars.  It can be produced by both unpasteurized beer and cider.  Some acetic acid bacteria are known for synthesizing cellulose.



Lactobacillus are found in the human intestines and vagina.  It means acid-loving milk bacteria.  It converts sugar to produce Vitamin K, bacteriocin, acidoline, lactase, and lactodin (all necessary in the production of dairy).  Human consumption of lactobacillus proves to be beneficial in a variety of instances.  Many lactobacilli do not requiew iron for growth and have an extremely high hydrogen peroxide tolerance.



Ruminococcus are found in the large intestines of herbivorous mammals, such as cattle.  It is a gram-positive bacteria beneficial in food digestion, such as digestion of cellulose.  This digestive action is provided by cellulase and turn cellulose into energy for animals.

Make a chart of the similarities and differences between cellular respiration and photosynthesis

Cellular Respiration	Photosynthesis
Equation:  C6H12O6 + 6 O2 = 6 CO2 + 6H2O	Equation: 6 CO2 + 6 H2O = C6H12O6 + 6 O2
Cellular respiration undergoes glycolysis, Kerb cycle, and oxidative phosphoration.	Photosynthesis undergoes light dependent reactions and Calvin cycle.
Glycolysis breaks glucose down to form two pyruvates, forming a net of 2 ATP and 2 NADH.	Light reactions depend on the light absorbed by the chloroplasts to initiate the reaction.  Carbon dioxide is absorbed by the stomata and water molecules are absorbed through the roots of the plant.  Under the light reactions, electrons undergo the photosystems ( I and II) and chemiosmosis.
The goal of Kerbs cycle is to take pyruvate and put it into Kerbs cycle, producing NADH and FADH2.  There are two steps, the first is the conversion of pyruvate to Acetyl CoA, and the second step is to converse all of carbon, hydrogen, and oxygen in  pyruvate end up as CO2 and H2O.    It produces 2 ATP, 8 NADH, and 2 FADH2 per glucose molecule.	Under the Calvin cycle,  it takes 3 turns to generate one sugar.  The first step requires 7 CO2, which undergoes carbon fixation.  It requires 3 ATP and 2 NADPH per turn.
ETC's goal is to break down NADH and FADH2, pumping H+ into the outer compartment of the mitochondria, creating a gradient which is used to produce ATP.  This produces 32 ATPs.
	In order to conserve water, there are three types of plants, C3, C4, and CAM.  (see other blog for specific difference)
Number of ATP produced: glycolysis  2 ATP Kerbs Cycle  2 ATP ETC  32 ATP NADH  2 ATP FADH2  2 ATP Net        36 ATP

Explain the difference between C3, C4, and CAM plants

The difference between C3, C4, and CAM plants are their process of light and dark reactions.    All three are alternatives to conserve water to limit the amount of water loss, to ultimately create more product through photosynthesis.

C3 plants close their stomata on hot, dry days to limit water loss.  Carbon dioxide enters the Calvin cycle and the first product of fixation is 3-phosphoglycerate.  When stomata closed, CO2  concentration in the leafs air spaces falls, slowing down the Calvin cycle.
   


C4 plants opened their stomata during the day.  C4 plants fix carbon dioxide into 4 carbon compounds.  Co2 is first added to PEP with adis of PEP carboxylase resulting 4 carbon compound formed in mesophyll cells.  These compounds are able to transport through bundle-sheath cells.  Compounds are broken down to release CO2, which initiate the Calvin cycle.

The CAM plants open their stomata during the night.  In doing so, they reverse the performance of regular plants.  The light reactions are conducted during the night while the Calvin cycle occurred during the day.  These plants are commonly cactus.  In the desert, it would be beneficial because the day time is usually really hot and these plants would conserve water during the day.

Five Things I Learned From 3D Molecular Models

1.  Glucose is a hexose of the aldose  type, which is called an aldohexose.  Glucose is the most stable form as glucopyranose. 


2. Cellulose is the major polysaccharide in wood and in structural parts of plants, usually the outer layer, such as stems and leaves.  Cellulose is formed by the linkage of D-glucose molecules through glycosidic beta bonds.



3.  Amino acids are made up of an amino group and a carboxyl group linked to the same carbon atom.  The letter R represents the rest of the molecule.  It is what differentiates one amino acid from the others.  Proteins are composed of 20 types of amino acids.



4. The tertiary structure of a protein is the whole 3D structure of a protein.  It is a combination of several different secondary structures on each part of the molecule.  The protein lysozyme under tertiary structure composed of several alpha helices, one beta sheet, and zones without a regular secondary structure. 


5. DNA are formed by linkage of deoxyribonucleotide monophosphates.  DNA is formed as a double helix and consists on two chains associated by means of hydrogen bonds between nitrogenous bases.

Describe how the structure of macromolecules affects their function?

Macromolecules, in simple terms, are long polymers.  Polymers are made up of basic building blocks called monomers.  When monomers link together, they form polymers.  According to the structure of the macromolecules, the functional group of the molecules change and affect the function of the macromolecule.  Functional group and the structure first affect the monomers of the macromolecules.  For example, although glucose and fructose are all six carbon sugar with the exact same functional groups, but the isomer, or the shape of the monomer change its function.  When monomers link, the way they link may affect the macromolecule.  For example, when cysteine (amino acids) link to form a peptide, cysteine forms disulfide bonds.  This is one of the special function of protein because protein is able to coil and fold based on the numerous bonds in the peptides.   The structure of macromolecule, such as protein, affect the function.  For a macromolecule like protein, protein only functions when the protein is in its folded structure.  If a protein is to denature and unfold, the protein would not even work.  Enzymes only work under a certain conditions, and if enzymes are to denature, then enzymes will no longer catalyze substrates.      

Biochemistry Wordle

Terms used: Biochemistry, atom, molecule, covalent-bond, monomers, polymers, solution, solute, solvent, ionic-bond, functional-group, nonpolar, polar, hydrogen-bond, amino acids, fatty acids, nucleotides, sugar, glucose, protein, carbohydrates, nucleic acids, lipids, DNA, RNA, Phospholipid, macromolecules, hydrolysis, dehydration, pH, acids, base, elections, neutrons, protons, valence, matter, water, specific-heat

Wordle link: http://www.wordle.net/show/wrdl/4198048/biochemistry

Why?
I choose these terms for the biochemistry chapters because they represent the most important aspects of the chapters.  While matter and chemical bonds take the overview of the biochemistry chapters by explaining the importance of chemistry in biology, the four macromolecules, carbohydrates, nucleic acids, lipids, and proteins illustrates how organic chemistry is essential part of both biology and chemistry.  Water is also another important aspect of biochemistry.  Water is the universal solvent and has special properties, such as surface tension and high specific heat.  The pH in an environment is also important.  By having a stable pH, most biological functions will work, however sometimes, in extreme acid or base environment, some functions very little, some cease to function.  Overall, the biochemistry chapter starts with the concept of matter and atoms.  The subparticle of atoms, especially electrons, play an important role in bonding and reacting with other atoms, to form molecules.  All organic molecules are built based on monomers, extended to polymers.

Ecology Unit Wordle

 Ecology Unit Wordle


http://www.wordle.net/show/wrdl/4112400/ECOLOGY_UNIT_WORD_CLOUD

Vocabulary Words Used: Terrestrial and aquatic biomes, Imprinting , Bartesian mimicry, Second succession , Endangered species, Disturbance, Competition, Innate Behavior, Invasive species, Territoriality, Biogeography, Predation, Ecological niche, Learned behavior, Energy transfer, Carrying capacity, Classical Conditioning, Interspecific interactions, Biodiversity, Mullerian mimicry, Diversity and unity, Eutrophication, Ecology, Biophilia, Threatened species, Taxis vs. kinesis, Stimulus, Conservation biology, Species richness, First-succession

Why?
The terms I used to create the wordle based on the ecology unit range from the over branching themes to the specific behaviors of animal.  The theme of unity and diversity is emphasized in the ecology unit, and how animals exhibit different behaviors based on the environment.  Certain key terms describe the animal behaviors.  For example, both kinesis and taxis are behaviors of animals, but one is the immediate reaction of the animal while other is the stimulus for the animal.  While these terms explain the animals' behaviors, other terms, such as competition, define the interaction between animals.  Furthermore, the ecology unit go broader than behaviors and interactions of animals.  Ecology is also the study of the animals and the environment.  Ultimately, ecology links to humans as well.  Conservation biology and our sense of biophilia connect humans to nature, justifying that human is part of nature.

Wordle: Word Cloud about Myself

Hi Ms. Malonek:

The following is the link to my personal word cloud.

http://www.wordle.net/show/wrdl/4071248/Untitled