C4 VS CAM Plants

Both C4 plants and CAM plants are for hot and dry environments, except CAM plants are plants that exist where it is impossible to collect carbon dioxide during the day because it'll lose too much water.

C4 plants collect carbon dioxide in the mesophyll cell, circulate it until it becomes oxaloacetate, and then it brings the carbon dioxide into the bundle-sheath cell to start the Calvin cycle.

In CAM plants, the stomata is closed during the day, meaning all the CO2 will have to be collected and stored inside the mesophyll cell, since photosynthesis can only happen during the day.  When the day approaches, the stomata closes again, and photosynthesis can start with the carbon dioxide that was stored during the night.

Review for Macromolecules

Guys, check it:  http://bilingualbiology11a.blogspot.com/2010_09_01_archive.html.  a bio teacher's blog.


Carbohydrates
-Carbs are made of a series of carbon chains with many hydroxyl bonds
-Four types:  monosaccharides, disaccharides, oligosaccharides and polysaccharides.
-Two types of monosaccharides:  aldose and ketose.  aldose comes from aldehyde end, and ketose has a ketose group, usually on second carbon of the carbohydrate chain.
-Carbohydrates can be in cyclical structures, for alpha, both hydroxyl ends are pointing down, while for beta, at least one hydroxyl end is pointing up.

-Amylose are fats inside plants that have alpha 1-4 bonds, which results in a linear shape
-Amylopectin are fats inside plants also, that have mainly alpha 1-4 bonds, but sometimes have alpha 1-6 bonds, which results in branches
-Glycogen are fats stored by animals.  They are similar in structure to Amylopectin, but have more alpha 1-6 bonds.
-Cellulose is made of glucose with beta 1-4 bonds.  Cellulose found in plant cell walls.
-Carbohydrate monosaccharides use glycosidic bonds to combine with each other (bonding between hydroxyl groups).  this results in production of H20, which is why glycosidic bonds are condensation.
-Glucose + Glucose = Maltose.  Condensation
-Glucose + Galactose = Lactose.  Condensation
-Sucrose = Fructose + Glucose.  Hydrolysis (requires water to break down bonds)

Proteins
-protein structure:  one carboxyl end and one amino end
-proteins made of amino acids linked by peptide bonds, a condensation reaction
-shape most important for proteins, four types:  Primary, Secondary, Tertiary, Quaternary
-Primary is just a straight chain
-Secondary is either alpha helix, or beta pleated sheet
-Tertiary is a combination of primary and secondary
-Quaternary is a combination of different primary, secondaries, and Tertiaries.
-Essential proteins are the ones humans need to eat; non-essential are the ones automatically produced by the human body

Lipids
-lipids are stored in animal body as triglycerides in adipose cells/fat cells
-triglycerides are made up of three fatty acids and a glycerol.
-saturated acids are linear because they only have single bonds
-unsaturated acids have double bonds, which creates the possibility of bending in the fats.
-unsaturated fats are healthier, as less can be stored, and they can be broken more easily because of their irregular shape.
-glycerol is hydrophilic and fatty acid is hydrophobic.
-a phospholipid is two fatty acids joined by a glycerol
-brown fat is baby fat, used for protection
-steroids are also a lipid
-excess carbs turn into lipids
-USES OF LIPIDS:  digestion, insulation, food storage (energy source), hormones (control), structure of cells, and vitamins to regulate body processes

Results: pH and Liver Catalyst

20% HCl
Start gas volume: 75 mL
Stop gas volume: 85 mL
Time: 1:58
* this was our first trial so we did it again because we thought we had made errors.

20% HCl (trial 2)
Start gas volume: 50 mL
Stop gas volume: 105 mL
Time: 0:22

40% HCl
Start gas volume: 85 mL
Stop gas volume: 500 mL (MAX)
Time: 0:23
*since this trial reached the maximum volume we did it again.

40% HCl (trial 2)
Start gas volume: 105 mL
Stop gas volume: 500 mL
Time: 0:34
*this one produced gas rapidly, then stopped, so time was stopped. Gas then suddenly continued being produced at the same pace, so time was started again.

60% HCl
Start gas volume: 50 mL
Stop gas volume: 225 mL
Time: 0:12

20% NaOH
Start gas volume: 60 mL
Stop gas volume: 500 mL (MAX)
Time: 0:55
*this one reached the max as well but we didn't have time to redo it.

40% NaOH
Start gas volume: 50 mL
Stop gas volume: ~550 mL
Time: 0:37
*this trial stopped about 50 mL after the 500 mL mark.

60% NaOH
Start gas volume: 60 mL
Stop gas volume: 400 mL
Time: 0:30

Importance of Entropy

Firstly, the definition for entropy is the measure of randomness or disorder in a collection of objects or energy; symbolized by S.  In layman terms connected to biology, entropy is the measure of the randomness of the particles in an object or system.  So an example would be when you add heat to an ice cube, the randomness of the particles increase, because the heat causes the particles to go from just vibrating to vibrating and moving fluidly into open space.

Entropy is also a part of the Thermodynamic Laws, namely being the second law.  The Second Law of Thermodynamics states:  All systems will spontaneously increase in entropy over time.

A good way to prove entropy:

1. Change of state
2. Energy Form
3. Number of particles

In addition, to quickly demonstrate a reaction has actually followed the laws of thermodynamics, balance the chemical equation.

Sanger Method - DNA Sequencing

ddNTP

Sanger Method

1. Start off with a single strand of DNA.  Occurs through denaturation of DNA, be being heated.
2. Radioactively labeled primer attached to four copies of single strand DNA.  (to help identify the starting point)
3. Each strand is put into individual test tubes.  Each test tube is filled with an abundant amount of dATP, dGTP, dCTP, dTTP.  
4. In each separate test tube, a small amount of ddNTP is added to each test tube.  One type of ddNTP for each test tube, e.g. ddATP in one, ddGTP in one, etc.  ddNTP stands for dideoxy nucleoside triphosphate.  It has NO oxygens on the carbon chain, and therefore cannot bond with any other dATPs, which terminates the DNA replication.
5. Polymerase 3 is added.
6. DNA replication occurs.  In each test tube, there will be strands where the replication automatically stops as a result of ddNTP.
7. Each individual test tube is loaded into four individual lanes on a gel.  The gel is run through an electrophoresis machine, and the DNA sequence can be read from bottom to the top, because it is radioactively labelled.  

PCR vs. Vector Cloning

Vector Cloning:

• Relatively cheaper compared to PCR
• replicates entire DNA
• requires bacteria and plasmid
• can be used to insert DNA and produce protein
• requires specific R.E. 
• Has practical uses in treating medical disorder (eg. somatropin for stunted growth)

PCR:

• Requires less time
• Higher probability of damage/corruption.  if only one DNA is replicated improperly, every DNA strand in that set will be negatively affected.
• Only replicates DNA, cannot produce protein
• Useful for forensics; PCR only requires one intact DNA strand.
• Medical uses more centred in help with diagnosis (diagnosis of HIV, looking for HIV genome)

Actually Starting on ISU

Got my paint together, got all the pots and soil and etc. together.

Started mixing paint.  And I suddenly ran into a foreseeable but unforseen problem.

Oil based paint does not dilute very well in water.  Not at all, actually.  Oil and water don't mix.  Duh.  Should've thought of that earlier.

So now I'm wondering if I should just go ahead with the environmentally friendly and acrylic paint and go without the last one, oil based, or find a substitute.  What a dilemma.

I decided to start another blog to keep track of my ISU progress.  Just cause I like blogs.  And cause I'm tired of putting together work logs for my ISUs (multiple curses upon my grade 11 and 12 physics ISUs...)
http://isuayjcc.blogspot.com/

Translation

1. Ribosomes are attracted to the G-cap.
2. Two subunits clamp onto mRNA, one bigger and one smaller.  *NOTE:  prokaryotic cells have a 30s small subunit and a 50s big subunit, and Eukaryotic ahve a 40s small subunit and 60s big subunit*
3. Ribosomes moves from 5' to 3' end.
4. Coding starts at AUG codon.
5. tRNA brings amino acids to ribosomes.  tRNA has a structure of a cloverleaf.  tRNA has a section of three bases called the anticodon arm, which attaches to the codon.  amino acid found on 3'end of tRNA, OH end.
6. Three sites in the ribosome:  A (acceptor) site, P (peptide) site, and E (exit site).
7. A tRNA reads the mRNA codon and attaches to the A site, attaches amino acids to its acid, moves to the P site.  another tRNA takes its spot in the A site and bonds the amino acid to itself, and moves to the P site.  the original tRNA moves to the E site and leaves the ribosome.  *NOTE: the first tRNA automatically goes to the P site.*

8. Peptide bonds are created between the amino acids as step number 7 repeats.  As the protein grows, it starts folding to protect itself.
9. Eventually, stop codon is read: UGA, UAG, or UAA.  No amino acids for these condons and so a protein called the release factor helps the polypeptide chain separate from the ribosome.

Note:  Wobble Hypothesis = third nucleotide can be swithced, but still code for the same amino acid.  prevents corruptions and errors.

Summary on Transcription

Vocab:  Coding strand = Sense
            Template = Antisense
            Upstream = Promoter Region = TATA box
            Downstream = Terminator Region = AAUAA ... box?
            pre-mRNA = RNA Transcript

1)  Find the TATA box sequence on the DNA.  The It should read from 3' to 5' (on the DNA) because all RNA and DNA code from 5' to 3'.  The TATA box is also known as the 'promoter region' or 'upstream'.

2)  TFs (transcription factor) find the TATA boxes and act as a 'beacon' for Polymerase II to bind to.  TFs are made of proteins.

3)  Polymerase II attaches to the TFs.

4)  TATA box, TF, and Polymerase II put together is known as the Initiation Process.

5)  Polymerase II elongates the pre-mRNA from 5' to 3'.  The RNA transcript is similar to the Coding Strand.

6)  When AAUAA is reached on RNA, coding of the RNA is finished.

7)  G-capping of the 5' end and poly (A) tail caps the 3' end to protect the RNA Transcript.  Poly (A) tail adds 50-250 adenine nucleotides.

8)  DNA Splicing occurs to fix any mutations and get rid of any unnecessary coding.  Spliceosomes are made of snRNPs and snRNAs.  snRNAs recognize the beginning and end of intron and help the spliceosome to attach to the RNA Transcript.  The snRNP part of the spliceosome brings the intron into a loop (to increase stability and decrease mutations) and severs the intron away from the exon.  The severed intron is not useless; sometimes becomes TFs.  The intron is the unwanted code.  the exon is the needed code.

9) Transcription is complete; the pre-mRNA / Transcript RNA is now a mRNA.

Steps 1-4 is known as Initiation, step 5 is known as Elongation, and steps 6-8 is known as Terimnator.

Note:  pre-mRNA is always found in nucleus.  Is only released into the cell's cytoplasm when it has undergone safeguarding by DNA splicing and capping.

Starting on ISU

So my ISU will be the study of the effect paint has on the environment.

I have decided to use beans to experiment with.  They are pretty much the quickest plants to grow with a quick turnover.  52-57 days.  If I start today, that will mean I will hopefully start getting results in a month's time.

I'll be watering the plants with different types of paints to study the effects of paint on the 'environment', which in this case is the plant and the soil.

Three types of paints will be used.  Environmentally friendly, regular oil based paint, and regular acrylic paint.  Two concentrations for each, one with 60% and the other with 40%.  Finally, two plants that just grow with regular water.

My biggest question now is... do I have to write up a hypothesis, and a prelab?  I have actually never done a formal experiment on my own before.

10 Really Important Things in Replication

1)  DNA always grows from 5' to 3'. The leading strand is always going into the fork, from 5' to 3'.

2)  DNA does not only replicate at the ends of the DNA at the fork.  The fork actually is part of a bubble, where DNA replicates on both ends.  And there are multiple bubbles on the DNA as it replicates.

3)  Initiation is the first stage of replication.  Helicase starts the process of replication in the DNA.  It unwinds the DNA.  Gyrase releases the tension in the DNA.  Single strand binding proteins (or SS binding proteins) keeps the separated strands stable.  RNA Primase creates primers for Polymerase III to attach to.

4) Elongation is the second stage of replication.  Polymerase III attaches to the DNA via the RNA Primers and adds bases.

5)  Termination is the final stage of replication.  DNA Polymerase I replaces the RNA Primer with DNA nucleotides.  It proofreads everything done so far.  Ligase glue the gaps in DNA caused by Okazaki Fragments.

6) Okazaki fragments occur because there are two strands in DNA replication:  leading and lagging strand.

Summary of points 1-6

7) Three types of bonds:  glycosol, phosphodiester, and hydrogen bonds.  Phosphodiester bonds along with sugar make up backbone of DNA.  Hydrogen bonds connect complementary bases.  Glycosol bonds sugar to DNA nucleotide (double check on Tuesday).

8)  DNA nucleoside is only sugar and nitrogenous base.  DNA nucleotide is sugar, nitrogenous base, and phosphate group put together.

Left side of diagram outlines where nucleoside and nucleotide begins.

9)  Counting carbons on a ribose:  DNA strand can only grow at carbon 3, and phosphate groups always bind to carbon 5.

10)  Anything that ends in -ase is an enzyme.  Strands in double helix are antiparallel.  One strand runs from 5' to 3' and the other from 3' to 5'.

11)... one more.  Watson and Crick came up with various models as to how DNA replicated.  The one that made the most sense was called semiconservative replication.  Happens when double helix separates so that each daughter molecule will have one old strand and one new strand.

Review for Grade 12 U Bio

So instructions for homework were to write down ten words from the list and to define them.  Obviously, the obvious choice would be the words that we don't know or understand.  Or have completely forgotten.

RNA:  one of three major macromolecules essential for lifeforms.  called the ribonucleic acid.  RNA is single stranded whereas DNA is double stranded.  also, RNA substitutes uracil in place of thymine.  RNA contains ribose sugar rather than deoxyribose.  found both in the nucleus and the cytoplasm.

Uracil:  is a base which can replace thymine.  found in RNA only.  replaces thymine when DNA transcription takes places (creating complementary copy of RNA for DNA sequence).

mRNA:  called the messenger RNA, it is one of three major classes of RNA molecules.  the mRNA acts as the intermediary between DNA and ribosomes.  translated into protein by ribosomes.  it is the end product of transcription of a gene.

Telomere:  long sequences of repetitive, noncoding DNA on end of chromosomes.  protects chromosomes from deterioration.

histones:  positively charged proteins that bind to negatively charged DNA in chromosomes.  found in the nucleus.  packages chromosomes into order.  key protein component of chromatin.  acts as spools around which DNA winds so that it has some sort of structure.

London Forces:  type of force acting between atoms and molecules. part of Van der Waals Force.  also known as dispersion forces.

Van der Waals Force:  intermolecular forces of attraction including London forces, dipole-dipole forces, and hydrogen bonds.

Cleavage Furrow:  indentation where cytokinesis starts.  only happens in animal cells, because plant cells have cell plates instead.  starts on outside of cell and moves inwards towards the middle. cell plates start in the middle and work outwards.

Genome:  The complete set of chromosomes of an organism containing all its genes and associated DNA

G1 and G2 are growth cycles.  S phase is when DNA gets replicated.

Cell Cycle:  the cycle that a cell goes through in life.

Intermolecular Bonds:  chemical bonds between molecules.

Intramolecular Bonds:  Covalent bond that holds atoms of a molecule together, and ionic  bond that holds ions together in a salt.

Germ cells:  opposite of somatic cells; cells that give rise to gametes of organisms that produce sexually.  undergo mitosis and meiosis to develop into gametes.

Ideas for ISU... Continued

1)  The effect paint has on our environment.  Asked Mr. Hendrickson and he said that paint was indeed toxic to environment, since all paints are either oil based or plastic based (acrylic).  So unsafe treatment of the paint might cause environmental harm.  Could test this hypothesis by watering plants with different concentrations of different paints.
2) Is laugher contagious? Just looked online and it actually is.  Scientists have already mapped the brain and what laughter does to it.  So it's a no go for experiment.  But perhaps I can turn it into a study, since laughter is also beneficially related to health.

Example Discussion

So today Mr. Chung did an example of what a discussion on Wednesday should look like.  He had:
1) Itinerary
2) Questions
3) Hook in the form of an activity/game/media (he had both a video and an activity)
4) 5 minute quiz
5) 15-20 minute discussion on findings, its usefulness and future reserach

Basically, a good discussion doesn't solve questions or create answers.  They create questions and promote critical thinking.

In other words... I'm having a horrible time finding a contact at a university for the ISU.  It seems like I'm a ball in a pinball machine, always getting pushed from one end to another in an endless chase for the perfect university supervisor.  Oh pooh.  Should've started earlier.  Should've spammed everybody on the list instead of being selective.  But I did find out something interesting.  Apparently there's a contest for students involved in science, something like our science fair...  http://www.ysf.ca/Competitions/CWSF/... unless this IS our ISU.  If it is one and the same ... does that mean Artin won money for his project?

Molecular Basis of Inheritance

1)  T.H. Morgan showed that genes are located on chromosomes through fruit fly experiments.  fruit flies have the scientific name Drosophila melanogaster.  Morgan arrived at the idea through comparisons in the phenotype of fruit flies and the research done by Mendel.  The traits skipped a generation in both cases.


2) Griffith discovered the genetic role of DNA in 1928.  Until then, the scientific community assumed that the protein carried the genetic code.  Discovery made through study of Streptococcus pneumoniae, a bacteria responsible for pneumonia.  in the experiment, dead pathogenic stains of bacteria (smooth) absorbed DNA material from harmless bacteria (rough) to function again and kill the mouse in experiment.
Transformation is the event where genotype and phenotype changes due to assimilation of DNA.

3)  Hershey and Chase did experiment on T2 Phage, a virus.  DNA and protein were stained respectively, and DNA of virus was confirmed to be found inside infected cell, not protein.
 4)  Chargaff developed series of rules based on observation of DNA.  There were four bases, adenine, thymine, guanine and cytosine.  They do not appear in equal ratio.  Equal % of adenine and thymine must exist, as well as equal % of guanine and cytosine.
5)  Wilkins and Franklin studied structure of DNA with X-ray crystallography.  Shot light through a crystal representation of DNA to get vague 3-D arrangement of DNA.  Light is diffracted upon leaving crystal.  Franklin did not receive proper recognition because she was female and was dead from cancer (overdose of X-Ray).

Example of X-Ray Crystallography

6)  Watson and Crick determined structure of DNA.  From data collected by Wilkins and Franklin, Watson arrived at double helix shape.  He determined the width of helix and space between bases.
There are minor groups and major groups in DNA.  Minor are shorter connections between bases, whereas major have longer connections between bases.  Hydrogen bonds connected two strands together.  Adenine and thymine would only form double bonds, and guanine and cytosine would only form triple bonds.

Murder Mystery

Today in class Mr. Chung introduced his friend, Mr. Relish.  Well... technically, Professor Relish.  But actually Captain Relish (air force, army, or navy?).  And that's not even his real name since he changed his name after his brief stint in jail.  So... I guess Mr. Chung wasn't kidding when he wrote that his friend has a mysterious past.  And now he's dead.  So that's something else to add to his list of accomplishments.

Anyways.  DNA Sequencing.  Apparently the order of the nucelotide bases.  Adenine, Guanine, Thymine, Cytosine.  So I guess... we have to figure out the correct order for the twelve ... sets of chromosomes?  Still kind of confused.  Google might be able to help a bit more than Wikipedia...

http://www.zerobio.com/sanger.htm helpful link?

Ideas for ISU

Ok.  So first of all, I had this awesome idea.  But it was unethical.  So it had to be scrapped.

Then I came up with a borderline ethical idea.  Experimentation involving deprivation of sunlight during growth in mammals.  But it turns out we actually can't experiment on live animals.  Bah humbug.

SO.  Some further ideas...
1) Effects of biting on your pencil.  You know it - lead poisoning!  Everybody's chewed on their pencil at least once... even if just out of curiosity.
2) Is stress contagious?  You would think so at AY Jackson.  Perfect school for such an experiment.  Too bad exam periods are over, data would be harder to come by.
3) Attention span.  Not sure what I can do with this... not sure about societal implications either.  I think this idea has potential though.  As our ability to share information and multi-task increases, our attention span seems to decrease dramatically.  Perhaps over time will alter human behavior.  Might be too much to hope for to see effects on human hormones/homeostasis... but I won't know that until hard evidence is in my hands.
4) Future technology.  With such a broad idea, there's bound to be future technology that involves biology/ecology/psychology.  Perhaps stem cells.  Overdone idea though.  Everybody knows what a stem cell is.  Any ordinary smuck on the street can probably tell you what a stem cell is.  Not interesting at all.  Maybe nano-technology?  But it's being discussed in class, will take away from ISU project... still, a good idea to pursue.
5) Linking physics and biology together.  We all know that without physics there would be no chemistry... but the extent to which biology and physics are related are hazy at best sometimes.  There might be a link somewhere that can be used.  Perhaps quantum biological computing.  Certainly sounds like something out of a comic book...
6) On the topic of comic books... perhaps superhero powers and how they might be biologically possible.  Goodness knows a lot of Marvel comic heroes involve some sort of radiation as a background to their powers... maybe Spiderman?.... or Captain America?  Captain America was injected with a cocktail serum to improve his puny muscles.  That just sounds like steroids now that I think about it... Or maybe Iron Man.  Remember how his body was getting poisoned in Iron Man 2 because of his impure core (or something like that...)?  Wow, now that I think about it, this is a really stupid idea.  But with a little bit more research, I might uncover something.  Or I might get killed because there might actually be a secret government project going on right now attempting to create a Captain America.  If I don't turn up to school on Monday, some nut-case American agency probably has me in a dungeon asking if I work for Russia, China, or the Middle East.
7) Everybody knows that the human head releases a lot of heat.  Lost energy.  Is there any way to harness that leakage?
8) Modified food.  Basically genetic engineered food... do a project on difference in terms of nutrient breakdown, benefits and consequences?
9) Edible paper.  We recycle paper a lot, but I don't think all of it is getting recycled.  Perhaps if we make paper more pleasant to taste and nutritional, people can be convinced to eat paper if they're too lazy to get off their butts to put it in the recycling bin.  Or if there's no recycling bin available at the time.  Because paper is technically edible... high in fiber.  Just... people don't eat it cause it's just not tasty.  So the project could possibly include the manufacturing process of paper, effect of ingestion of paper on human body, and... different ways to modify paper flavour?  O.o Will have to think more on this.


Hmm... not very good ideas after all.  Not one of them are good in terms of both quantitative observations and interests...  Must go back to the drawing board.  Good thing I never left it.

Carlos