Biology Blog #5: Twenty Points From Pg. 58-77

1. Living organisms must continually capture, store and use energy, which is the ability to do work.
2. The sum of all anabolic and catabolic processes in a cell or organism is called metabolism.
3. Work is done when one object applies a force on another object and changes its position or state in motion. 
4. All forms of energy can be classified as either kinetic energy, which is the energy possessed by all moving objects and can turn into heat energy (movement of particles), mechanical energy (coordinated motions of particles), electromagnetic energy (motion of light) and electrical energy (motion of charged particles).
5. Potential energy is stored energy. Created when position changes within an attractive or repulsive force; comes in two different forms, gravitational potential energy (attraction of electrons to protons in a chemical bond) and chemical potential energy (the attraction of electron to protons in a chemical bond)
6. Bond energy is the minimum energy required to break one mole of bonds between two species of atoms; a measure of the stability in a chemical bond.
7. Activation Energy is the difference between the potential energy level of te transition state and the potential energy of reacting molecules.
8. In a chemical reaction, a temporary condition in which the bonds within reactants are breaking and the bonds between products are forming is called the transition state.
9. Entropy: a measure of the randomnesss or disorder in a collection of objects or energy
10. Free energy: energy that can do useful work.
11. Exergonic reaction: a chemical reaction in which the energy of the product is less than the enrgy of the reactants.
12. Endergonic reaction: a chemical reaction in which the energy of the products is more that the enrgy of the reactants.
13. Oxidation: a chemical reaction in which an atom loses one or more electrons
14. Redox reaction: a chemical reaction involving the transfer of one or more electrons from one atom to another
15. Reducing agent: a substance that loses an electron in a redox reaction.
16. Oxidixing agent: a substance taht gains an electron in a redox reaction.
17. Substrate: the reactant that an enzyme acts on when it catalzyes a chemical reaction.
18. Active site: the location where the substrate binds to a material
19. Competitive inhibitors: substances that complete with the substrate for an enzyme's active site.
20. Non competitive inhibitors: substances that attach to a binding site on an enzyme on an enzyme other than the active site.

^CAN YOU FEEL THE ENERGY?!?!?! IT'S OVER 9000!!!!!

Biology Blog #4: Ten Things To Know for the Biotechnology Test

Polymerase Chain Reaction

1. PCR: Polymerase Chain Reaction consists of three steps: Heating, Cooling and Replication, which helps produce an exponentially increasing population of DNA molecules
2. Targeted strand is only heated after the third cycle
3. Heating denatures the DNA turning them into single stranded

Recombinant DNA

1. Using the restriction enzyme, the recognition sites are cut, and the sticky ends are connected to another pair. then using lygase, the two sticky ends are joined together.
2. EcoRI, SalI, and HindIII will make sticky ends. sticky ends are DNA molecule fragments missing their pairs.
3. SmaI and AluI make blunt ends, which are DNA molecules with their corresponding pair.

Genetic Engineering

1. A plasmid is taken out of a bacterium and a piece of human chromosome is taken out. with sticky ends attached, a new recombined plasmid or chimera is created, and it is re-inserted into bacterium, which reproduces with the chimera inside. thus all of the new bacteria now have plasmids.

Gel Electrophoresis:

1. Separates macromolecules by the rate of movement through an electric field.

Story time:

Let's say that there are three groups of knights who are chasing after a reaallllllyyyyy hot princess. They have to fight through dragons and warriors and other castle-like things in order to get to the girl. So the first group is just made up of three knights, three fat horses and their esquires. naturally, they're going to get caught in the thicket, and the dragon kills them all... their charred corpses are there as markers now. then the second group is made up of just a knight and his esquire, they get past the dragon and slay it, but then all these rebel warriors come and kill them... the swords sticking out of their bodies are the markers. then some uber powered knight-magician guy comes along and wipes out everything and gets to the girl.

Restriction Fragment Length Polymorphisms (RFLP)

1.  so when the gel electrophoresis separates the DNA fragments, they can they be taken apart and put under Restriction fragment analysis
2. southern blotting lets us transfer the DNA in the same sequence of gel electrophoresis. southern blotting also works on non-coding DNA

Biology Blog #3b: PCR vs DNA sequencing - October 9,2011

PCR                                                                                                                         DNA SEQUENCING
   VS       

Similarities:

• It all starts somewhere... like the test tubes! It's like the clone wars! :O
• Both need DNA polymerization
• Used to amplify DNA sequence

Differences:

• DNA sequencing is a method of finding out the actual numbers of sequencing.
• PCR only enlarges the quality to a usable amount

Biology Blog #3a: PCR vs. Vector Cloning - October 8, 2011

Polymerase Chain Reaction:

1. it's a technique used to replicate the same small strand of DNA over and over again. 
2. DNA is denatured at high temperatures
3. five steps to it: 
1. Initialization step:
2. Denaturation step: 
3. Annealing step: 
4. Extension/elongation step: 
5. Final elongation: 
6. Final hold

Vector Cloning:

1. restriction enzymes used to cut gene of interest and original at specific points so that the sticky ends match
2. DNA must be artificially created to ensure that the gene is there.

Biology Blog #2: Ten Things To Know For The First Test - October 1, 2011

1. Remember! 5' to 3' is always needed!
2. Adenine and Guanine are called purines, double bonded, and Cytosine and Thymine are called pyrimidines, single bonded.
3. Remember the codons! You don't need to memorize all 64 of them, but for the most part, remember that AUG/ Met is the start codon, while UAA, UAG, UGA is the stop codon. Kinda reminds you of U.A.O.H. from Chouriki Sentai Ohranger haha.
4. Transcription in four parts: Initiation, RNA polymerase binds to double helical DNA at promotor 5'TATA3' (Tata box ;D) region. Unwound and shows template strands. Elongation: mRNA is synthesized from 5'-3'. Remember that T is no longer there. Termination, it's stopped. Like Arnold Schwarzenegger, AAUAA!
5. Introns are inside, and exons are outside. Introns are discard because they are coding, while exons code. Simple?
6. Enzymes. Somehow science has a lot of them.
1. DNA helicase: Unwinds the double helix.
2. DNA ligase: it's like the glue stick. it holds all the DNA together at the end when it comes to recombinant DNA.
3. Dna gyrase: relieves the tension of unwinding DNA during replication. now if only there was something like that for long days of school
7.  The lagging strands have short segments called Okazaki fragments built on them by the DNA polymerase III.
8. Remember the old folks.
1. Rosalind Franklin: Used X-Ray imaging to find hazy images of DNA and what it looked like.
2. James Watson and Francis Crick: the crooks that took Franklin's findings to prove their own theory.
3. Frederick Griffith: discovered teh process of transformation.
4. Erwin Chargaff: discovered and founded Chargaff's rule: A=T and G=C
5. Alfred Hershey and Martha Chase: suggested DNA is hereditary material.
9. DNA polymerase II is really RNA polymerase II
10. RNA doesn't like "T"ea. That's why when it drinks "T"ea, Uracil is excreted instead. (Vulgar, yes, but it helps me.)

Biology Blog #1: Deaf By Design Reflection - October 1, 2011

Deaf By Design introduces the concept of Deaf Culture, and a brief genetic history of how children were born deaf.
First things first, about 20% of the time, deafness in the United States is caused by a mutation in genes for proteins called connexins 26 and 30. These proteins affect the ear's sound sensitive cochlea (See below).

Above is a simple diagram of the cochlea, courtesy of Wikipedia.
With so many deaf people now getting married, and Deaf culture becoming more commonplace in the world, a lot of Deaf couples want deaf babies, and want them a lot over hearing babies. As a result, prenatal genetic testing is being used a lot more widely to figure out if the child is deaf.

Reflecting back upon this, I don't really think that's there is anything wrong with wanting a deaf child. And knowing how a deaf baby is made was really interesting. There are many different ways of becoming deaf, and I know someone that is progressively becoming deaf, because her hearing is deteriorating. However, it's not because of the mutations in her proteins.

The video, Sound and Fury, was also useful and relevant to the topic, because it showed good emotional and visual support for the article.