20 points from section 1.3 to 1.4

1.       Energy is the ability to do work. Work is the transfer of energy from one body to another. Metabolism is the sum of all anabolic and catabolic process in a cell or organism

2.       First law of thermodynamic – the total amount of energy in the universe is constant. Energy cannot be created or destroyed but only converted from one form into another.

3.       Kinetic energy is the energy possessed by moving object. Potential energy is the energy stored by virtue of an object’s position within an attractive or repulsive force field.

4.       Bond energy is the minimum energy required to break one mole of bond between two species of atom.

5.       To show the change in potential energy that take place during a chemical reaction one would need a potential energy diagram.

6.       Activation energy is the difference between the potential energy level of the transition state and the potential energy of reacting molecules.

7.       Transition state in a chemical reaction is a temporary condition in which bonds within reactants are breaking and the bonds between products are forming.

8.       Exothermic reaction results in a net amount of energy released, while endothermic reaction results in a net amount of energy absorbed. An example of exothermic reaction is combustion.

9.       Entropy is a measure of the randomness or disorder in energy or in a collection of object.

10.   Exothermic reactions that increase in entropy occur spontaneously at all temperature. If it decreases in entropy, the reaction only occurs spontaneously at low temperature. Endothermic reaction that increases entropy only occurs spontaneously in high temperature and if it doesn’t increase entropy it will only occur with a net input of energy.

11.   Free energy is energy that can do useful work.

12.   The second law of thermodynamics – the entropy of the universe increases with any change that occurs.

13.   Exergonic reaction is a chemical reaction in which the energy of the product is less than the energy if the reactant. This is related to exothermic reaction. Endergonic reaction is a chemical reaction in which the energy of the product is more that the energy of the reactant. This is related to Endothermic reaction

14.   Metabolic reactions are reversible. When reversible reaction reaches equilibrium they become a dead cell.

15.   ATP (adenosine triphosphate) is the primary source of free energy in living cell.

16.   Redox reaction is a chemical reaction involving oxidation (atom loses one or more electron) and reduction (gaining one or more electron). The substance that loses an electron is called reducing agent while the substance that gains an electron is called an oxidizing agent.

17.   Enzymes are used to catalyze a reaction. Substrates are the reactant that an enzyme acts on when it catalyzes chemical reaction. Active site is the location where the substrate binds to an enzyme. The interaction between the substrate and the amino acids causes the protein to change its shape. This is known as the induced-fit model.

18.   Enzyme requires cofactor or coenzymes to work properly.

19.   Enzyme inhibitors are used to control enzyme activity. Enzyme activities can also be controlled by allosteric regulation. Feedback inhibition is a method of metabolic control in which product formed later in a sequence of reaction allosterically inhibits an enzyme that catalyzes a reaction occurring earlier in the process.

20.   There are many commercial and industrial use of enzyme such as using proteases to coagulate milk for the manufacture of cheese.

Things to know for biotech quiz

REs

-used to cut DNA fragment from a sequence.

-Sticky and blunt are the two type of cuts that REs can cut.

Vector Cloning

-target gene is inserted into a recombinant DNA and reinserted back into the bacterium where transformation occurs.

PCR

-Taq polymerase is used because of its ability to survive in heat.

-target sequence is obtained at the 3^rd cycle

Gel electrophoresis

-used to locate desired gene base on DNA fragment size.

-DNA is negatively charged and the larger fragment stays on the top while the smaller fragment travels further.

RFLP

-used to detect certain differences in DNA sequence.

DNA sequencing

-adds 0.01% of ddNTP to create fragment of different length.

-used to determine the DNA sequence.

Comparing PCR

PCR vs Vector cloning

VS

Similarity – Both uses gel electrophoresis to locate the desired gene.  

They both are used to create huge quantities of DNA.

Difference –Vector cloning uses plasmid, bacteria, ands REs. PCR uses Taq polymerase, dNTP, ddNTP.

Vector cloning involves multiple steps and is not as quick as PCR.

PCR creates lot of DNA sequence, while Vector cloning creates modified bacteria containing the genes to create the desired proteins.

PCR  vs DNA sequence

VS

Similarity – both uses gel electrophoresis to identify the fragments.

Both uses dNTP to create large quantity of DNA sequence.

Both uses heating and cooling.

Difference – PCR tries to create a lot of the target sequence. DNA sequence tries to determine the sequence of ATGC.

DNA sequence uses small amount of ddNTP to create DNA fragment of different length, While PCR only uses dNTP to create complete fragment.

10 things to remember

1. Frederick Griffith discovers DNA contains the genetic information through his experiment with the phenomenon he dubbed as ‘Transformation’.

2. Watson and crick discovered the DNA structure – the double helix- with the help of Rosalind’s x-ray of DNA.

3. Nucleotide are made of phosphate (negatively charged), Sugar (DNA lack one oxygen), and Nitrogenous base. Nucleoside doesn’t have phosphate.

4. A%=T%, G%=C%. A and G are purines. T and C are pyrimidine.

5. All new strand of RNA or DNA are made from 5’ --> 3’.

6. Transcription beings from the 5’ TATA 3’ box and ends with the AAUAA sequence on the RNA.

7. RNA mod #1: 5’ G cap + 3’ poly a tail protects the mRNA.

8. RNA mod #2: RNA splicing cuts out the intron with spliceosome to make sure there’s no mutation.

9. Translation beings with 5’ AUG 3’, reads codons and ends with UAA, UAG, UGA.

10. Enzymes are very important.

-Polymerase I: Proof reads the new DNA strand and replaces RNA with DNA nucleotide. (DNA replication)

-Polymerase II: Binds to TFs, untwist the double helix, reads the template strand and grabs RNA nucleotides to form pre mRNA. (Transcription)

-Polymerase III: elongate the new DNA strand by grabbing DNA nucleotides. (DNA replication)

-Primase: Makes primer to initiate elongation. (DNA replication)

-Ligase: joins gaps between Okazaki fragments. (DNA replication)

-TFs: binds to the promoter region at the initiation. (Transcription)

-Helicase: untwist DNA and splits DNA into single strand. (DNA replication)

-SSBP: stabilise single strand DNA. (DNA replication)

-Gyrase: release tension made by Helicase by splitting the DNA. (DNA replication)

-Spliceosone: cuts the introns out of the mRNA. (Transcription)

Reflection: Deaf by design

Deaf by design is a very interesting article about deaf parents and their quest for a deaf baby. The deaf community being closely knit keeps them quite isolated from the outside world. They often reply on one another for support. And out of fear of not knowing how to raise their child to be a ‘hearing’, or having a negative opinion of the ‘hearing’ society. Those thoughts would lead them to make the decision of having a deaf child. Some deaf parents would even abort a healthy baby just to have a deaf one.

Through this study, it addresses the issue of should we be selecting for traits. My subjective view on this topic is quite hypocritical because I believe that it is okay to allow people to select for traits as long as the trait being selected is socially considered ‘good’. For example, I believe it is okay to abort baby with deaf hearing but you cannot abort baby if they are perfectly healthy. The reason for this is because I believe being deaf is a disability. Being deaf removes one’s ability to hear clearly and being able to hear doesn’t prevent one from learning things deaf people learn.  Also, I believe sign language is just another language that becomes an advantage for one to have just as any other language. Objectively I understand that we have to be fair. So if someone can abort because of a ‘bad’ trait we should be able to abort because of a ‘good’ trait especially when ‘bad’ and ‘good’ are such loose words.

Another problem that arises from this is what is considered good and what is considered bad. Suppose we decide to put regulation on this issue. Drawing the line between what is acceptable for abortion and what isn’t is quite difficult. I cannot say where the line should be draw because of my limited knowledge in the field; however I do believe that there should be a line.

My final opinion on this topic is that we should have minimum regulation on this issue. The regulation should be enough to prevent everyone from selecting for traits. This should be done to prevent the lost of genetic variation amongst the population. Genetic variation is very important to the survival of our species.