20 points on Metabolism and Enzymes

1. All organisms do work in order to do all their daily activities, from repairing damaged tissues to reproduction. To do this, organisms need energy.

2. Metabolism is divided into two categories: Anabolic and catabolic processes.

Anabolic processes break down substances. (e.g. starch breaking down into simple sugars).

Catabolic processes build up substances (e.g. transcription and translation).

3. Energy is categorized into two fundamental types: Kinetic and potential energy

Kinetic energy is the energy that is possessed by moving substances (e.g. heart pumping blood).

Potential energy is the energy stored in a certain form (e.g. ATP storing energy to be released).

4. The First Law of Thermodynamics

“The total amount of energy in the universe is constant. Energy can neither be created nor destroyed but only converted from one form to another. If an object or process gains an amount of energy, it does so at the expense of a loss in energy somewhere else in the universe” (Nelson Biology 12, p. 58).

For example: a roller coaster has all its energy as potential energy at the start. When the ride starts, this energy is converted into kinetic energy and is continuously changing between these two energies until the ride stops.

5. Energy is not readily served in the environment. For example, plants produce energy from the sun by the process of photosynthesis. For human beings, through the process of cellular respiration, we get our energy from glucose which in turn is converted into ATP. ATP releases energy that we use for work.

6. Bond energy is the measurement of the stability of a covalent bond. Through the first law of thermodynamics, an equal amount of the bond energy is needed to break the bond (called the activation energy)

7. These two graphs illustrate the chemical reactions that take place within an organism (changes in potential energy). The reactants go through what is called a transition state by the activation energy. The transition state is when the products of the chemical reaction are produced. The one on the left represents the endothermic reaction and the right diagram represents the exothermic reaction

8. Endothermic versus Exothermic

Endothermic reactions: When the reactants release energy, the energy is absorbed (e.g. ATP releasing energy).

Exothermic reactions: The process in which the reactants release energy and the energy is lost (converted into another form). An example would be combustion.

9. Entropy is a measure of disorder in energy (symbol is S). Entropy increases when disorder increases. This explains why endothermic reactions occur as the products are more unstable than their reactants.

The Second Law of Thermodynamics states that “the entropy of the universe increases with any change that occurs. Mathematically, Delta S > 0” (Nelson Biology 12).

10. Entropy (S) increases when the following happen:

- Solids become liquids, or gases

- Liquids become gases

- A smaller amount of reactants form a larger amount of products

- When decomposition occurs (complex to simple)

- When diffusion or osmosis occur (solutes moving from high concentration to low concentration)

11. Free energy (Gibbs free energy): Energy that can do useful work.

So for exergonic reactions, the reactions are spontaneous and have a decrease in free energy. For endergonic reaction is not spontaneous and have an increase in free energy.

12. All the anabolic and catabolic reactions of metabolism are reversible. When a cell’s reversible reactions reach equilibrium (so zero free energy), it is dead.

13. ATP (Adenosine triphosphate) is the main source of energy for all organisms. It consists of adenine (nitrogenous base), the sugar (5 carbons) which is attached to 3 phosphate groups. ATP goes through hydrolysis to release 31 kJ/mol (in a lab) of free energy (about 54 kJ/mol in a living cell).

14. Redox Reactions: a chemical reaction where atoms transfer electrons to other atoms, in other words it is reduction (gaining electrons) and oxidation (losing electrons). An example would be the transfer of 1 electron of sodium to 1 chlorine to form sodium chloride. Redox reactions are exothermic as they release energy to make a new substance.

15. What are enzymes: Enzymes are protein catalysts that speed up chemical reactions, meaning that the reactants become the products much faster. They are usually tertiary or quaternary strucutures.

16. Enzymes do not affect the change in amount of free energy there is in chemical reactions. It cannot change an endergonic reaction into an exergonic reaction or vice versa. It can only reduce the amount of activation energy that is put into the transition state. This means that chemical reactions will become faster.

17. The reactants of chemical reactions that enzymes catalyze are called substrates. The substrate binds onto a specific site of an enzyme. For example, the substrate amylose is catalyzed by the enzyme amylase to produce maltose. Notice that each substrate has their special enzyme.

18. The area that the substrate attaches to the enzyme is called the active site. When the substrate is attached to the enzyme, the protein actually changes shape to better accommodate the substrate. This protein and reactant combination is called the enzyme-substrate complex.

19. Enzyme inhibition: When a competitive substance takes place of the active site of a non-competitive substance. Competitive inhibitors can block non-competitive inhibitors as they have very similar shapes compared to the non-competitive inhibitors. An example would be oxygen binding to hemoglobin. Oxygen is a non-competitive inhibitor while carbon monoxide is a competitive inhibitor. If one continuously keeps breathing in carbon monoxide, the hemoglobin of the body will only carry carbon monoxide and not oxygen. This results in oxygen not being delivered to all the parts of the body and ultimately death.

20. Applications of Enzymes: There are many uses of enzymes in industrial and commercial industries such as cleaning, cheese making, starch production, wine, pulp and paper and more.

Sources used: Nelson Biology 12

Top Ten Points I need to know about the Biotechnology Test

1. When transcribing DNA, follow the following steps:

     1. Look for 5’ TATA 3’

     2. Look for AATAA on the coding strand

     3. Look for the intronic sequences

     4. Look for 5’ ATG 3’ on the coding strand

     5. Choose which strand is the coding and template and start transcribing and translating

2. Vector cloning:

For this technique, the gene of interest is isolated from the old organism. The gene and the plasmid is cut by the same restricted enzyme (when orientation is not important). The gene of interest is then attached to the plasmid through DNA ligase. The plasmid is inserted into the bacteria and it is left to grow. Through selection, the bacteria with the desired plasmid are induced into the new organism.

3. PCR (Polymerase Chain Reaction):

The double stranded DNA is mixed with Taq polymerase, primers bind to DNA, and DNA nucleotides. The mixture is heated and cooled several times. During this time, the hydrogen bonds of the double helix is broken and rebuilt, creating more DNA fragments.

4. RFLP (Restriction Fragment Length Polymorphism)

Created by Frederick Sanger, RFLP is a method of DNA sequencing. The DNA in question is mixed with nucleotides, primers, polymerase along with dideoxynucleotides. ddNTPs have no hydroxyl group so they do not react. Four test tubes have the mixture along with the ddNTPs for adenine, guanine, cytosine and thymine. After some time, the four mixtures are run through gel electrophoresis to determine the DNA sequence

5. RFLP always involves COMPLETE digestion by the restriction enzymes.

6. Gel electrophoresis 1

 DNA runs from the top to the bottom as the top is negatively charge and the bottom is positively charged. Since DNA is negatively charged, it is attracted to the positively charged bottom. Since smaller DNA fragments run faster down than large fragments, therefore the bands at the bottom are smaller than the ones up top.

7. Gel electrophoresis 2

A gel electrophoresis consists of:

Ladder, Lane 1, Lane 2, Lane 3, etc.

To complete each lane, one has to know which restriction enzyme is used and whether it is complete or incomplete digestion. If it is complete, all the restriction sites and cut. If it is incomplete digestion, there could be 0 cuts to the number of restriction sites that are on the DNA. Each fragment has a certain about of bp (base pairs) and are labelled as bands on the gel electrophoresis.

8. Restriction enzymes: blunt and sticky

The sticky ends of the gene of interest are needed to place it in the plasmid. Blunt ends however are not designed to be placed on the plasmid. It is used to cut up foreign DNA. An example would be a mosquito putting its DNA into one’s bloodstream. The blunt ends are used to cut them up to prevent disease, infections, etc.

9. Orientation of restriction enzymes

Orientation of the gene of interest is not important when only 1 restriction enzyme is used, as it is cut on both sites of the plasmid. However, orientation is important when 2 restriction enzymes are used to cut one of each side as they both have to match the sites on the plasmid.

10. Objectives

PCR: To amplify a piece of DNA.

Vector cloning: To produce a protein product and to induce a new gene into an organism

RFLP: To determine the DNA sequence. 

PCR vs. DNA sequencing

1. The difference of the objective

PCR: Used to make more of the DNA.

DNA sequencing: Has the DNA strands stop at certain A’s, T’s, C’s and G’s.

2. At some point, each process uses Gel electrophoresis

PCR: To separate the truncated strands from the longer strands.

DNA sequencing: To find out the location of each adenine, thymine, guanine, and cytosine on the DNA strand.

3. Number of test tubes used

PCR: At least one test tube is needed as one just puts all the tools and waits for an hour to get the amplified DNA

DNA sequencing: Four test tubes are used in DNA sequencing for each nitrogenous base: adenine, thymine, cytosine, and guanine.

4. Each process uses the same tools with one major difference

PCR: Needs some modified polymerase, lots of nucleotides and short pieces of single-stranded DNA as primers, along with the DNA fragment.

DNA sequencing: Needs all of the tools of PCR plus the dideoxynucleotides: ddATP, ddCTP, ddGTP, and ddTTP, to terminate elongation because dideoxynucleotides do not have a hydroxyls like in DNA or RNA.

5. Each process has a different result

PCR: A large amount of the amplified DNA is obtained for use to detect mutations, when you need to recombine, when you need to find out who the daddy is and when you need to solve a crime.

DNA sequencing: The sequence of adenine, thymine, cytosine, and guanine of the DNA strand is revealed. 

PCR vs. Vector Cloning

1. At some point, both processes use gel electrophoresis 

PCR: To separate the truncated strands from the longer strands.

Vector cloning: Use gel electrophoresis to determine which band is the gene of interest.

2. Type of replication

PCR: DNA is amplified (artificial replication).

Vector cloning: the gene (like DNA) is cloned, through the bacteria growing exponentially with the plasmids as the genes (regular replication).

3. Different tools are used in each process

PCR: Needs some modified polymerase, lots of nucleotides and short pieces of single-stranded DNA as primers.

Vector Cloning: Needs plasmids, bacteria, restriction enzymes, and restriction

4. Each process has a different result

PCR: A large amount of the amplified DNA is obtained for use in forensics and to find out who the daddy is.

Vector cloning: A genetically modified organism is the result for better or worse.

5. PCR is very short, where vector cloning is a very long process

PCR: Just add some polymerase, nucleotides and primers with the DNA, heat and cool it, separate through gel electrophoresis and you get the DNA.

Vector cloning: Cut the gene from the organism, run it through gel electrophoresis, choose the gene, place it in plasmid, insert plasmid into bacteria, choose bacteria culture with plasmid, and introduced to the desired new organism.

Top Ten Points I need to know about the Genetics Test

1. Griffith (along with Hershey and Chase): Discovery of DNA as the carrier of genetic material.

2. Purines versus Pyrimidines: 

Purines (2-rings): Adenine and Guanine

Pyrimidine s (1-ring): Thymine and Cytosine

3. DNA structure:

DNA is made up of three components: phosphate (have a negative charge, therefore DNA is NEGATIVELY CHARGED), sugar, and the nitrogenous bases. The double helix is also anti-parallel.

4. DNA Replication: The process in which DNA is cloned (Semi-conservative replication). First, Helicase unwinds the helical structure. Primase begins the replication via primers and DNA polymerase III adds nucleotides to form a new DNA strand.

5. Transcription: The process in which RNA is made. First the initiation complex is made from TFs, RNA polymerase II and promoters. RNA polymerase starts transcribing from the template and  grabs RNA nucleotide. It stops when the coding strand is at AAUAA (termination sequence).

6. Introns versus Exons: Introns are cut out (to become TFs for other DNA strands) and Exons stay in.

7. Ways to protect RNA mutation: Through splicing the introns and the wobble effect of the tRNA (codons).

8. Translation: The process in which pre-mRNA is run through the ribosomes of the ER to form a polypeptide chain. 

Deaf by Design Reflection

When I first read the article, Deaf by Design, my first impression was that wanting to have a child to have a “disability” was insane. I reasoned that it would be hard for Deaf children to be able to communicate with other children who could hear (not to mention a lonely childhood). They would be discriminated or at least people would pity them for being Deaf. And when they grow older, they would have trouble finding a career as communication is very important in today’s society. I really believed that being Deaf was one of the worst things that can happen to a child. However, after watching the documentary, Sound and Fury, I learned that the Deaf had their own small community. They are able to form intimate relationships easily as they share a common characteristic.In addition. The documentary coupled with the discussions changed my opinion on the issue. Now I believe a child should be given a choice whether to stay deaf or to get hearing implants, whether to be happy in their Deaf community or to be able to form a link between the hearing and the deaf. Because no one wants to be forced to do something (in this case to get hearing implants or not).

The article can be found here: Deaf byDesign