METABOLISM

1. ENERGY the ability to do work is needed for the survivial of living organisms.
Catabolic Reactions:  reactions that result in the breakdown of complex substances.
Anabolic Reactions: cells build complex substances from simpler subunits (such as DNA from nucleotides.)
Metabolism: The sum of all anabolic and catabolic processes in a cell or organism.

2. LAWS OF THERMODYNAMICS:
1. Energy cannot be created or destroyed but only converted forom one form into another. (The total amount of energy in the universe is constant.)
2. The entropy (measure of randomness or disorder in energy or in a collection of objects) of the universe increases with any change that occurs.
3. abosolute zero

3. All forms of energy can be classified as KINETIC ENERGY or POTENTIAL ENERGY

4. Potential energy diagram is a diagram showing the changes in potential energy that take placeduring a chemical reaction

5. Endothermic reaction: the reactants have more energy than the products
Exothermic reaction: the products have more energy than the reactants

6. Entropy increases when:
- solid reactants become liquids or gaseous products
- liquid reactants become gaseous products
- fewer moles of reactant molecule form a greater number of moles of product molecules

7. FREE ENERGY: energy that can do work

8. ATP (adenosine triphosphate) is the primary source of free energy in living cells.

9. PHOSPHORYLATION: the process of attaching a phosphate group to an organic molecule

10. OXIDIZATION: a chemical reaction in which an atom loses one or more electrons.

11. REDUCTION: a chemical reaction in which an atom gains one or more electrons.

12. REDOX REACTION: (oxidization-reduction) is a chemical reaction involving the transfer of one or more electrons from one atom to another.
13. ENZYME: a biological protein catalyst.

14. SUBSTRATE: the reactant that an enzyme acts on when it catalyzes a chemical reaction.    
                                                                           
15ACTIVE SITE: the location where the substrate binds to an enzyme
16. COMPETITIVE INHIBITORS: substances that compete with the subtrate for an enzymeès acitive site.
17. NONCOMPETITIVE INHIBITORS: substances that attach to a binding site on an enzyme other than the active site causing a change in the enzymes shape and a loss of affinity for its substrate

19. FEEDBACK INHIBITION: method used by cells to control metabolic pathways in which a product formedd later in the sequence of reaction steps allosterically inhibits an enzyme that catalyzes a reaction occuring earler in the process
 
 
20. Enzymes are used in many commercial and industrial process such as cleaning and brewing.  

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Top Ten Points for BIOTECHNOLOGY

Examples of blunt and sticky end enzymes
1. STICKY ENDS: fragment end of DNA molecule with short single stranded overhangs. Both fragments have DNA nucleotides that are kacking complementary bases.
2. BLUNT ENDS: fragment ends of DNA molecule that are fully based pairs.

3. Sticky ends are more useful. They can be easily joined to other sticky ends that have been cut by the same restriction enzyme.

4. RECOGNITION SITE: a specific sequence within double stranded DNA that restriction enzymes recognizes and cuts

5. GEL ELECTROPHORESIS: seperation of DNA fragments on the basis of sides by sorting through a gel meshwork.
The process of using plasmids during vector cloning
- Shorter fragments move faster through the agarose gel because they can navigate through the pores of the gel easier

6. PLASMIDS: small circular pieces of DNA that can exit and enter bacterial cells. They are uses as vectors because the plasmids lack a protein coat and are independant of the chromosome of the bacterial cell. Basically, it can be easily taken in and put back into a cell without messing up any of the cell's biological functions.

7. A use of VECTOR CLONING is that it can take a gene for something useful such as insulin, and isolate it into a vector and it can be expressed (cloned) by bacterial cells. In other words, this insulin gene is inserted into bacterial cells that express the gene and build the protein insulin.

A simplified process of PCR
8. ddNTPS: are dNTP whose deoxyribose sugar is missing -OH group on its 3' carbon. These are the chain terminators.

9. PCR can be seperated into three main parts ... 1. HEAT used to seperate DNA strands 2. COOL to attack primers 3. HEAT to extend primers using Taq polymerase

10. RFLP (restriction fragment length polymorphism) can be used to find any difference in DNA sequence, non coding and coding that can be detected between individuals. This is useful in forensics to where a piece of DNA at the scene of the crime can be processed through the RFLP technique to see if it match's any suspets DNA.

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PCR vs. DNA Sequencing

DNA sequencing, the Sanger dideoxy method, is a technique based on DNA replication that uses dideoxy nucleoside triphosphates. The ddNTPS are dNTP whose deoxyribose sugar is missing -OH group on its 3' carbon. They are the chain terminators.

SIMILARITIES:
- Use electrophoresis
- Both methods use DNA polymerase

DIFFERENCES:
- DNA sequencing uses radioactively labelled primers, DNA polymerase, dNTPs, single stranded DNA template and most importantly ddNTPs
- DNA sequencing  uses a large sample of DNA sequence and replicates it
- PCR uses a small sample of DNA and amplifies it
- DNA sequencing maps specific nucleotides in a sequence wheras the main purpose of PCR is to produce large quantities of a specific DNA

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PCR vs. Vector Cloning

The polymerase chain reaction (PCR) is a process that amplifies a single or a few copies of a piece of DNA generating thousands to millions of copies of a particular  DNA sequence.

Vector Cloning involves vectors (vehicles by which DNA may be introduced into host cells by) that are introduced into host cells. Fragments of the DNA introduced into the cell are identically cloned when the cell replicates and divides.


SIMILARITIES:
- Produce a sequence of DNA in large quantities
- DNA is produced at a fast rate
- Use electrophoresis

DIFFERENCES:
- PCR uses DNA primers, Taq polymerase, and dNTPS
- Vector cloning requires a plasmid vector and a bacterial host
- PCR produces a pure sample of the DNA of interest
- Vector cloning expresses the gene (the gene of interest that was cloned can produce proteins)

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Top 10 Points for Molecular Genetics

1. Nucleoside have only a sugar and nitrogen base. (whereas nucleotides have sugar, nitrogen base, and phosphate group.)

There is a hydroxyl (-OH group) in the structure of RNA. 

2. RNA is more reactive than DNA because it is single stranded and it has one extra oxygen. This means that it cannot form a double helix strcuture because of the extra oxygen bond. The oxygen bond will react with something, such as the nearby phosphate group, and break the ladder structure if the RNA where to create a helix structure.

A portion of a DNA molecule with the helix unwound,
showing the complementary base pairs.  


3. In base pairing, adenine and thymine always bind together (double hydrogen bonds) and guanine and cytosine bind together (triple hydrogen bonds).



4. There are three types of nucleotide bonds:
    1. Glycosyl - sugar + nitrogenous base (intramolecular)
    2. Phosphodiester - sugar + phosphate (intramolecular)
    3. Hydrogen - between nitrogenous bases (bonds connecting the nucleotides and nucleosides) (intermolecular)

    Friffith's experiment proving that DNA is genetic material.
    5. Discovery of the genetic code began with research by Frederick Griffith in 1928. He discovered transformation, which is a change in genotype and phenotype due to the assimilation of a foreign substance by a cell. Through his experiments, it was proven that protein was not the hereditary material.






    6. REPLICATION Summary:

    <>   <>   
    Acts

    Names

    Characters

    Roles
       I
    Initiation

    -Helicase

    -SSBP

    -Gyrase

    -Primase

    -Untwists DNA, provides the direction of replication

    -Stabilizes single stranded DNA

    -Release tension

    -Makes primers to initiate elongation

    II

    Elongation

    -DNA Pol. III

    -Elongates new DNA strands

    -Replication (5’-3’)



    III

    Termination

    -DNA Pol. I

    -Ligase

    -Proofreads the new strand (replace RNA with DNA)

    -Joins gaps between okazi fragments



    7.  Ribosomes are composed of 30 and 50 subunits (70s total) in prokaryotes, 40 and 60 subunits (80s total) in eukaryotes.
    
    
    <> <>     <> <>     <> <>
    Exons are excised (cut out) before translation.

    8. RNA splicing removes introns (the noncoding segments) and joins exons to creat an mRNA molecule.




    9. Three ways in which DNA can be replicated:
    Possible ways DNA is replicated in.
    The two original strands of DNA are shown in yellow (light);
    newly synthesized DNA is blue (dark).
    Conservative replication would leave intact the original DNA molecule and generate a completely new molecule.
    Dispersive replication would produce two DNA molecules with sections of both old and new DNA interspersed along each strand.
    Semiconservative replication would produce molecules with both old and new DNA, but each molecule would be composed of one old strand and one new one.
    10. DNA replicates 5' to 3'. 

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    Deaf by Design

    Getting our first real taste of genetics in the real world, we were introduced to an article called "Deaf by Design". The article tells the story of how a deaf couple want to concieve a deaf child, the world of deaf people, and the controversial side of having prenatal genetic testing to select a "desired" child.
    Having never associated or known a deaf person, this article was an interesting and eye opening experience into the deaf community. I don't see deaf people any different than us, but I do feel concerned because they are usually isolated. They cannot hear or talk to people who do not know sign language and they can never hear music, the radio and television. The Deaf cannot hear their own children's laughter, cries, or anything that inspires all of the hearing people hearing from their children. It sound a little devasting but it seems as if the Dead don't see being deaf as a handicap. They've got their own tight knit community and their own culture, and they I'm sure they view their lifestyles as an alternative way of life, just as valuable as the life of hearing individuals.

    As to them wanting a deaf child rather than a hearing one .... sure, why not. To each their own. If they think they can be better parents and it would lead to a stronger bond between the family, it seems as if it's the obvious answer to let them have what they want. As to aborting a fetus that can hear, it's not the most reassuring thing to hear and there definitely should be limitations and boundaries to this sticky topic.

    While watching the documentary involving decision to getting a cochlear implant for a child, there was really one thing running through my mind. And that is how cool sign language is. Really, it's fascinating how sign language can be such a powerful way communicating from just using hand shapes to convey meaning.

    As to getting a cochlear implant .... I'm not against anything that will improve life. The technology can help a Deaf person go so far beyond in the future, because after all, most people on this planet don't use sign language to communicate. It all comes down to whether the parents make the right decision. No one can interject and argue with the family on whats the best decision for the child. Outsiders never know the whole story.

    A video of a baby hearing for the first time. Ridiculously adorable.

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