20 Points: Metabolism

1. Living organisms must continually capture, store, and use energy to carry out the function of life.

2. Catabolic Reaction - breaking down complex structures
Anabolic Reaction - building complex substances from simpler subunits

3. Energy is absorbed when reactant bonds break and energy is released when product bonds form

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

5.  Exothermic - release free energy - (-/\ G) - spontaneous ; endothermic - gain free energy - (/\ G) - not spontaneous

6. Free energy - energy that can do useful work

7. Phosphorylation - attatching a phosphate group to an organic molecule (i.e. ADP) ; therefore making it more reactive

8. Redox reaction - a chemical reaction involving the transwer of one or more electrons from one atom to another; where reduction and oxidation occurs

9. Reducing again - loses an electron ; Oxidizing agent - takes an electron ; oxidation - process of losing ; reduction - process of gaining

10. Enzymes are protein catalyst; catalyst - a substance that speeds up a chemical reaction without being consumed in the process

11. Catalyst doesn't change /\ G; only decrease potential energy level in transition state

12. Substrate - reactant that an enzyme acts on when it catalyzes a chemical reaction

13. Substrate only binds to a particular site on the enzyme to which it is attracted to; generally won't bind to isomers of the substrate; must possess compatible shape

14. Without energy, work cannot be done and life would cease to exist.

15. Activation Energy - amount of energy needed to strain and break reactants' bonds.

16. Enzymes are either tertiary or quaternary structures with complex formation.

17. Competitive inhibitors - similar to the enzyme's substrate that they are able to enter the enzymes active site and block the normal substrate from binding

18. Non-competitive inhibitors - they latch to another site on the enzymes, causing a change in the enzyme's shape

19. Non-competitive inhibitor then loses its affinity for its substrate

20. Entropy - measure of randomness or disorder in energy

Top 10: Biotechnology

1. Polymerase Chain Reaction (PCR) requires the polymerase called Taq polymerase.  This polymerase comes from hot springs.

2. It is not until after the 3rd crycle that the desired segment of DNA is replicated solely on its own.

3. Sanger's Sequencing requires dideoxyribose nucleotides (ddNTPs)

4. The bacterial plasmid is used to insert a foreign gene as it reproduces very quickly, is easy to obtain, and because we know a lot about the plasmid and bacteria.

5.Restriction enzymes cut the phosphodiester bonds on both strands of DNA in either sticky ends or blunt ends.

6. PCR has three steps: heating, cooling, and replication

7. Southern blotting is used to transfer DNA fragments from the gel to a sheet of nitrocellulose paper.

8. Gel electrophoresis separates macromolecules

9. RFLP markers serve as genetic markers

10. Recombinant DNA is when two genes from different sources are combined. 

PCR vs. DNA Sequencing

PCR

Similarities

-Sanger's method is similar to PCR
-only requires a small part of DNA (though larger parts will still work)

Differences
-PCR is to amplify a segment of DNA, while DNA Sequencing is to map the DNA sequence
-DNA Sequencing uses dideoxyribose nucleotides
-to interpret the sequence, you must run it through gel electrophoresis

PCR vs. Vector Cloning

PCR

VC

Purpose
PCR- to amplify a piece of DNA in small amount of time
Vector Cloning- to replicate the plasmid containing the recombinant DNA

Application
PCR- often used by forensic scientists when there are not a lot of DNA samples
VC- to insert a specific foreign gene into an organism

Requirement
PCR- DNA segment
VC- plasmid, bacterium, and recombinant DNA

Process
PCR- a three step cycle of heating, cooling, then replicating
VC- gene is inserted into the plasmid, which is placed back into bacterium where it will replicate with the recombinant plasmid

Top 10: Genetics

1. DNA and RNA are replicated, transcript-ed and translated from 5' to 3'

2.When DNA is replicated, it is done by semi conservative replication.  This meaning that the new daughter molecule will have one newly made strand and an old strand.  Watson and Crick made up this model.

3. After the introns are spliced out of the premRNA, the 5' end is capped with the "5' cap" and the 3' end is called with the "polyAtail".  This is to protect the mRNA from hydrolytic enzymes.

4. The wobble positions exists as many amino acids have more than one codon.  For example, UUU and UUC both code for Phe.  Therefore, the third base of the codon and anticodon have more than one option.  

The third base are blue, which are wobble base pairs.

5. The promotor in transcription is the 5TATA3 and the terminator is AAUAA.

6. Translation is initiated at 5'AUG3' and terminated with either UAA, UAG, or UGA.

7. Spliceosomes are made up of snRNPS (protein) and snRNA (RNA nucleotides)

8. There are always three parts in replication, transcription, and translation: Initiation, Elongation, and Termination.

9. Purines have two rings and are adenine and guanine.  Pyrimidines have one ring and are thymine and cytosine.  Purines are therefore more stable because they have two rings.

10.Watson deduced the width of the helix and the spacing between the bases.