Notes for october 21st

An exam review story about PCR, CSI, and LSD.
I. Characteristics of Proteins
• Made out of Amino Acids (Amino acids in a chain)
- Amino Acids are linked together in a chain
- 20 different amino acids which can be arranged in many different orders
- All Amino Acids have different properties
- Interaction between amino acids in protein give protein its shape, function
- Adhesions are proteins on the pili that allow the bacterium to move along surfaces.
a. Both hydrophobic and Hydrophilic amino acids in the protein
i. Denatured mean a protein has lost its shape
External environment also determines proteins shape
Properties of animo acids and external environment of protein determine how amino acids interact, thus determine protein’s shape
b. To denature: heat, detergent for hydrophobic, or change pH its in (interactions between amino acids changed by changes in pH, increase in temperature) (changes in interaction between amino acid = denature protein) (same)
i. Once changed never returns to the original shape
II. Characteristics of DNA
• Made out of nucleotides (made out of bases linked together via sugar-phosphate backbone
- Four Bases: cytosine, guanine, adenine, thymine (CG complementary: 3 H-Bonds) (AT complementary: 2 H-bonds
a. Sugar in backbone is deoxyribose (warmer the DNA is the more CG present)
b. Heating DNA (does not break the base and sugars or the sugars in the backbone.) doesn’t destroy bases linked (covalently) to sugar phosphate backbone – but does break the H-bonds between the complementary bases (if broken DNA strands separate)
III. How is DNA replicated?
• DNA polymerase  key enzyme that brings in bases complementary to DNA strand being copied and links those bases into a new chain with a sugar-phosphate backbone
• For DNA to begin being copied by DNA polymerase
1. Must be “unzipped” from partner strand
2. Must have DNA or RNA “primer” complementary to first few bases in strand being copied for DNA polymerase to bind to
IV. Extremophilic Bacteria
• Bacteria on screen are Thermus aquaticus, live at ~ 100*C
• Hyperthermophiles live in water right at the boiling point and are happy at that temperature.
V. Polymerase Chain Reaction (PCR)
• Could copy a whole bunch of copies of DNA if you had a DNA polymerase not denatured by heat.
a. Out DNA sample in a test tube with lots of bases and primers and DNA polymerase from Thermos aquaticus
b. Heat that test tube to just under 100*C  DNA strands separate
c. Cool to ~ 60*C  DNa polymerase copies several strands
d. Repeating the same 2 steps over and ove again (30 times or so) it stands to reason that you start with one strand of DNA which separate and copy. TO having more that 1 billion copies of that DNA strand which could be handy
VI. Applications of PCR
Could allow crimes to be solved even if only a little DNA is present becaue same strand could be replicated the same alot
VII. Kary Mullis, Nobel Laureate, weirdos
Found you could use enzymes to make DNA was high and helps you be smart with insight.

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