Notes 10-21

Notes from class!! :) Good luck on the exam!

An Exam Review Story About PCR, CSI, and LSD

• Characteristics of proteins
o Composed of amino acids in a chain
• 20 amino acids that can be arranged in many different orders
• Each amino acid has different properties
• Ex. Hydrophobic, hydrophilic, acidic, basic
o Interactions between amino acids in protein give protein it’s shape and function
• Heat causes proteins to denature – lose it’s shape
• External environment also determines how those amino acids interact with each other thus determine protein’s shape
o Interactions between amino acids changed by changes in pH, increase in temperature (also denaturing)
o Once a protein has been denatured it is PERMENANT
o Ex. Adhesins – twitching motility
• Gram negative (pili)
• Part of molecule would have to contain hydrophilic particles and hydrophobic particles to interact with both the inside world and the outside world
• Characteristics of DNA
o Bases are linked together by sugar-phosphate backbone
• Sugar in phosphate background is Deoxyribose
• DNA composed of 4 bases that connect to the sugars:
• Cytosine (C)
• Guanine (G)
o CG – complementary with 3 H-bonds
• Adenine (A)
• Thymine (T)
o AT – complementary with 2 H-bonds
• Strands are connected in an antiparallel action (5’ to 3’)
• When DNA is heated – the bonds between the complementary bases break (H-bonds break) and the two strands separate from each other – will probably come back together in the future
• How is DNA replicated?
o DNA polymerase - is the key enzyme that copies the DNA stand – by bringing in bases complementary to DNA strand being copied, and links those bases into a new chain with a sugar-phosphate backbone
o Before the DNA strand can be copied by DNA polymerase is has to be unattached from it’s sister strand
• 1. Must be ‘unzipped’ from partner strand
• 2. Also there must be a primer which is a little swatch of DNA or RNA that DNA polymerase can bind to before it begins it’s copying
• Primer is complementary to the first few bases in strand being copied
• DNA polymerase binds to primer and moves on down the line synthesizing the strand and copying it
• The DNA polymerase cannot copy the section of the strand that the primer binds to
• Extremophilic bacteria
o Ex. Thermos aquaticus
• Live at ~100C – hyperthermophiles
o Do everything that normal bacteria do, but they just do it at higher temperatures
o Live in water right at 100C
o DNA polymerase would denature at this high of a temperature
• Polymerase chain reaction (PCR)
o You could copy a bunch of copies of DNA IF you have a DNA polymerase that will not be denatured by heat
• Put DNA sample in tube with bases and primers for the DNA & the DNA polymerase from thermos aquaticus
• Heat tube to ~95C and that would separate the DNA strands
• Cool it down just a little bit ~60C – the DNA polymerase will then synthesize a new strand of DNA to match each of those that have been separated by the heating – let it hang out for a little bit to have ample time to finish
• Repeat the heating and cooling steps over and over again 30+ times – and you would have many DNA strands (a billion +)
• Applications of PCR
o PCR will allow you to take a tiny sample from a crime scene and run off a bunch of copies so that you have enough to do a bunch of tests to determine DNA of a suspect
• Kary Mullis, Nobel Laureate, weirdo
o Won an award discussing that proteins at a hot springs are different from other ones
o Worked at a chemical plant

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