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Unit 6: Gene Expression and Regulation

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Deoxyribonucleic Acid (DNA):
A polymer made up of many monomers
Nucleotide: (monomer)
Sugar (pentose, deoxyribose C5H10O5): 5 carbon sugar, in a pentagon shape
A ribose minus an oxygen
Phosphate Group (PO3)
Nitrogenous Base: what changes between nucleotides
Cing Tut == pyrimidines
Adenine (purine == double ring structure)
Thymine (pyrimidine == single ring structure)
Guanine (purine)
Cytosine (pyrimidine)
A always bonded to T and G always bonded C
DNA has two strands of nucleotides, and nitrogenous bases are held together by hydrogen bonds
Antiparallel: DNA strands runs in opposite directions, one strand runs 5 to 3 and the other runs 3 to 5 (important for DNA replication)
5 Prime Side: there are five carbons (where the point of the pentose sugar points)
3 Prime Side: where three carbons at end of the pentos (fat side of the pentose points to the end)
DNA Backbone: sides of the nitrogenous base ladder rung structure, made up of sugar and phosphate, keep the DNA together
Double Helix: DNA twists around, made up of two strands of DNA
Proteins were considered genetic information for a while before discovering DNA, bec. There were 20 amino acids, which makes more sense for complex combinations than 4 bases
Frederick Griffith’s Experiment: mixed a rough strain of a disease (harmless) with a heat-killed smooth (virulent) strain and the mouse died
There was a transforming factor, from the heat-killed bacteria to the rough strain → DNA
Avery McCarty Macleod Experiments: wanted to discover Griffith’s transforming factor
Isolated the bacterial RNA, proteins, and DNA
Used enzymes that broke down each of those things until they could find out what caused the bacteria strain to transform
When they broke down DNA, they found that the bacteria could no longer transform → found life was based off DNA (not definitively)
Alfred Hershey and Martha Chase Blender Experiment: is it DNA or is it proteins that actually drive life (definitively)?
Dyed sulfur and phosphorus in a virus that invades a bacterial cell
Sulfur is found in proteins but not DNA
Phosphorus found in DNA and not proteins
Showed that the only one that was transforming the cell was the phosphorus → therefore DNA was hereditary material
Watson and Crick: credited for discovering DNA’s structure combining Chargaff’s ATGC levels and Wilkins and Franklin’s helical structure
Maurice Wilkins and Rosalind Franklin: discovered the crystallographic helical structure of DNA (basically had the data that Watson and Crick would use)
Erwin Chargaff: looked at the amounts of bases: ATGC
Found that A and T amounts correlated; G and C amounts correlated
Must be pairs: Chargaff’s Rule
during the S phase of interphase
Semiconservative Model (of replication): original/parental strands of DNA separate, and two new strands fill in with each parental strand. Each new copy of DNA is composed of one old parental strand and one newly made strand
DNA only dies if you don’t pass it down, “the immortal thread”
Every new DNA molecule is made up partly of old DNA
MESELSON AND STAHL Experiment: discovered semiconservative model
At the time, there were two other models of DNA that were proposed:
Dispersive Model: DNA was broken up, and each little DNA model was made up of old and new
Conservative Model: original parental molecule was conserved, and a two new strands were formed
Grew bacteria in heavy nitrogen, all DNA made in bacteria contained heavy nitrogen-15
Original bacteria has two strands of DNA both with nitrogen-15
Would have low band on centrifuge because of high density
Grew bacteria in nitrogen-14, all new DNA would be made using nitrogen-14 (lighter)
Two new daughter strands made using nitrogen-14 but the old strands are all originally nitrogen-15
After first round of replication, each DNA strand was half 15 and half 14
Got a medium band on the centrifuge
Third Round of Replication
Centrifuge results:
Light Band: daughter strand of second round, paired with a new strand
Medium Band: old 15 band from original paired again with another new daughter strand
Never goes away because original nitrogen-15 DNA strand stays
Origin of Replication “bubbles”: different in prokaryotes vs eukaryotes
Where replication begins in each cell
Bacterial DNA is unicircular has only one origin of replication and extends outward in both directions around the circle until completely replicated
Eukaryotic DNA: multiple origins of replication with linear strands of DNA
“Bubbles” at origins get bigger and bigger until they converge → multiple origins of replication make the process go faster and proves semiconservativeness
Contains two replication forks: extends outward at each fork
Creation of the Replication Bubble (made up of two replication forks)
DNA Helicase: responsible for opening DNA up and making the replication bubble → breaks hydrogen bonds of helix
Topoisomerase keeps theDNA unwound and stop hydrogen bonds from reconnecting “little clamps” DNA doesn’t want to stay apart
Single-strand Binding Proteins: keep the bubble open, and binds to the unpaired bases of DNA to stop them from rematching up
Making new DNA strands: (S phase of interphase)
Primase: not made up of DNA, made up of RNA, lays down a primerto begin DNA creation
5 to 3 == leading strand
Replication happens easily in the leading strand
3 to 5 == lagging strand
DNA Polymerase 3: the enzyme that actually makes the new DNA, can’t start from nothing, it can only extend preexisting nucleotides, needs to go off the primase’s primer
***can only operate in one direction ONLY operates to make 5 prime to 3 prime so it starts at the 3’ side of the leading strand to make a complementary 5’ to 3’, builds a complementary strand that’s opposite prime to opposite prime, by reading the template
Starts at the 3 prime side of the template original/parental strand to make DNA 5 prime to three prime
Then how do you make DNA for the other parental 5 to 3 strand but polymerase 3 can only go the opposite way
See DNA Replication Sheet on Drive
In the lagging strand, multiple not just one like leading strand, primers are going to be laid down, and polymerase 3 operates in between the primers
Okazaki Fragments: only found in the lagging strand, a segment where DNA is replicated in the opposite direction, but stops at each primer, and then moves to the left, then replicates to the right, and moves to the left…
P→ P→ P→
Overall direction: ←
All fragments are polymerased simultaneously, so it is quicker than just two primers on the end
Polymerase 1: removes the RNA primers and replaces with DNA
Ligase: connects fragments of DNA together, connects Okazaki Fragments to make a continuous strand of DNA
New daughter strands are IDENTICAL
If there is a mutation: Polymerase 3 screwed up
You get all of your materials from your food
Where do Polymerases get their nucleotides?
Nucleoside Triphosphate: an adenine nucleotide with two extra phosphates to which is ATP
Polymerase cuts off the phosphoruses and you get Adenine
Releases energy required to build DNA
There are also CTP, GTP, TTP, other energy sources that when phosphorylated become all of the other nucleotides in the body.
BUT, if at the very end of each DNA fragment, there’s nothing for Polymerase 1/3 to latch on to; end DNA is never replicated
With every single replication of DNA, your DNA gets shorter
Telomeres: contain non-coding DNA, long sequences of repetitive DNA at the end of each chromosome, it can be burned up through the process of DNA replication as to not affect your coding DNA
When telomeres run up, you die because you start eating into your genes when you replicate
Telomerase: enzyme found in germline cells (sperm/egg) that extend telomeres so you pass on full DNA
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