Chapter 9 Flashcards
How do you recognize an inverted and an inserted gene on a dot plot?
Inversion:
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Insertion:
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What is the purpose of a phylogenetic tree? Define: branch, clade, node, outgroup, ingroup.
To visualize the evolution of a gene!
- Branches: show the path of transmission of genetic information from one generation to the next
- Clade: a group of organisms that includes a single ancestor and all of its descendants
- Node: a branching point from the ancestral population
- Outgroup: a more distantly related group of organisms that serves as a reference group when determining the evolutionary relationships of the ingroup
- Ingroup: the group of living organisms whose relationships are being studied (CLOSELY RELATED!)
What is a motif?
A region of protein or DNA sequence that codes for a specific structure. Motifs are candidates for functionally important sites.
What is topology?
Studying linkage sites (to determine whether DNA will be coiled or supercoiled)
What is the function of Telomerase? Why are they so important?
An enzyme in cells that helps keep them alive by adding DNA to telomeres (the ends of chromosomes). Each time a cell divides, the telomeres lose a small amount of DNA and become shorter. Over time, the chromosomes become damaged and the cells die.
What can topoisomerase do?
They cause coiling and undo coiling by creating small, reversible cuts in the DNA. Topoisomerase enzymes can be thought of as tiny surgeons who wield molecular scissors.
What are “topoisomers”? Why to “topoisomers” exist?
Topological Isomers: DNA with same chemical formula but wound differently. DNA can be negatively or positively supercoiled, with the twisting in different directions.
What is supercoiling? What is the difference between positive and negative supercoiling? (NOTE: don’t worry about the linking number, just answer conceptually)
Supercoiling: DNA twisting into a superhelix. (like old-school phone chords)
- In positive supercoiling, the DNA helix is overwound or twisted in the same direction as the helical turns of the DNA.
- In negative supercoiling, the DNA helix is underwound or twisted in the opposite direction to the helical turns of the DNA.
How does supercoiling affect the ability of DNA to run on a gel?
Supercoiling makes DNA travel faster! (smaller and more compact than relaxed DNA -> TRAVELS FARTHER)
How do polymerases cause supercoiling?
Polymerases themselves do not cause supercoiling; rather, the process of DNA replication can introduce supercoiling. Supercoiling arises due to the unwinding of the DNA double helix during processes such as replication and transcription. LAGGING AND LEADING STRANDS will result in more coiling on one side than the other.
What are topoisomerases? What do they have to do with topoisomers?
Topoisomerases are enzymes that play a crucial role in the regulation of DNA topology by managing the supercoiling of the DNA double helix. Topoisomers (Topological Isomers) are chemically identical but structurally different DNA
How do type I topoisomerases work?
How do type II topoisomerases work?
TYPE I: Change linking number (Lk) by “Nicking” (cutting) only 1 strand and passing the unbroken strand through the break. This relaxes supercoiled DNA and alleviate the DNA helical constraints.
TYPE II: Cleave both DNA strands in concert and pass another double strand through the break. These enzymes are able to remove superhelical twists from DNA and resolve knotted or tangled duplex molecules.
What is gyrase? How does it differ from type I topoisomerases?
Gyrase introduces negative supercoils into DNA by breaking both strands of the double helix, passing another segment of the DNA through the break, and then resealing the break. Type I can either introduce negative or positive supercoils but typically relax supercoiled DNA.
Define writhe and twists in DNA. How does changing one effect the other?
Twist refers to the number of helical turns in the DNA molecule. (approximately 10 base pairs)
Writhe describes the coiling or supercoiling of the DNA double helix upon itself.
The linking number is the sum of twist and writhe. When one changes, the other must compensate to maintain the overall linking number constant.
Describe Type I and II Bacterial Topoisomerases
Type I Topoisomerase
- no ATP
- uses a nick to cut one strand
- reduces twist and writhe
Type II Topoisomerase
(ex: DNA Gyrase)
- uses 2 ATP to cut
- double-stranded break
- turns twice
- ligates same strands together
- leaves strands twisted
- increases supercoils
