Chapter 9 Flashcards
How do you recognize an inverted and an inserted gene on a dot plot?
Inversion:
\
/
\
Insertion:
\
\
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
Describe Type I and II Eukaryotic Topoisomerases
Type I Topoisomerase
- no ATP
- uses nick to cut one strand
- reduces twist & writhe
* HELPS WITH CHROMOSOME CONDENSING! (makes DNA wound around histones looser so that the whole chromosome can condense better)
Type II Topoisomerase
- uses ATP to cut
- reduces writhe
What is the linking number (LK) equation?
LK# = Writhe + Twist
What happens to the chromosome in each phase of the cell cycle?
INTERPHASE
- Growth (G1) Phase: Chromosomes are loose and spread out like spaghetti. The cell is growing and doing its usual jobs.
- Synthesis (S) Phase: Chromosomes duplicate, making exact copies of themselves. Now, each chromosome has a twin, connected at the middle.
- Growth (G2) Phase: Chromosomes start to condense, getting ready for division. The cell checks for mistakes in the copied DNA and prepares for the next step.
MITOTIC (M) PHASE
- Prophase: Chromosomes coil up tightly and become visible under a microscope. The cell’s nucleus disappears, and tiny fibers called spindle fibers start to form.
- Metaphase: Chromosomes line up neatly in the middle of the cell, ready to be split. Spindle fibers attach to the middle of each chromosome pair.
- Anaphase: The chromosome pairs are pulled apart by the spindle fibers, with one half going to each side of the cell.
- Telophase: The separated chromosomes reach opposite ends of the cell, and the nucleus reforms around them.
- Cytokinesis: The cell pinches in the middle, splitting into two new cells, each with its own set of chromosomes.
What proteins are made in G1 and G2 phases. What proteins are used in the S and M phases?
What are SMC proteins? How is cohesion used? How is condensin used and when is it no longer needed? How is separase used?
Structural Maintenance Proteins
SMC Proteins (Cohesins)
in G1 phase, the “lifesavors” are loaded onto the chromosome, then during S phase they ensure that the DNA is safe while DNA is being synthesized into sister chromatids
Separase
Releases Cohesions during anaphase (after sister chromatids separate during metaphase)
Condensins (nerds)
Help Condense Chromosomes beginning in prophase and ending after telophase
What are Histones made up of? What does the DNA do in relation to histones?
8 proteins (8 subunits). DNA wraps around each histone ~ 2 times (200bp)
