9 | DNA Topology Flashcards
The number, size and potential length of shortest human chromosome?
Chromosome #21 has 47 million base pairs and would be 16mm stretched out
Human Cell Size
7-30 microns
Centromere
Serve as attachment point to link chromosome(s) to mitotic spindle during metaphase
Telomeres
Sequences at the ends of chromosomes that provide stability and protection from nucleases
HAC
Human Artificial Chromosome
Three Requirements for a Stable Artificial Chromosome
1) Centromere
2) Telomere
3) Appropriate number of replication origins
Somatic Gene Therapy
Process of correcting disease causing gene errors in somatic cells
Contour Length
Length along the axis of the double-helical DNA
or the circumference, in the event of circular chromosome
Replicative Form
Specific types of viral DNA
dsRNA
Plasmid
Small DNA free in the cytosol and capable of autonomous replication
What is the primary structural compaction of DNA called?
Helical Coil
DNA Supercoiling
Further coiling of double-helix in DNA
Supercoiling is a manifestation of ________?
Structural strain
Relaxed DNA
When there is no secondary bending or coiling of DNA upon itself
DNA Topology
Conformational change due to thermal motion, stretching or interaction with other proteins or other molecules
Discontinuous deformation results from ______?
DNA breakage
DNA ligation
Joining of two DNA backbones
Closed-circular DNA
Circular DNA with no breakage or discontinuity on either strand
B-form DNA (turns/bp)
1 turn per 10.4 bp
DNA underwinding
When a DNA molecule has fewer turns than would be expected in B-form DNA
Deviation from the stability of B-form in DNA causes ______?
Thermodynamic strain
Strand separation can be caused by ________.
DNA underwinding
Linking Number (lk)
Topological feature of double-stranded DNA that cannot change when bent or deformed. Always an integer.
My convention, if two strands of DNA are interwound in a _______ the “lk” is positive (+) and negative (-) if they are wound in a _______.
Right-handed helix; left-handed helix
Linking number for DNA is undefined if _______.
Either strand is broken or discontinuous
Linking number is equal to _______ / ________.
Base pairs; base pairs per turn
A change in linkage number can be used to express ________.
Underwound DNA
Superhelical Density (σ)
The change in number of turns divided by the number of turns in the relaxed DNA.
General degree of DNA under-winding in cellular DNA falls between _____ and _____.
5% (σ= -0.05); 7% (σ= -0.07)
Negative supercoiling
Supercoiling of underwound DNA
Positive supercoiling
Supercoiling of overwound DNA
Linkage number can be changed +/- 1 by breaking one-strand and rotating it 360° about the other strand than reattachment. This process is catalyzed in cells by _____.
Topoisomerases
Topoisomers are _____.
Two forms of circular DNA who only differ topologically (i.e. linking number)
Linking number can be broken down into two structural components _____ and _____.
Writhe (Wr); Twist (Tw)
Lk = Wr + Tw
Twist (Tw)
Local, spatial twisting relationship between base pairs
Writhe (Wr)
The coiling of the helical axis
Underwinding of right-handed helix can facilitate short regions of _____ or _____.
Left-handed helix; Z-DNA
Plectonemic supercoiling
Whenever the helical structure exists in a simple or regular state. (Helical axis = ~40% of strand length)
Solenoidal supercoiling
The addition of tight left-hand turns to further compaction beyond the plectonemic supercoiling alone.
Plectonemic supercoiling provides stability in _____ while solenoidal supercoiling can be stabilized by ____ and provides a far greater degree of ____.
solution; protein binding; compaction
____ is the primary mechanism by which underwinding contributes to compaction.
Solenoidal supercoiling
DNA supercoiling (underwinding) is ____ regulated and effects many aspects of DNA ____.
precisely; metabolism
The underwinding and/or relaxation of DNA is catalyzed by ____.
Topoisomerases
There are two (2) classes of topoisomerases: ____ & ____.
Type I; Type II
Type I Topoisomerases carry out the following four (4) tasks:
(1) Break one of the two DNA strands
(2) Pass the unbroken strand through the break
(3) Ligate the broken ends
(4) Lk changed in increments of 1
Type II Topoisomerases carry out the following two (2) tasks:
(1) Break both strands of DNA
(2) Lk changed in increments of 2
How is uncontrolled relaxation during topological change avoided?
Topoisomerases never release the DNA while catalyzing the change.
In bacteria, the following functions are carried out by Topoisomerase I, II(_____), III and IV; respectively:
(DNA gyrase) I: Supercoil relaxation II: Supercoil introduction III: Specializes in DNA repair and replication IV: Replicated chromosomal decatenation
In eukaryotes, the following functions are carried out by Topoisomerase I, IIα, IIβ and III; respectively (in-particular):
I: (-) supercoil relaxation (DNA replication)
IIα/IIβ: (+/-) supercoil relaxation
(chromatin condensation, replication, transcription)
III: Specializes in DNA repair and replication
Topoisomerase activity can be observed via _____ because it will separate them based on _____ _____.
Gel electrophoresis; topoisomeric form
SMC Proteins (Structural Maintenance of Chromosomes)
Class of enzymes facilitate the further condensation/compaction of cellular DNA by forming reversible loops that link DNA segments
Bacterial, circular, daughter/sister chromosomes that are intertwined (while still continuous) are referred to as _____?
Catenanes
Pairing of SMC1 and SMC3 form a functional unit called _____.
Cohesin
Pairing of SMC2 and SMC4 form a functional unit called _____.
Condensin
Cohesion _____ while Condensin_____.
link sister chromatids during mitosis immediately following replication; facilitate condensation as mitosis begin via positive supercoiling
