Week 3 - Genomes and Chromosomes Flashcards
packaging
DNA must be packaged as they are too long but they must be packaged carefully so that they are able to retain genetic information
plasmids
- synthetically manufactured to carry genetic info. for bacteria
- can carry genes that counter “virulence”
intron
- non-coding regions
- 28% of genome
exon
- gene regions expressed
- 2% of genome
transposes
- most are silent
- copies and inserts themselves, therefore the genome gets bigger
- can cause problems if they land on a functioning gene
- 45% of genome
supercoiling
molecule writhes in response to to torsional strain (increases free energy) when helix is overwound or underwound
helical turns/twists/linking number
of times DNA turn in 360 degrees
relaxed linking number (L0)
of expected helical turns of dsDNA (10 bp per turn for B-form)
underwinding
introduces negative supercoils that will writhe in the same direction
overwinding
introduces positive supercoils that will writhe in the opposite direction
writhe requirements
- CCC DNA
- ends are anchored in protein if linear
- prevents the DNA from relaxing
topoisomerase
- topological isomer
- catalyzes underwinding or overwinding in helical turns
- type 1 and type 2
- produces topoisomers
type 1 topoisomerase
- changes linking number by 1 per catalytic cycle
- breaks a phosphodiester bond
- does not use ATP therefore there is no energy input and it cannot add torsional strain
- will only RELIEVE strain
- only alters linking number if DNA is already writhed
type 2 isomerase
- changes linking number by 2 per catalytic cycle
- breaks both backbones
- can use ATP therefore it can add writhe
- only adds writhe in prokaryotes
- only modifies existing writhe in eukaryotes
writhes
- enzyme is in a closed conformation and has a tyrosine is close to a phosphodiester bond, therefore it will attack as a Nu-
- bond will get cleaved creating 2 strands from the one
- enzyme changes to open conformation and the unbroken strand can rotate and change linking
- enzyme changes to closed conformation and the 3’OH will attack phosphate group to cleave DNA strands
- enzyme will either stay bound (therefore, Tyr will attack again) or it will dissociate
topoisomers
- dsDNA that have the same bp, therefore same L0 (relaxed)\
- differ in L (writhe), therefore it will be under or overwound
topoisomerases in gel electrophoresis
- highly supercoiled DNA will move faster
- uncompacted DNA will move slower
- over time, the highly compacted DNA will return to an uncompacted form
naturally-occuring DNA
- found in negatively charged supercoiled, therefore a reduced L, as they must unwind for translation and transcription
- A-form is the least likely to form when negative supercoils are added to B-form DNA
consequences of negative supercoiling
- DNA compacts
- helix is partially unwound’
- cruciforms > Z- form = H-form are likely to form
cruciforms in negative supercoiling
there is less energy needed to flip and form as it is already unwound
Z-form in negative supercoiling
there is less energy needed to go from a right handed helix to a left handed helix as it is already unwound
H-form in negative supercoiling
there is less energy needed to pair the regions in both triple helix and ss regions as it is already unwound
plectonemic negative supercoiling
DNA molecules in soln
solenoidal negative supercoiling
- DNA molecules with proteins
- more compaction
- eukaryotes
chromatin
- also known as “beads-on-a-string”
- contains proteins and DNA in equal amounts
- DNA is wound in histones and linked by linker DNA
- topoisomerases in formation of eukaryotic chromatins
histone modifications
- changing the shape will change the function, therefore affecting the ability of modified side chains to interact with DNA
- changes chromatin function
- post-translational modifications of amino acid side chains
post-translational modifications
- phosphortylation
- acetylation
- glycosylation
- methylation
nucleosome
- “bead”
- DNA that’s wrapped around a lot
H1
brings nucleosomes together to be wrapped into solenoid
formation of nucleosome
will make negative supercoiling (reduced L)
negative supercoiling in nucleosome formation
- DNA wraps around histone left-hand causing right handed writhe (increased L)
- bound histone has negative supercoiling and unbound DNA has positive supercoiling
- topoisomerase will only unwind the positive unbound supercoiling
- results in a net negative supercoiling
euchromatin
- highly transcribed (less ordered) DNA
- exists in interphase
- lower levels of H1
heterochromatin
- untranscribed/silent (more ordered) DNA
- exists in interphase
- increase in H1 levels
- increase in topoisomerases
heterochromatin to euchromatin
histone modifications to get from one form to another
