Week 3 - Genomes and Chromosomes

Question 1

packaging

Answer 1

DNA must be packaged as they are too long but they must be packaged carefully so that they are able to retain genetic information

Question 2

plasmids

Answer 2

• synthetically manufactured to carry genetic info. for bacteria
• can carry genes that counter “virulence”

Question 3

intron

Answer 3

• non-coding regions

- 28% of genome

Question 4

exon

Answer 4

• gene regions expressed

- 2% of genome

Question 5

transposes

Answer 5

• 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

Question 6

supercoiling

Answer 6

molecule writhes in response to to torsional strain (increases free energy) when helix is overwound or underwound

Question 7

helical turns/twists/linking number

Answer 7

of times DNA turn in 360 degrees

Question 8

relaxed linking number (L0)

Answer 8

of expected helical turns of dsDNA (10 bp per turn for B-form)

Question 9

underwinding

Answer 9

introduces negative supercoils that will writhe in the same direction

Question 10

overwinding

Answer 10

introduces positive supercoils that will writhe in the opposite direction

Question 11

writhe requirements

Answer 11

• CCC DNA
• ends are anchored in protein if linear
• prevents the DNA from relaxing

Question 12

topoisomerase

Answer 12

• topological isomer
• catalyzes underwinding or overwinding in helical turns
• type 1 and type 2
• produces topoisomers

Question 13

type 1 topoisomerase

Answer 13

• 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

Question 14

type 2 isomerase

Answer 14

• 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

Question 15

writhes

Answer 15

1. enzyme is in a closed conformation and has a tyrosine is close to a phosphodiester bond, therefore it will attack as a Nu-
2. bond will get cleaved creating 2 strands from the one
3. enzyme changes to open conformation and the unbroken strand can rotate and change linking
4. enzyme changes to closed conformation and the 3’OH will attack phosphate group to cleave DNA strands
5. enzyme will either stay bound (therefore, Tyr will attack again) or it will dissociate

Question 16

topoisomers

Answer 16

• dsDNA that have the same bp, therefore same L0 (relaxed)\

- differ in L (writhe), therefore it will be under or overwound

Question 17

topoisomerases in gel electrophoresis

Answer 17

• highly supercoiled DNA will move faster
• uncompacted DNA will move slower
• over time, the highly compacted DNA will return to an uncompacted form

Question 18

naturally-occuring DNA

Answer 18

• 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

Question 19

consequences of negative supercoiling

Answer 19

• DNA compacts
• helix is partially unwound’
• cruciforms > Z- form = H-form are likely to form

Question 20

cruciforms in negative supercoiling

Answer 20

there is less energy needed to flip and form as it is already unwound

Question 21

Z-form in negative supercoiling

Answer 21

there is less energy needed to go from a right handed helix to a left handed helix as it is already unwound

Question 22

H-form in negative supercoiling

Answer 22

there is less energy needed to pair the regions in both triple helix and ss regions as it is already unwound

Question 23

plectonemic negative supercoiling

Answer 23

DNA molecules in soln

Question 24

solenoidal negative supercoiling

Answer 24

• DNA molecules with proteins
• more compaction
• eukaryotes

Question 25

chromatin

Answer 25

• 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

Question 26

histone modifications

Answer 26

• 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

Question 27

post-translational modifications

Answer 27

• phosphortylation
• acetylation
• glycosylation
• methylation

Question 28

nucleosome

Answer 28

• “bead”

- DNA that’s wrapped around a lot

Question 29

H1

Answer 29

brings nucleosomes together to be wrapped into solenoid

Question 30

formation of nucleosome

Answer 30

will make negative supercoiling (reduced L)

Question 31

negative supercoiling in nucleosome formation

Answer 31

1. DNA wraps around histone left-hand causing right handed writhe (increased L)
2. bound histone has negative supercoiling and unbound DNA has positive supercoiling
3. topoisomerase will only unwind the positive unbound supercoiling
4. results in a net negative supercoiling

Question 32

euchromatin

Answer 32

• highly transcribed (less ordered) DNA
• exists in interphase
• lower levels of H1

Question 33

heterochromatin

Answer 33

• untranscribed/silent (more ordered) DNA
• exists in interphase
• increase in H1 levels
• increase in topoisomerases

Question 34

heterochromatin to euchromatin

Answer 34

histone modifications to get from one form to another