Quiz 1

Question 1

What enzyme removes overwound regions that stall DNA replication (Diffuses the tension of the super coiled region)
-breaks DNA, relieving/introducing twists

Answer 1

topoisomerase

Question 2

What is topology

Answer 2

The study of geometric properties and spatial relations unaffected by the continuous change of shape or size of figures

Question 3

The flexibility of DNA is constrained by what two things

Answer 3

Surrounding ionic environment(water, salt), and the protein bound with the DNA

Question 4

What is the linking number

Answer 4

Number of times two DNA strands need to be passed over each other to be entirely separate from the other
Always an integer
-The only way to change the linking number is to introduce a break in one or both DNA strands, rotate the two DNA strands relative to the other and seal the break
L(k) = T(w) + W(r)

Question 5

What is twist

Answer 5

Number of helical crossings/turns
-not always an integer
Twist = #base pairs / 10.5 bp per turn

Question 6

What is writhe and what are the subtypes

Answer 6

# of super helical crossings
Superhelical turns can be either interwound/plectonemic (prokaryote) or toroidal/donut shaped O ring (eukaryote chromos)
-can be any real number

Question 7

Bubble formation in circular DNA

Answer 7

Bubble formation decreases twist, must therefore result in increased in writhe

• in relaxed or positively super coiled DNA, bubble formation increases writhe but in negatively super coiled DNA, bubble formation decreases writhe
• bubble formation is disfavoured by positive super coiling, but favoured by negative super coiling

Question 8

What enzyme helps deal with the Tension and super coiling during DNA replication caused by positive super coiling

Answer 8

DNA Gyrase causes negative super coiling that reverses the positive super coiling due to DNA replication
-DNA gyrase is a type 11 topoisomerase that introduces neg. supercoils and is responsible for the negative supercoiling of chromos in prokaryotes

Question 9

Topoisomers

Answer 9

Identical DNAs with different thinking numbers

-they have different superhelical density and run different on agarose gels

Question 10

Change in L(k)= L(k) - L(k)°
What does it mean if:
Change in L(k)=0
Change in L(k)<0
Change in L(k)>0
->measures the extent of supercoiling

Answer 10

No torsional strain
Negative supercoiled
Positive supercoiled

Question 11

What is physiological linking number L(k)°

Answer 11

L(k)° = # of bp in DNA/10.5

Question 12

Negative super coiling in DNA is usually seen in life except where?

Answer 12

Except in thermal files. If organism lives in hot environment, DNA can be positively super coiled to prevent unwanted DNA uncoiling

Question 13

Describe the two classes of Topoisomerases

Answer 13

Class 2: cuts twice and Changes the linking number by two. Requires ATP

• It can fixed joint rings, nodded, and entangled DNA
• only DNA gyrase induces negative supercoiling by passing double strand through break before resealing

Class 1: only cuts once and without ATP

• Can only fix 15 he is already next on one strand
• The cleaved DNA ends don’t float off, one end attaches to topoisomerase 1 and it then induces Confirmational change

Question 14

Catenated replication ?

Answer 14

If circular DNA is joined like rings

Question 15

Three ways RNA differs from DNA

Answer 15

It is not a 2’-deoxyribose sugar but a ribose, uses uracil instead of thymine and not a gene carrier
-also does not form B-helixes due to 2’-OH

Question 16

What are some of the roles RNA can take

Answer 16

Ribosomal RNA- ribosomes are complexes that incorporate several RNA subunits in addition to numerous protein units
transfer RNA- transport amino acids to ribosome during translation
splicosome-(does intron splicing) is a complex with several RNA units
micro RNA- regulatory roles
mRNA- carrying info from DNA to make proteins
-can be an enzyme, regulate genes expression (mRNA folding)
-Many viral genomes (e.g. HIV, Ebola viruses) use RNA-encoding (not DNA!)

Question 17

What are the stem loop structures (discrete structure classes of secondary structures)

Answer 17

Bulge: sticks out one side, bases on exterior
Internal loop: sticks out both sides.
Stem: complementary base pairing stretch.
Hairpin loop: at end of stem
Junctions: Meeting of three stems

Question 18

What is a pseudoknot

Answer 18

Where a stem loop structure bulges out, pairing with a hairpin loop elsewhere

• bps that are not contiguous
• can be important part of RNA containing enzymes
• are structures that have non-local pairing, are conserved (e.g., RNaseP ) and functional

Question 19

Ribozymes

Answer 19

RNA-based enzymes

-because of many secondary, tertiary structures available to RNA, they can also carry out catalysis themselves
- first one was RNaseP endoribonuclease that cleaves precursor tRNA to generate the mature tRNA (RNA cleaving RNA!-Could this hint at early life)
nobel prize

Question 20

What are the three stages of prebiotic evolution

Answer 20

Geophysical- what did the earths crust and atmosphere look like when life originated

• early atmosphere likely made of gaseous hydrogen, nitrogen, carbon monoxide and CO2
• inorganic chemical soup in a very different environment

chemical-How can building blocks of life been made
-In reducing environment, amino acids and bases are easy to synthesize from naturally occurring molecules (unlike the oxidizing environment now)

biological-How did the building blocks organize into living organisms

• hammerhead ribozyme is part of infectious viroids infecting plants and may hint at early replication
• these viroids can self-cleave to create individual units of itself (so could a hypothetical RNA-based RNA polymerase replicate itself?)

Question 21

SELEX=

Answer 21

=systemic evolution of ligands by exponential amplification
Current day SELEX experiments yield simple metabolic ribozymes
-**Can now randomly make RNA ribozymes and select for them on the basis of activity **
-SELEX is directed evolution that selects RNAs with randomized sequences that can bind small molecules/protein (such RNAs are known as aptamers)
-can use PCR and mutagenesis to enrich for aptamers that have an even higher affinity for the molecules

Question 22

What is the RNA world hypothesis***

Answer 22

-How could life have arisen if the DNA could multiply, be transcribed, and translated only in the presence of proteins? The RNA W.H. is the idea that protein-based life arose from earlier life-forms based on RNA molecules.
Neither the nucleic acid nor the enzyme came first but molecules that simultaneously;
1) contain the genetic information
2) are able to self replicate
3) had a catalytic activity

= The all in one RNA molecule was start of life
(life probably evolved from an RNA world)

Question 23

Evolution from RNA to DNA

Answer 23

RNA polymers, RNA world, RNA – protein
system, DNA – RNA – protein system
-a DNA-to-protein system seems like a leap too far
-RNA world hypothesis proposes stepwise increase in complexity

Question 24

A directional writhing number can be determined bylooking at the crossings of the DNA on a flat surface

• middle and forefinger represent ?
• right and left hand are?

Answer 24

• Forefinger along undercrossing
• Middle finger along overcrossing

Right-handed triple = -1
Left-handed triple = +1

Question 25

what kind of supercoiling does DNA replication cause?

Answer 25

positive supercoiling

Question 26

what is LK^0

Answer 26

the linking number of a fully relaxed cccDNA under physiological conditions
-free of supercoiling
- 10.5 bps per turn
=# of bp / 10.5

Question 27

is DNA neg or pos supercoiled and why?

Answer 27

negatively supercoiled because the neg supercoils act as a store of free energy that aids in the processes that require strand separation (replication/transcription)
-strand separation can be accomplished more easily in negatively supercoiled DNA than in relaxed DNA

Question 28

how does topoisomerase use covalent protein-DNA linkage to cleave and rejoin DNA strands

Answer 28

tyrosine residue in the active site of the topoisomerase attacks a phosphodiester bond in the backbone of the target DNA, this causes a break in the DNA and the enzyme is covalently linked to one of the broken ends via . a phosphotyrosine linkage
-the OH group from one broken DNA end attacks the phospho-tyrosine bond reforming the DNA phosphodiester bond

Question 29

what does ethidium do to DNA

Answer 29

used as a stain to visualize DNA
-increases the spacing between successive bps, distorts the regular sugar-phosphate backbone, and decreases the twist of the helix

Question 30

what is relaxed DNA

Answer 30

free of writhe and has 10.5 bp per turn

Question 31

what is non-canonical’ base pairing

Answer 31

other bases besides the usual pairs will sometimes pair

- such as U and G or can even get a triple base interaction (U:A:U)

Question 32

why can’t RNA form a B-form Helix like DNA

Answer 32

RNA that is in the form of a double helix cannot be in B-form because it has 2’-hydroxyls in the RNA backbone
-it instead resembles the A-form of DNA

Question 33

the miller-Urey experiment

Answer 33

• they addressed the question of whether the conditions of primitive earth could have sustained chemical reactions capable of creating organic molecules
• showed that organic molecules (amino acids) could be created from water, methane, ammonia and hydrogen
• mimicked early earth environment that was reducing and full of methane?