Quiz 1 Flashcards
(33 cards)
What enzyme removes overwound regions that stall DNA replication (Diffuses the tension of the super coiled region)
-breaks DNA, relieving/introducing twists
topoisomerase
What is topology
The study of geometric properties and spatial relations unaffected by the continuous change of shape or size of figures
The flexibility of DNA is constrained by what two things
Surrounding ionic environment(water, salt), and the protein bound with the DNA
What is the linking number
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)
What is twist
Number of helical crossings/turns
-not always an integer
Twist = #base pairs / 10.5 bp per turn
What is writhe and what are the subtypes
# 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
Bubble formation in circular DNA
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
What enzyme helps deal with the Tension and super coiling during DNA replication caused by positive super coiling
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
Topoisomers
Identical DNAs with different thinking numbers
-they have different superhelical density and run different on agarose gels
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
No torsional strain
Negative supercoiled
Positive supercoiled
What is physiological linking number L(k)°
L(k)° = # of bp in DNA/10.5
Negative super coiling in DNA is usually seen in life except where?
Except in thermal files. If organism lives in hot environment, DNA can be positively super coiled to prevent unwanted DNA uncoiling
Describe the two classes of Topoisomerases
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
Catenated replication ?
If circular DNA is joined like rings
Three ways RNA differs from DNA
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
What are some of the roles RNA can take
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!)
What are the stem loop structures (discrete structure classes of secondary structures)
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
What is a pseudoknot
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
Ribozymes
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
What are the three stages of prebiotic evolution
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?)
SELEX=
=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
What is the RNA world hypothesis***
-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)
Evolution from RNA to DNA
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
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?
- Forefinger along undercrossing
- Middle finger along overcrossing
Right-handed triple = -1
Left-handed triple = +1
