Base

scaffold

connector 

Which is which?

Base

scaffold

connector 

Which is which?

Base= A, G,C,T

scaffold= Sugar

connector =phosphate

Where does the Phosphates bind in DNA?

Where does the base bind to the sugar in DNA?

1. 5 prime and 3 prime positions 

2. The 1 prime position

[image]

How does a DNA sugar look like? 

What is special about it compared to RNA?

[image]

A 2 prime position there is OH instead of H in RNA.

How does adenine look like? 

Difference in sugar:

(ribose for RNA and deoxyribose for DNA)

Uracil ( RNA) and thymine (DNA)

Nucleic acid codes

B-form

1. It is an antiparallel double helix.
   
   
2. It is a right-handed helix.
   
   
3. The base-pairs are perpendicular to the axis of the helix. (Actually, they are very slightly tilted - at an angle of 4 degrees)
   
   
4. The axis of the helix passes through the centre of the base pairs.
   
   
5. Each base pair is rotated by 36 degrees from the adjacent base pair.
   
   
6. The base-pairs are stacked 0.34 nm apart from one another.
   
   
7. The double helix repeats every 3.4 nm, i.e. the pitch of the double helix is 3.4 nm.
   
   
8. B-DNA has two distinct grooves: a MAJOR groove; and, a MINOR groove. These grooves form as a consequence of the fact that the beta-glycosidic bonds of the two bases in each base pair are attached on the same edge. However, because the axis of the helix passes through the centre of the base pairs, both grooves are similar in depth.

DNA conformations?

Right /left?

A= turns right

B =turns right

Z =turns left

Supercoiling involves?

w...

t...

L..

Formula?

Writhe 

Twist

Link

L= T+ W

Topoisomerase?

How many types and what is special about them?

ATP ?

Topo 1 = breaks single strand

Topo 2 = breaks double strand

Topo 1 does not use ATP

Topo 2 uses ATP

What is hyperchromicity?

At which wavelength of UV important for detection?

Effect depends on what?

Tm?

Semi conservative replication of DNA

2 methods?

Using isotypes of Nitrogen

BrdU

>10

Cannot:

Melt DNA/unwind

Initiate replication

Replication starts only at Origin

DNA strand grows in 5 p to 3 p direction

DNA reads in 3 p to 5 p direction

DNA unwound by?

Dna B composed of how many subunits?

Dna B aided by what?

What is pre priming complex?

Dna B

6 subunits

Dna C --> delivers DNA b to template

--> in DNA replication, an assembly of proteins that include dnaB-dnaC complex and proteins n, n′, n′′ and i, formed at an intermediate time during DNA replication.

What is ARS?

Autonomously replicatiing sequence

It has lots of AT bonds

--> consensus sequence

Dna B

Dna C

SSB

Dna G --> RNA pol primase

Dna B

Dna C

SSB

Dna G --> RNA pol primase 

After priming the setup is called primosome 

DNA synthesis in which direction?

RNA pol synthesis in which direction

Ribosome moves in which direction?

Exonuclease in which direction?

Endonuclease in which direction?

RNA and DNA pol reads in 3 to 5 but makes in 5 to 3

Ribosome reads in 5 to 3.

Exonuclease attack from the end by taking one base at a time. They work on only one strand and start either from 3 prime end or 5 prime end.

Negative supercoiling where needed?

Positive supercoiling where does it occur?

Negative supercoiling needed before replication can take place ==> by topo2

Positive supercoils removed after a few cycles of replication by topo 1.

DNA pol I and III, what do they do?

DNA pol III binds where?

DNA pol III is the main one which does the replication

DNA pol I removes primers and fills gaps.

Ligase seals the gaps.

---> binds OriC ..always needs an origin.

RNA polymerase, what are the subunits?

Binds where?

-->holoenzyme:

see script

--> binds the promoter with help of sigma factor.

Ribosome binds where?

Consensus sequence: Shine Dalgarno for prokaryotes and Kozak for Eukaryotes.

A sigma factor (σ factor) is a prokaryotic transcription initiation factor that enables specific binding of RNA polymerase to gene promoters

-35 region --> recognition domain

-10 region ( TATA box/ pribnow box)---> unwinding domain.

2 types:

Terminator sequences are found close to the ends of coding sequences. Bacteria possess two types of these sequences. In rho-independent terminators, inverted repeat sequences are transcribed; they can then fold back on themselves inhairpin loops, causing RNA pol to pause and resulting in release of the transcript. On the other hand, rho-dependent terminators make use of a factor called rho, which actively unwinds the DNA-RNA hybrid formed during transcription, thereby releasing the newly synthesized RNA.

What the sites in ribosomes?

Which unit binds first to RNA?

Which one contains the complementary strand to the RBS?

RBS= ribosome binding site

P, A and catalytic site

small subunit binds the RBS 

BER and NER repair pathway? 

How does it work and what is the difference?

Can you mention some diseases related to errors in those repair pathways?