DNA Topology Parameters
This section calculates the Linking Number (Lk) and Base Pairs per Turn (BPT) for the given DNA molecule based on its topological properties.
Linking Number Calculation
The Linking Number (Lk) represents the total number of times one DNA strand winds around the other. It is determined by the sum of the Topological Winding Number (Tw) and the Writhing Number (Wr).
Formula: $ Lk = Tw + Wr $
Given Values:
- Topological Winding Number ($Tw$) = $191$
- Writhing Number ($Wr$) = $-4$
Calculation:
$ Lk = 191 + (-4) $
$ Lk = 191 - 4 $
$ Lk = 187 $
The calculated Linking Number is $187$.
Base Pairs per Turn Calculation
The Number of Base Pairs per Turn (BPT) indicates the helical pitch of the DNA under specific conditions. It is calculated by dividing the total number of base pairs in the DNA molecule by its Linking Number.
Formula: $ BPT = \frac{\text{Total Base Pairs}}{\text{Linking Number}} $
Given Values:
- Total Base Pairs = $2.0 \text{ kb} = 2000$
- Linking Number ($Lk$) = $187$
Calculation:
$ BPT = \frac{2000}{187} $
$ BPT \approx 10.695187... $
Rounding to two decimal places, the calculated Number of Base Pairs per Turn is $10.69$.
Important Questions from Molecular Structure of Genes and Chromosomes
Consider the following multiple sequence alignment of four DNA sequences.
$\begin{matrix}A & C & T & A \\ A & C & T & G \\ A & G & T & C \\ A & G & C & T \end{matrix} $
Shannon's entropy of the above alignment is ________.
- All pseudogenes DO NOT code for a __________.
- C-value paradox refers to
The transcription factor X binds a 10 base pair DNA stretch. In the DNA of an organism, X was found to bind at 20 distinct sites. An analysis of these 20 binding sites showed the following distribution:
Base Position in the binding site 1 2 3 4 5 6 7 8 9 10 A 11 0 0 0 16 2 4 0 4 3 T 3 0 19 0 1 3 4 20 2 4 G 4 20 0 0 2 4 6 0 12 2 C 2 0 1 20 1 11 6 0 2 11 What is the consensus sequence for the binding site of X?
- Which of the following statements are CORRECT when a protein sequence database is searched using the BLAST algorithm?
P. A larger E-value indicates higher sequence similarity
Q. E-value < $10^{-10}$ indicates sequence homology
R. A higher BLAST score indicates higher sequence similarity
S. E-value > $10^{10}$ indicates sequence homology
