Nucleic Acids 2 Flashcards
In what instance can AFM achieve higher resolution than STM?
On very flat crystalline 2D samples with sharp single atom tip where repulsive forces dominate over attractive forces.
What is a heteropolymer and a homopolymer?
Heteropolymers are polymers that contain multiple types of monomer.
Homopolymers are polymers that contain one type of monomer.
What is the persistence length of dsDNA?
About 50nm.
Which models are best used for the structure of RNA and ssDNA, and dsDNA?
For RNA and ssDNA: FJC and FRC are the best models, but we can also use WLC with a bond length, l, of about twice the nucleotide repeat along the chain.
For dsDNA: WLC model
Describe the force-extension behaviour for ssDNA.
The applied force stretches the molecule out against entropy until straight and then the force rises rapidly upon bond extension until breakage.
Describe the force-extension behaviour for dsDNA.
Increasing force: dsDNA→Double-helix unwinds→Ladder structure→Connections between two strands start to break off (overstretch transition)(at about 65pN)→Splits into two single strands
A force plateau is reached just after full extension of the entropic coil conformation (during overstretch transition) and after the overstretch transition it behaves like ssDNA. One strand is only held to the other by intermolecular forces.
Is dsDNA melting reversible?
Melting is reversible if the force is released before breakage (i.e. the double-helix can re-anneal if the normalised extension is dropped below 1 again)
What factor affects DNA reannealing kinetics?
Salt concentration as ions affect many intermolecular forces.
What is the central dogma of molecular biology?
The genetic information flow from DNA to proteins.
DNA replicates using DNA polymerase. Information from DNA is transferred in RNA by transcription (copying a segment of DNA into RNA) using RNA polymerase.
Information is transferred from the RNA to a protein by translocation (ribosome).
How do DNA polymerase and RNA polymerase obtain chemical energy?
DNA polymerase uses deoxyribonucleoside triphosphates (dNTPs) to obtain chemical energy by breaking a covalent bond within the dNTP molecule.
RNA polymerase does the same with ribonucleoside triphosphates (rNTPS).
What is a genome?
All the genetic material in an organism.
What is a gene?
A section of DNA that codes for a particular sequence of amino acids to make a specific protein .
What is DNA hybridisation? What is required for this process to occur?
The process in which two complementary ssDNA and/or RNA molecules bond together to form dsDNA.
The two molecules must be complements of each other (i.e. Watson-Crick base pairings (A-T and C-G) must form along the entire sequence) unless the DNA is long enough in which case there can be up to a few mismatched bases (DNA sequence mutations) for hybridisation to occur.
What is a fully complementary dsDNA molecule?
One in which all the bases in the strands form A-T and C-G base pairings with each other.
What factors affect the melting temperature of DNA?
Melting temperature increases with increasing strand length as well as an increasing number of G-C base pairings.
