Nucleic Acids Flashcards
Very briefy describe the structure of DNA.
DNA has a double helix structure with the genetic bases on the inside.
What are the two forms of DNA and which is most common in biological systems?
A-form dsDNA (dehydrated) and B-form dsDNA (hydrated).
B-form dsDNA is the most common form of DNA in biological systems.
What are the 4 DNA bases and how do they pair?
Adenine pairs with Thymine (A-T).
Cytosine pairs with Guanine (C-G).
What is DNA?
DNA = Deoxyribonucleic acid.
DNA is a very stiff polymer molecule made from monomer units called nucleotides which have the form: phosphate group-sugar-base (A, T, C, or G).
Why is DNA called an acid?
The phosphate group loses an H+ ion in aqueous solution (i.e. is a proton donor).
How does RNA differ to DNA?
RNA has one extra oxygen atom connected to the sugar ring.
RNA has uracil instead of thymine.
RNA tends to be single stranded (but can fold to form base-paired double strand regions).
What mechanism acts as a gene expression switch?
Cytosine bases modified by enzymes called DNA methylases interfere with DNA transcription (gene expression). Methylation of cytosine acts as a gene expression switch. Methylation silences (turns off) genes.
How is the double helix of B-form DNA stabilised?
By hydrogen bonding between base pairs and base-stacking interactions (hydrophobic effect).
Which AFM mode is best used for biological molecules and why?
AC-tapping mode. Biological molecules are liquid/liquid-crystal so cannot support shear forces and are deformed by DC-contact mode AFM so AC-tapping mode tends to be used instead (as force is always normal to surface and isn’t continuous).
What are advantages of AFM over STM?
STM only works on conducting or semi-conducting surfaces.
What are useful properties of AFM?
AFM works in all environments (e.g. hydrating environments (e.g. liquid)).
Large dynamic range: 25nm-65μm.
Good signal-to-noise for single molecules.
What is DNA binded to during SPM (AFM and STM) and why?
Muscovite mica, as it can be easily cleaved to produce a fresh, uncontaminated, atomically flat surface and in aqueous environments the surface carries a negative charge.
What factor affects AFM resolution?
Tip sharpness. Atomic tips are better than molecular tips.
Why in practice does STM have higher imaging resolution than AFM on most samples?
The force in AFM has both attractive and repulsive contributions and the interaction volume of the AFM tip with the surface is typically larger than for STM.
