Nucleic Acids Flashcards
What is the difference beween a nucleoside and a nucleotide
A nucleoside is a nitrogenous base + a pentose sugar, with no phosphate group. A nucleotide has a phosphate group
Purines have a ____-ring struncture, and pyrimidines have a ____- ring structrue
Purines have a two-ring struncture, and pyrimidines have a one- ring structrue
Name the mmnenonic for purines and pyrimidines
pure as gold (purines = adenine and guanine)
CUT the PIE (cytosine, uracil, thymine for CUT and PIE reminds you of the first two letters in pyrimidines)
Uracil is the demethylated version of what nitrogenous base?
Thymine
adenine and guanine differ by adenine’s ____ group and guanine’s ____ group
adenine and guanine differ by adenine’s amine group and guanine’s carbonyl group
cytosine is the only pyrmidine with one ____ group
primary amine
the phosphodiester bond is the linkage between the 3’ carbon atom of one sugar molecule and the 5’ carbon atom of another, deoxyribose in DNA and ribose in RNA
phosphodiester bond
We read DNA strands from the 5’ end to the 3’ end. The 5’ end is by the ____ group, and the 3’ end is by the ____ group
The 5’ end is by the phosphate group, and the 3’ end is by the OH group
Name this molecule
ATP!
Name this molcule
GTP!
Note, the nitrogenous base is a guanine
Name this molecule
Cyclic adenosine monophosphate cAMP
crucial intracellular signaling molecule
in nucleotide monophosphates, a single phosphate group can attach to both 3’ and 5’ carbons, such as in cAMP
True or false
In shorthand form, nitrogenous bases are always written in the 5’ to 3’ direction, but nitrogenous bases are connected by 3’ to 5’ phosphodiester bonds
True
FAD, FMN, NAD, NADP+ and CoA are all ____
nucleotides that are cofactors
How many hydrogen bonds form between A and T?
2
How many hydrogen bonds are between C and G?
3
stands with more C-G pairs require higher temperatures for the strands to denature because there are more bonds
True or False
Purines pair with each other, and so do pyrimidines
False
purines pair with pyrimidines and vice versa
Name this term
In DNA there is always equality in quantity between the bases A and T and between the bases G and C
Chargaff’s rule
%A=%T. %C = %G
There are three types of DNA, A, B, and Z. The most commonly known one in which Watson and Crick applied their principles is B-DNA. Compare and contrast these 3 types of DNA
- B-DNA is the typical right-handed double stranded helix, 10.5 bp per turn
- A-DNA is deyhydrated & tighter than B-DNA, 11 bp per turn
- Z-DNA is found in methylated DNA, is left-handed and looser, and has 12 bp per turn
the over- or under-winding of a DNA strand, and is an expression of the strain on that strand
supercoiling
a DNA segment that is overwound is ____ supercoiled, and one that is underwound is ____ supercoiled
a DNA segment that is overwound is positively supercoiled, and one that is underwound is negatively supercoiled
a typical DNA strand is ____ supercoiled, making unwinding of the double helix for transcription more energetically favorable
negatively
negatively supercoiled = underwound
the process in which complementary base pairs combine
Hybridization
the driving force of this is formation of hydrogen bonds between pairs
the melting of annealed (joined) strands via heat application; can cause the reversible dissociation of the base-paired complex
in DNA, not in proteins
thermal denaturation
the heat causes the double stranded helix to unwind as the hydrophobic interactions between bases become insufficient to maintain a base-paired complex
the temperature at which half of the DNA strands in a sample are in their single stranded (ssDNA) state
melting temperature (Tm)
depends on nucelotide length and sequence
C-G requires more heat to denature than A-T
what is the significance of denaturation and hybridization in PCR?
Denaturation is used to seperate strands and subsequent hybridization is used right before the amplification process to anneal the strands
