5. Nucleic Acids Flashcards
Two phosphates bound together via an an-hydride linkage produce what?
Pyrophosphate. The P-O-P bond in pyrophoshate is high energy with a negative ΔG.
- their negative charges repel each other
- orthophosphate has resonance stabilization
- orthophosphate interacts more favorably with biological solvents.
Explain the structure of a nucleotide.
A ribose or deoxyribose sugar (5 carbons). Bound to the first carbon is a purine or pyrimidine base (nitrogenous aromatic system). Joined to the sugars 5th carbon is 1-3 phosphate groups.
The sugar-phosphate backbone provide the core for DNA / RNA, while the nitrogen base binding determines the genetic code.
Compare the structure of purines to pyrimidines.
purines have 2 aromatic rings whereas pyrimidines have 1 (longer name, less rings).
What is a nucleoside?
A nucleoside is a sugar bound to its corresponding nitrogenous base, but lacks the phosphate groups in a nucleotide (the monomer of nucleic acids).
In the beta-glycosidic linkage between a pentose sugar and its nitrogenous base, is the base above or below the plane in a Haworth projection?
Beta linkages are above the plane.
Its Better to B UP.
alpha linkages are below (remember how they are drawn)
What is the difference between adenine / thymine ans adenosine / thymidine?
adenine / thymine - these are free nitrogenous bases
adenosine / thymidine - these are nucleosides (bound to a pentose sugar).
What is a phosphodiester bond?
A phosphodiester bond is what covalently links nucleotides together to form a polymer of nucleic acid. This occurs between the 3’OH of the sugar and the 5’ phosphate group of the next sugar.
hence, DNA is synthesized (and RNA is transcribed) in the 5’ to 3’ direction
A always H-bonds with T, G always H-bonds with C. Explain the H-bonds.
A-T - 2 hydrogen bonds per pair
G - C - 3 hydrogen bonds per pair
True or false, the temperature at which 50% of DNA has denatured is called the melting temperature (Tm).
true
note that GC rich regions of DNA (more H-bonds) will have higher Tm values.
Why does methylated DNA (which bind DNA phosphate groups) have a higher Tm than non-methylated DNA?
The phosphates in regular DNA electrostatically repel each other. When you bind them with methyl groups, they lose their negative charge. Thus, losing the force of electric repulsion makes denaturing the DNA more difficult, which increases the Tm.
How many bases take up one full turn of the right-hand helix of DNA?
10 bases complete a turn, which is approximately 34 angstroms. (thus, bases are 3.4 A apart).
How many chromosomes do humans have?
46 chromosomes, 23 from each parent.
22 allosomes, and 1 sex chromosome from each parent.
How do prokaryotes condense their DNA?
They use DNA Gyrase which super-coils the circular DNA (single circular chromosome).
DNA wrapped around an octamer of histones is called?
nucleosomes
What amino acid residues are likely found in histones?
Basic histones (lysine, arginine, histidine) since DNA is acidic (phosphate groups - nucleic acid).
