M2M Notes Flashcards
what are the building blocks of nucleic acids
Ribonucleotide and 2’deoxy-nucleotide residues
which oxygen is missing from ribose and why
2’, makes deoxy-ribose (RNA v DNA)
what is the mechanism of caffeine action
prevent cyclic AMP from being decyclicized
how many rings in purines
double ring bases
how many rings in pyrimidines
triple ring bases
order of solubility for nucleoside, nucleotide, and base
nucleotide > nucleoside > base
two diseases from accumulation in tissues of low-solubility purines
Gout and Lesch-Nyhan
what is the polarity of DNA and RNA
5’ -> 3’
What is the central dogma of life
DNA –> RNA –> Protein
Genome -> Transcriptome -> Proteome
what does rapid DNA/RNA replication signify
cancer, bacterial or viral infection
what are non-specific drug targets
transcription and translation
what are specific drug targets
protein products (efficacy is structure-dependent
What are the two classes of “high energy” bonds
thioester and phosphate
high energy thioester molecule?
C-S bond in acetyl CoA
high energy phosphate molecules?
phosphoanhydride (P-O-P) in ATP
phosphocreatine (P-N)
phosphoenolpyruvate (C-O-P)
What defines a “high energy” bond
not instability, but delta-Go’ <= -6 kcal/mol
equation for Gibbs Free Energy
delta-G = delta-Go’ + 2.3RTlog Q
Q = [products]/[reactants]
standard conditions for biochemistry
T = 298K (25 degC) P = 1 atm pH = 7.0 [H2O] = 55.5 molar 1M reactants AND products 1mM Mg++ in solution
theoretical delta-G for releasing energy in glucose
-686 kcal/mol
theoretical ADP -> ATP yield per glucose
90 ATP
actual ADP -> ATP yield per glucose
32 ATP (~35% effficiency)
chemical delta-G
delta-G = delta-H -T*delta-S
concentration gradient delta-G
delta-G = 2.3*RT log([C2]/[C1])
electric field gradient potential delta-G
delta-G = zF*delta-psi
redox rxn delta-G
delta-G = -nF*deltaE
What types of work do cells perform
change concentration gradients
synthesize macromolecules
mechanical work of motion (filaments, cilia, chromosome movements)
membrane voltage potential
50-70 mV
Units of Energy currency
ADP -> ATP
NAD+ -> NADH
NADP+ -> NADPH
FAD -> FADH2
what is 5-mC
5-methyl Cytosine
what is 5-methyl Cytosine
methyl group added at 5’ carbon, important consequences for gene regulation
what is a major cause of mutations
deamination of bases (amino group removal)
depurination, leads to phosphate backbone fragility
give an example of deaminiation
5-methyl Citosine -> Thymine
thymine also a naturally occuring base, leads to unintentional mutation
what is a major cause of DNA damage?
oxidative damage by hydroxyl radicals
UV light covalently links thymines, kinks DNA backbone, transcription/translation problems
what is DNA intercalation
drug or other molecular interference with DNA by inserting into grooves of helix
What is Actinomycin D
intercalating agent frequently used in cancer therapy, target actively dividing cells
complex, multi-ring molecule
What is doxorubicin (adrinmycin)
intercalating agent frequently used in cancer therapy, target dividing cells
How do retroviruses work
use reverse transcriptase to transcribe DNA from RNA
reverse transcriptase
make DNA from RNA
not part of human genome
Chargaff’s Rule
[A] = [T] [G] = [C]
what groove of DNA is used by proteins for access
major groove
what is the periodicity of DNA
- 0 nm helix diameter
3. 5 nm periodicity (10 steps)
What is the orientation of purine/pyrimidine bonds in DNA
sugar-phosphate backbone is external, AT and GC bonds are internal
What are the strengths of hydrogen bonds in DNA
G-C -> 14.1 kcal/mol
A-T -> 5.7 kcal/mol
are stacked dimers energetically favored or disfavored in DNA structure
favored
