M2M Notes

Question 1

what are the building blocks of nucleic acids

Answer 1

Ribonucleotide and 2’deoxy-nucleotide residues

Question 2

which oxygen is missing from ribose and why

Answer 2

2’, makes deoxy-ribose (RNA v DNA)

Question 3

what is the mechanism of caffeine action

Answer 3

prevent cyclic AMP from being decyclicized

Question 4

how many rings in purines

Answer 4

double ring bases

Question 5

how many rings in pyrimidines

Answer 5

triple ring bases

Question 6

order of solubility for nucleoside, nucleotide, and base

Answer 6

nucleotide > nucleoside > base

Question 7

two diseases from accumulation in tissues of low-solubility purines

Answer 7

Gout and Lesch-Nyhan

Question 8

what is the polarity of DNA and RNA

Answer 8

5’ -> 3’

Question 9

What is the central dogma of life

Answer 9

DNA –> RNA –> Protein

Genome -> Transcriptome -> Proteome

Question 10

what does rapid DNA/RNA replication signify

Answer 10

cancer, bacterial or viral infection

Question 11

what are non-specific drug targets

Answer 11

transcription and translation

Question 12

what are specific drug targets

Answer 12

protein products (efficacy is structure-dependent

Question 13

What are the two classes of “high energy” bonds

Answer 13

thioester and phosphate

Question 14

high energy thioester molecule?

Answer 14

C-S bond in acetyl CoA

Question 15

high energy phosphate molecules?

Answer 15

phosphoanhydride (P-O-P) in ATP
phosphocreatine (P-N)
phosphoenolpyruvate (C-O-P)

Question 16

What defines a “high energy” bond

Answer 16

not instability, but delta-Go’ <= -6 kcal/mol

Question 17

equation for Gibbs Free Energy

Answer 17

delta-G = delta-Go’ + 2.3RTlog Q

Q = [products]/[reactants]

Question 18

standard conditions for biochemistry

Answer 18

T = 298K (25 degC)
P = 1 atm
pH = 7.0
[H2O] = 55.5 molar
1M reactants AND products
1mM Mg++ in solution

Question 19

theoretical delta-G for releasing energy in glucose

Answer 19

-686 kcal/mol

Question 20

theoretical ADP -> ATP yield per glucose

Answer 20

90 ATP

Question 21

actual ADP -> ATP yield per glucose

Answer 21

32 ATP (~35% effficiency)

Question 22

chemical delta-G

Answer 22

delta-G = delta-H -T*delta-S

Question 23

concentration gradient delta-G

Answer 23

delta-G = 2.3*RT log([C2]/[C1])

Question 24

electric field gradient potential delta-G

Answer 24

delta-G = zF*delta-psi

Question 25

redox rxn delta-G

Answer 25

delta-G = -nF*deltaE

Question 26

What types of work do cells perform

Answer 26

change concentration gradients synthesize macromolecules mechanical work of motion (filaments, cilia, chromosome movements)

Question 27

membrane voltage potential

Answer 27

50-70 mV

Question 28

Units of Energy currency

Answer 28

ADP -> ATP NAD+ -> NADH NADP+ -> NADPH FAD -> FADH2

Question 29

what is 5-mC

Answer 29

5-methyl Cytosine

Question 30

what is 5-methyl Cytosine

Answer 30

methyl group added at 5' carbon, important consequences for gene regulation

Question 31

what is a major cause of mutations

Answer 31

deamination of bases (amino group removal) | depurination, leads to phosphate backbone fragility

Question 32

give an example of deaminiation

Answer 32

5-methyl Citosine -> Thymine thymine also a naturally occuring base, leads to unintentional mutation

Question 33

what is a major cause of DNA damage?

Answer 33

oxidative damage by hydroxyl radicals UV light covalently links thymines, kinks DNA backbone, transcription/translation problems

Question 34

what is DNA intercalation

Answer 34

drug or other molecular interference with DNA by inserting into grooves of helix

Question 35

What is Actinomycin D

Answer 35

intercalating agent frequently used in cancer therapy, target actively dividing cells complex, multi-ring molecule

Question 36

What is doxorubicin (adrinmycin)

Answer 36

intercalating agent frequently used in cancer therapy, target dividing cells

Question 37

How do retroviruses work

Answer 37

use reverse transcriptase to transcribe DNA from RNA

Question 38

reverse transcriptase

Answer 38

make DNA from RNA not part of human genome

Question 39

Chargaff's Rule

Answer 39

``` [A] = [T] [G] = [C] ```

Question 40

what groove of DNA is used by proteins for access

Answer 40

major groove

Question 41

what is the periodicity of DNA

Answer 41

2. 0 nm helix diameter | 3. 5 nm periodicity (10 steps)

Question 42

What is the orientation of purine/pyrimidine bonds in DNA

Answer 42

sugar-phosphate backbone is external, AT and GC bonds are internal

Question 43

What are the strengths of hydrogen bonds in DNA

Answer 43

G-C -> 14.1 kcal/mol A-T -> 5.7 kcal/mol

Question 44

are stacked dimers energetically favored or disfavored in DNA structure

Answer 44

favored