Lecture 4

Question 1

If A2 < A1:

Answer 1

Delta G is negative, and transfer is favorable

Question 2

Other source of Free Energy in a cell:

Answer 2

1. conecentration gradients
2. redox reactions

Question 3

If A2 > A1:

Answer 3

Delta G is positive and transfer is unfavorable

Question 4

If A2 = A1:

Answer 4

Delta G is 0 and the system is at equilibrium

Question 5

Diffusion:

Answer 5

1. Two solutions of A with concentrations [A]1 and [A]2 are separated by a porous membrane through which A can pass in either direction
2. If the initial concentration is higher in region 1, the driving force for transport of A across the membrane will result in movement of A from region 1 to region 2 until equal concentrations are obtained

Question 6

Oxidation:

Answer 6

the removal of electrions

Question 7

Reduction

Answer 7

the gain of electrons

Question 8

Oxidant:

Answer 8

molecule causing the reduction

Question 9

Reductor:

Answer 9

molecule causing the oxidation

Question 10

Excellent electron acceptor:

Answer 10

oxygen, used in the context of the electron transport chain

Question 11

REDOX reaction in iron and copper:

Answer 11

1. Fe2+ -> Fe3+: reducdant, oxidized
2. Cu2+ -> Cu+: oxidant, reduced

Question 12

Measuring reduction potential:

Answer 12

1. Iron and hydrogen can exist in oxidized or reduced form
2. Solutions of Fe3+ and Fe2+ are added to the cathode, and solutions of H+ and H2 are added to the anoide
3. Connect the two to measure the direction and strength (voltage) of electron flow
4. If electrons flow from reference (H+/H2) cell to the test cell, then H2 is giving up elecrons to Iron, oxidizing H2 and reducing Fe3+ to Fe2+

Question 13

Voltmeter:

Answer 13

placed between the two half-cells and measures the electromotive force in volts, whch is the measure of potential electrons to flow from one cell to the other

Question 14

Electron movement:

Answer 14

electrons tend to move based on the ions’ tendency to accept or donate electrons

Question 15

If E knot is positive:

Answer 15

strong oxidizing agent: test cell is positive w/ respect to standard cell and acecpts electrons

Question 16

If E knot is negative:

Answer 16

strong reducing agent: any redox couple that donates electrons to the standard hydrogen cell

Question 17

E knot prime:

Answer 17

the standard oxidation-reduction potential (pH 7 and 25 C)

Question 18

Gibbs Free Energy (redox reactions)

Answer 18

Question 19

Oxidation of ethanol by NAD+ (catalyzed by Alcohol Dehydrogenase)

Answer 19

unfavorable reaction

Question 20

Gibbs Free Energy (Metabolic reactions)

Answer 20

Question 21

Gibbs Free Energy (Protein folding)

Answer 21

Question 22

Electron Transport Chain:

Answer 22

regeneration of ATP from ADP requires an input of energy, which is supplised by the protein gradient in the motochondrial membrane. Proton gradient comes from redox reactions (NADH + O2 -> NAD+)

Question 24

Nucleic Acids:

Answer 24

primary, secondary, and tertiary structure and transmisison of genetic information

Question 25

Properties of nucleic acids:

Answer 25

* began evolution * carry the potential for self duplication necessary to pass information from on generation to the next

Question 26

The first genome to be sequenced:

Answer 26

bacteriophage, a viral genome with only 5,368 bp

Question 27

The first eukaryote to be sequenced:

Answer 27

yeast in 1989

Question 28

Properties of nucleotides:

Answer 28

* phosphate group is highly acidic * negatively charged at phys. pH (7) * phosphodiester linkages (covalent bonds) attach to the 5' hydroxyl on one monomer and the 3' hydroxyl on theo ther monomer * glycosidic linkages (covalent bonds) * at optimal pH 7, the O groups are reduced for oxidized proteins

Question 29

The difference between ribonucleic acids (RNA) vs. deoxyribonucleic acid (DNA)

Answer 29

in deoxyribose, the 2' hyrdroxyl group is relaced by H (which can be catalytically active)

Question 30

Backbone of nucleic acids:

Answer 30

phosphate groups and sugars

Question 31

Pyrimidines:

Answer 31

cytosine, thymine, and uracil

Question 32

Purines:

Answer 32

adenine and guanine

Question 33

Number of hydrogen bonds between A and T:

Answer 33

2 bonds

Question 34

Number of hydrogen bonds between A and U/ A and T

Answer 34

stronger, 3 bonds

Question 35

Nucleoside:

Answer 35

base + sugar * deoxyadenosine * deoxyguanosine * deoxycytidine * uridine, thymidine

Question 36

Nucleotide Monophosphate (NMP):

Answer 36

base + sugar + phosphate group = nucleoside + 5' phosphate

Question 37

Polynucleotides:

Answer 37

nucleic acids are polymers of nucleotides with different bases attached, via a glycosidic bond

Question 38

Nucleic acid optimal wavelength:

Answer 38

~260 nm

Question 39

Spectrophotometer of nucleic acids:

Answer 39

* conjugated double-bonds in the bases allow light to be absorbed in the UV spectrum * can be used to quantify in solution * 260 nm: 280 nm: purity, comparison between nucleic acids and proteins

Question 40

Self-catalysis in RNA:

Answer 40

1. Mix RNA with a base 2. Pull hydrogen off from the 2' OH group 3. Will attack the phosphate group, and breaks the phosphate bond that would hold an addition nucleotide

Question 41

Catalyst of DNA/RNA replication:

Answer 41

DNA/RNA polymerase

Question 42

Dehydration of two nucleotide monophosphates:

Answer 42

highly unfavorable, +25 kJ/mol. Equilibrium lies on the side of hyrolysis of phosphodiester bond

Question 43

Favorability of joining a phosphodiester bond?

Answer 43

1. adding a triphosphate 2. breaks and releases a pyrophosphate by polymerase 3. releases energy to make the reaction more favorable 4. coupling or anabolic reaction

Question 44

Written direction of DNA/RNA:

Answer 44

5' to 3'

Question 45

Experiment 1/ Transformation:

Answer 45

the transfer of DNA from a pathogenic bacteria to a nonpathogenic bacteria, could make them pathogenic

Question 46

Hershey-Chase Experiment:

Answer 46

1. bacteriophage were grown in radioactive sulfur and phosphorus, which labels proteins and nucleic acids, respectively 2. phosphorus was transferred during infection and was sufficient to direct formation of new bacteriophage 3. new phage particles contained radiolabeled phosphorus, but no radioactive sulfur 4. DNA can be replicated, not protein