Lecture 4 Flashcards
If A2 < A1:
Delta G is negative, and transfer is favorable
Other source of Free Energy in a cell:
- conecentration gradients
- redox reactions
If A2 > A1:
Delta G is positive and transfer is unfavorable
If A2 = A1:
Delta G is 0 and the system is at equilibrium
Diffusion:
- 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
- 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
Oxidation:
the removal of electrions
Reduction
the gain of electrons
Oxidant:
molecule causing the reduction
Reductor:
molecule causing the oxidation
Excellent electron acceptor:
oxygen, used in the context of the electron transport chain
REDOX reaction in iron and copper:
- Fe2+ -> Fe3+: reducdant, oxidized
- Cu2+ -> Cu+: oxidant, reduced
Measuring reduction potential:
- Iron and hydrogen can exist in oxidized or reduced form
- Solutions of Fe3+ and Fe2+ are added to the cathode, and solutions of H+ and H2 are added to the anoide
- Connect the two to measure the direction and strength (voltage) of electron flow
- 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+
Voltmeter:
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
Electron movement:
electrons tend to move based on the ions’ tendency to accept or donate electrons
If E knot is positive:
strong oxidizing agent: test cell is positive w/ respect to standard cell and acecpts electrons
If E knot is negative:
strong reducing agent: any redox couple that donates electrons to the standard hydrogen cell
E knot prime:
the standard oxidation-reduction potential (pH 7 and 25 C)
Gibbs Free Energy (redox reactions)
Oxidation of ethanol by NAD+ (catalyzed by Alcohol Dehydrogenase)
unfavorable reaction
Gibbs Free Energy (Metabolic reactions)
Gibbs Free Energy (Protein folding)
Electron Transport Chain:
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+)
Nucleic Acids:
primary, secondary, and tertiary structure and transmisison of genetic information
Properties of nucleic acids:
- began evolution
- carry the potential for self duplication necessary to pass information from on generation to the next
The first genome to be sequenced:
bacteriophage, a viral genome with only 5,368 bp
The first eukaryote to be sequenced:
yeast in 1989
Properties of nucleotides:
- 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
The difference between ribonucleic acids (RNA) vs. deoxyribonucleic acid (DNA)
in deoxyribose, the 2’ hyrdroxyl group is relaced by H (which can be catalytically active)
Backbone of nucleic acids:
phosphate groups and sugars
Pyrimidines:
cytosine, thymine, and uracil
Purines:
adenine and guanine
Number of hydrogen bonds between A and T:
2 bonds
Number of hydrogen bonds between A and U/ A and T
stronger, 3 bonds
Nucleoside:
base + sugar
* deoxyadenosine
* deoxyguanosine
* deoxycytidine
* uridine, thymidine
Nucleotide Monophosphate (NMP):
base + sugar + phosphate group = nucleoside + 5’ phosphate
Polynucleotides:
nucleic acids are polymers of nucleotides with different bases attached, via a glycosidic bond
Nucleic acid optimal wavelength:
~260 nm
Spectrophotometer of nucleic acids:
- 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
Self-catalysis in RNA:
- Mix RNA with a base
- Pull hydrogen off from the 2’ OH group
- Will attack the phosphate group, and breaks the phosphate bond that would hold an addition nucleotide
Catalyst of DNA/RNA replication:
DNA/RNA polymerase
Dehydration of two nucleotide monophosphates:
highly unfavorable, +25 kJ/mol. Equilibrium lies on the side of hyrolysis of phosphodiester bond
Favorability of joining a phosphodiester bond?
- adding a triphosphate
- breaks and releases a pyrophosphate by polymerase
- releases energy to make the reaction more favorable
- coupling or anabolic reaction
Written direction of DNA/RNA:
5’ to 3’
Experiment 1/ Transformation:
the transfer of DNA from a pathogenic bacteria to a nonpathogenic bacteria, could make them pathogenic
Hershey-Chase Experiment:
- bacteriophage were grown in radioactive sulfur and phosphorus, which labels proteins and nucleic acids, respectively
- phosphorus was transferred during infection and was sufficient to direct formation of new bacteriophage
- new phage particles contained radiolabeled phosphorus, but no radioactive sulfur
- DNA can be replicated, not protein
