∆S, measure of microscopic disorder in a system
∆H, measure of energy of a thermodynamic system
Define Gibbs Free Energy
∆G, Amount of work that can extracted from a system
Name some high energy compounds
ATP, Glucose, NADH
What is a Redox reaction?
A chemical reaction in which atoms have their oxidation state changes (i.e. the exchange of electrons between atoms or compounds)
Define First Law of Thermodynamics
Energy is always conserved (i.e. energy cannot be created or destroyed)
Define Second Law of Thermodynamics
The entropy of the universe if always increasing (i.e. it takes energy to put things in an orderly fashion)
List and define the four kinds of kinetic energy
Radiant: energy from sun carried by photonsThermal: KE from temperatureMechanical: KE from motionElectrical: movement of charged particles down gradients of electric potential
What are the four ways that potential energy is stored?
Chemical bonds, concentration gradients, in redox pairs, in electric fields from charge separation
What are the three basic thermodynamic equations?
∆G = ∆H - T∆S∆G˚ = ∆G - RTlnKeq∆G = ∆G˚ + RT*ln([prod]/[react])FYI: [prod]/[react] = Q
If ∆G is negative which way does the reaction proceed?
Forward (i.e. the forward reaction is spontaneous)
What does it mean when ∆G is zero?What does K equal at this point?
The reaction is at equilibrium1
What is K when ∆G is positive?
K < 1
What equation does one use to relate Gibbs Free Energy to Redox potential
∆G = -nF∆EWhere n = number of electrons transferred, F = Faraday’s constant (96,500 C/Mol of e-),∆E = difference in reduction potential in (volts)
What might the system be doing if it is moving electrons?
Creating energy! (I acknowledge this is a dumb card. Sorry.)
How might one make a reaction with a +∆G move in the forward direction?
Couple it with a spontaneous reaction
What are some high energy compounds used in biological systems?
Lipids and Carbohydrates
What are the two main classes of high energy bonds?
Thioester (Sulfur - Carbon)High energy phosphate bonds (e.g. ATP)
Which nitrogenous bases are purines?Pyrimidines?
Purines: AGPyrimidines: CTU
What is the difference between ribose and deoxyribose?
ribose has a hydroxyl group at the 2’ carbon and deoxyribose does not
What is the difference between ribonucleoside and deoxyribonucleoside?
A nucleoside is a sugar + base.A deoxyribonucleoside is doesn’t have a hydroxyl group at the 2’ carbon
What is the difference between a nucleoside and nucleotide?
A nucleotide has a 5’ phosphate group, a nucleoside does not
What is the difference between a nucleoside diphosphate and nucleoside triphosphate?
Nucleoside triphosphate (ATP) has three phosphate groups, nucleoside diphosphate (ADP) has two phosphate groups
Rank the relative solubilities of bases, nucleotides, and nucleosidesPyrimidines vs. Purines
Nucleotides > Nucleosides > BasesPyrimidines > Purines
What is an example of a disease caused by the insolubility of bases?
Gout - An accumulation of uric acid in joints as a precipitate of purines
What makes DNA and RNA polar?
The 3’ hydroxyl group and the 5’ phosphate group. Nucleotides are always added to the 3’ prime end b/c it is nucleophilic. Nothing is ever added to the 5’ prime end.
Define phosphodiester linkage.
The key to the DNA/RNA backbone. Caused by the nucleophilic 3’ hydroxyl group attacking the 5’ phosphate group.
What critical experiment helped establish DNA as the basic genetic material?
Avery, McCarty, and McCloud:Isolated DNA from virulent bacteria. Inserted into non-virulent bacteria. Kills the mouse.
List Chargaff’s Rules.
C=G, A=TC - Cytosine, G - Guanine, A - Adenine, T - Thymine(Think DNA)
Describe the Watson-Crick model for DNA structure
Double stranded sugar-phosphate backbone. Internal base pairing (Chargaff’s Rules).
What is the major groove?Minor groove?
DNA has two grooves, the major is bigger, minor is smaller.
What four things affect the stability of DNA double helix structure in solution?
- [salt], higher [salt] = more stable2. Extremes of pH destabilize3. Length, longer strand = more stable4. GC/AT ratio, higher ratio = more stable
Describe linear, circular, relaxed and supercoiled forms of DNA.
Linear = non circular dna (eurkaryotic)Circular = found in prokaryotes (ecoli)Relaxed = straight ribbon with normal twistingSupercoiled = DNA with torsion applied (important for eukaryotes)
What is methylation (with regard to DNA) and how does it lead to disease?
When there is a C & G adjacent to one another on same side of helix the C is usually methylated = 5 methylcytosine (80-90% of time). Without such methylation such C-G areas are associated with gene promoters and can lead to over transcription of genes.
What is deamination (with regard to DNA) and how does it lead to disease?
When a base loses an amine group mutations occur. W/o proper repair - leads to disease.For example C turns to U or When G is deaminated it becomes X which pairs with T. Then DNA repair converts X to A. Thus G-C has been converted to AT.
What is depurination (with regard to DNA) and how does it lead to disease?
The removal of a purine base from a deoxyribose sugar.Now missing base = no bueno. Plus, this weakens the phosphodiester backbone of DNA.
How does UV light damage DNA?
It covalently binds thymines together which distorts the helix and can block replication enzymes.
How is DNA polymerized?
New nucleotides are added to the 3’ end.
How are nucleoside analogues used as drugs?
When the cell is replicating DNA the free floating analogues are recruited to the new strand. Their structure, however, causes the new strand to be nonfunctional.
Differences between DNA and RNA?
DNA has no 2’ Hydroxyl group.RNA binds Uracil instead of ThymineRNA is single stranded
What are the 3 main classes of RNA and their components?
Information containing: mRNA (messenger)Structural: rRNA (ribosomal), snRNA (small nuclear)Regulatory: miRNA (micro), siRNA (small interfering)
What does rRNA do?
Ribosomes are made of rRNA. Ribosomes translates mRNA.
What does snRNA do?
Small nuclear RNA helps with splicing, regulation of transcription factors, and maintenance of telomeres.
What do miRNA and siRNA do?
They regulate gene expression.
What does mRNA do?
Contains information (codons) to translated into proteins by ribosomes (rRNA).
Describe the chemical basis for nucleic acid melting.How can it be used to detect one specific sequence in total cellular DNA?
Heating up the DNA breaks the H-bonds between the strands (base pairs)Add tagged probe of 20-25 base pairs which will anneal onto a strand if they have the complementary sequence.