Nucleic Acids and Bioenergetics

Question 1

Define Entropy

Answer 1

∆S, measure of microscopic disorder in a system

Question 2

Define Enthalpy

Answer 2

∆H, measure of energy of a thermodynamic system

Question 3

Define Gibbs Free Energy

Answer 3

∆G, Amount of work that can extracted from a system

Question 4

Name some high energy compounds

Answer 4

ATP, Glucose, NADH

Question 5

What is a Redox reaction?

Answer 5

A chemical reaction in which atoms have their oxidation state changes (i.e. the exchange of electrons between atoms or compounds)

Question 6

Define First Law of Thermodynamics

Answer 6

Energy is always conserved (i.e. energy cannot be created or destroyed)

Question 7

Define Second Law of Thermodynamics

Answer 7

The entropy of the universe if always increasing (i.e. it takes energy to put things in an orderly fashion)

Question 8

List and define the four kinds of kinetic energy

Answer 8

Radiant: energy from sun carried by photonsThermal: KE from temperatureMechanical: KE from motionElectrical: movement of charged particles down gradients of electric potential

Question 9

What are the four ways that potential energy is stored?

Answer 9

Chemical bonds, concentration gradients, in redox pairs, in electric fields from charge separation

Question 10

What are the three basic thermodynamic equations?

Answer 10

∆G = ∆H - T∆S∆G˚ = ∆G - RTlnKeq∆G = ∆G˚ + RT*ln([prod]/[react])FYI: [prod]/[react] = Q

Question 11

If ∆G is negative which way does the reaction proceed?

Answer 11

Forward (i.e. the forward reaction is spontaneous)

Question 12

What does it mean when ∆G is zero?What does K equal at this point?

Answer 12

The reaction is at equilibrium1

Question 13

What is K when ∆G is positive?

Answer 13

K < 1

Question 14

What equation does one use to relate Gibbs Free Energy to Redox potential

Answer 14

∆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)

Question 15

What might the system be doing if it is moving electrons?

Answer 15

Creating energy! (I acknowledge this is a dumb card. Sorry.)

Question 16

How might one make a reaction with a +∆G move in the forward direction?

Answer 16

Couple it with a spontaneous reaction

Question 17

What are some high energy compounds used in biological systems?

Answer 17

Lipids and Carbohydrates

Question 18

What are the two main classes of high energy bonds?

Answer 18

Thioester (Sulfur - Carbon)High energy phosphate bonds (e.g. ATP)

Question 19

Which nitrogenous bases are purines?Pyrimidines?

Answer 19

Purines: AGPyrimidines: CTU

Question 20

What is the difference between ribose and deoxyribose?

Answer 20

ribose has a hydroxyl group at the 2’ carbon and deoxyribose does not

Question 21

What is the difference between ribonucleoside and deoxyribonucleoside?

Answer 21

A nucleoside is a sugar + base.A deoxyribonucleoside is doesn’t have a hydroxyl group at the 2’ carbon

Question 22

What is the difference between a nucleoside and nucleotide?

Answer 22

A nucleotide has a 5’ phosphate group, a nucleoside does not

Question 23

What is the difference between a nucleoside diphosphate and nucleoside triphosphate?

Answer 23

Nucleoside triphosphate (ATP) has three phosphate groups, nucleoside diphosphate (ADP) has two phosphate groups

Question 24

Rank the relative solubilities of bases, nucleotides, and nucleosidesPyrimidines vs. Purines

Answer 24

Nucleotides > Nucleosides > BasesPyrimidines > Purines

Question 25

What is an example of a disease caused by the insolubility of bases?

Answer 25

Gout - An accumulation of uric acid in joints as a precipitate of purines

Question 26

What makes DNA and RNA polar?

Answer 26

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. 

Question 27

Define phosphodiester linkage.

Answer 27

The key to the DNA/RNA backbone. Caused by the nucleophilic 3' hydroxyl group attacking the 5' phosphate group.

Question 28

What critical experiment helped establish DNA as the basic genetic material?

Answer 28

Avery, McCarty, and McCloud:Isolated DNA from virulent bacteria. Inserted into non-virulent bacteria. Kills the mouse.

Question 29

List Chargaff's Rules.

Answer 29

C=G, A=TC - Cytosine, G - Guanine, A - Adenine, T - Thymine(Think DNA)

Question 30

Describe the Watson-Crick model for DNA structure

Answer 30

Double stranded sugar-phosphate backbone. Internal base pairing (Chargaff's Rules). 

Question 31

What is the major groove?Minor groove?

Answer 31

DNA has two grooves, the major is bigger, minor is smaller. 

Question 32

What four things affect the stability of DNA double helix structure in solution?

Answer 32

1. [salt], higher [salt] = more stable2. Extremes of pH destabilize3. Length, longer strand = more stable4. GC/AT ratio, higher ratio = more stable

Question 33

Describe linear, circular, relaxed and supercoiled forms of DNA.

Answer 33

Linear = non circular dna (eurkaryotic)Circular = found in prokaryotes (ecoli)Relaxed = straight ribbon with normal twistingSupercoiled = DNA with torsion applied (important for eukaryotes)

Question 34

What is methylation (with regard to DNA) and how does it lead to disease?

Answer 34

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. 

Question 35

What is deamination (with regard to DNA) and how does it lead to disease?

Answer 35

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. 

Question 36

What is depurination (with regard to DNA) and how does it lead to disease?

Answer 36

The removal of a purine base from a deoxyribose sugar. Now missing base = no bueno. Plus, this weakens the phosphodiester backbone of DNA. 

Question 37

How does UV light damage DNA?

Answer 37

It covalently binds thymines together which distorts the helix and can block replication enzymes.

Question 38

How is DNA polymerized?

Answer 38

New nucleotides are added to the 3' end. 

Question 39

How are nucleoside analogues used as drugs?

Answer 39

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. 

Question 40

Differences between DNA and RNA? 

Answer 40

DNA has no 2' Hydroxyl group.RNA binds Uracil instead of ThymineRNA is single stranded

Question 41

What are the 3 main classes of RNA and their components?

Answer 41

Information containing: mRNA (messenger)Structural: rRNA (ribosomal), snRNA (small nuclear)Regulatory: miRNA (micro), siRNA (small interfering)

Question 42

What does rRNA do?

Answer 42

Ribosomes are made of rRNA. Ribosomes translates mRNA.

Question 43

What does snRNA do?

Answer 43

Small nuclear RNA helps with splicing, regulation of transcription factors, and maintenance of telomeres.

Question 44

What do miRNA and siRNA do?

Answer 44

They regulate gene expression.

Question 45

What does mRNA do?

Answer 45

Contains information (codons) to translated into proteins by ribosomes (rRNA).

Question 46

Describe the chemical basis for nucleic acid melting. How can it be used to detect one specific sequence in total cellular DNA?

Answer 46

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.