# Nucleic Acids and Bioenergetics Flashcards Preview

## M2M - Unit 1 > Nucleic Acids and Bioenergetics > Flashcards

Flashcards in Nucleic Acids and Bioenergetics Deck (46)
1
Q

Define Entropy

A

∆S, measure of microscopic disorder in a system

2
Q

Define Enthalpy

A

∆H, measure of energy of a thermodynamic system

3
Q

Define Gibbs Free Energy

A

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

4
Q

Name some high energy compounds

A

5
Q

What is a Redox reaction?

A

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

6
Q

Define First Law of Thermodynamics

A

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

7
Q

Define Second Law of Thermodynamics

A

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

8
Q

List and define the four kinds of kinetic energy

A

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

9
Q

What are the four ways that potential energy is stored?

A

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

10
Q

What are the three basic thermodynamic equations?

A

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

11
Q

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

A

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

12
Q

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

A

The reaction is at equilibrium1

13
Q

What is K when ∆G is positive?

A

K < 1

14
Q

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

A

∆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)

15
Q

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

A

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

16
Q

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

A

Couple it with a spontaneous reaction

17
Q

What are some high energy compounds used in biological systems?

A

Lipids and Carbohydrates

18
Q

What are the two main classes of high energy bonds?

A

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

19
Q

Which nitrogenous bases are purines?Pyrimidines?

A

Purines: AGPyrimidines: CTU

20
Q

What is the difference between ribose and deoxyribose?

A

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

21
Q

What is the difference between ribonucleoside and deoxyribonucleoside?

A

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

22
Q

What is the difference between a nucleoside and nucleotide?

A

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

23
Q

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

A

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

24
Q

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

A

Nucleotides > Nucleosides > BasesPyrimidines > Purines

25
Q

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

A

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

26
Q

What makes DNA and RNA polar?

A

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.

27
Q

A

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

28
Q

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

A

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

29
Q

List Chargaff’s Rules.

A

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

30
Q

Describe the Watson-Crick model for DNA structure

A

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

31
Q

What is the major groove?Minor groove?

A

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

32
Q

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

A
1. [salt], higher [salt] = more stable2. Extremes of pH destabilize3. Length, longer strand = more stable4. GC/AT ratio, higher ratio = more stable
33
Q

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

A

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

34
Q

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

A

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.

35
Q

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

A

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.

36
Q

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

A

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

37
Q

How does UV light damage DNA?

A

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

38
Q

How is DNA polymerized?

A

New nucleotides are added to the 3’ end.

39
Q

How are nucleoside analogues used as drugs?

A

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.

40
Q

Differences between DNA and RNA?

A

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

41
Q

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

A

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

42
Q

What does rRNA do?

A

Ribosomes are made of rRNA. Ribosomes translates mRNA.

43
Q

What does snRNA do?

A

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

44
Q

What do miRNA and siRNA do?

A

They regulate gene expression.

45
Q

What does mRNA do?

A

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

46
Q

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

A

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.