Micro test 2

1. Define thermodynamics.

science that analyzes energy changes in a collection of matter called a system

2A. 1st law of thermodynamics

energy can not be created or destroyed

2B. 2nd law of thermodynamics

physical and chemical processes occur in a way such that entropy in the universe is constantly increasing

2C. Define entropy

amount of randomness in a system

3. What is the relevance of the laws of thermodynamics in chemical reactions?

Chemical reactions can not create or destroy energy and will proceed towards entropy. To work against entropy, energy is required

4. What does “life obeys laws of thermodynamics” mean?

It means life must get energy from the environment since it can not create its own

5. Define the standard reduction potential

A measure of how willing the donor of a half reaction is to donate electrons

6. Why does aerobic growth generate the highest amount of energy (ATP)?

Aerobic respiration generates more ATP because fermentation does not have an ETC (also has a final acceptor pyruvate). Fermentation generates ATP via substrate level phosphorylation. Anaerobic respiration uses a terminal acceptor that is not oxygen. This yields less ATP bc of the incomplete oxidation of the sugar molecule (since O2 is not present).

7. How does E0 play a role in the organization of the electron transport system?

Electron carriers with more negative E0 will be at front of the ETC (better oxidizer) and electron carriers with more positive E0 will be at end of system

8.Compare the E’0 of aerobic and anaerobic respiration.

Aerobic ETC has more negative E0 all the way to the TEA while anaerobic has more positive E0. Aerobic respiration requires oxygen, and the E0red is much greater than the E0red of anaerobic respiration.

9. True or False: A redox pair with more negative reduction potential will spontaneously donate electrons to a pair with more positive potential.

True

10. Electron transport chains are composed of several \__________

Electron Carriers

11. Components of Electron transport chains in bacteria are found in \_________

plasma membrane

12. Components of Electron transport chains in eukaryotes are found in \_________

Inner mitochondrial membrane

13. True or False: The first electron carrier in an ETC has the most negative E’0

True

14. True or False: The more positive the reduction potentials, the greater the affinity for electrons.

True

15. True or False: ETC are associated with plasma membranes or mitochondrial/chloroplast internal membranes

True

16A. True or False: All molecules found in ETC are capable of transferring both electrons and protons

False

16B. What molecules can carry both electrons and protons

Prosthetic groups like Flavin and quinones like coenzyme Q

17. Describe the flow of electrons in fermentation

No ETC, NADH is produced by the EmbdenMeyerhof pathway during glycolysis. NADH still needed to be oxidized, slow down pyruvate dehydrogenase (enzyme that feeds pyruvate to TCA cycle). The pyruvate used as EA .

18. Describe the flow of electrons in respiration

aerobic respiration: Sugar oxidized> electron transferred to NADH and FADH2, then to the ETC and terminal acceptor. Anaerobic respiration does the same, it just uses a terminal acceptor that is not O2.

19. What is the final electron acceptor in fermentation?

pyruvate or derivative

20. What is the final electron acceptor in respiration?

O2 or NO3, SO4 ,CO2,Fe3+

21. True or False: Examples of Final electron acceptors in fermentation include both organic and inorganic molecules

False (organic only)

22. True or False: Examples of Final electron acceptors in anaerobic respiration include both organic and inorganic molecules

True

23. True or False: Final electron acceptor in aerobic respiration is always oxygen

True

24. Describe how enzymes are involved in chemical reactions

Enzymes speed up reactions by lowering activation energy

25. Define apoenzyme

protein component of enzyme

26. Define cofactor

nonprotein component of enzyme that assists in creating a reaction, tryptophan and trP

27. Define prosthetic group

Cofactor that is firmly attached to apoenzyme. Capable of carrying electrons and protons. Used in redox reactions.

29A. How are enzymatic activities inhibited?

competitive and non competitive inhibition

29B. Define Competitive inhibition

Inhibitor directly binds and competes for the site of activation

29C. Define noncompetitive inhibition

inhibitor binds at site other than active site and changes shape of enzyme to decrease activity

29D. How are enzymatic activities regulated?

metabolic channeling, regulation of synthesis, direct stimulation or inhibition of critical enzymes

29E. Define metabolic channeling

localization of enzymes and metabolites

30. How is Sulfanilamide used in competitive inhibition to control enzymes involved in synthesis of folic acid?

​​Sulfanilamide is similar in shape to normal substrate and binds to active site of the enzyme. This prevents other substrates from binding thus rx is blocked.

33. What are enzymes made of?

protein and non protein components

34. What are riboszymes made of?

RNA

37. What is covalent modification?

direct stimulation/inhibition by modifying enzyme by adding or removing chemical group

38. How do environmental factors effect enzymatic activities?

increased temp and pH can denature enzyme causing it to lose function

39. What chemical intermediate links pyruvate to TCA cycle?

Acetyl CoA

41. Do any of the eukaryotes perform fermentation?

Yes, all eukaryotic and most prokaryotic organisms are facultative anaerobic. Ex: certain yeasts (eukaryotic and facultatively anaerobic)

42. List the three chemoorganotrophic fueling processes

aerobic and anaerobic Respiration and fermentation.

43. What are the important features of Chemoorganotrophs?

Derive their energy and electrons from organic molecules

44. Can Chemoorganotrophs use the same compound as a C source, energy source, and as a source for reducing power?

Yes

45. What is meant by CO2 fixation?

Process of which inorganic CO2 is converted to complex organic molecules like glucose

46. List three pathways used by microbes to fix CO2

Calvin Cycle, Reductive TCA cycle, 3 hydroxypropionate cycle, AcetylCoA pathway

47A. Define photolithotroph

ES: light, CS: CO2, E: inorganic

47B. Define photoorganoheterotroph

ES: light, CS: organic, E: organic

47C. Define Chemolithoautotroph

ES: inorganic, CS: CO2, E: inorganic

47D. Define Chemolithoheterotroph

ES: inorganic , CS: organic, E: inorganic

47E. Define chemoorganoheterotroph

ES: organic, CS: organic, E: organic

49A. ATP synthesis in respiration and fermentation

i. Respiration and fermentation both synthesize ATP from ADP. , ii. Pathways: respiration involves the passage of electrons down ETC and ATP created via oxidative phosphorylation. iii. Fermentation involves the passage of electrons to endogenous acceptors and creation of ATP through substrate level phosphorylation in glycolysis. iv. Glucose can be an electron donor in both respiration and fermentation

49B. Electron carriers in respiration and fermentation

Respiration: exogenous compounds (aerobic\=O2, anaerobic\=organic/inorganic).Fermentation: endogenous electron acceptors which must be regenerated

49C. Number of ATP produced in respiration and fermentation

38 ATP\=aerobic (2 ATP in glycolysis and 36 in Krebs cycle), 34 ATP\=anaerobic, 3 ATP Fermentation

50. Describe how proton motive force (PMF) is generated

chemiosmotic theory

51. What is the central role of PMF?

synthesis of ATP and motility

52A. Define substrate level phosphorylation

Involves the creation of ATP using energy from another high energy compound

52B. Define Oxidative phosphorylation

Involves the creation of ATP from scratch, using the PMF that is established as electrons are passed through the electron transport chain

53A. Which form of phosphorylation is associated with Glycolysis?

substrate level phosphorylation

53B. Which form of phosphorylation is associated with Krebs cycle?

substrate level phosphorylation

53C. Which form of phosphorylation is associated with the ETC?

oxidative phosphorylation

55. Define and give examples of amphibolic pathways

Function both as catabolic and anabolic pathways. Examples: glycolysis, embden meyerhof pathway, pentose phosphate pathway, TCA cycle

56A. List and describe and compare three common routes of glucose conversion to pyruvate

Pentose phosphate pathway, Entner Dourdoroff pathway, and Embden Meyerhof pathway

56B. Describe pentose phosphate pathway

an amphibolic pathway that can operate aerobically/anaerobically. Oxidation of glucose followed by the synthesis of 5carbon pentose sugars (precursors for making nucleic acids)

56C.Describe Entner Doudoroff pathway

not amphibolic, low energy pathway that provides 1 NADPH, 1 NADH and 1 ATP for synthesis per glucose molecule. It combines elements of glycolysis and pentose phosphate pathway.

56D. Describe Embden Meyerhof pathway

(glycolysis): most common glycolytic pathway produces 2 ATP

57. How are anabolism and catabolism intertwined in glycolysis and TCA cycle?

Both processes are amphibolic processes

58. What is the significance of glycolysis and TCA cycle in providing skeleton carbon to the cell?

They produce intermediates that serve as carbon skeletons in anabolic pathways

59. List possible molecules that are used as final electron acceptor in anaerobic respiration.

Fe3+, sulfate, nitrate, sulfur, and organic

60. List several possible end products of fermentation

lactate, ethanol, formic acid

61. What are the environmental impacts of nitrification, and denitrification?

nitrification increases soil fertility while denitrification decreases fertility

62. What are the environmental impacts of Chemolithotrophs activities?

important in nitrogen, suflur, and iron cycles

65. What organisms use oxygenic photosynthesis?

eukaryotes and cyanobacteria

65B. What organisms use anoxygenic photosynthesis?

bacteria

67. True or False: Both organic and inorganic compounds may be used as electron acceptor in anaerobic respiration

True

68. True or False: Only inorganic compound may be used as electron acceptors in aerobic respiration

True

69. How are lipids catabolized

triglycerides broken down to glycerol which is phosphorylated and oxidized to intermediate in EMP, or broken down by B oxidation

70. What is meant by deamination?

removal of amino group from amino acid

71A. Light reaction in photosynthesis

light energy is trapped and converted to chemical energy

71B. Dark reaction in photosynthesis

energy from light reaction is used to reduce CO2 and synthesis compounds

73. True or False: Calvin cycle is used by both prokaryotes and eukaryotes

True

74. True or False: Calvin cycle is used by both photosynthetic and nonphotosynthetic bacteria

false

75. What are the roles of amphibolic enzyme?

catalyze a pathway in both directions, anabolic and catabolic

76. Griffith transformation experiment demonstrated that a cellular component transformed nonpathogenic bacteria into pathogenic bacteria. Name this compound.

DNA

77. Briefly explain how Hershey Chase experiment ruled out protein as being the genetic material.

Labeled protein and DNA in phages, infected cells and observed which compound transferred

78. Define semiconservative replication

DNA strands are separated and used as a template to construct a new complementary strand. Resulting in DNA with one old strand and one new strand

83. Define exonuclease activities

remove incorrect mismatched base from 3’ end, proofreading

85. List the events occurs during initiation of replication with regards to OriC, helicase, topoisomerase, primer, ssDNA binding proteins

replication begins at OriC by DnaA binding, Helicase binds and unwinds dna, primase synthesizes primer, ssDNA binding proteins protect dna from damage, topoisomerase relieves tension from unwinding

86. Describe proofreading process in replication. List the enzymes involved in this process

DNA polymerase III and core enzyme detect and remove mismatched bases

88. Which one is complementary to mRNA?

coding strand

89B. DnaA

initiates replication; binds origin of replication

89C. DnaB

helicase 5 to 3, breaks H bonds and unwinds double helicase

89D. SSB proteins

bind single stranded DNA after separated by helicase, protect DNA

89E. DnaC

loads helicase, directs DnaB

89F. DNA primase

synthesizes RNA primer

89G. DNA pol III holoenzyme

~20 polypep, catalyzes DNA synthesis and 3 to 5 exonuclease activity

89H. Ribonuclease H

removes RNA primer

89I. DNA ligase

seals nicked DNA and joins fragments

89J. Tus

terminates replication