Week 6

Question 1

What is Metabolism ?

Answer 1

Catabolism + Anabolism = Metabolism.

Metabolism is the sum of catabolic, which is the break down of chemical reactants to create energy for anabolic processes, which is the build up of chemical reactants.

Question 2

What are the metabolic requirements for all cells ?

Answer 2

• Water
• Free energy ( energy required to do work)
• Reducing power ( generates free energy and necessary for some biosynthetic reactions)
• precursor metabolites for biosynthesis

Question 3

What is ATP ? How is it used?

Answer 3

ATP is an energy carrying molecule, found in the cells of all living things. ATP captures chemical energy and uses it to fuel other processes. phosphorylation is the addition of a phosphate group and hydrolysis is the removal of a phosphate group.

Question 4

what molecules are High energy phosphate and sulfur carriers ? What is their Gibbs free energy ?

Answer 4

Phosphoenolpyruvate -61.9
1,3 Bisphosphoglycerate -49.4 
Acetyl phosphate  -44. 8 
ATP -31.8 
ADP -31.8 
Acetyl-CoA -35.7 ( sulfur) 
AMP -14.2
Glucose 6 phosphate -13.8

Question 5

How is ATP generated ?

Answer 5

Substrate level phosphorylation: Formation of ATP from ADP using a substrate and no inorganic phosphate.

Oxidative phosphorylation: The proton motive force is used to power ATP synthase and make ATP. The PMF is generated by transfer of electrons and its very efficient.

Photophosphorylation: The PMF powers ATP synthase, and the PMF is generated by light energy.

Question 6

Redox Reactions

Answer 6

Oxidation and reduction the transfer of electrons

LEO- loss of electrons is oxidation
GER- gain of electrons is reduction

Question 7

How does the redox tower work ?

Answer 7

It shows the reduction potential, and how badly a molecule wants electrons, and how easily a molecule can be reduced.

The tower shows half reactions.

The oxidized reagent is on the left and the reduced reagent is on the right. The reduced form has electrons and the oxidized doesn’t.

The electron donor is higher on the tower and will give electrons to the electron acceptor which is lower on the tower.

Question 8

What is Gibbs free energy ?

Answer 8

Gibbs free energy is the energy available to do work
If delta G is negative, reaction produces energy.
If delta G is positive, reaction requires energy.
Reactions are not spontaneous , have activation energy which exists because you have to break bonds and form bonds.

Question 9

What are electron carriers ?

Answer 9

When a molecule has a lot of energy, these electron carriers are able to carry energy.

-NAD+/NADH
FAD/FADH2
Ubiquinone/Ubiquinol
Fe3+/Fe2+

Question 10

NAD+/NADH & NADP+/NADPH

Answer 10

• Nicotinamide adenine dinucleotide
  
  • • comes from the positively charged Nitrogen on the nicotinamide
  • Can accept 2 protons and 2 electrons
  • 2 protons and 2 electrons convert NAD+ to NADH
  • In NADP, the hydroxyl group is replaced with a phosphate
    
    • NADP is used in anabolic reactions

Question 11

FAD+/FADH & FMN+/FMNH

Answer 11

• Flavin adenine dinucleotide and flavin mononucleotide
  (riboflavin phosphate)
  -Bound to proteins

Question 12

Coenzyme Q 
(Ubiquinone)

Answer 12

• Lipid-linked
  
  • Hydrophobic
  • A long molecule
  • Found in the membrane

Question 13

Fe2+/Fe3+

Answer 13

Iron can go from 2+ to 3+ state
Fe2+ is oxidized Fe3+ is reduced

Fe2+ = Heme

Fe3+ = Iron-sulfur clusters

Question 14

How are Enzymes helpful when used in a reaction ?

Answer 14

Enzymes decrease activation energy.

When enzymes are used they help to :
• Increase the amount of substrates at the active site
• Orient the substrates so they form the transition-state complex
• Enzyme and substrate interact

Enzyme activity is impacted by:
• The substrate and product concentration
• The pH
• The temperature

Question 15

How does an Enzyme decrease activation energy ?

Answer 15

Activation energy is the minimum amount of energy needed for a reaction to start.

Gibbs free energy stays the same whether an enzyme is used or not.

Enzymes decrease activation energy by:
• Desolvation ( loss of water molecules)
• Hydrogen bonds
• Vander Wals forces

Question 16

What is a chemotroph and what are the two kinds ?

Answer 16

Chemotroph means that chemicals are used as the energy source

Chemoorganotrophs: use organic chemicals as electron donors and catabolic processes lead to the release of energy which can be stored as ATP.

Chemolithotrophs: use inorganic compounds as electron donors and these inorganic compounds can be oxidized, eventually leading to the formation of ATP. Chemolithotrophs are extremophiles.

S, SO42-, NO3, O2 are the terminal electron acceptors for both.

Question 17

What are the steps involved in Glycolysis ?

Answer 17

Glycolysis has 2 stages , stage 1 is where all the building blocks are made and stage 2 is where the redox reactions occur. There are 2 redox reactions.

The steps of glycolysis

1. Glucose is phosphorylated to form glucose 6 phosphate 
2. Glucose 6 phosphate is then changed to Fructose 6 phosphate by the enzyme isomerase ( 6 carbon to 5 carbon molecule)
3. Fructose 6 phosphate is phosphorylated and becomes fructose 1,6 bisphosphate  * ATP consumption steps* 
4. The enzyme aldolase splits fructose 1,6-bisphosphate into two 3-carbon molecules, glyceraldehyde 3-phosphate and its isomer, dihydroxyacetone phosphate.
5. Dihydroxyacetone phosphate is converted into glyceraldehyde 3-phosphate. 
6. Redox step: glyceraldehyde 3-phosphate is oxidized to 1,3-bisphosphoglyceric acid (occurs twice, once for each of the two glyceraldehyde 3-phosphates NAD+ is reduced to NADH by G-3-P dehydrogenase) 
7. Each Glyceraldehyde 3-phosphate is phosphorylated by the addition of  inorganic phosphate
8. ATP is synthesized by substrate-level phosphorylation when: 
	(1) each molecule of 1,3-bisphosphoglyceric acid is converted to 3-phosphoglyceric acid, and
	 (2) each molecule of phosphoenolpyruvate is converted to pyruvate

During the first two stages of glycolysis, two ATP molecules are consumed and four ATP molecules are synthesized. The net energy yield in glycolysis is two molecules of ATP per molecule of glucose fermented.

Question 18

What are the 3 mains ways chemoorganotrophs get energy ?

Answer 18

Fermentation

Oxidative phosphorylation

Photophosphorylation

Question 19

What are the fates of pyruvate ?

Answer 19

turned into amino acids like alanine.

It can go straight into the citric acid cycle as citrate and coA or as oxaloacetate.

converted into acetaldehyde and ethanol.

It can also go back into glycolysis as phosphoenolpyruvate.

Question 20

What is acetyl coA needed for ? How is it made ?

Answer 20

• Carbohydrate metabolism
  
  • Fatty acid metabolism
  • Steroid synthesis
  • Amino acid metabolism
  • Acetylation ( post translational modification)
  • Carbon storage ( Beta-hydroxybutyrate)

It is made from pyruvate. Pyruvate is oxidized to acetyl coA.

Question 21

What is beta oxidation ? what molecule does it use ?

Answer 21

Fatty acids are oxidized by Beta-oxidation.

The two carbons of the fatty acid split off, the beta carbon is the one that is oxidized.

Acetyl CoA and a new fatty acid ( 2 carbons shorter than the original) are formed

Question 22

What is hydrogen degradation ?

Answer 22

• hydrocarbons become acids
• catalyzed by a monooxygenase
• one of the atoms of O2 is incorporated, typically at a terminal carbon atom
• End product of the reaction sequence is a fatty acid of the same length as the original hydrocarbon
• The fatty acid can be beta-oxidized

Question 23

Are cells able to grow using just glycolysis ?

Answer 23

Cells are not able to grow with just glycolysis:

There is no way to convert the reducing power created into something useful.

You can run out of NADH and FADH2 if you keep converting them.

Question 24

When does an organism use fermentation ? Why ? What molecules are involved ?

Answer 24

Fermentation occurs when there is no oxygen, or in organisms like yeast when there is an abundance of sugars. Here NADH reduces pyruvate to lactate. Pyruvate is the organic molecule and the final electron acceptor.

Allows for glycolysis to occur when there is no oxygen around. Need to regenerate the NAD+ because NADH would be collecting lots of electrons.

Fermentation is not efficient because one glucose will produce 2 net ATP.

Question 25

Name the different types of fermentation

Answer 25

Alcoholic fermentation: Hexose --> 2 ethanol + 2 CO2 uses a pyruvate derivative. Produces alcohol and CO2 (Yeast, Zymomonas) Homolactic fermentation: hexose --> 2 lactate + 2H+ + 2 ATP. The protons acidify the environment as they accumulate. (Streptococcus, Lactobacillus) Heterolactic fermentation: Hexose --> Lactate + ethanol + CO2 + H+ . A mix of alcoholic and homolactic fermentation, Alcohol and an acidic environment are produced. (Leuconostoc, Lactobacillus) Lactic acid fermentation: uses pyruvate. Pyruvate becomes lactate Mixed acid: the hexose is converted to a bunch of things. Such as lactate, acetate, succinate, formate, ethanol, hydrogen gas and CO2. (Enteric Bacteria. E.coli, Salmonella, Shigella)

Question 26

Name the 3 categories of Final Electron Acceptors

Answer 26

Aerobic: Uses oxygen as the final electron acceptor ( oxidative phosphorylation) Anaerobic: Uses an inorganic molecule other than oxygen ( NO3-, SO42-,CO2, Fe3+) Fermentation: Uses an organic molecule as a final electron acceptor. Doesn’t use the ETC, PMF, or oxidative phosphorylation.

Question 27

Electron transport chain vs Oxidative phosphorylation how are they different ?

Answer 27

ETC only has to do with the 4 complexes, electrons and protons. The ETC uses FADH and NADH which were created from the Citric acid cycle. Oxidative phosphorylation: the electron transport chain and ATP synthesis combined. The uses of a proton gradient, and electron transport to create ATP.

Question 28

Steps of the Electron Transport Chain

Answer 28

There are two entry points to the ETC. Complex 1 or 2, will get electrons and pass them on to Co enzyme Q reducing ubiquinone to ubiquinol. Complex 1 oxidizes NADH --> NAD+ + H+ It gains 2 electrons, and 4 protons are pumped into the periplasm. Complex 1 can pump protons from cytoplasm to periplasm. Complex 2 is succinate dehydrogenase, which is part of the citric acid cycle. It oxidizes FADH2 to FAD+ and passes the electrons to co enzyme Q reducing it from ubiquinone to ubiquinol. Complex 2 can not pump protons so complex 1 produces more energy due to the 4 H+'s. Complex 3 takes 2 electrons and 2 protons from ubiquinol, and it also pumps 2 protons from the cytoplasm to the periplasm. Complex 3 also transfers electrons to cytochrome C and transfers protons to the cytosol. Cytochrome C transfers electrons to complex 4, complex 4 also pumps 2 protons from the cytoplasm to the periplasm. Complex 4 also reduces the final electron acceptor oxygen and turns it to 2 water molecules. If the ETC starts at complex 1 using NADH a total of 10 protons are transported through to O2 If the ETC starts at complex 2 using FADH2 a total of 6 protons are transported through to O2

Question 29

Electron Transport Chain Facts

Answer 29

There are 4 complex involved in the ETC. The electrons go from a high energy state to a low energy state. Complex 1, 3, and 4 shift protons from the mitochondrial matrix to the inner membrane space setting up the PMF. (eukaryotes) Complex 1, 3, and 4 shift protons from the cytoplasm to the periplasm setting up the PMF. (bacteria) The electron transport chain is located in the plasma membrane of chemoorganotrophs in bacteria and archaeal cells it is located in the inner mitochondrial membrane of eukaryotic cells. A series of electron carriers that work together to transfer and FADH2 and NADH to a terminal electron acceptor ( O2, NO3-, SO42- and CO2). Electrons flow from carrier with more negative reduction potential to carriers with a more positive reduction potential.

Question 30

What is ATP Synthase ? How does ATP synthase work ?

Answer 30

ATP synthase uses the flow of protons to make ATP from ADP and inorganic phosphate. 3 Protons are needed to create 1 ATP. F0- rotor in the membrane F1- the head, catalyzes ATP formation. There is a channel in protein A which protons can enter though, this causes the C ring to spin along with the epsilon and gamma subunits, this causes a conformational change in alpha and beta subunits which do not spin as they are anchored in place by B- proteins. If there is a high volume of ATP then ATP synthase will work in reverse and hydrolyze ATP.

Question 31

What are the different ATP yield of the chemoorganotrophic organisms ?

Answer 31

Glycolysis alone yields 2 ATP per glucose • Electron transport chain: • NADH results in a maximum of 10 H+ ions pumped across the membrane • FADH2 results in a maximum of 6 H+ ions pumped across the membrane • Oxidative phosphorylation take ~3 H+ ions to make one ATP • Glycolysis + citric acid cycle yields a potential 38 ATP per glucose (4 from substrate level phosphorylation and 34 from oxidative phosphorylation) * Factors affecting yield: * PMF is also used for other things (motility, active transport) * Intermediates may be used to synthesize other molecules * ETC may be shorter in some bacteria/archaea

Question 32

Citric acid Cycle

Answer 32

* View Diagram* The citric acid cycle begins when the two-carbon compound acetyl-CoA condenses with the four-carbon compound oxaloacetate to form the six-carbon compound citrate (citric acid). A series of oxidation reactions converts citrate back to oxaloacetate

Question 33

How is metabolism Diverse? what are the different classifications of metabolic organisms?

Answer 33

Chemoorganotrophs, use organic electron donors for fermentation, anaerobic respiration and aerobic respiration Chemolithotrophs use inorganic electron donors for anaerobic and aerobic respiration Phototrophs use light. Anoxygenic photosynthesis occurs without H20, sulfur is usually used and oxygenic photosynthesis occurs using H20. Electrons don’t generate the PMF, light does. Light helps make ATP but reducing power is still needed.

Question 34

Why is E.coli Special ?

Answer 34

It does all 3 types of metabolism E. Coli uses fermentation when oxygen and nitrate are absent. It uses anaerobic respiration when oxygen is absent, and makes nitrate the final electron acceptor. It uses the enzyme nitrate reductase which changes nitrate to nitrite and pumps a total of 6 protons. E. Coli can also use aerobic respiration where oxygen is the final electron acceptor and pump a total of 8 protons, they use an enzyme called cytochrome bo3.

Question 35

What is bacteriochlorophyll ? How dies it differ from chlorophyll ?

Answer 35

Bacteriochlorophyll, is the major light capturing molecule it is structurally similar to heme but has Mg2+ instead of Fe2+. Bacteriochlorophyll absorbs light at different wavelengths than chlorophyll.

Question 36

What are the steps of photosynthesis ?

Answer 36

Light is harvested by protein complexes containing bacteriochlorophyll Converts p870 into a strong electron donor Reduces ubiquinone to ubiquinol Transfers protons and electrons to cytochrome bc, same as for chemoheterotrophs Electrons (lower energy) are transferred back to p870 Accessory pigments used in photosynthesis help transfer light energy to chlorophylls, they absorb light at different wavelengths than chlorophylls

Question 37

How do archaea get energy ?

Answer 37

They are non-photosynthetic autotrophs and they use a protein called bacteriorhodopsin. Used in Archaea, the PMF is made without the ETC, only the protein Bacteriorhodopsin is used. The amino acids on the protein get protonated and deprotonated