Metabolism

1. Metabolism

2. Oxidation-Reduction • Two truisms: • Chemistry is the study of the movement of electrons between atoms • Life is applied chemistry • Oxidation: a molecule loses an electron • LEO: Lose Electron Oxidation • Reduction: a molecule gains an electron • GER: Gain Electron Reduction • In living cells, there are no free electrons: every time an electron leaves one molecule, it goes to another one. • Thus, all oxidation reactions are coupled with reduction reactions: one compound is oxidized while the other is reduced. “Redox” reactions • Electrons are often accompanied by H+ ions. Thus, FAD is the oxidized form, and FADH2 is the reduced form: it has 2 more electrons (and H’s) than FAD. • For this reason, enzymes that perform oxidations are usually called dehydrogenases.

3. Redox Potential • Redox potential is a measure of the affinity of compounds for electrons. The more positive a compound’s redox potential is, the greater its tendency to acquire electrons. • Redox potential is measured in millivolts (mV), relative to hydrogen at 1 atm pressure. Compounds are at 1 M concentration. • H2 2 H+ + 2 e- • The idea is, if your compound was mixed with hydrogen gas, would electrons flow from your compound to the hydrogen (compound has a negative redox potenitial), or from the hydrogen to your compound (compound has a positive redox potenital)? • Redox potential is affected by the concentration of the reactants and also by the redox potential of the environment • When electrons in compounds with lower (more negative) redox potentials are moved to compounds with higher potentials, energy is released. Organisms capture this energy to live on.

4. Some Redox Reactions Used in Bacteria

5. Some Lithotrophic Reactions

6. Fermentations • Fermentation is defined as a process where organic molecules are both the electron • donor and the electron acceptor. • Since the complete oxidation of organic molecules ends at carbon dioxide, fermentations are by definition incomplete oxidations: there is always some potential energy left in the products of a fermentation. • And thus the fermentation products excreted by one species are often used as food sources for another species. • The best known fermentations involve the products of glycolysis. • Glucose is oxidized to pyruvate, but the electrons from glucose are used to convert NAD+ to NADH. • To get rid of these electrons, NADH is used to reduce pyruvate to lactate (as in anaerobic human muscle) or to ethanol (as in yeast). Both of these pathways are used in various bacteria.

7. Other Fermentations

8. Aerobic Respiration • The most efficient way of producing energy is by oxidizing organic compounds to carbon dioxide = respiration. This is the process used by most eukaryotes and aerobic bacteria.

9. Energy Generation • Energy in the cell is generated and used in the form of ATP. • Two basic way s of generating ATP: • substrate-level phosphorylation. The simplest form: transfering a phosphate group from another molecule to ADP, creating ATP. • chemiosmotic: generation of a proton (H+) gradient across a membrane. This gradient is called “proton-motive force”.

10. Chemiosmotic Theory • The same basic process in the mitochondria as in many bacteria. • High energy electrons from an electron donor are used to pump H+ ions out of the cell, into the periplasmic space • This drains energy from the electrons • Electron transport • There are thus more H+ ions outside than inside: the pH outside is lower than inside. • The H+ ions are then allowed back into the cell by passing them through the ATP synthase protein, which uses the energy of the H+ ions flowing down the gradient to attach phosphate (Pi) to ADP, creating ATP. • the gradient is both chemical: more H+ outside than inside, and electrical: more + charge outside than inside

11. Carbon Assimilation • Heterotrophic organisms obtain organic carbon compounds from pre-existing organic molecules. • often the same molecules they are using for energy: glucose for example. • Autotrophs “fix” carbon dioxide into organic carbon. • 4 pathways: • Calvin cycle (ribulose bis-phosphate pathway. Used in plants and many bacteria: the most common pathway • Reductive TCA cycle: run the Krebs cycle backwards • Reductive acetyl CoA pathway, which requires hydrogen gas and produces carbon monoxide as an intermediate. • 3-hydroxypropiuonate cycle. Seems to mostly be in Archaea

12. Carbon Assimilation Pathways

13. Nitrogen Assimilation • Most of the nitrogen on Earth is nitrogen gas, N2, which is strongly held together by a triple bond. • nitrogen fixation, converting nitrogen to ammonia, is very energy-intensive and carried out by a small group of bacteria, including some Clostridium. • some nitrogen is also fixed by lightning. • Nitrogen’s major use in the cell is as a component of amino acids, in the ammonium form: -NH2 • Many organisms get their nitrogen from organic nitrogen compounds • some organisms perform ammonification, which means splitting the amino group off organic compounds, releasing ammonium ions. • Nitrogen is also found as nitrate. Most bacteria can reduce nitrate (NO3-) to nitrite (NO2-) and then to ammonia: assimilatory nitrate reduction. • nitrate is also degraded back into nitrogen gas by other bacteria: denitrification. • the reverse process, converting ammonia into nitrate and nitrite, is used as an energy source by some lithotrophs. It is called nitrification.

14. More Nitrogen Assimilation • When nitrogen is taken into the cell in the form of ammonium ions, it is attached to glutamate, forming glutamine, using the enzyme glutamine synthetase. • Alpha-ketoglutarate, glutamate, and glutamine can all be interconverted. • this is the source of the amino group of amino acids and amino sugars.

15. Assimilation of Other Elements • Cells use several other elements: C, H, O, and N are the major ones • also covalently bound: P, S, Se • ions: Na, K, Mg, Ca, Cl • trace elements (mostly as enzyme co-factors): Fe, Mn, Co, Cu, Ni, Zn, others.... • Sulfur can be incorporated from organic sources, but it is often taken into the cell as sulfate (SO4-2). Getting into the cell requires attaching it to the ATP derivative APS, after which it is reduced to sulfide (S-2) and then attached to serine, converting it to cysteine. • phosphate (PO4-3) is generally found in the same form as it is used. It just needs to be transported into the cell.

16. Intermediary Metabolism • Lots of interconversions. • it is necessary to make: • amino acids (proteins) • nucleotides (DNA, RNA, and ATP) • sugars (part of nucleotides, food, structure) • lipids: food storage and membrane • several co-factors for enzymes: biotin, cytochromes, panthothenic acid, NAD, riboflavin, cobalamin, ubiquinone, etc. • The central metabolic pathways of glycolysis and the Krebs cycle have several side branches that feed these biosynthetic pathways.

18. Enzyme Nomenclature • Every chemical interconversion requires an enzyme to catalyze it. • Nearly all enzyme names end in –ase • Enzyme functions: which reactants are converted to which products • Across many species, the enzymes that perform a specific function are usually evolutionarily related. However, this isn’t necessarily true. There are cases of two entirely different enzymes evolving similar functions. • Enzyme functions are given unique numbers by the Enzyme Commission. • E.C. numbers are four integers separated by dots. The left-most number is the least specific • For example, the tripeptide aminopeptidases have the code "EC 3.4.11.4", whose components indicate the following groups of enzymes: • EC 3 enzymes are hydrolases (enzymes that use water to break up some other molecule) • EC 3.4 are hydrolases that act on peptide bonds • EC 3.4.11 are those hydrolases that cleave off the amino-terminal amino acid from a polypeptide • EC 3.4.11.4 are those that cleave off the amino-terminal end from a tripeptide • Top level E.C. numbers: • E.C. 1: oxidoreductases (often dehydrogenases): electron transfer • E.C. 2: transferases: transfer of functional groups (e.g. phosphate) between molecules. • E.C. 3: hydrolases: splitting a molecule by adding water to a bond. • E.C. 4: lyases: non-hydrolytic addition or removal of groups from a molecule • E.C. 5: isomerases: rearrangements of atoms within a molecule • E.C. 6:ligases: joining two molecules using energy from ATP

19. Detailed Pathways • For many compounds, there can be more than one way to produce it. Some organisms have more than one pathway to a given compound, and sometimes different organisms produce it by different mechanisms. • KEGG (Kyoto Encyclopedia of Genes and Genomes) has a comprehensive set of pathway maps, with individual species differences noted. • KEGG also has information about individual enzymes and ligands. You can get there by clicking the elements of the map. • http://www.genome.ad.jp/kegg/pathway.html