Chapter 11 Anabolism: The Use of Energy in Biosynthesis

1. Chapter 11 Anabolism: The Use of Energy in Biosynthesis CHAPTER GLOSSARY Anaplerotic回補 reactions Assimilatory趨向sulfate reduction Calvin cycle Gluconeogenesis Glyoxylate cycle Macromolecule Nitrogen fixation Nucleoside Nucleotide Purine Pyrimidine Ribulose-1,5-bisphosphata carboxylase Transaminases Transpeptidation

2. Anabolism • energy from catabolism is used for biosynthetic pathways • using a carbon source and inorganic molecules, organisms synthesize new organelles and cells • antibiotics inhibit anabolic pathways • a great deal of energy is needed for anabolism • turnover • continual degradation and resynthesis of cellular constituents by nongrowing cells • metabolism is carefully regulated • for rate of turnover to be balanced by rate of biosynthesis • in response to organism’s environment

4. Principles Governing Biosynthesis • macromolecules are synthesized from limited number of simple structural units (monomers) • saves genetic storage capacity, biosynthetic raw material, and energy • many enzymes do double duty • catabolic and anabolic pathways are not identical as some enzymes function in only one direction

5. More principles… • to synthesize molecules efficiently, anabolic pathways must operate irreversibly in the direction of biosynthesis • done by coupling breakdown of ATP to certain reactions in biosynthetic pathways • drives the biosynthetic reaction to completion • anabolic and catabolic reactions are physically separated • located in separate compartments • allows pathways to operate simultaneously but independently • catabolic and anabolic pathways use different cofactors • catabolism produces NADH • NADPH used as electron donor for anabolism • large assemblies (e.g., ribosomes) form spontaneously from macromolecules by self-assembly

6. Precursor Metabolites • generation of precursor metabolites is critical step in anabolism • carbon skeletons are used as starting substrates for biosynthetic pathways • examples are intermediates of the central metabolic pathways • most are used for the biosynthesis of amino acids

7. The Organization of Anabolism

8. Figure 11.4 The Precursor Metabolites

9. The Fixation of CO2 by Autotrophs • the Calvin cycle • the reductive TCA cycle • the hydroxypropionate cycle • the acetyl-CoA pathway • the 3-hydroxypropionate/4-hydroxybutyrate pathway Calvin cycle • used by most autotrophs to fix CO2 • also called the reductive pentose phosphate cycle • in eukaryotes, occurs in stroma of chloroplasts • in cyanobacteria, some nitrifying bacteria, and thiobacilli, may occur in carboxysomes • inclusion bodies that may be the site of CO2 fixation

10. Calvin Cycle • consists of 3 phases • the carboxylation phase • the reduction phase • the regeneration phase • three ATPs and two NADPHs are used during the incorporation of one CO2 The Carboxylation Phase • catalyzed by the enzyme ribulose 1.5-bisphosphate carboxylase, also called ribulosebisphosphatecarboxylase/oxygenase (rubisco) • rubisco catalyzes addition of CO2 to ribulose-1,5-bisphosphate (RuBP), forming 2 molecules of 3-phosphoglycerate

11. The Reduction and Regeneration Phases • 3-phospho-glycerate reduced to glyceraldehyde 3-phosphate • RuBP regenerated • carbohydrates (e.g., fructose and glucose) are produced Summary 6CO2 + 18ATP + 12NADPH + 12H+ + 12H2O  glucose + 18ADP + 18Pi + 12NADP+

12. Other CO2-Fixation Pathways • the reductive TCA cycle • used by some chemolithoautotrophs • runs in reverse direction of the oxidative TCA cycle

13. Other CO2-Fixation Pathways • the hydroxypropionate cycle • used by some archael genera and the green nonsulfur bacteria (also anoxygenic phototrophs)

14. Other CO2-Fixation Pathways • the acetyl-CoA pathway • methanogens use portions of the acetyl-CoA pathway for carbon fixation • involves the activity of a number of unusual enzymes and coenzymes

15. The 3-Hydroxypropionate/ 4-Hydroxybutyrate Pathway • first described in 2007 in an archeon • uses 3-hydroxypropionate cycle • uses unique reaction to produce 3-hydroxybutryate

16. Synthesis of Sugars and Polysaccharides • Gluconeogenesis • Monosaccharides • Polysaccharides • Peptidoglycan

17. Gluconeogenesis • synthesis of glucose and related sugars from nonglucose precursors • glucose, fructose, and mannose are gluconeogenic intermediates or made directly from them • galactose is synthesized with nucleoside diphosphate derivatives • bacteria and algae synthesize glycogen and starch from adenosine diphosphate glucose • functional reversal of glycolysis, but the two pathways are not identical • 7 enzymes shared • 4 enzymes are unique to gluconeogenesis

18. Gluconeogenesis

19. Synthesis of Monosaccharides • several sugars are synthesized while attached to a nucleoside diphosphate such as uridinediphosphate glucose (UDPG)

20. Synthesis of polysaccharides • also involves nucleoside diphosphate sugars • e.g., starch and glycogen synthesis ATP + glucose 1-P  ADP-glucose + PPi (glucose)n + ADP-glucose  (glucose)n+1 + ADP Peptidoglycan Synthesis • complex process • involves use of UDP derivatives • also usesbactroprenol, a lipid carrier, to transport NAG-NAM-pentapeptide units across the cell membrane • cross links are formed by transpeptidation

21. Synthesis of UDP-NAG and UDP-NAM Pentapeptide

23. Bactoprenol-NAM Bactoprenol is attached to N-acetylmuramic acid (NAM)

24. Transpeptidation

25. Patterns of Cell Wall Formation • autolysins • carry out limited digestion of peptidoglycan • activity allows new material to be added to wall and division to occur • inhibition of peptidoglycan synthesis can weaken cell wall and lead to lysis • many commonly used antibiotics inhibit cell wall formation

26. The Synthesis of Amino Acids • Nitrogen assimilation • Sulfur assimilation • Amino acid biosynthetic pathways • Anaplerotic reactions and amino acid biosynthesis • many precursor metabolites are used as starting substrates for synthesis of amino acids • carbon skeleton is remodeled • amino group and sometimes sulfur are added

27. Nitrogen Assimilation • major component of protein, nucleic acids, coenzymes, and other cell constituents • nitrogen addition to carbon skeleton is an important step • potential sources of nitrogen: ammonia, nitrate, or nitrogen • most cells use ammonia or nitrate • ammonia nitrogen easily incorporated into organic material because it is more reduced than other forms of inorganic nitrogen Ammonia Incorporation into Carbon Skeletons • ammonia N can be directly assimilated by • transaminase activity • glutamate dehydrogenase • glutamine synthetase-glutamate synthase systems • once incorporated, nitrogen can be transferred to other carbon skeletons by transaminases

28. Ammonia Assimilation by Reductive Amination and Transaminase

29. Glutamine Synthetase and Glutamate Synthase

30. Ammonia Incorporation Using Glutamine Synthetase, Glutamate Synthase and Transaminases • This route is effective at low ammonia concentration.

31. Assimilatory Nitrate Reduction • used by bacteria to reduce nitrate to ammonia and then incorporate it into an organic form • nitrate reduction to nitrite catalyzed by nitrate reductase • reduction of nitrite to ammonia catalyzed by nitrite reductase

32. Nitrogen Fixation • reduction of atmospheric nitrogen to ammonia • catalyzed by nitrogenase • found only in bacteria and archaea Nitrogen Reduction • requires large ATP expenditure

33. Mechanism of Nitrogenase Activity • occurs in 3 steps to reduce N2 to 2 molecules of NH3 • requires large ATP expenditure • once reduced, NH3 can be incorporated into organic compounds

34. Sulfur Assimilation • sulfur needed for • synthesis of amino acids cysteine and methionine • synthesis of several coenzymes • sulfur obtained from • external sources • intracellular amino acid reserves Use of Sulfate as a Sulfur Source • sulfate = inorganic sulfur source • assimilatory sulfate reduction • sulfate reduced to H2S and then used to synthesize cysteine • cysteine can then be used to form sulfur containing organic compounds

35. Assimilatory Sulfate Reduction • involves sulfate activation through formation of phosphoadenosine 5’-phosphosulfate (PAPS) followed by reduction of the sulfate Activated sulfate (PAPS)

36. Incorporation of Sulfur from H2S

37. Amino Acid Biosynthesis – Branching Pathways • used in the synthesis of multiple amino acids • a single precursor metabolite can give rise to several amino acids • biosynthetic pathways for aromatic amino acids also share intermediates Aromatic Amino Acid Synthesis

38. Anaplerotic Reactions • TCA cycle intermediates are used in many amino acid biosynthetic pathways • replenishment of these intermediates is provided by anaplerotic reactions • allow TCA cycle to function during periods of active biosynthesis • e.g., anaplerotic CO2 fixation • e.g., glyoxylate cycle Anaplerotic CO2 fixation • phosphoenolpyruvate (PEP) carboxylase • phosphoenolpyruvate + CO2 oxaloacetate + Pi • pyruvate carboxylase • pyruvate + CO2 + ATP + H2O  oxaloacetate + ADP + Pi • reaction requires the cofactor biotin

39. Glyoxalate cycle • other anaplerotic reactions are part of the glyoxalate cycle, a modified TCA cycle

40. Phosphorus Assimilation • phosphorus found in nucleic acids as well as proteins, phospholipids, ATP, and some coenzymes • most common phosphorus sources are inorganic phosphate and organic phosphate esters • inorganic phosphate (Pi) • incorporated through the formation of ATP by • photophosphorylation • oxidative phosphorylation • substrate-level phosphorylation • organic phosphate esters • present in environment in dissolved or particulate form • hydrolyzed by phosphatases, releasing Pi

41. The Synthesis of Purines, Pyrimidines, and Nucleotides • most microbes can synthesize their own purines and pyrimidines • purines • cyclic nitrogenous bases consisting of 2 joined rings • adenine and guanine • pyrimidines • cyclic nitrogenous bases consisting of single ring • uracil, cytosine, and thymine • nucleoside = nitrogenase base-pentose sugar • nucleotide= nucleoside-phosphate

42. Purine Biosynthesis • complex pathway in which several different molecules contribute parts to the final purine skeleton • initial products are ribonucleotides • deoxyribonucleotides formed by reduction of nucleoside diphosphates or nucleoside triphosphates inosinic acid

43. Pyrimidine Biosynthesis • begins with aspartic acid and high energy carbamoyl phosphate • ribonucleotides are initial products • deoxy forms of U and C nucleotides formed by reduction of ribose to deoxyribose

44. Lipid Synthesis • lipids • major required component in cell membranes • most bacterial and eukaryal lipids contain fatty acids • fatty acids • synthesized then added to other molecules to form other lipids such as triacylglycerols and phospholipids Fatty Acids • synthesized from acetyl-CoA, malonyl-CoA, and NADPH by fatty acid synthase system • during synthesis the intermediates are attached to the acyl carrier protein • double bonds can be added in two different ways

45. Fatty acid synthesis • catalyzed by fatty acid synthetase • involves activity of acyl carrier protein (ACP)

46. Triacylglycerols and phospholipids • eukaryotic microbe and a few gram-positive bacteria can store carbon and energy as triacylglycerol • made from fatty acids and glycerol phosphate • phosphatidic acid is an important intermediate in this pathway

47. Phospholipids • major components of eucaryotic and bacterial cell membranes • synthesized from phosphatidic acid by forming CDP-diacylglycerol, then adding an amino acid