Anabolism - Microbial metabolism

1. Photosynthesis1.1 Light dependent reactions

a. Cyclic photophosphorylationb. Noncyclic photophosphorylation

1.2 Light independent reactions2. Other Anabolic Pathways3. Integration and Regulation of

Metabolic Functions

Photosynthesis• Photosynthesis is the single most important chemical

process on earth. It is the process by which plants use solar energy to manufacture food.

• It changes light energy into food (chemical) energy.• Photosynthesis sustains green plants and as a result all

other living things as well.• Wood and fossil fuels — coal, oil and natural gas formed

from plants and animals that lived millions of years ago — provide much of our electricity and heat.

• Green plants are the source of gasoline that we use to power buses and cars.

• Fresh fruits, vegetables and grain, as well as meat from animals that eat plants, give us the energy to work and play and think

Chemicals and structures in photosynthesis

• Photosynthesis is a process in which light energy is captured by pigment molecules (called chlorophylls) and transferred to ATP and metabolites.

• Photosystems, photosystem I (PS I) and photosystem II (PS II), are networks of chlorophyll molecules and other pigments held within a protein matrix in membranes called thylakoids.

• Prokaryotic thylakoids are infoldings of the cytoplasmic membrane

• Eukaryotic thylakoids are infoldings of the inner membranes of chloroplasts.

• Stacks of thylakoids within chloroplasts are called grana.

Mechanism of photosynthesis

Light dependent reactions• The light absorption and redox reactions of

photosynthesis are classified as lightdependent reactions (light reactions) and light-independent reactions (dark reactions).

• A reaction center chlorophyll is a special chlorophyll molecule of photosystem I, which is excited by transferred energy absorbed by pigment molecules elsewhere in the photosystem.

• Excited electrons from the reaction center are passed to an acceptor of an electron transport chain

• Protons are pumped across the membrane,• A proton motive force is created, and ATP is generated

in a process called photophosphorylation which can be either cyclic or noncyclic

Reaction center chlorophyll

Cyclic Photophosphorylation• In cyclic photophosphorylation

electrons return to the original reaction center chlorophyll after passing down the electron transport chain.

• The resulting proton gradient produces ATP by chemiosmosis.

Cyclic photophosphorylation

Noncyclic Photophosphorylation• In noncyclic photophosphorylation,

photosystem II works with photosystem I, and the electrons are used to reduce NADP+ to NADPH.

• Therefore, in noncyclic photophosphorylation, a cell must constantly replenish electrons to PS II.

• In oxygenic organisms, the electrons come from H2O.

• In anoxygenic organisms, the electrons come from inorganic compounds such as H2S.

Noncyclic photophosphorylation

Light-Independent Reactions• The light-independent reaction synthesize glucose from

carbon dioxide and water regardless of light conditions.• ATP and NADPH from the light-dependent reactions

drive the synthesis of glucose in the light-independent pathway of photosynthesis.

• The Calvin-Benson cycle of the light-independent pathway occurs in three steps:

i. carbon fixation in which CO2 is reduced; ii. reduction by NADPH to form molecules of G3P, which

join to form glucose;iii. and regeneration of RuBP (ribulose 5-phosphate)

[also produced by PPP] to continue the cycle.

The Calvin-Benson cycle of the light-independent pathway

Other Anabolic Pathways• Because anabolic reactions are synthesis

reactions, they require energy and metabolites, both of which are often the products of catabolic reactions.

• Amphibolic reactions are metabolic reactions that can proceed toward catabolism or toward anabolism depending on the needs of the cell.

• Examples are found in the biosynthesis of carbohydrates, lipids, amino acids, and nucleotides.

Carbohydrate Biosynthesis• Gluconeogenesis refers to metabolic pathways that

produce sugars, starch, cellulose, glycogen, peptidoglycan, etc. from noncarbohydrate precursors such as amino acids, glycerol, and fatty acids

• It is highly endergonic requiring adequate supply of energy.

• G3P from Calvin cycle, Acetyl-CoA, and DHAP(dihydroxyacetone phosphate) from glycerol (from fat) forms:

• (1)Fructose1,6,biphosphate --- • (2)--fructose 6-phosphate (peptidoglycan) ---- • (3)--glucose 6- phosphate (glycogen) ----• (4)--glucose (starch, cellulose)

Lipid Biosynthesis• Lipids are diverse group of organic molecules

that function as energy-storage compounds and as components of membranes e.g. Pigments carotenoids in bacteria and plant photosystems

• Lipids are synthesized by a variety of routes. • Steroids result from complex pathways involving

polymerizations and isomerizations of sugar and amino acid metabolites.

• Fat is synthesized from glycerol and three molecules of fatty acid—a reverse of the catabolic reaction.

Steps in lipid biosynthesis p.157 Bauman

• G3P (glyceraldehyde 3-phosphate) obtained from Calvin-Benson cycle and from glycolysis

• It converts into DHAP(dihydroxyacetone phosphate), glycerol and fats

• Acetyl-CoA from glycolysis undergoes reverse of beta-oxidation to form fatty acids and fats

Amino Acid Biosynthesis

• Precursor metabolites for amino acid synthesis are derived from glycolysis, Krebs cycle, PPP, and other amino acids

• E. coli and most plants and algae synthesize all their amino acids from precursor metabolites (exception Lactobacillus)

• Humans need essential amino acids in diets because they cannot synthesize amino acids

Precursor metabolitesDerived from glycolysis:

i. Glucose 6-phosphate synthesize lipopolysacharideii. Fructose 6-phosphate synthesize peptidoglycaniii. Glyceraldehde 3-phosphate synthesize glycerol portion of proteinsiv. Phosphoglyceric acid synthesize amino acidsv. Phosphoenolpyruvic acid (PEP) synthesize amino acids, phenylalanine, trytophan, tyrosinevi. Pyruvic acid synthesize amino acids, alanine, leucine, valine

Precursor metabolitesDerived from Pentose phosphate pathway:

i. Ribose 5-P synthesize DNA, RNA, amino acid and histidineii. Erythrose 5-P synthesize amino acids, phenylalanine, trytophan, tyrosine

Derived from Krebs cycle:i. Acetyl CoA synthesize portion of fatty acidsii. Alfa-ketoglutaric acid synthesize amino acidsiii. Succinyl –CoA synthesize heme (cytochrome electron carrier)iv. Oxaloacetate synthesize amino acids

Amino acid and protein synthesis• Precursor metabolites are converted to amino

acids by an addition of amine group by:• Amination when the amine group comes from

ammonia(NH3) e.g. Formation of aspartic acid and the Krebs cycle intermediate oxaloacetic acid

• Transamination, a reversible reaction in which an amine group is transferred from one amino acid to another by the action of enzymes (transaminase) using coenzyme pyridoxal phosphate derived from vitamin B6

• Ribosomes and ribozymes polymerize amino acids into proteins

Nucleotide Biosynthesis

• Nucleotides are produced from precursor metabolites derived from:

1. glycolysis 2. the Krebs cycle: ribose and deoxyribose

from ribose-5 phosphate, 3. phosphate from ATP 4. purines and pyrimidines from the amino

acids glutamine and aspartic acid.

Nucleotide synthesis

Integration and Regulation of Metabolic functions

• Energy released in catabolic reactions is used to drive anabolic reactions.

• Catabolic pathways produce metabolites to use as substrates for anabolic reactions.

• Cells use a variety of mechanisms to regulate metabolism including control of gene expression, which controls enzyme production needed for metabolic pathways, and control of metabolic expression in which the cells control enzymes that have been produced.

Pathways of cellular metabolism• The pathways of cellular metabolism can

be categorized into 3 groups:• pathways synthesizing macromolecules

(proteins, nucleic acids, polysaccharides, and lipids),

• intermediate pathways, • and pathways that produce ATP and

precursor molecules (glycolysis, Krebs cycle, pentose phosphate pathway, and Entner-Doudoroff pathway).

Regulation of metabolismCells regulate metabolism by the following:• Cells synthesize or degrade or channel and

transport proteins to regulate the concentration of chemicals in the cytosols or organelles

• They synthesize enzymes needed to catabolize a particular sustrate or stop the production of beta-oxidation enzymes when there are no fatty acids to catabolize

• If 2 energy sources are available, cells catabolize the more energy efficient of the two

• They synthesize the metabolites they need and cease synthesis if a nutrient is available as a metabolite

Metabolism regulation• Eukaryotic cells isolate particular enzymes for

different metabolic processess so as to avoid their interference in the pathways

• Cells use inhibitory sites on enzymes to control their activities

• Feedback inhibition slows or stops anabolic pathways when product is in abundance

• The same substrate molecules used in catabolic and anabolic pathways can be regulated by using different coenzymes for each pathway e.g. NADH is used almost exclusively with catabolic enzymes, whereas NADPH is typically used for anabolism