Food for thought? • Why would a bowl sugar provide energy, but it would not spoil?
Macro-nutrients Element Source Supplied as media ingredient Carbon (C) CO 2 or organics Glucose, malate, acetate, pyruvate, amino acids, etc... Hydrogen (H) Water, organics Water, organics Oxygen (O) H 2 O, O 2 , Organics H 2 O, O 2 , organics Nitrogen (N) NH 3 , NO 3 -, N 2 , organic NH 4 Cl, (NH 4 ) 2 SO 4 , KNO 3 , N 2 nitrogen Amino acids, nucleotides Phosphorus (P) PO 4 3- KH 2 PO 4 , Na 2 HPO 4 2- , organic S Sulphur (S) H 2 S, SO 4 Na 2 SO4, Na 2 S, cysteine compounds, metal sulphides Potassium (K) K+ in solution KCl, KH 2 PO 4 Mg 2+ in solution Magnesium (Mg) MgCl 2 , MgSO 4 Ca 2+ in solution Calcium (Ca) CaCl 2 Fe 2+ , Fe 3+ in solution, FeS, Iron (Fe) FeCl 3 , FeSO 4 , various chelated Fe(OH) 3 iron solutions
Micro-nutrients Element Cellular function Boron (B) Involved in quorum sensing; some polyketide antibiotics Cobalt (Co) Vitamin B 12 , some enzymes Copper (Cu) Respiration, cytochrome c oxidase, photosynthesis, some superoxide dismutases; ammonia/methane oxidation (some enzymes) Iron (Fe) Cytochromes, catalases, peroxidase, iron-sulfur proteins, oxygenases, all nitrogenases Manganese (Mn) Activator for many enzymes, certain superoxide dismutases, enzyme in photosystem II Molybdenum Flavin containing enzymes, some nitrogenases, nitrate (Mo) reductases, sulfite oxidases, DMSO-TMOA reductases, some formate dehydrogenases
Micro-nutrients Element Cellular function Nickel (Ni) Most hydrogenases, coenzyme F430 of methanogens, carbon monoxide dehydrogenase, urease Selenium (Se) Formate dehydrogenases; amino acid selenocysteine Tungsten (W) Some formate dehydrogenases; oxotransferase of hyperthermophiles Vanadium (V) Vanadium nitrogenase; bromoperoxidase Zinc (Zn) Carbonic anhydrase; alcohol dyhydrogenase; RNA/DNA polymerases and many DNA-binding proteins
Vitamin growth factors Element Cellular function p-aminobenzoic acid Precursor of folic acid Folic acid One-carbon metabolism; methyl group transfer Biotin Fatty acid synthesis; b-decarboxylations; some CO 2 fixation reactions Cobalamin (B12) Reduction or and transfer of single carbon fragments; synthesis of deoxyribose Lipoic acid Transfer of acyl groups in decarboxylation of pyruvate and a-ketoglutarate Nicotinic acid (niacin) Precursor of NAD+; electron transfer in oxidation-reduction reactions Panthothenic acid Precursor of coenzyme A; activation of acetyl and other acyl derivatives Riboflavin Precursor of FMN, FAD in flavoproteins involved in electron transport Thiamine (B1) a-decarboxylations; transketolases Vitamin B6 Amino acid and keto acid transformations Vitamin K Electron transport Hydroxamates Iron binding compounds; transport of iron into cell
Carbon • Many cellular structures • Energy • Autotrophs – able to build all of their cellular structures from carbon dioxide • Heterotrophs – acquire carbon from organic compounds
Nitrogen • Proteins • Nucleic acids • Several cellular constituents • All bacteria can assimilate NH 3 (ammonia) • Many can uptake NO 3 (nitrate), NO 2 (nitrite) • Some can take up N 2
Phosphorus • ATP (energy) • Nucleic acids • Some lipid compounds • Cells can only assimilate inorganic phosphate • Cannot take up organic-P • Incorporated into ATP pathways • Phosphatases hydrolyse P from organic compounds
Oxygen • Electron acceptor (some organisms) • Cellular components • Aerobes – require oxygen for respiration • Anaerobes – do not require oxygen for respiration – Facultative – can survive in presence of O 2 – Obligate – cannot survive in presence of O 2
Sulphur • Many proteins • Detoxification mechanisms • Metal coordination in enzymes • Sulphide (H 2 S), most reduced state, only present in anaerobic environments • Sulphate (SO 4 2- ), found in aerobic environments (difficult uptake) • Organic-S compounds
Iron • Cellular respiration – Cytochromes – Electron transport • Some cells would produce siderophores that bind iron and transport into the cell
Metabolism • Guiding principle is the optimisation of energy and biomass production • Catabolism – reactions that lead to energy production – Substrates with highest energy yield are preferentially used • Anabolism – reactions that lead to biomass production – Substrates with lowest required energy input to biomass are preferentially used
Catabolism • Energy is conserved in the formation of certain compounds that contain energy-rich phosphate or sulphur bonds • Most common = adenosine tri-phosphate (ATP) • Long-term = formation of polymers, which can be consumed to yield ATP
Glycolysis • Glycolysis is a major pathway of fermentation (anaerobic metabolism) • Precursor for respiration • Yields 2 ATP and fermentation products from each glucose consumed
Respiration • The citric acid cycle plays a major role in the respiration of organic compounds • It follows the initial steps of glycolysis
Respiration • The energy (electrons) from NADH, FADH2 are shuttled through electron transport train • Shifted protons outside the membrane forms the proton motive force .
Respiration • Sequential series of redox reactions • The electron transport chain include flavins, quinones, cytochrome complex, and other cytochromes.
Respiration • Cells use the proton motive force (electro- chemical gradient each side of membrane) as a “battery” to make ATP • ATP synthase (ATPase) ADP + P ATP
ATP yields RESPIRATION: 38 ATP v. FERMENTATION 2 ATP
Catabolic alternatives • In anaerobic respiration, electron acceptors other than O 2 can function as terminal electron acceptors for energy • E.g., NO 3 , SO 4 2- , sulphur (S 0 ), Fe +3 , etc. (more later)
Catabolic alternatives • Chemolithotrophs use inorganic compounds as electron donors (S 2- , NH 3 , H 2 , S 0 , Fe 2+ , etc.) • Phototrophs use light to form a proton motive force. • Proton motive force is involved in all forms of respiration and photosynthesis.
Eukaryotic system? • How would this mechanism work in eukaryotic cells?
2. Anabolism
Miller Urey experiment (1952) • Using: – Water – Methane – Ammonia – Hydrogen • Created over 20 amino acids
Graham Cairns-Smith • Clay hypothesis – Replication and natural selection of clays – Crystals preserve their formal arrangement as they fragment and grow (as based on a template) – Slight changes in template may create a “better” clay (e.g., stickier) – Change may be noticed in further crystals…
Cairns-Smith (1985) • Proto-life was inorganic and existed on solid surfaces such as clays • Clays catalysed formation of complex molecules • Clays acted like template for RNA self-assembly and evolved into RNA • Natural selection enhanced replication potential
Andromeda Strain
Andromeda Strain • Requires specific pH • Crystalline structure • Lacks DNA, RNA, proteins, amino acids • One version = silicon • 2008 version = sulphur based
Si for Life • “Scientists and science fiction authors have long speculated that because silicon atoms bond to other atoms in a manner similar to carbon, silicon could form the basis of an alternative biochemistry of life. • “Scientists reported in San Diego at the ACS that they have evolved a bacterial enzyme that efficiently incorporates silicon into simple hydrocarbons – a first for life.” • - Science , 18 March 2016
“What is Life?” is… a linguistic trap. To answer according to the rules of grammar, we must supply a noun, a thing. But life on Earth is more like a verb. It repairs, maintains, re- creates, and outdoes itself.” Lyn Margulis (1995)
Introduction
Introduction
Sugars
Polysaccharides • Via glycosidic bonds • They can contain other compounds such as lipids and proteins
Fatty acids
Lipids • Triglyceride • Phospholipid
Nucleic acid • Nucleic acids • Nucleotides • DNA/ RNA
Amino acids Proteins • Amino acids • Polypeptides • Proteins
Anabolism • If not provided the building blocks, either from – nature (environment) – culture media • They must be bio-synthesised from simpler components (anabolism)
Substrates Products Catabolism ATP Anabolism Biosynthesis Monomers Macromolecules
Review
Nucleotides + amino acids Glucose-6-P Ribulose-5-P + CO2 Ribose-5-P Ribonucleotides Ribonucleotide RNA Deoxyribonucleotide DNA
Nucleotides + amino acids Amino acids are formed from carbon skeletons generated during catabolism.
Amino acids
Nucleotides + amino acids Purines Nucleotides are synthesised from multiple carbon sources Pyrimidines
Fatty Acids + Lipids • Fatty acids are synthesised 2-carbons at a time • Then attached to glycerol to form lipids
Food for thought? • Why would a bowl sugar provide energy, but it would not spoil?
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