Food for thought? Why would a bowl sugar provide energy, but it - - PowerPoint PPT Presentation

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) CO2 or organics Glucose, malate, acetate, pyruvate, amino acids, etc... Hydrogen (H) Water, organics Water, organics Oxygen (O) H2O, O2, Organics H2O, O2, organics Nitrogen (N) NH3, NO3-, N2, organic nitrogen NH4Cl, (NH4)2SO4, KNO3, N2 Amino acids, nucleotides Phosphorus (P) PO4

3-

KH2PO4, Na2HPO4 Sulphur (S) H2S, SO4

2-, organic S

compounds, metal sulphides Na2SO4, Na2S, cysteine Potassium (K) K+ in solution KCl, KH2PO4 Magnesium (Mg) Mg2+ in solution MgCl2, MgSO4 Calcium (Ca) Ca2+ in solution CaCl2 Iron (Fe) Fe2+, Fe3+ in solution, FeS, Fe(OH)3 FeCl3, FeSO4, various chelated iron solutions

Micro-nutrients

Element Cellular function Boron (B) Involved in quorum sensing; some polyketide antibiotics Cobalt (Co) Vitamin B12, 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,

• xygenases, all nitrogenases

Manganese (Mn) Activator for many enzymes, certain superoxide dismutases, enzyme in photosystem II Molybdenum (Mo) Flavin containing enzymes, some nitrogenases, nitrate 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 CO2 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 NH3 (ammonia)
• Many can uptake NO3 (nitrate), NO2 (nitrite)
• Some can take up N2

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 O2 – Obligate – cannot survive in presence of O2

Sulphur

• Many proteins
• Detoxification mechanisms
• Metal coordination in enzymes
• Sulphide (H2S), most reduced state, only present in

anaerobic environments

• Sulphate (SO4

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 O2 can function as terminal electron acceptors for energy

• E.g., NO3, SO4

2-, sulphur (S0), Fe+3, etc.

(more later)

Catabolic alternatives

• Chemolithotrophs use inorganic compounds as

electron donors (S2-, NH3, H2, S0, Fe2+, 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

Nucleotides are synthesised from multiple carbon sources

Purines 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?