Photosynthesis: Carbon reactions

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Photosynthesis: Light Reactions (For UG students)

 

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Nitrogen Metabolism

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Biological Nitrogen Fixation

 

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 Enzyme

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Metabolism 

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Metabolism is the sum of all chemical transformations taking place in a cell or organism.

It occurs through a series of enzyme-catalyzed reactions that constitute metabolic pathway.

In this multistep sequence, the product of one step serves as the substrate for the next step. These metabolic intermediates are called metabolites.

Multiple metabolic pathways remain interconnected to form a meaningful well-coordinated network that determines the overall functioning of the cell.

Complexity of metabolic pathways as depicted in KEGG: Kyoto Encyclopedia of Genes and Genomes

 

             

Catabolism

• The degradative phase of metabolism 
• Organic nutrient molecules (carbohydrates, fats, and proteins) are converted into smaller, simpler end products (such as lactic acid, CO2, NH3) 
• Release energy:
• A part is conserved in the form of ATP and reduced electron carriers (NADH, NADPH, and FADH2)
• The rest is lost as heat

Anabolism

• The biosynthetic phase of metabolism
• Small, simple precursors are built up into larger and more complex molecules (lipids, polysaccharides, proteins, and nucleic acids)
• Require input of energy (phosphoryl group transfer potential of ATP and reducing power of NADH, NADPH, and FADH2)

Some pathways can be either anabolic or catabolic, depending on the energy conditions in the cell. They are referred to as amphibolic pathways.

Example: Citric acid cycle

Metabolic pathways may linear, branched or cyclic.

Catabolic pathways are convergent and anabolic pathways divergent.

• Converging catabolism: convert several starting materials into a single product
• Diverging anabolism: yielding multiple useful end products from a single precursor
• Cyclic pathway: one starting component is regenerated in a series of reactions that converts another starting component into a product

Metabolic processes are regulated in three principal ways:

• by controlling the accessibility of substrates
• by controlling the amounts of enzymes
• by controlling their catalytic activities

Controlling the accessibility of substrates

• At low substrate concentration (near or below Km), rate of reaction depends on substrate concentration.
• Controlling the flux of substrates also regulates metabolism. 
• The transfer of substrates from one compartment of a cell to another (e.g., from the cytosol to mitochondria) can serve as a control point.
• Compartmentalization segregates opposed reactions. For example, fatty acid oxidation takes place in mitochondria, whereas fatty acid synthesis takes place in the cytosol. 

Controlling the amounts of enzymes

• The amount of a particular enzyme depends on:
• its rate of synthesis
• its rate of degradation
• The level of most enzymes is adjusted primarily by changing the rate of transcription of the genes encoding them.

Controlling their catalytic activities

The catalytic activity of enzymes is controlled by: 

• Reversible allosteric control: Key enzymes in many biosynthetic pathways is allosterically inhibited by a metabolic intermediate or coenzyme or the  ultimate product of the pathway. 
• Reversible covalent modification: Activation/deactivation of enzymes by phosphorylation/deposphorylation of particular residues.
• Hormones-mediated reversible modification of key enzymes: Hormones or growth factors coordinate metabolic relations between different tissues, often by regulating the reversible modification of key enzymes.

Classification of the Bryophytes (Goffinet, Buck and Shaw; 2008)

Mosses display a wide range of structural diversity from which relationships and lineages can be inferred. Historically, bryophyte systematics has focused on peristome teeth complexity and sex organ distribution to define taxonomic units.

Modern classifications reflect systematic concepts proposed by Fleischer (1920) and Brotherus (1924, 1925), wherein the peristomate mosses were classified as follows:

• Nematodontous
• Arthrodontous

Based on the position of perichaetia, arthrodontous mosses were sub-divided into:

• Acrocarpous 
• Pleurocarpous

Based on the architecture of the outer ring of peristome teeth, arthrodontous mosses were sub-divided into:

• Haplolepideous
• Diplolepideous

Sphagnum, Andreaea, Andreaeobryum, and Takakia represent additional groupings distinguished by the presence of a pseudopodium and the mode of sporangial dehiscence.

The classification of the Bryophyta is undergoing constant revisions, particularly in the light of phylogenetic inferences. The classification proposed by Goffinet, Buck, and Shaw (2008) builds on those presented by Buck & Goffinet (2000) and Goffinet & Buck (2004). Their classification is outlined below:

BRYOPHYTA

        SUPERCLASS I

                CLASS TAKAKIOPSIDA: Leaves divided into terete filaments; capsules dehiscent by a single longitudinal spiral slit; stomata lacking. Example: Takakia

Takakia sp.

        SUPERCLASS II

                        CLASS SPHAGNOPSIDA: Branches usually in fascicles; leaves composed of a network of chlorophyllose and hyaline cells; setae lacking; capsules elevated on a pseudopodium; stomata lacking. Example: Sphagnum

Sphagnum

        SUPERCLASS III

                CLASS ANDREAEOPSIDA: Plants on acidic rocks, generally autoicous; cauline central strand absent; calyptrae small; capsules valvate, with four valves attached at apex; seta absent, pseudopodium present; stomata lacking. Example: Andreaea

Andreaea

                CLASS ANDREAEOBRYOPSIDA: Plants on calcareous rocks, dioicous; cauline central strand lacking; calyptrae large and covering whole capsule; capsules valvate, apex eroding and valves free when old; stomata lacking; seta present. Example: Andreaeobryum

Andreaeobryum

        SUPERCLASS V

         CLASS OEDIPODIOPSIDA: Leaves unicostate; calyptrae cucullate; capsule symmetric and erect, neck very long; stomata lacking; capsules gymnostomous. Example: Oedipodium

Oedipodium

                    CLASS POLYTRICHOPSIDA: Plants typically robust, dioicous; cauline central strand present; stems typically rhizomatous; costa broad, with adaxial chlorophyllose lamellae; peristome nematodontous, mostly of (16)32–64 teeth. Example: Polytrichum

Polytrichum

                    CLASS TETRAPHIDOPSIDA: Leaves unicostate; calyptrae small conic; capsule symmetric and erect, neck short; peristome nematodontous, of four erect teeth. Example: Tetraphis

Tetraphis

                       CLASS BRYOPSIDA: Plants small to robust; leaves costate or not, typically lacking lamellae; capsules operculate; peristome at least partially arthrodontous. Example: Bryum

Bryum

Features of the classification system:

• The rank of superclass is adopted to unite all arthrodontous mosses in one taxon (i.e. Superclass V).
• Although this system of classification aimed at accepting only monophyletic taxa, given the limited number of ranks available, paraphyletic taxa were incorporated (e.g. Bryanae). 
• Effort was made to resolve the relationships among genera of the Hypnanae.
• Due to the lack of sequence data and availability of information of many taxa at regional level only, the authors have been unable to expand their classification system to a global scale.                                        

Further reading: 

Buck WR, Shaw AJ, Goffinet B. Morphology, anatomy, and classification of the Bryophyta. In: Bryophyte Biology: Second Edition, ed. B. Goffinet & A. J. Shaw. Cambridge University Press; 2008. p. 55–138.