L08 Metabolism and Protein Secretion

Metabolism

Metabolism is the total of all chemical reactions in the cell and is divided into two parts

catabolism 异化作用；分解代谢
anabolism 同化作用；合成代谢

Contribute to cycling of elements in ecosystems

some cycling reactions performed only by microbes

一、 Catabolism: Energy Release and Conservation

Diversity

1. Requirements for Carbon, Hydrogen, and Oxygen

Often satisfied together

carbon source often provides H, O, and electrons

Carbon Sources
Autotrophs 自养生物	CO2 sole or principal biosynthetic carbon source
Heterotrophs 异养生物	Reduced, preformed, organic molecules from other organisms

Energy Sources
Phototrophs 光养型生物	Light
Chemotrophs 化能生物	Oxidation of organic or inorganic compounds

Electron Sources
Lithotrophs 无机营养型	Reduced inorganic molecules
Organotrophs 有机营养型	Organic molecules

2. Major Nutritional Types

3. Fueling Reactions 供能反应

Despite diversity of energy, electron, and carbon sources used by organisms, they all have the same basic needs

ATP as an energy currency
Reducing power to supply electrons for chemical reactions
Precursor metabolites for biosynthesis

Chemoorganotrophy 化能有机营养

Carried out by chemoorganoheterotrophs

Example Processes

aerobic respiration
anaerobic respiration
fermentation

1. Respiration

aerobic respiration 需氧呼吸

final electron acceptor is oxygen

anaerobic respiration 无氧呼吸

final electron acceptor is different exogenous acceptor such as :

organic acceptors may also be used

ATP made primarily by oxidative phosphorylation , Generally yields less energy

Electron Transport Chain

In eukaryotes the $e^{-}$ transport chain carriers are in the inner mitochondrial membrane, connected by coenzyme Q and cytochrome c

(1) Bacterial and Archaeal ETCs

Located in plasma membrane

Some resemble mitochondrial ETC, but many are different

different electron carriers
may be branched
may be shorter
may have lower P/O ratio

Example: Paracoccus denitrificans 脱氮副球菌

Facultative, soil bacterium

2. Fermentation

Fermentation

No ETC (Electron Transport Chain) and PMF (Proton Motivation Force)

Uses an endogenous electron acceptor

ATP synthesized only by SLP

An Special Outer membrane protein Called SLP

Chemolithotrophy 化能无机营养

Carried out by chemolithotrophs

Inorganic molecule and TEC

ATP synthesized by oxidative phosphorylation 磷酸化作用

Examples:

1. Energy Sources

Much less energy is available from oxidation of inorganic molecules than glucose oxidation

2. Major Groups of Chemolithotrophs

Have ecological importance

Several bacteria and archaea oxidize hydrogen

Nitrifying bacteria oxidize ammonia to nitrate

Sulfur-oxidizing microbes

hydrogen sulfide ($H_{2} S$), sulfur ($S^{0}$), thiosulfate ($S_{2} O_{3} ^{2-}$)

Sulfur-Oxidizing Bacteria

ATP can be synthesized by both oxidative phosphorylation and substrate-level phosphorylation

3. Reverse Electron Flow by Chemolithotrophs

Many energy sources used by chemolithotrophs have higher redox potential than NAD+(P)/NAD(P)H

use reverse electron flow to generate NAD(P)H

Phototrophy 光营养

1. Light Reactions in Oxygenic Photosynthesis

Photosynthetic eukaryotes and cyanobacteria

Oxygen is generated

Most important pigments are chlorophylls

2. The Light Reaction in Anoxygenic Photosynthesis

H2O not used as an electron source; therefore O2 is not produced

Only one photosystem involved

Uses bacteriochlorophylls

Carried out by phototrophic green bacteria, phototrophic purple bacteria, and heliobacteria

3. Comparision Between Photosynthetic Systems

4. Bacteriorhodopsin-Based Phototrophy

Some archaea use bacteriorhodopsin

a membrane protein
functions as a light-driven proton pump

A proton motive force is generated

二、Anabolism: Synthesis of Peptidoglycan

Peptidoglycan（肽聚糖） Synthesis

Complex process involving UDP derivatives

Figure 12.9:

Steps：

UDP derivatives of NAM and NAG are synthesized (Figure 12.9)
Sequential addition of amino acids to UDP-NAM to form the NAM-pentapeptide (figure 12.9b).
NAM-pentapeptide is transferred to bactoprenol phosphate. They are joined by a pyrophosphate bond.
UDP transfers NAG to the bactoprenol-NAM-pentapeptide. If a pentaglycine interbridge is required, it is created using special glycyl-tRNA molecules but not ribosomes. Interbridge formation occurs in the membrane.
The bactoprenol carrier transports the completed NAG-NAM-pentapeptide repeat unit across the membrane.
The NAG-NAM-pentapeptide is attached to the growing end of a peptidoglycan chain, increasing the chain’s length by one repeat unit.
The bactoprenol carrier moves back across the membrane. As it does, it loses one phosphate, becoming bactoprenol phosphate. It is now ready to begin a new cycle.
Peptide cross-links between peptidoglycan chains are formed by transpeptidation