Bacteriology at UW-Madison Bakteriologis pada UW-Madison

The Microbial World Dunia mikroba

Lectures in Microbiology by Kenneth Todar PhD University of Wisconsin-Madison Department of Bacteriology Kuliah di Mikrobiologi oleh Todar PhD University Kenneth of Wisconsin-Madison Department of Bacteriology

Diversity of Microbial Metabolism Keragaman Metabolisme Mikroba

© 2009 Kenneth Todar PhD © 2009 Kenneth Todar PhD

Introduction Pengantar

A lot of hoopla is made about microbial diversity . Banyak kehebohan dibuat tentang keanekaragaman mikroba. Although eucaryotic microbes, especially the protista, exhibit a great deal of structural diversity, the procaryotes are without this distinction. Meskipun mikroba eukariotik, terutama Protista tersebut, menunjukkan banyak keanekaragaman struktural, procaryotes yang tanpa perbedaan ini. However, based on their modes of metabolism, the procaryotes are much more diverse than all eucaryotes, and the real real explanation for "microbial diversity" rests fundamentally on some aspect procaryotic metabolism, especially with regards to energy-generating metabolism and synthesis of secondary metabolites. Namun, berdasarkan mode mereka metabolisme, yang procaryotes jauh lebih beragam daripada semua eucaryotes, dan penjelasan yang nyata nyata "keragaman mikroba" terletak mendasar pada beberapa aspek metabolisme prokariot, khususnya berkaitan dengan metabolisme energi dan sintesis menghasilkan metabolit sekunder . Microbial diversity translates to metabolic diversity. The procaryotes, as a group, conduct all the same types of basic metabolism as eucaryotes, but, in addition, there are several types of energy-generating metabolism among the procaryotes that are non existent in eucaryotic cells or organisms. menerjemahkan keragaman mikroba terhadap keanekaragaman metabolik,. The procaryotes sebagai sebuah kelompok, melakukan semua jenis yang sama metabolisme dasar sebagai eucaryotes, tetapi, di samping itu, ada beberapa jenis yang menghasilkan metabolisme energi antara procaryotes yang tidak ada dalam sel-sel eukariotik atau organisme. These include Ini termasuk

Unique fermentation pathways that produce a wide array of end products Unik jalur

fermentasi yang menghasilkan beragam produk akhir

Anaerobic respiration : respiration that uses substances other than O 2 as a final electron acceptor Respirasi anaerob: pernapasan yang menggunakan zat lain dari O 2 sebagai akseptor elektron terakhir

Lithotrophy : use of inorganic substances as sources of energy Lithotrophy: penggunaan zat anorganik sebagai sumber energi

Photoheterotrophy : use of organic compounds as a carbon source during bacterial photosynthesis Photoheterotrophy: penggunaan senyawa organik sebagai sumber karbon selama fotosintesis bakteri

Anoxygenic photosynthesis : uses special chlorophylls and occurs in the absence of O 2 fotosintesis Anoxygenic: menggunakan klorofil khusus dan terjadi tanpa adanya O 2

Methanogenesis : an ancient type of archaean metabolism that uses H 2 as an energy source and produces methane Methanogenesis: tipe kuno metabolisme Archaean yang menggunakan H 2 sebagai sumber energi dan menghasilkan metana

Light-driven nonphotosynthetic energy production : unique archaean metabolism that converts light energy into chemical energy; occurs in the archaea (extreme halophiles) Light-driven nonphotosynthetic produksi energi: metabolisme yang unik Archaean yang mengubah energi cahaya menjadi energi kimia; terjadi dalam archaea (halophiles ekstrim)

Unique mechanisms for autotrophic CO 2 fixation , including primary production on anaerobic habitats Unik mekanisme untuk autotrophic fiksasi CO 2, termasuk produksi primer pada habitat anaerobik

What is metabolism? Apa itu metabolisme?

The term metabolism refers to the sum of the biochemical reactions required for energy generation and the use of energy to synthesize cell material from small molecules in the environment. Metabolisme merujuk pada jumlah reaksi biokimia yang diperlukan untuk generasi energi dan penggunaan energi untuk mensintesis bahan sel dari molekul kecil di lingkungan. Hence, metabolism has an energy-generating component , called catabolism , and an energy-consuming , Oleh karena itu, metabolisme memiliki komponen yang menghasilkan energi, yang disebut katabolisme, dan mengkonsumsi energi, biosynthetic component , called anabolism . biosintesis komponen, anabolism disebut. Catabolic reactions or pathways produce energy as ATP , which can be utilized in anabolic reactions to build cell material from nutrients in the environment. reaksi katabolik atau jalur menghasilkan energi ATP, yang dapat digunakan dalam reaksi anabolik untuk membangun bahan sel dari nutrisi di lingkungan. The relationship between catabolism and anabolism is illustrated in Figure 1 below. Hubungan antara katabolisme dan anabolisme diilustrasikan pada Gambar 1 di bawah ini.

Figure 1. Gambar 1. The relationship between catabolism and anabolism in a cell. Hubungan antara katabolisme dan anabolisme dalam sel. During catabolism, energy is changed from one form to another, and keeping with the laws of thermodynamics, such energy transformations are never completely efficient, ie, some energy is lost in the form of heat. Selama katabolisme, energi berubah dari satu bentuk ke bentuk lain, dan sesuai dengan hukum termodinamika, transformasi energi tersebut pernah benar-benar efisien, yaitu, beberapa energi hilang dalam bentuk panas. The efficiency of a catabolic sequence of reactions is the amount of energy made available to the cell (for anabolism) divided by the total amount of energy released during the reactions. Efisiensi dari urutan reaksi katabolik adalah jumlah energi tersedia untuk sel (untuk anabolism) dibagi dengan jumlah energi yang dilepaskan selama reaksi.

Metabolism is usually visualized as as a series of biochemical reactions mediated by enzymes, referred to as a metabolic pathway . Catabolic pathways lead to end products, which are "waste products" and result in the generation of energy which is temporarily conserved as adenosine triphosphate (ATP). Metabolisme biasanya divisualisasikan sebagai sebagai serangkaian reaksi biokimia dimediasi oleh enzim, disebut sebagai jalur metabolisme. Jalur katabolik menyebabkan produk akhir, yang "produk sampah" dan menghasilkan generasi energi yang sementara dilestarikan sebagai adenosin trifosfat ( ATP). In heterotrophs, the most common catabolic pathways are the Emden-Meyerhof pathway for degradation of sugars as energy sources (glycolysis and the tricarboxylic acid cycle (TCA cycle), which can be linked to the further degradation of almost any organic compound and further leads to the synthesis of ATP. Dalam heterotrophs, jalur katabolik yang paling umum adalah jalur Emden-Meyerhof untuk penurunan gula sebagai sumber energi (glikolisis dan siklus asam tricarboxylic (siklus TCA), yang dapat dihubungkan dengan semakin rusaknya hampir semua senyawa organik dan lebih mengarah ke sintesis ATP.

Model of a catabolic pathway. Model jalur katabolik. Each reaction in the pathway is mediated by a specific en zyme . Setiap reaksi dalam jalur dimediasi oleh tertentu en zyme. s x y z s x y z sugar--------> X--------> Y--------> Z--------> Intermediate + ATP gula --------> X --------> --------

Y> Z --------> Intermediate + ATP

Anabolic pathways utilize ATP to provide energy for the synthesis of the monomeric compounds that are required for the manufacture of the small molecules needed in cells, ie, carbohydrates, lipids, amino acids, nucleotides, vitamins, etc. Anabolic memanfaatkan jalur ATP untuk menyediakan energi untuk sintesis senyawa monomer yang diperlukan untuk pembuatan molekul kecil yang diperlukan dalam sel, yaitu, karbohidrat, lemak, asam amino, nukleotida, vitamin, dll

Model of an anabolic pathway. Model jalur anabolik. Each reaction in the pathway is mediated by a specific en zyme. Setiap reaksi dalam jalur dimediasi oleh tertentu en zyme.

a b c d a c b d Intermediate + ATP--------> A--------> B--------> C--------> Final product Intermediate + ATP --------> A --------> B --------> C -------- produk Akhir>

ATP ATP

During catabolism, useful energy is temporarily conserved in the "high energy bond" of ATP - adenosine triphosphate . Selama katabolisme, energi yang berguna untuk sementara kekal dalam "ikatan energi tinggi" ATP - adenosin trifosfat. No matter what form of energy a cell uses as its primary source, the energy is ultimately transformed and conserved as ATP. Tidak peduli apa bentuk energi sel digunakan sebagai sumber utama, energi yang pada akhirnya berubah dan dilestarikan sebagai ATP. ATP is the universal currency of energy exchange in biological systems. ATP adalah mata uang universal pertukaran energi dalam sistem biologi. When energy is required during anabolism, it may be spent as the high energy bond of ATP which has a value of about 8 kcal per mole. Ketika energi yang dibutuhkan selama anabolism, mungkin akan menghabiskan ikatan energi tinggi dari ATP yang memiliki nilai sekitar 8 kkal per mol. Hence, the conversion of ADP to ATP requires 8 kcal of energy, and the hydrolysis of ATP to ADP releases 8 kcal. Oleh karena itu, konversi ADP menjadi ATP memerlukan 8 kkal energi, dan hidrolisis ATP menjadi ADP rilis 8 kkal.

Figure 2. Gambar 2. The structure of ATP. Struktur ATP. ATP is derived from the nucleotide adenosine monophosphate (AMP) or adenylic acid, to which two additional phosphate groups are attached through pyrophosphate bonds (~P). ATP berasal dari nukleotida adenosin monofosfat (AMP) atau asam adenylic, di mana dua gugus fosfat tambahan yang terpasang melalui obligasi pirofosfat (~ P). These two bonds are energy rich in the sense that their hydrolysis yields a great deal more energy than a corresponding covalent bond. Kedua Obligasi ini energi kaya dalam arti bahwa hasil hidrolisis mereka jauh lebih banyak energi daripada ikatan kovalen yang sesuai. ATP acts as a coenzyme in energetic coupling reactions wherein one or both of the terminal phosphate groups is removed from the ATP molecule with the bond energy being used to transfer part of the ATP molecule to another molecule to activate its role in metabolism. ATP bertindak sebagai koenzim dalam reaksi kopling energik dimana salah satu atau kedua kelompok terminal fosfat dihapus dari molekul ATP dengan energi ikatan yang digunakan untuk mentransfer bagian dari molekul ATP molekul lain untuk mengaktifkan perannya dalam metabolisme. For example, Glucose + ATP -----> Glucose-P + ADP or Amino Acid + ATP -----> AMP-Amino Acid + PPi. Sebagai contoh, Glukosa + ATP -----> Glukosa-P + ADP atau Asam Amino -----> + ATP AMP-Asam Amino + PPi.

Because of the central role of ATP in energy-generating metabolism, expect to see its involvement as a coenzyme in most energy-producing processes in cells. Karena peran sentral ATP dalam metabolisme energi yang menghasilkan, berharap untuk melihat keterlibatannya sebagai koenzim dalam proses produksi energi yang paling dalam sel.

NAD NAD

Another coenzyme commonly involved in metabolism, derived from the vitamin niacin, is the pyridine nucleotide, NAD ( Nicotinamide Adenine Dinucleotide) . Koenzim lain umumnya terlibat dalam metabolisme, berasal dari niacin vitamin, adalah nukleotida piridin, NAD (Nicotinamide Adenin dinukleotida). The basis for chemical transformations of energy usually involves oxidation/reduction reactions. Dasar untuk transformasi kimia energi biasanya melibatkan oksidasi / reaksi reduksi. For a biochemical to become oxidized, electrons must be removed by an oxidizing agent. Untuk biokimia untuk menjadi teroksidasi, elektron harus dikeluarkan oleh agen pengoksidasi. The oxidizing agent is an electron acceptor that becomes reduced in the reaction. Agen pengoksidasi adalah akseptor elektron yang menjadi berkurang

reaksi. During the reaction, the oxidizing agent is converted to a reducing agent that can add its electrons to another chemical, thereby reducing it, and reoxidizing itself. Selama reaksi berlangsung, agen pengoksidasi dikonversi menjadi agen mengurangi yang dapat menambah elektron untuk kimia lain, sehingga mengurangi itu, dan reoxidizing sendiri. The molecule that usually functions as the electron carrier in these types of coupled oxidation-reduction reactions in biological systems is NAD and its phosphorylated derivative, NADP . Molekul yang biasanya berfungsi sebagai pembawa elektron dalam jenis reaksi oksidasi-reduksi digabungkan dalam sistem biologis adalah NAD dan derivatif terfosforilasi nya, NADP. NAD or NADP can become alternately oxidized or reduced by the loss or gain of two electrons. NAD atau NADP bisa menjadi bergantian teroksidasi atau dikurangi dengan kerugian atau keuntungan dari dua elektron. The oxidized form of NAD is symbolized NAD; the reduced form is symbolized as NADH 2 . Bentuk teroksidasi NAD dilambangkan NAD; bentuk pengurangan disimbolkan sebagai NADH 2. The structure of NAD is drawn below. Struktur NAD digambar di bawah ini.

Figure 3. Gambar 3. The Structure of NAD. Struktur NAD. (a) Nicotinamide Adenine Dinucleotide is composed of two nucleotide molecules: Adenosine monophosphate (adenine plus ribose-phosphate) and nicotinamide ribotide (nicotinamide plus ribose-phosphate). (A) Nicotinamide Adenin dinukleotida terdiri dari dua molekul nukleotida: Adenosin monofosfat (adenin ditambah ribosa-fosfat) dan ribotide nicotinamide (nicotinamide plus-fosfat ribosa). NADP has an identical structure except that it contains an additional phosphate group attached to one of the ribose residues. NADP memiliki struktur yang sama kecuali bahwa ia mengandung sebuah gugus fosfat tambahan yang terpasang pada salah satu residu ribosa. (b) The oxidized and reduced forms of of the nicotinamide moiety of NAD. (B) dan mengurangi bentuk teroksidasi dari bagian nicotinamide NAD. Nicotinamide is the active part of the molecule where the reversible oxidation and reduction takes place. Nicotinamide adalah bagian aktif dari molekul mana reversibel oksidasi dan reduksi terjadi. The oxidized form of NAD has one hydrogen atom less than the

reduced form and, in addition, has a positive charge on the nitrogen atom which allows it to accept a second electron upon reduction. Bentuk teroksidasi NAD memiliki satu atom hidrogen kurang dari bentuk dikurangi dan, di samping itu, memiliki muatan positif pada atom nitrogen yang memungkinkan untuk menerima elektron kedua pada pengurangan. Thus the correct way to symbolize the reaction is NAD + + 2H -----> NADH + H + . Jadi cara yang benar untuk melambangkan reaksi NAD + + 2H -----> NADH + H +. However, for convenience we will hereafter use the symbols NAD and NADH 2 . Namun, untuk kenyamanan kita selanjutnya akan menggunakan simbol dan NADH NAD 2.

ATP Synthesis Sintesis ATP

The objective of a catabolic pathway is to make ATP, that is to transform either chemical energy or electromagnetic (light) energy into the chemical energy contained within the high-energy bonds of ATP. Tujuan dari lintasan katabolik adalah membuat ATP, yang baik adalah untuk mengubah energi kimia atau elektromagnetik (cahaya) energi ke energi kimia yang terkandung dalam ikatan energi tinggi ATP. Cells fundamentally can produce ATP in two ways: substrate level phosphorylation and electron transport phosphorylation . Sel dasarnya dapat menghasilkan ATP dalam dua cara: fosforilasi tingkat substrat dan transportasi fosforilasi elektron.

Substrate level phosphorylation (SLP) is the simplest, oldest and least-evolved way to make ATP. Tingkat substrat fosforilasi (SLP) adalah dan paling sederhana, tertua-cara berevolusi untuk membuat ATP. In a substrate level phosphorylation, ATP is made during the conversion of an organic molecule from one form to another. Dalam fosforilasi tingkat substrat, ATP dilakukan selama konversi dari sebuah molekul organik dari satu bentuk ke bentuk lainnya. Energy released during the conversion is partially conserved during the synthesis of the high energy bond of ATP. Energi yang dilepaskan selama konversi sebagian kekal selama sintesis ikatan energi tinggi dari ATP. SLP occurs during fermentations and respiration (the TCA cycle), and even during some lithotrophic transformations of inorganic substrates. SLP terjadi selama fermentasi dan respirasi (siklus TCA), dan bahkan selama beberapa transformasi lithotrophic substrat anorganik.

Figure 4. Gambar 4. Three examples of substrate level phosphorylation. Tiga contoh tingkat fosforilasi substrat. (a) and (b) are the two substrate level phosphorylations that occur during the Embden Meyerhof pathway, but they occur in all other fermentation pathways which have an Embden-Meyerhof component. (A) dan (b) adalah dua phosphorylations tingkat substrat yang terjadi selama jalur Meyerhof Embden, tetapi mereka terjadi pada semua jalur fermentasi lain yang memiliki komponen-Meyerhof Embden. (c) is a substrate level phosphorylation found in Clostridium and Bifidobacterium. These are two anaerobic (fermentative) bacteria who learned how to make one more ATP from glycolysis beyond the formation of pyruvate. (C) tingkat substrat fosforilasi ditemukan di Clostridium dan Bifidobacterium. Ini adalah dua anaerobik (fermentasi) bakteri yang belajar bagaimana membuat satu lagi ATP dari glikolisis luar pembentukan piruvat.

Electron Transport Phosphorylation (ETP) is a much more complicated affair that evolved long after SLP. Transportasi Elektron Fosforilasi (ETP) adalah urusan yang lebih rumit banyak yang berevolusi lama setelah SLP. Electron Transport Phosphorylation takes place during respiration, photosynthesis, lithotrophy and possibly other types of bacterial metabolism. Transportasi Elektron Fosforilasi berlangsung selama respirasi, fotosintesis, lithotrophy dan mungkin jenis lain dari metabolisme bakteri. ETP requires that electrons removed from substrates be dumped into an electron transport system (EST) contained within a membrane. ETP mensyaratkan bahwa elektron dihapus dari substrat dibuang ke dalam sistem transpor elektron (EST) yang terkandung dalam membran. The electrons are transferred through the EST to some final electron acceptor in the membrane (like O 2 in aerobic respiration) , while their traverse through the ETS results in the extrusion of protons and the establishment of a proton motive force ( pmf ) across the membrane. Elektron ditransfer melalui EST ke beberapa akseptor elektron terakhir dalam membran (seperti O 2 dalam respirasi aerobik), sementara mereka menelusuri hasil ETS dalam ekstrusi proton dan pembentukan kekuatan motif proton (PMF) di membran . An essential component of the membrane for synthesis of ATP is a membrane-bound ATPase (ATP synthetase) enzyme. Komponen penting dari membran untuk sintesis ATP adalah yang terikat ATPase membran (ATP sintetase) enzim. The ATPase enzyme transports

protons, thereby utilizing the pmf (protons) during the synthesis of ATP. Enzim ATPase transport proton, sehingga memanfaatkan PMF (proton) selama sintesis ATP. The idea in electron transport phosphorylation is to drive electrons through an ETS in the membrane, establish a pmf, and use the pmf to synthesize ATP. Ide dalam fosforilasi transpor elektron adalah mengarahkan elektron melalui ETS dalam membran, membentuk PMF, dan gunakan PMF untuk mensintesis ATP. Obviously, ETP take a lot more "gear" than SLP, in the form of membranes, electron transport systems, ATPase enzymes, etc. Jelas, ETP mengambil banyak lebih "gigi" daripada SLP, dalam bentuk membran, sistem transpor elektron, ATPase enzim, dll

A familiar example of energy-producing and energy-consuming functions of the bacterial membrane, related to the establishment and use of pmf and the production of ATP, is given in the following drawing of the plasma membrane of Escherichia coli . Contoh akrab energi-memproduksi dan memakan fungsi energi dari membran bakteri, terkait dengan pendirian dan penggunaan PMF dan produksi ATP, diberikan dalam gambar berikut membran plasma Escherichia coli.

Figure 5. Gambar 5. The plasma membrane of Escherichia coli. The membrane in cross-section reveals various transport systems, the flagellar motor apparatus (S and M rings), the respiratory electron transport system, and the membrane-bound ATPase enzyme. Membran plasma Escherichia coli Bagian ini. Membran di lintas mengungkapkan berbagai sistem transportasi, aparat motor flagellar (S dan cincin M), transpor elektron sistem pernapasan, dan terikat enzim-ATPase membran. Reduced NADH + H+ feeds pairs of electrons into the ETS. Mengurangi NADH + H + feed pasangan elektron ke ETS. The ETS is the sequence of electron carriers in the membrane [FAD --> FeS --> QH2 (Quinone) --> (cytochromes) b --> b --> o] that ultimately reduces O 2 to H 2 O during respiration. ETS adalah urutan pembawa elektron dalam membran [FAD -> FeS - QH2> (kuinon) -> (sitokrom) b -> b -> o] yang pada akhirnya mengurangi O 2 H 2 O selama respirasi. At certain points in the electron transport process, the electrons pass "coupling sites" and this results in the translocation of protons from the inside to the outside of the membrane, thus establishing the proton motive force (pmf) on the membrane. Pada titik tertentu dalam proses transpor elektron, elektron lulus "situs kopling" dan hasil ini dalam translokasi proton dari dalam ke luar membran, sehingga membentuk motif gaya proton (PMF) pada membran. The pmf is used in three ways by the bacterium to do work or conserve energy: active transport (eg lactose and proline symport; calcium and sodium antiport);

motility (rotation of the bacterial flagellum), and ATP synthesis (via the ATPase enzyme during the process of oxidative phosphorylation or electron transport phosphorylation). PMF ini digunakan dalam tiga cara oleh bakteri untuk melakukan pekerjaan atau menghemat energi: transpor aktif (misalnya laktosa dan symport prolin, kalsium dan natrium antiport); motilitas (rotasi dari flagel bakteri), dan sintesis ATP (melalui enzim ATPase selama proses fosforilasi oksidatif atau transportasi fosforilasi elektron).

Heterotrophic Types of Metabolism Jenis heterotrofik Metabolisme

Heterotrophy (ie, chemoheterotrophy) is the use of an organic compound as a source of carbon and energy. Heterotrophy (yaitu, chemoheterotrophy) adalah penggunaan senyawa organik sebagai sumber karbon dan energi. It is the complete metabolism package. Ini adalah paket metabolisme lengkap. The cell oxidizes organic molecules in order to produce energy (catabolism) and then uses the energy to synthesize cellular material from these the organic molecules (anabolism). Sel mengoksidasi molekul organik untuk menghasilkan energi (katabolisme) dan kemudian menggunakan energi untuk mensintesis bahan selular dari molekul-molekul organik (anabolisme). We animals are familiar with heterotrophic metabolism. Kami hewan yang akrab dengan metabolisme heterotrofik. Fungi and protozoa are all heterotrophs; many bacteria, but just a few archaea, are heterotrophs, Heterotrophic fungi and bacteria are the masters of decomposition and biodegradation in the environment. Jamur dan protozoa semua heterotrophs; banyak bakteri, namun hanya beberapa archaea, yang heterotrof, jamur dan bakteri heterotrofik adalah penguasa dekomposisi dan biodegradasi dalam lingkungan. Heterotrophic metabolism is driven mainly by two metabolic processes: fermentations and respirations. Metabolisme heterotrofik didorong terutama oleh dua proses metabolisme: fermentasi dan respirasi.

Fermentation Fermentasi

Fermentation is an ancient mode of metabolism, and it must have evolved with the appearance of organic material on the planet. Fermentasi adalah modus kuno metabolisme, dan harus telah berevolusi dengan munculnya bahan organik di planet ini. Fermentation is metabolism in which energy is derived from the partial oxidation of an organic compound using organic intermediates as electron donors and electron acceptors . Fermentasi adalah metabolisme di mana energi berasal dari oksidasi parsial dari suatu senyawa organik menggunakan intermediet organik sebagai donor elektron dan akseptor elektron. No outside electron acceptors are involved; no membrane or electron transport system is required; all ATP is produced by substrate level phosphorylation . Tidak ada akseptor elektron luar yang terlibat, tidak ada membran atau sistem transportasi elektron diperlukan; semua ATP dihasilkan oleh tingkat fosforilasi substrat.

By definition, fermentation may be as simple as two steps illustrated in the following model. Menurut definisi, fermentasi dapat sederhana seperti dua langkah digambarkan dalam model berikut. Indeed, some amino acid fermentations by the clostridia are this simple. Memang, beberapa fermentasi asam amino oleh Clostridia yang sederhana ini. But the pathways of fermentation are a bit more complex, usually involving several preliminary steps to prime the energy source for oxidation and substrate level phosphorylations. Namun jalur fermentasi sedikit lebih kompleks, biasanya melibatkan beberapa langkah awal utama sumber energi untuk oksidasi dan substrat phosphorylations tingkat.

Figure 6. Gambar 6. Model fermentation. Model fermentasi. L. The substrate is oxidized to an organic intermediate; the usual oxidizing agent is NAD. L. substrat ini dioksidasi menjadi perantara organik; biasa oksidator adalah NAD. Some of the energy released by the oxidation is conserved during the synthesis of ATP by the process of substrate level phosphorylation. Beberapa energi yang dilepaskan oleh oksidasi adalah kekal selama sintesis ATP oleh proses fosforilasi tingkat substrat. Finally, the oxidized intermediate is reduced to end products. Akhirnya, teroksidasi menengah berkurang menjadi produk akhir. Note that NADH 2 is the reducing agent, thereby balancing its redox ability to drive the energy-producing reactions. Perhatikan bahwa NADH 2 adalah agen mengurangi, sehingga keseimbangan redoks kemampuan untuk drive-menghasilkan reaksi energi. R. In lactic fermentation by Lactobacillus, the substrate (glucose) is oxidized to pyruvate, and pyruvate becomes reduced to lactic acid. R. Dalam fermentasi laktat oleh Lactobacillus, substrat (glukosa) teroksidasi untuk piruvat, dan menjadi piruvat direduksi menjadi asam laktat. Redox balance is maintained by coupling oxidations to reductions within the pathway. Keseimbangan redoks dikelola oleh oksidasi kopling untuk pengurangan dalam jalur tersebut. For example, in lactic acid fermentation via the EmbdenMeyerhof pathway, the oxidation of glyceraldehyde phosphate to phosphoglyceric acid is coupled to the reduction of pyruvic acid to lactic acid. Misalnya, dalam fermentasi asam laktat melalui jalur EmbdenMeyerhof, oksidasi fosfat gliseraldehida menjadi asam phosphoglyceric digabungkan dengan pengurangan asam piruvat menjadi asam laktat.

In biochemistry, for the sake of convenience, fermentation pathways start with glucose. Dalam biokimia, demi kenyamanan, jalur fermentasi mulai dengan glukosa. This is because it is the simplest molecule, requiring the fewest enzymatic ( catalytic) steps, to enter into a pathway of glycolysis and central metabolism. Hal ini karena itu adalah molekul sederhana, membutuhkan paling sedikit enzimatik (katalitik) langkah, untuk masuk ke dalam jalur glikolisis dan metabolisme pusat.

In the bacteria there exist three major pathways of glycolysis (the dissimilation of sugars): the classic Embden-Meyerhof pathway , which is also used by most eucaryotes, including yeast ( Saccharomyces ): the heterolactic pathway used by lactic acid bacteria, and the Entner-Doudoroff pathway used by vibrios and pseudomonads, including Zymomonas. Although the latter two pathways have some interesting applications in the manufacture of dairy products and alcoholic beverages, they will not be discussed further in this section.. Pada bakteri terdapat tiga

jalur utama glikolisis (yang disimilasi gula): jalur Embden-Meyerhof klasik, yang juga digunakan oleh sebagian besar eucaryotes, termasuk ragi (Saccharomyces): heterofermentatif jalur yang digunakan oleh bakteri asam laktat, dan Entner -Doudoroff jalur yang digunakan oleh Vibrio dan pseudomonad, termasuk Zymomonas. Meskipun dua terakhir jalur memiliki beberapa aplikasi yang menarik dalam pembuatan produk susu dan minuman beralkohol, mereka tidak akan dibahas lebih lanjut dalam bagian ini ..

The Embden-Meyerhof Pathway The-Meyerhof Pathway Embden

This is the pathway of glycolysis most familiar to biochemists and eucaryotic biologists, as well as to brewers, breadmakers and cheese makers. Ini adalah jalur glikolisis yang paling akrab bagi ahli biokimia dan ahli biologi eukariotik, serta bir, breadmakers dan pembuat keju. The pathway is operated by Saccharomyces to produce ethanol and CO 2 . jalur ini dioperasikan oleh cerevisiae untuk menghasilkan etanol dan CO 2. The pathway is used by the lactic acid bacteria to produce lactic acid, and it is used by many other bacteria to produce a variety of fatty acids, alcohols and gases. jalur tersebut digunakan oleh bakteri asam laktat untuk menghasilkan asam laktat, dan digunakan oleh bakteri lain untuk menghasilkan berbagai lemak, alkohol asam dan gas. Some end products of Embden-Meyerhof fermentations are essential components of foods and beverages, and some are useful fuels and industrial solvents. Beberapa produk akhir fermentasi Embden-Meyerhof merupakan komponen penting dari makanan dan minuman, dan beberapa bahan bakar yang berguna dan pelarut industri. Diagnostic microbiologists use bacterial fermentation profiles (eg testing an organism's ability to ferment certain sugars, or examining an organism's array of end products) in order to identify them, down to the genus level. Diagnostik mikrobiologi menggunakan profil fermentasi bakteri (misalnya uji kemampuan organisme untuk fermentasi gula tertentu, atau memeriksa array organisme produk akhir) dalam rangka untuk mengidentifikasi mereka, sampai ke tingkat genus.

Figure 7. Gambar 7. The Embden Meyerhof pathway for glucose dissimilation. The Embden Meyerhof jalur untuk disimilasi glukosa. The overall reaction is the oxidation of glucose to 2 pyruvic acid. Reaksi keseluruhan adalah oksidasi glukosa menjadi asam piruvat 2. The two branches of the pathway after the cleavage are identical. Dua cabang dari jalur setelah pembelahan adalah identik.

The first three steps of the pathway prime (phosphorylated) and rearrange the hexes for cleavage into 2 triodes (glyceraldehyde phosphate). Fructose 1,6-diphosphate aldolase is the key (cleavage) enzyme in the EM pathway. Tiga langkah pertama dari jalur utama (terfosforilasi) dan mengatur ulang heks untuk pembelahan menjadi 2 triodes (fosfat gliseraldehida) adalah Fruktosa 1,6-difosfat. Aldolase enzim (belahan dada) kunci dalam jalur EM. Each triose molecule is oxidized and phosphorylated followed by two substrate level phosphorylations that yield 4 ATP during the drive to pyruvate. Setiap molekul triose fosforilasi teroksidasi dan diikuti oleh dua phosphorylations tingkat substrat yang menghasilkan 4 ATP selama berkendara ke piruvat.

Lactic acid bacteria reduce the pyruvate to lactic acid; yeast reduce the pyruvate to alcohol (ethanol) and CO 2 as shown in Figure 8 below. bakteri asam laktat piruvat untuk mengurangi asam laktat, ragi mengurangi piruvat untuk alkohol (etanol) dan CO 2 seperti yang ditunjukkan pada Gambar 8 di bawah ini.

Figure 8. Gambar 8. (a) The Embden Meyerhof pathway of lactic acid fermentation in lactic acid bacteria (Lactobacillus) and (b) the Embden Meyerhof pathway of alcohol fermentation in yeast (Saccharomyces). (A) Embden Meyerhof jalur fermentasi asam laktat pada bakteri asam laktat (Lactobacillus) dan (b) Embden Meyerhof jalur fermentasi alkohol dalam ragi (Saccharomyces). The pathways yield two moles of end products and two moles of ATP per mole of glucose fermented. Jalur menghasilkan dua mol produk akhir dan dua mol ATP per mol glukosa difermentasi. The steps in the breakdown of glucose to pyruvate are identical. Langkah-langkah dalam pemecahan glukosa menjadi piruvat adalah identik. The difference between the pathways is the manner of reducing pyruvic acid, thereby giving rise to different end products. Perbedaan antara jalur adalah cara mengurangi asam piruvat, sehingga menimbulkan produk akhir yang berbeda.

Besides lactic acid, Embden-Meyerhof fermentations in bacteria can lead to a wide array of end products depending on the pathways taken in the reductive steps after the formation of pyruvic acid. Selain asam laktat, Embden-Meyerhof fermentasi dalam bakteri dapat menyebabkan beragam produk akhir tergantung pada jalur yang diambil dalam langkah-langkah reduktif setelah pembentukan asam piruvat. Usually, these bacterial fermentations are distinguished by their end products into the following groups. Biasanya, bakteri fermentasi ini dibedakan dengan produk akhir mereka ke dalam kelompok berikut.

1. Homolactic Fermentation . Lactic acid is the sole end product. 1 Fermentasi. Homolactic asam laktat. Adalah satu-satunya produk akhir. Pathway of the homolactic acid bacteria ( Lactobacillus and most streptococci). Jalur dari bakteri asam homolactic (Lactobacillus dan streptokokus paling). The bacteria are used to ferment milk and milk products in the manufacture of yogurt, buttermilk, sour cream, cottage cheese, cheddar cheese, and most fermented dairy products. Bakteri yang digunakan untuk memfermentasi susu dan produk susu dalam pembuatan yogurt, buttermilk, krim asam, keju cottage, keju cheddar, dan produk susu yang paling fermentasi.

2. Mixed Acid Fermentations . 2. Fermentasi Asam Campuran. Mainly the pathway of the Enterobacteriaceae. End products are a mixture of lactic acid , acetic acid , formic acid , succinate and ethanol , with the possibility of gas formation ( CO 2 and H 2 ) if the bacterium possesses the enzyme formate dehydrogenase, which cleaves formate to the gases. Terutama jalur produk End. Enterobacteriaceae adalah campuran asam laktat, asam asetat, asam format, suksinat dan etanol, dengan kemungkinan pembentukan gas (CO 2 dan H 2) jika bakteri tersebut memiliki enzim dehidrogenase formate, yang memotong formate ke gas.

2a. Butanediol Fermentation . 2a. Fermentasi butanadiol. Forms mixed acids and gases as above, but, in addition, 2,3 butanediol from the condensation of 2 pyruvate. campuran asam Formulir dan gas seperti di atas, tetapi, di samping itu, 2,3 butanadiol dari kondensasi 2 piruvat. The use of the pathway decreases acid formation (butanediol is neutral) and causes the formation of a distinctive intermediate, acetoin . Penggunaan jalur menurun pembentukan asam (butanadiol netral) dan menyebabkan pembentukan, menengah acetoin khas. Water microbiologists have specific tests to detect low acid and acetoin in order to distinguish non fecal enteric bacteria (butanediol formers, such as Klebsiella and Enterobacter ) from fecal enterics (mixed acid fermenters, such as E. coli, Salmonella and Shigella ). mikrobiologi air harus menjalani tes khusus untuk mendeteksi asam rendah dan acetoin untuk membedakan tinja bakteri enterik non (pembentuk butanadiol, seperti Klebsiella dan Enterobacter) dari enterics tinja (fermentor asam campuran, seperti E. coli, Salmonella dan Shigella).

3. Butyric acid fermentations , as well as the butanol-acetone fermentation (below), are run by the clostridia, the masters of fermentation. 3 adalah asam butirat. Fermentasi, serta butanol-aseton fermentasi (bawah), dijalankan oleh Clostridia tersebut, para empu fermentasi. In addition to butyric acid, the clostridia form acetic acid, CO 2 and H 2 from the fermentation of sugars. Selain asam butirat, bentuk Clostridia asam asetat, CO 2 dan H 2 dari fermentasi gula. Small amounts of ethanol and isopropanol may also be formed. Sejumlah kecil etanol dan isopropanol juga mungkin terbentuk.

3a. Butanol-acetone fermentation . 3a.-Aseton fermentasi Butanol. Butanol and acetone were discovered as the main end products of fermentation by Clostridium acetobutylicum during the World War I. This discovery solved a critical problem of explosives manufacture (acetone is required in the manufacture gunpowder) and is said to have affected the outcome of the War. Butanol dan aseton ditemukan sebagai produk akhir utama dari fermentasi oleh acetobutylicum Clostridium selama Perang Dunia I. Penemuan ini memecahkan masalah kritis pembuatan bahan peledak (aseton diperlukan dalam pembuatan mesiu) dan dikatakan telah mempengaruhi hasil dari Perang . Acetone was distilled from the fermentation liquor of Clostridium acetobutylicum,

which worked out pretty good if you were on our side, because organic chemists hadn't figured out how to synthesize it chemically. Aseton adalah disuling dari fermentasi minuman keras acetobutylicum Clostridium, yang bekerja di luar cukup bagus jika Anda berada di pihak kita, karena ahli kimia organik belum menemukan cara untuk mensintesis itu kimiawi. You can't run a war without gunpowder, at least you couldn't in those days. Anda tidak dapat menjalankan perang tanpa mesiu, setidaknya Anda tidak bisa pada waktu itu.

4. Propionic acid fermentation . 4. Propionat fermentasi asam. This is an unusual fermentation carried out by the propionic acid bacteria which include corynebacteria, Propionibacterium and Bifidobacterium . Ini adalah fermentasi yang tidak biasa dilakukan oleh bakteri asam propionat yang meliputi Corynebacteria, Propionibacterium dan Bifidobacterium. Although sugars can be fermented straight through to propionate, propionic acid bacteria will ferment lactate (the end product of lactic acid fermentation) to acetic acid, CO 2 and propionic acid. Meskipun gula dapat difermentasi langsung pada propionat, bakteri asam propionat akan memfermentasi laktat (produk akhir fermentasi asam laktat) menjadi asam asetat, CO 2 dan asam propionat. The formation of propionate is a complex and indirect process involving 5 or 6 reactions. Pembentukan propionat merupakan proses yang kompleks dan tidak langsung yang melibatkan 5 atau 6 reaksi. Overall, 3 moles of lactate are converted to 2 moles of propionate + 1 mole of acetate + 1 mole of CO 2 , and 1 mole of ATP is squeezed out in the process. Secara keseluruhan, 3 mol laktat yang dikonversi menjadi 2 mol propionat + 1 mol asetat + 1 mol CO 2, dan 1 mol ATP meremas dalam proses. The propionic acid bacteria are used in the manufacture of Swiss cheese, which is distinguished by the distinct flavor of propionate and acetate, and holes caused by entrapment of CO 2 . Bakteri asam propionat digunakan dalam pembuatan keju Swiss, yang dibedakan dengan rasa yang berbeda propionat dan asetat, dan lubang yang disebabkan oleh jeratan CO 2.

The Embden-Meyerhof pathway for glucose dissimilation (Figure 8), as well as the TCA cycle discussed below (Figure 10), are two pathways that are at the center of metabolism in nearly all organisms. Jalur Embden-Meyerhof untuk disimilasi glukosa (Gambar 8), serta siklus TCA dibahas di bawah ini (Gambar 10), adalah dua jalur yang berada di pusat metabolisme pada hampir semua organisme. Not only do these pathways dissimilate organic compounds and provide energy, they also provide the precursors for biosynthesis of macromolecules that make up living systems. Tidak hanya jalur-jalur dissimilate senyawa organik dan memberikan energi, mereka juga menyediakan prekursor untuk biosintesis makromolekul yang membentuk sistem kehidupan. These are sometimes called amphibolic pathways since the have both an anabolic and a catabolic function. Ini kadang-kadang disebut jalur amphibolic sejak memiliki dua anabolik dan fungsi katabolik.

Respiration Pernafasan

Compared to fermentation as a means of oxidizing organic compounds, respiration is a lot more complicated. Dibandingkan dengan fermentasi sebagai sarana untuk mengoksidasi senyawa organik, respirasi jauh lebih rumit. Respirations result in the complete oxidation of the substrate by an outside electron acceptor . Respirations mengakibatkan oksidasi lengkap substrat oleh akseptor elektron luar. In addition to a pathway of glycolysis, four essential

structural or metabolic components are needed: Selain jalur glikolisis, empat komponen struktural atau metabolisme penting diperlukan:

1. 1. The tricarboxylic acid (TCA) cycle (also known as the citric acid cycle or the Kreb's cycle): when an organic compound is utilized as a substrate, the TCA cycle is used for the complete oxidation of the substrate. Siklus tricarboxylic (TCA), asam (juga dikenal sebagai siklus asam sitrat atau siklus Kreb's): bila suatu senyawa organik digunakan sebagai substrat, siklus TCA digunakan untuk oksidasi lengkap substrat. The end product that always results from the complete oxidation of an organic compound is CO 2 . Produk akhir yang selalu hasil dari oksidasi lengkap dari senyawa organik adalah CO 2.

2. 2. A membrane and an associated electron transport system (ETS) . Sebuah membran dan sistem transpor elektron yang terkait (ETS). The ETS is a sequence of electron carriers in the plasma membrane that transports electrons taken from the substrate through the chain of carriers to a final electron acceptor. ETS adalah suatu urutan pembawa elektron dalam membran plasma yang mengangkut elektron diambil dari substrat melalui rantai pembawa ke akseptor elektron terakhir. The electrons enter the ETS at a very low redox potential (E' o ) and exit at a relatively high redox potential. Elektron memasuki ETS pada redoks potensial rendah sangat ('o E) dan keluar pada redoks potensi tinggi relatif. This drop in potential releases energy that can be harvested by the cells in the process of ATP synthesis by the mechanisms of electron transport phosphorylation . Ini rilis penurunan energi potensial yang dapat dipanen oleh sel dalam proses sintesis ATP oleh mekanisme transportasi fosforilasi elektron. The operation of the ETS establishes a proton motive force (pmf) due to the formation of a proton gradient across the membrane. Pengoperasian ETS menetapkan kekuatan proton motif (PMF) karena pembentukan gradien proton melintasi membran.

3. 3. An outside electron acceptor ("outside", meaning it is not internal to the pathway, as is pyruvate in a fermentation). Sebuah akseptor elektron luar ("luar", yang berarti tidak internal untuk jalur, seperti piruvat pada fermentasi a). For aerobic respiration the electron acceptor is O 2 , of course. Untuk respirasi aerobik akseptor elektron adalah O 2, tentu saja. Molecular oxygen is reduced to H 2 0 in the last step of the electron transport system. Molekul oksigen direduksi menjadi H 2 0 pada langkah terakhir dari sistem transportasi elektron. But in the bacterial processes of anaerobic respiration , the final electron acceptors may be SO 4 or S or NO 3 or NO 2 or certain other inorganic compounds, or even an organic compound, such as fumarate. Namun dalam proses respirasi anaerob bakteri, akseptor elektron terakhir mungkin SO 4 atau S atau NO 3 atau NO 2 atau tertentu senyawa anorganik lainnya, atau bahkan senyawa organik, seperti fumarat.

4. 4. A transmembranous ATPase enzyme (ATP synthetase). Sebuah enzim ATPase transmembranous (ATP sintetase). This enzyme utilizes the proton motive force established on the membrane (by the operation of the ETS) to synthesize ATP in the process of electron transport phosphorylation . Enzim ini memanfaatkan kekuatan motif proton didirikan pada membran (oleh pengoperasian ETS) untuk mensintesis ATP dalam proses fosforilasi transport elektron. It is believed that the transmembranous Fo subunit is a proton transport system that transports 2H + to the F1 subunit (the actual ATPase) on the inside of the membrane. Hal ini diyakini bahwa transmembranous Untuk subunit adalah transportasi proton sistem yang

mengangkut 2H + ke subunit F1 (yang ATPase aktual) di bagian dalam membran. The 2 protons are required and consumed during the synthesis of ATP from ADP plus Pi. 2 proton yang diperlukan dan dikonsumsi selama sintesis ATP dari ADP plus Pi. See Figure 6 -the membrane of E. Lihat Gambar 6-membran E. coli. The reaction catalyzed by the ATPase enzyme is ADP + Pi + 2 H + <----------> ATP. coli. Reaksi dikatalisis oleh enzim ATPase adalah ADP + Pi + 2 H + <----------> ATP. (It is important to appreciate the reversibility of this reaction in order to account for how a fermentative bacterium, without an ETS, could establish a necessary pmf on the membrane for transport or flagellar rotation. If such an organism has a transmembranous ATPase, it could produce ATP by SLP, and subsequently the ATPase could hydrolyze the ATP, thereby releasing protons to the outside of the membrane.) (Hal ini penting untuk menghargai berbaliknya reaksi ini dalam rangka untuk menjelaskan bagaimana bakteri fermentasi, tanpa ETS, dapat membentuk suatu PMF diperlukan pada membran untuk transportasi atau rotasi flagellar Jika seperti organisme memiliki ATPase transmembranous,. Itu bisa memproduksi ATP oleh SLP, dan selanjutnya ATPase bisa menghidrolisis ATP, sehingga melepaskan proton ke luar membran.)

The diagram below of aerobic respiration (Figure 9) integrates these metabolic processes into a scheme that represents the overall process of respiratory metabolism. Diagram di bawah respirasi aerobik (Gambar 9) mengintegrasikan proses-proses metabolisme ke dalam skema yang merupakan keseluruhan proses metabolisme pernapasan. A substrate such as glucose is completely oxidized to to CO 2 by the combined pathways of glycolysis and the TCA cycle. Sebuah substrat seperti glukosa sepenuhnya teroksidasi untuk untuk CO 2 oleh gabungan jalur glikolisis dan siklus TCA. Electrons removed from the glucose by NAD are fed into the ETS in the membrane. Elektron dihapus dari glukosa dengan NAD dimasukan pada ETS dalam membran. As the electrons traverse the ETS, a pmf becomes established across the membrane. Sebagai melintasi elektron ETS, PMF yang menjadi didirikan di membran. The electrons eventually reduce an outside electron acceptor, O 2 , and reduce it to H 2 0. Elektron akhirnya mengurangi akseptor elektron luar, O 2, dan mengurangi ke H 2 0. The pmf on the membrane is used by the ATPase enzyme to synthesize ATP by a process referred to as "oxidative phosphorylation". The PMF pada membran yang digunakan oleh enzim ATPase untuk mensintesis ATP dengan proses yang disebut sebagai "fosforilasi oksidatif".

Figure 9. Gambar 9. Model of Aerobic respiration . Model respirasi aerobik.

The overall reaction for the aerobic respiration of glucose is Reaksi keseluruhan untuk respirasi aerobik glukosa

Glucose + 6 O 2 ----------> 6 CO 2 + 6 H 2 O Glukosa + 6 O 2 ----------> CO 2 6 + 6 H 2 O

In a heterotrophic respiration, glucose is dissimilated in a pathway of glycolysis to the intermediate, pyruvate, and it the pyruvate that is moved into the TCA cycle, eventually becoming oxidized to 3 CO 2 . Dalam respirasi heterotrofik, glukosa dissimilated dalam jalur glikolisis ke, menengah piruvat, dan yang piruvat yang dipindahkan ke dalam siklus TCA, akhirnya menjadi teroksidasi menjadi 3 CO 2. Since 2 pyruvate are formed from one glucose, the cycle must turn twice for every molecule of glucose oxidized to 6 CO 2 . Sejak 2 piruvat terbentuk dari satu glukosa, siklus harus mengaktifkan dua kali untuk setiap molekul glukosa teroksidasi hingga 6 CO 2. The TCA cycle (including the steps leading into it) accounts for the complete oxidation of the substrate and it provides 10 pairs of electrons (from glucose) for transit through the ETS. Siklus TCA (termasuk tangga menuju ke dalamnya) account untuk oksidasi lengkap substrat dan memberikan 10 pasang elektron (dari glukosa) untuk transit melalui ETS. For every pair of electrons put into the ETS, 2 or 3 ATP may be produced, so a huge amount of ATP is produced in a respiration, compared to a fermentation. Untuk setiap pasangan elektron dimasukkan ke ETS, 2 atau 3 ATP dapat dihasilkan, sehingga sejumlah besar ATP dihasilkan dalam respirasi, dibandingkan dengan fermentasi sebuah.

The TCA cycle is an important amphibolic pathway, several intermediates of the cycle may be withdrawn for anabolic (biosynthetic) pathways (See Figure xx). Siklus TCA merupakan jalur amphibolic penting, beberapa intermediet siklus dapat ditarik untuk anabolik (biosintetik) jalur (Lihat xx Gambar).

Figure 10. Gambar 10. The tricarboxylic acid (TCA) or Kreb's cycle. Asam tricarboxylic (TCA) atau dalam siklus Kreb. Also called the citric acid cycle because citric acid is one of the first intermediates formed during the cycle. Juga disebut siklus asam sitrat karena asam sitrat merupakan salah satu intermediet pertama terbentuk selama siklus. When an organic compound is utilized during respiration it is invariably oxidized via the TCA cycle. Ketika sebuah senyawa organik yang digunakan selama respirasi itu selalu dioksidasi melalui siklus TCA. Combined with the pathway(s) of glycolysis (eg Embden-Meyerhof) TCA is central to the metabolism of all heterotrophic respiratory organisms.....worth memorizing if you are a biologist. Dikombinasikan dengan jalur (s) glikolisis (misalnya Embden-Meyerhof) TCA merupakan pusat metabolisme semua organisme heterotrofik pernapasan. ..... Layak menghafal jika Anda seorang yang ahli biologi

Anaerobic Respiration Respirasi anaerobik

Respiration in some procaryotes is possible using electron acceptors other than oxygen (O 2 ). Respirasi di beberapa procaryotes adalah akseptor elektron menggunakan kemungkinan lain selain oksigen (O 2). This type of respiration in the absence of oxygen is referred to as anaerobic

respiration . Jenis ini respirasi tanpa adanya oksigen disebut anaerobik respirasi sebagai. Although anaerobic respiration is more complicated than the foregoing statement, in its simplest form it represents the substitution or use of some compound other than O 2 as a final electron acceptor in the electron transport chain . Meskipun respirasi anaerob lebih rumit daripada pernyataan tersebut, dalam bentuknya yang sederhana itu merupakan pengganti atau penggunaan beberapa senyawa lain dari O 2 sebagai akseptor elektron terakhir dalam rantai transpor elektron. Electron acceptors used by procaryotes for respiration or methanogenesis (an analogous type of energy generation in archaea) are described in the table below. akseptor elektron digunakan oleh procaryotes untuk respirasi atau gas metan (jenis analog dari generasi energi di archaea) yang dijelaskan dalam tabel di bawah ini.

Table 1. Tabel 1. Electron acceptors for respiration and methanogenesis in procaryotes Akseptor elektron untuk respirasi dan gas metan di procaryotes electron acceptor akseptor elektron

reduced end product mengurangi produk akhir

name of process Nama proses

organism organisme

O 2 O 2 H 2 O H 2 O aerobic respiration respirasi aerobik

Escherichia , Streptomyces Coli, Streptomyces

NO 3 NO 3 NO 2 , NH 3 or N 2 NO 2, NH 3 atau N 2

anaerobic respiration: denitrification respirasi anaerob: denitrifikasi

Bacillus , Pseudomonas Bacillus, Pseudomonas

SO 4 SO 4 S or H 2 S S atau H 2 S anaerobic respiration: sulfate reduction respirasi anaerob: reduksi sulfat

Desulfovibrio Desulfovibrio

fumarate fumarat succinate suksinat

anaerobic respiration: respirasi anaerob:

using an organic e- acceptor menggunakan e akseptor-organik

Escherichia Coli

CO 2 CO 2 CH 4 CH 4 methanogenesis metanogenesis

Methanococcus Methanococcus

Biological methanogenesis is the source of methane (natural gas) on the planet. methanogenesis biologis adalah sumber metana (gas alam) di planet ini. Methane is preserved as a fossil fuel (until we use it all up) because it is produced and stored under anaerobic conditions, and oxygen is needed to oxidize the CH 4 molecule. Metana yang diawetkan sebagai bahan bakar fosil (sampai kita menggunakan semuanya) karena diproduksi dan disimpan dalam kondisi anaerob, dan oksigen diperlukan untuk mengoksidasi molekul CH 4. Methanogenesis is not really a form of anaerobic respiration, but it is a type of energy-generating metabolism that requires an outside electron acceptor in the form of CO 2 . Methanogenesis tidak benar-benar sebuah bentuk

respirasi anaerobik, tetapi merupakan jenis yang menghasilkan metabolisme energi yang memerlukan akseptor elektron luar dalam bentuk CO 2.

Denitrification is an important process in agriculture because it removes NO 3 from the soil. Denitrifikasi merupakan proses penting dalam pertanian karena menghilangkan NO 3 dari tanah. NO 3 is a major source of nitrogen fertilizer in agriculture. NO 3 adalah sumber utama pupuk nitrogen dalam pertanian. Almost one-third the cost of some types of agriculture is in nitrate fertilizers The use of nitrate as a respiratory electron acceptor is usually an alternative to the use of oxygen. Hampir sepertiga biaya beberapa jenis pertanian di pupuk nitrat Penggunaan nitrat sebagai akseptor elektron pernafasan biasanya merupakan alternatif dari penggunaan oksigen. Therefore, soil bacteria such as Pseudomonas and Bacillus will use O 2 as an electron acceptor if it is available, and disregard NO 3 . Oleh karena itu, tanah bakteri seperti Pseudomonas dan Bacillus akan menggunakan O 2 sebagai akseptor elektron jika tersedia, dan mengabaikan NO 3. This is the rationale in maintaining well-aerated soils by the agricultural practices of plowing and tilling. E. Ini adalah alasan dalam mempertahankan-aerasi tanah baik oleh praktek-praktek pertanian membajak dan mengolah. E. coli will utilize NO 3 (as well as fumarate) as a respiratory electron acceptor and so it may be able to continue to respire in the anaerobic intestinal habitat. coli akan menggunakan NO 3 (serta fumarat) sebagai akseptor elektron pernapasan dan sehingga mungkin dapat terus bernafas dalam habitat usus anaerobik.

Sulfate reduction is not an alternative to the use of O 2 as an electron acceptor. reduksi Sulfat bukan merupakan alternatif dari penggunaan O 2 sebagai akseptor elektron. It is an obligatory process that occurs only under anaerobic conditions. Ini merupakan proses wajib yang terjadi hanya dalam kondisi anaerobik. Methanogens and sulfate reducers may share habitat, especially in the anaerobic sediments of eutrophic lakes such as Lake Mendota, where they crank out methane and hydrogen sulfide at a surprising rate. Methanogen dan pengecil sulfat dapat berbagi habitat, terutama dalam sedimen anaerobik eutrofik danau seperti Danau Mendota, di mana mereka engkol keluar metana dan hidrogen sulfida pada tingkat yang mengejutkan.

Anaerobic respiring bacteria and methanogens play an essential role in the biological cycles of carbon, nitrogen and sulfur. bakteri anaerobik respiring dan methanogen memainkan peran penting dalam siklus biologis karbon, nitrogen dan sulfur. In general, they convert oxidized forms of the elements to a more reduced state. Secara umum, mereka mengubah bentuk teroksidasi elemen untuk keadaan yang lebih berkurang. The lithotrophic procaryotes metabolize the reduced forms of nitrogen and sulfur to a more oxidized state in order to produce energy. The procaryotes lithotrophic memetabolisme bentuk mengurangi nitrogen dan belerang ke keadaan yang lebih teroksidasi dalam rangka untuk menghasilkan energi. The methanotrophic bacteria, which uniquely posses the enzyme methane monooxygenase, can oxidize methane as a source of energy. Bakteri methanotrophic, yang unik yang dimiliki monooxygenase metan enzim, dapat mengoksidasi metana sebagai sumber energi. Among all these groups of procaryotes there is a minicycle of the elements in a model ecosystem. Di antara semua kelompok procaryotes ada minicycle elemen dalam ekosistem model.

Lithotrophic Types of Metabolism Lithotrophic Jenis Metabolisme

Lithotrophy is the use of an inorganic compound as a source of energy. Lithotrophy adalah penggunaan senyawa anorganik sebagai sumber energi. Most lithotrophic bacteria are aerobic respirers that produce energy in the same manner as all aerobic respiring organisms: they remove electrons from a substrate and put them through an electron transport system that will produce ATP by electron transport phosphorylation. Kebanyakan bakteri lithotrophic respirers aerobik yang menghasilkan energi dengan cara yang sama seperti semua organisme respiring aerobik: mereka menghilangkan elektron dari substrat dan menempatkan mereka melalui sistem transpor elektron yang akan menghasilkan ATP oleh fosforilasi transpor elektron. Lithotrophs just happen to get those electrons from an inorganic, rather than an organic, compound. Lithotrophs hanya terjadi untuk mendapatkan orang-orang elektron dari anorganik, bukan senyawa, organik.

Some lithotrophs are facultative lithotrophs , meaning they are able to use organic compounds, as well, as sources of energy. Beberapa lithotrophs yang lithotrophs fakultatif, yang berarti mereka dapat menggunakan senyawa organik, juga, sebagai sumber energi. Other lithotrophs do not use organic compounds as sources of energy; in fact, they won't transport organic compounds. lithotrophs lain tidak menggunakan senyawa organik sebagai sumber energi, bahkan, mereka tidak akan mengangkut senyawa organik. CO 2 is the sole source of carbon for the methanogens and the nitrifying bacteria and a few other species scattered about in other groups. CO 2 adalah satu-satunya sumber karbon untuk methanogen dan bakteri nitrifikasi dan beberapa spesies lain tersebar dalam kelompok-kelompok lain.

Most lithotrophs get their carbon from from CO 2 and are thus autotrophs and are properly referred to as lithoautotrophs or chemoautotrophs . Kebanyakan lithotrophs mendapatkan karbon dari dari CO 2 dan dengan demikian autotroph dan benar disebut sebagai lithoautotrophs atau chemoautotrophs. The lithotrophs are a very diverse group of procaryotes, united only by their ability to oxidize an inorganic compound as an energy source. Para lithotrophs adalah kelompok yang sangat beragam procaryotes, bersatu hanya dengan kemampuan mereka untuk mengoksidasi senyawa anorganik sebagai sumber energi.

Lithotrophy runs through the Bacteria and the Archaea . Lithotrophy berjalan melalui Bakteri dan Archaea. If one considers methanogen oxidation of H 2 a form of lithotrophy, then probably most of the Archaea are lithotrophs. Jika satu menganggap metanogen oksidasi H 2 bentuk lithotrophy, maka mungkin sebagian besar adalah lithotrophs Archaea. Lithotrophs are usually organized into "physiological groups" based on their inorganic substrate for energy production and growth (see Table 2 below). Lithotrophs biasanya diatur dalam "kelompok fisiologis" berdasarkan substrat anorganik mereka untuk produksi energi dan pertumbuhan (lihat Tabel 2 di bawah).

Table 2. Tabel 2. Physiological groups of lithotrophs Fisiologis kelompok lithotrophs

physiological group fisiologis kelompok

energy source sumber energi

oxidized end product teroksidasi produk akhir

organism organisme

hydrogen bacteria hidrogen bakteri

H 2 H 2 H 2 O H 2 O Alcaligenes , Pseudomonas Alcaligenes, Pseudomonas

methanogens H 2 H 2 H 2 O H 2 O Methanobacterium

methanogen Methanobacterium

carboxydobacteria carboxydobacteria

CO CO CO 2 CO 2 Rhodospirillum , Azotobacter Rhodospirillum, Azotobacter

nitrifying bacteria* nitrifikasi bakteri *

NH 3 NH 3 NO 2 NO 2 Nitrosomonas Nitrosomonas

nitrifying bacteria* nitrifikasi bakteri *

NO 2 NO 2 NO 3 NO 3 Nitrobacter Nitrobacter

sulfur oxidizers oksidasi belerang

H 2 S or S H 2 S atau S

SO 4 SO 4 Thiobacillus , Sulfolobus Thiobacillus, acidocaldarius

iron bacteria bakteri besi Fe ++ Fe + + Fe +++ Fe + + + Gallionella , Thiobacillus Gallionella, Thiobacillus

* The overall process of nitrification , conversion of NH 3 to NO 3 , requires a consortium of microorganisms. * Proses keseluruhan nitrifikasi, konversi NH 3 terhadap NO 3, memerlukan sebuah konsorsium mikroorganisme.

The hydrogen bacteria oxidize H 2 (hydrogen gas) as an energy source. Bakteri mengoksidasi hidrogen H 2 (gas hidrogen) sebagai sumber energi. The hydrogen bacteria are facultative lithotrophs as evidenced by the pseudomonads that fortuitously possess a hydrogenase enzyme that will oxidize H 2 and put the electrons into their respiratory ETS. Bakteri hidrogen lithotrophs fakultatif sebagaimana dibuktikan oleh pseudomonad yang kebetulan memiliki enzim hydrogenase yang akan mengoksidasi H 2 dan menempatkan elektron ke ETS pernapasan mereka. They will use H 2 if they find it in their environment even though they are typically heterotrophic. Mereka akan menggunakan H 2 bila mereka menemukannya di lingkungan mereka meskipun mereka biasanya heterotrofik. Indeed, most hydrogen bacteria are nutritionally versatile in their ability to use a wide range of carbon and energy sources. Memang, bakteri hidrogen kebanyakan gizi serbaguna dalam kemampuan mereka untuk menggunakan berbagai sumber karbon dan energi. the bacterial electron transport system. sistem transportasi bakteri elektron.

The methanogens used to be considered a major group of hydrogen bacteria - until it was discovered that they are Archaea . The methanogen digunakan untuk dianggap sebagai kelompok utama dari bakteri hidrogen - sampai ditemukan bahwa mereka Archaea. The methanogens are able to oxidize H 2 as a sole source of energy while transferring the electrons from H 2 to CO 2 in its reduction to methane. Para methanogen mampu mengoksidasi H 2 sebagai satu-satunya sumber energi sementara mentransfer elektron dari H 2 menjadi CO 2 dalam pengurangan untuk metana. Metabolism of the methanogens is absolutely unique, yet methanogens represent the most prevalent and diverse group of Archaea . Metabolisme dari methanogen benar-benar unik, namun methanogen mewakili lazim dan beragam kelompok kebanyakan Archaea. Methanogens use H 2 and CO 2 to produce cell material and methane. Methanogen menggunakan H 2 dan CO 2 untuk menghasilkan bahan sel dan metana. They have unique enzymes and electron transport processes. Mereka memiliki enzim yang unik dan proses transpor elektron. Their type of energy generating metabolism is never seen in the Bacteria , and their mechanism of autotrophic CO 2 fixation is very rare, except in methanogens. jenis mereka

menghasilkan metabolisme energi tidak pernah terlihat di Bakteri, dan mekanisme mereka autotrophic fiksasi CO 2 sangat jarang, kecuali di methanogen.

The carboxydobacteria are able to oxidize CO (carbon monoxide) to CO 2 , using an enzyme CODH ( carbon monoxide dehydrogenase ). carboxydobacteria yang mampu mengoksidasi CO (karbon monoksida) untuk CO 2, dengan menggunakan CODH enzim (karbon monoksida dehidrogenase). The carboxydobacteria are not obligate CO users, ie, some are also hydrogen bacteria, and some are phototrophic bacteria. Interestingly, the enzyme CODH used by the carboxydobacteria to oxidize CO to CO 2 , is used by the methanogens for the reverse reaction - the reduction of CO 2 to CO - in their unique pathway of CO 2 fixation.

The nitrifying bacteria are represented by two genera, Nitrosomonas and Nitrobacter. Together these bacteria can accomplish the oxidation of NH 3 to NO 3 , known as the process of nitrification . No single organism can carry out the whole oxidative process. Nitrosomonas oxidizes ammonia to NO 2 and Nitrobacter oxidizes NO 2 to NO 3 . Most of the nitrifying bacteria are obligate lithoautotrophs , the exception being a few strains of Nitrobacter that will utilize acetate. CO 2 fixation utilizes RUBP carboxylase and the Calvin Cycle. Nitrifying bacteria grow in environments rich in ammonia, where extensive protein decomposition is taking place. Nitrification in soil and aquatic habitats is an essential part of the nitrogen cycle.

Lithotrophic sulfur oxidizers include both Bacteria (eg Thiobacillus ) and Archaea (eg Sulfolobus ). Sulfur oxidizers oxidize H 2 S (sulfide) or S (elemental sulfur) as a source of energy. Similarly, the purple and green sulfur bacteria oxidize H 2 S or S as an electron donor for photosynthesis, and use the electrons for CO 2 fixation (the dark reaction of photosynthesis). Obligate autotrophy, which is nearly universal among the nitrifiers, is variable among the sulfur oxidizers. Lithoautotrophic sulfur oxidizers are found in environments rich in H 2 S, such as volcanic hot springs and fumaroles, and deep-sea thermal vents. Some are found as symbionts and endosymbionts of higher organisms. Since they can generate energy from an inorganic compound and fix CO 2 as autotrophs, they may play a fundamental role in primary production in environments that lack sunlight. As a result of their lithotrophic oxidations, these organisms produce sulfuric acid (SO 4 ), and therefore tend to acidify their own environments. Some of the sulfur oxidizers are acidophiles that will grow at a pH of 1 or less. Some are hyperthermophiles that grow at temperatures of 115 degrees C.

Iron bacteria oxidize Fe ++ (ferrous iron) to Fe +++ (ferric iron). At least two bacteria probably oxidize Fe ++ as a source of energy and/or electrons and are capable of lithoautotrophic growth: the stalked bacterium Gallionella , which forms flocculant rust-colored colonies attached to objects in nature, and Thiobacillus ferrooxidans , which is also a sulfur-oxidizing lithotroph.

Figure 11. Gambar 11. Lithotrophic oxidations. These reactions produce energy for metabolism in the nitrifying and sulfur oxidizing bacteria.

Phototrophic Metabolism

Phototrophy is the use of light as a source of energy for growth, more specifically the conversion of light energy into chemical energy in the form of ATP. Procaryotes that can convert light energy into chemical energy include the photosynthetic cyanobacteria, the purple and green bacteria, and the "halobacteria" (actually archaea). The cyanobacteria conduct plant photosynthesis, called oxygenic photosynthesis ; the purple and green bacteria conduct bacterial photosynthesis or anoxygenic photosynthesis ; the extreme halophilic archaea use a type of nonphotosynthetic photophosphorylation mediated by a pigment, bacteriorhodopsin, to transform light energy into ATP.

Photosynthesis is the conversion of light energy into chemical energy that can be used in the formation of cellular material from CO 2 . Photosynthesis is a type of metabolism separable into a catabolic and anabolic component. The catabolic component of photosynthesis is the light reaction , wherein light energy is transformed into electrical energy, then chemical energy. The anabolic component involves the fixation of CO 2 and its use as a carbon source for growth, usually called the dark reaction . In photosynthetic procaryotes there are two types of photosynthesis and two types of CO 2 fixation.

The Light Reactions depend upon the presence of chlorophyll, the primary light-harvesting pigment in the membrane of photosynthetic organisms. Absorption of a quantum of light by a chlorophyll molecule causes the displacement of an electron at the reaction center. The displaced electron is an energy source that is moved through a membrane photosynthetic electron transport system, being successively passed from an iron-sulfur protein (X ) to a quinone to a cytochrome and back to chlorophyll (Figure 12 below). As the electron is transported, a proton motive force

is established on the membrane, and ATP is synthesized by an ATPase enzyme. This manner of converting light energy into chemical energy is called cyclic photophosphorylation .

Figure 12. Photosystem I: cyclical electron flow coupled to photophosphorylation

The functional components of the photochemical system are light harvesting pigments , a membrane electron transport system , and an ATPase enzyme. The photosynthetic electron transport system of is fundamentally similar to a respiratory ETS, except that there is a low redox electron acceptor (eg ferredoxin ) at the top (low redox end) of the electron transport chain, that is first reduced by the electron displaced from chlorophyll.

There are several types of pigments distributed among various phototrophic organisms. Chlorophyll is the primary light-harvesting pigment in all photosynthetic organisms. Chlorophyll is a tetrapyrrole which contains magnesium at the center of the porphyrin ring. It contains a long hydrophobic side chain that associates with the photosynthetic membrane. Cyanobacteria have chlorophyll a , the same as plants and algae. The chlorophylls of the purple and green bacteria, called bacteriochlorophylls are chemically different than chlorophyll a in their substituent side chains. This is reflected in their light absorption spectra. Chlorophyll a absorbs light in two regions of the spectrum, one around 450nm and the other between 650 -750nm; bacterial chlorophylls absorb from 800-1000nm in the far red region of the spectrum.

The chlorophylls are partially responsible for light harvesting at the photochemical reaction center. The energy of a photon of light is absorbed by a special chlorophyll molecule at the reaction center, which becomes instantaneously oxidized by a nearby electron acceptor of low redox potential. The energy present in a photon of light is conserved as a separation of electrical charge which can be used to generate a proton gradient for ATP synthesis.

Carotenoids are always associated with the photosynthetic apparatus. They function as secondary light-harvesting pigments , absorbing light in the blue-green spectral region

between 400-550 nm. Carotenoids transfer energy to chlorophyll, at near 100 percent efficiency, from wave lengths of light that are missed by chlorophyll. In addition, carotenoids have an indispensable function to protect the photosynthetic apparatus from photooxidative damage. Carotenoids have long hydrocarbon side chains in a conjugated double bond system. Carotenoids "quench" the powerful oxygen radical, singlet oxygen, which is invariably produced in reactions between chlorophyll and O 2 (molecular oxygen). Some nonphotosynthetic bacterial pathogens, ie, Staphylococcus aureus, produce carotenoids that protect the cells from lethal oxidations by singlet oxygen in phagocytes.

Phycobiliproteins are the major light harvesting pigments of the cyanobacteria. They also occur in some groups of algae. They may be red or blue, absorbing light in the middle of the spectrum between 550 and 650nm. Phycobiliproteins consist of proteins that contain covalently-bound linear tetrapyrroles ( phycobilins ). They are contained in granules called phycobilisomes that are closely associated with the photosynthetic apparatus. Being closely linked to chlorophyll they can efficiently transfer light energy to chlorophyll at the reaction center.

Figure 17. The distribution of photosynthetic pigments among photosynthetic microorganisms.

All phototrophic bacteria are capable of performing cyclic photophosphorylation as described above and in Figure 16 and below in Figure 18. This universal mechanism of cyclic photophosphorylation is referred to as Photosystem I . Bacterial photosynthesis uses only Photosystem I (PSI), but the more evolved cyanobacteria, as well as algae and plants, have an additional light-harvesting system called Photosystem II (PSII). Photosystem II is used to reduce Photosystem I when electrons are withdrawn from PSI for CO 2 fixation. PSII transfers electrons from H 2 O and produces O 2 , as shown in Figure 20.

Figure 18. The cyclical flow of electrons during bacterial (anoxygenic) photosynthesis. A cluster of carotenoid and chlorophyll molecules at the Reaction Center harvests a quantum of light. A bacterial chlorophyll molecule becomes instantaneously oxidized by the loss of an electron. The light energy is used to boost the electron to a low redox intermediate, ferredoxin, (or some other iron sulfur protein) which can enter electrons into the photosynthetic electron transport system in the membrane. As the electrons traverse the ETS a proton motive force is established that is used to make ATP in the process of photophosphorylation. The last cytochrome in the ETS returns the electron to chlorophyll. Since light energy causes the electrons to turn in a cycle while ATP is synthesized, the process is called cyclic photophosphorylation. Compare bacterial photosynthesis with the scheme that operates in Photosystem I in Figure 16 above. Bacterial photosynthesis uses only Photosystem I for the conversion of light energy into chemical energy.

Figure 19. The normally cyclical flow of electrons during bacterial photosynthesis must be opened up in order to obtain electrons for CO 2 fixation. In the case of the purple sulfur bacteria, they use H 2 S as a source of

electrons. The oxidation of H 2 S is coupled to PSI. Light energy boosts an electron, derived from H 2 S, to the level of ferredoxin, which reduces NADP to provide electrons for autotrophic CO 2 fixation.

Figure 20. Electron flow in plant (oxygenic) photosynthesis. Photosystem I and the mechanisms of cyclic photophosphorylation operate in plants, algae and cyanobacteria, as they do in bacterial photosynthesis. In plant photosynthesis, chlorophyll a is the major chlorophyll species at the reaction center and the exact nature of the primary electron acceptors (X or ferredoxin) and the components of the ETS are different than bacterial photosynthesis. But the fundamental mechanism of cyclic photophosphorylation is the same. However, when electrons must be withdrawn from photosystem I (ferredoxin--e - -->NADP in upper left), those electrons are replenished by the operation of Photosystem II. In the Reaction Center of PSII, a reaction between light, chlorophyll and H 2 O removes electrons from H 2 O (leading to the formation of O 2 ) and transfers them to a component of the photosynthetic ETS (primary electron acceptor). The electrons are then transferred through a chain of electron carriers consisting of cytochromes and quinones until they reach chlorophyll in PSI. The resulting drop in redox potential allows for the synthesis of ATP in a process called noncyclic photophosphorylation. The operation of photosystem II is what fundamentally differentiates plant photosynthesis from bacterial photosynthesis. Photosystem II accounts for the source of reductant for CO 2 fixation (provided by H 2 O), the production of O 2 , and ATP synthesis by noncyclic photophosphorylation

Most of the phototrophic procaryotes are autotrophs, which means that they are able to fix CO 2 as a sole source of carbon for growth. Just as the oxidation of organic material yields energy, electrons and CO 2 , in order to build up CO 2 to the level of cell material (CH 2 O), energy (ATP) and electrons (reducing power) are required. The overall reaction for the fixation of CO 2 in the Calvin cycle is CO 2 + 3ATP + 2NADPH 2 ----------> CH 2 O + 2ADP + 2Pi + 2NADP. The light reactions operate to produce ATP to provide energy for the dark reactions of CO 2 fixation. The dark reactions also need reductant (electrons). Usually the provision of electrons is in some way connected to the light reactions. A model for coupling the light and dark reactions of photosynthesis is illustrated in Figure 21 below.

Figure 21. Model for coupling the light and dark reactions of photosynthesis.

The differences between plant and bacterial photosynthesis are summarized in Table 3 below. Bacterial photosynthesis is an anoxygenic process. The external electron donor for bacterial photosynthesis is never H 2 O, and therefore, purple and green bacteria never produce O 2 during photosynthesis. Furthermore, bacterial photosynthesis is usually inhibited by O 2 and takes place in microaerophilic and anaerobic environments. Bacterial chlorophylls use light at longer wave lengths not utilized in plant photosynthesis, and therefore they do not have to compete with oxygenic phototrophs for light. Bacteria use only cyclic photophosphorylation (Photosystem I) for ATP synthesis and lack a second photosystem.

Table 3. Tabel 3. Differences between plant and bacterial photosynthesis

plant photosynthesis bacterial photosynthesis

organisms organisme plants, algae, cyanobacteria purple and green bacteria

type of chlorophyll chlorophyll a klorofil a

absorbs 650-750nm

bacteriochlorophyll

absorbs 800-1000nm

Photosystem I

(cyclic photophosphorylation) present hadir present hadir

Photosystem I

(noncyclic photophosphorylation) present hadir absent absen

Produces O 2 yes ya no tidak ada

Photosynthetic electron donor H 2 O H 2 O H 2 S, other sulfur compounds or

certain organic compounds

While photosynthesis is highly-evolved in the procaryotes, it apparently originated in the Bacteria and did not spread or evolve in Archaea . But the Archaea, in keeping with their unique ways, are not without representatives which can conduct a type of light-driven photophosphorylation. The extreme halophiles , archaea that live in natural environments such as the Dead Sea and the Great Salt Lake at very high salt concentration (as high as 25 percent NaCl) adapt to the high-salt environment by the development of " purple membrane ", actually patches of light-harvesting pigment in the plasma membrane. The pigment is a type of rhodopsin called bacteriorhodopsin which reacts with light in a way that forms a proton gradient on the membrane allowing the synthesis of ATP. This is the only example in nature of non photosynthetic photophosphorylation . These organisms are heterotrophs that normally respire by aerobic means. The high concentration of NaCl in their environment limits the availability of O 2 for respiration so they are able to supplement their ATP-producing capacity by converting light energy into ATP using bacteriorhodopsin.

Autotrophic CO 2 fixation

The use of RUBP carboxylase and the Calvin cycle is the most common mechanism for CO 2 fixation among autotrophs. Indeed, RUBP carboxylase is said to be the most abundant enzyme on the planet (nitrogenase, which fixes N 2 is second most abundant). This is the only mechanism of autotrophic CO 2 fixation among eucaryotes, and it is used, as well, by all cyanobacteria and purple bacteria. Lithoautotrophic bacteria also use this pathway. But the green bacteria and the methanogens, as well as a few isolated groups of procaryotes, have alternative mechanisms of autotrophic CO 2 fixation and do not possess RUBP carboxylase.

RUBP carboxylase ( ribulose bisphosphate carboxylase ) uses ribulose bisphosphate (RUBP) and CO 2 as co-substrates. In a complicated reaction the CO 2 is "fixed" by addition to the RUBP, which is immediately cleaved into two molecules of 3-phosphoglyceric acid (PGA). The fixed CO 2 winds up in the -COO group of one of the PGA molecules. Actually, this is the reaction which initiates the Calvin cycle (Figure 22 below).

The Calvin cycle is concerned with the conversion of PGA to intermediates in glycolysis that can be used for biosynthesis, and with the regeneration of RUBP, the substrate that drives the cycle. After the initial fixation of CO 2 , 2 PGA are reduced and combined to form hexose-phosphate by reactions which are essentially the reverse of the oxidative Embden-Meyerhof pathway. (Now is a good time to go back to Figure 8 and look at the EM pathway for the location of PGA and glucose-phosphate). The hexose phosphate is converted to pentose-phosphate, which is phosphorylated to regenerate RUBP. An important function of the Calvin cycle is to provide the

organic precursors for the biosynthesis of cell material. Intermediates must be constantly withdrawn from the Calvin cycle in order to make cell material. In this regard, the Calvin cycle is an anabolic pathway. The fixation of CO 2 to the level of glucose (C 6 H 12 O 6 ) requires 18 ATP and 12 NADPH 2 .

Figure 22. The Calvin cycle and its relationship to the synthesis of cell materials.

The methanogens, a very abundant group of procaryotes, use CO 2 as a source of carbon for growth, and as a final electron acceptor in an energy-producing process that produces methane. If a methanogen is fed labeled CO 2 as a sole form of carbon, 95 percent of the label winds up in methane and 5 percent winds up in cell material. The methanogens fix CO 2 by means of the enzyme CODH ( carbon monoxide dehydrogenase ) and the Acetyl CoA pathway (Figure 23 below). Methanogens predominate in anaerobic habitats including the deep sea with its volcanos, thermal vents and fumaroles, and hence they perform a significant amount of CO 2 fixation on the planet.

Figure 23. The CODH or acetyl CoA pathway of CO 2 fixation in the methanogens. The pathway of methanogenesis steadily reduces CO 2 to the methyl (CH 3 ) level, mediated by the coenzyme methanopterin (MP), related to folic acid. MP-CH 3 may be reduced to methane (not shown) or the MP may be replaced by a vitamin B 12 -like molecule to enter the pathway of CO 2 fixation. The "B 12 "-CH 3 is substrate for CO fixation mediated by the CODH. CODH reduces CO 2 to CO and adds the CO to "B12"CH3 to form acetyl-[CODH]. Coenzyme A (CoA) then replaces the CODH, resulting in the formation of Acetyl CoA, which is in the heart of biosynthetic metabolism. The net effect is the reduction of 2 CO 2 to Acetyl CoA.

Biosynthesis Biosintesis

The pathways of central metabolism (ie, glycolysis and the TCA cycle), with a few modifications, always run in one direction or another in all organisms. The reason - these pathways provide the precursors for the biosynthesis of cell material. When a pathway, such as the Embden-Meyerhof pathway or the TCA cycle, functions to provide energy in addition to chemical intermediates for the synthesis of cell material, the pathway is referred to as an amphibolic pathway . Pathways of glycolysis and the TCA cycle are amphibolic pathways because they provide ATP and chemical intermediates to build new cell material. The main metabolic pathways, and their relationship to biosynthesis of cell material, are shown in Figure 24 below.

Biosynthesis or intermediary metabolism is a topic of biochemistry, more so than microbiology. It will not be dealt with in detail here. The fundamental metabolic pathways of biosynthesis are similar in all organisms, in the same way that protein synthesis or DNA structure are similar in all organisms. When biosynthesis proceeds from central metabolism as drawn below, some of the main precursors for synthesis of procaryotic cell structures and components are as follows.

Polysaccharide capsules or inclusions are polymers of glucose and other sugars .

Cell wall peptidoglycan (NAG and NAM) is derived from glucose phosphate .

Amino acids for the manufacture of proteins have various sources, the most important of which are pyruvic acid , alpha ketoglutaric acid and oxalacetic acid .

Nucleotides ( DNA and RNA ) are synthesized from ribose phosphate . ATP and NAD are part of purine (nucleotide) metabolism.

Triose-phosphates are precursors of glycerol , and acetyl CoA is a main precursor of lipids for membranes

Vitamins and coenzymes are synthesized in various pathways that leave central metabolism. In the example given in Figure 24, heme synthesis proceeds from the serine pathway, as well as from succinate in the TCA cycle.

Figure 24. The main pathways of biosynthesis in procaryotic cells

Written and Edited by Kenneth Todar. All rights reserved. All rights reserved.

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