Cellular respiration

Cellular respiration, also known as 'oxidative metabolism', is one of the key ways a cell gains useful energy. It is the set of the metabolic reactions and processes that take place in organisms' cells to convert biochemical energy from nutrients into adenosine triphosphate (ATP), and then release waste products. The reactions involved in respiration are catabolic reactions that involve the oxidation of one molecule and the reduction of another.

Nutrients commonly used by animal and plant cells in respiration include glucose, amino acids and fatty acids, and a common oxidizing agent (electron acceptor) is molecular oxygen (O₂). Bacteria and archaea can also be lithotrophs and these organisms may respire using a broad range of inorganic molecules as electron donors and acceptors, such as sulfur, metal ions, methane or hydrogen. Organisms that use oxygen as a final electron acceptor in respiration are described as aerobic, while those that do not are referred to as anaerobic.

The energy released in respiration is used to synthesize ATP to store this energy. The energy stored in ATP can then be used to drive processes requiring energy, including biosynthesis, locomotion or transportation of molecules across cell membranes.

Aerobic Respiration

The pyruvate produced in glycolysis undergoes further breakdown through a process called aerobic respiration in most organisms. This process requires oxygen and yields much more energy than glycolysis. Aerobic respiration is divided into two processes: the Krebs cycle, and the Electron Transport Chain, which produces ATP through chemiosmotic phosphorylation. The energy conversion is as follows:

C₆H₁₂O₆ + 6O_<2 -> 6CO₂ + 6H₂O + energy (ATP)

Krebs Cycle

The pyruvate molecules produced during glycolysis contain a lot of energy in the bonds between their molecules. In order to use that energy, the cell must convert it into the form of ATP. To do so, pyruvate molecules are processed through the Kreb Cycle, also known as the citric acid cycle.

1. Prior to entering the Krebs Cycle, pyruvate must be converted into acetyl CoA (pronounced: acetyl coenzyme A). This is achieved by removing a CO₂ molecule from pyruvate and then removing an electron to reduce an NAD⁺ into NADH. An enzyme called coenzyme A is combined with the remaining acetyl to make acetyl CoA which is then fed into the Krebs Cycle. The steps in the Krebs Cycle are summarized below:

2. Citrate is formed when the acetyl group from acetyl CoA combines with oxaloacetate from the previous Krebs cycle..

3. Citrate is converted into its isomer isocitrate..

4. Isocitrate is oxidized to form the 5-carbon α-ketoglutarate. This step releases one molecule of CO₂ and reduces NAD⁺ to NADH₂⁺.

5. The α-ketoglutarate is oxidized to succinyl CoA, yielding CO₂ and NADH₂⁺.

6. Succinyl CoA releases coenzyme A and phosphorylates ADP into ATP.

7. Succinate is oxidized to fumarate, converting FAD to FADH₂.

8. Fumarate is hydrolized to form malate.

9. Malate is oxidized to oxaloacetate, reducing NAD⁺ to NADH₂⁺.

We are now back at the beginning of the Krebs Cycle. Because glycolysis produces two pyruvate molecules from one glucose, each glucose is processes through the kreb cycle twice. For each molecule of glucose, six NADH₂⁺, two FADH₂, and two ATP.

Electron Transport Chain

What happens to the NADH₂⁺ and FADH₂ produced during the Krebs cycle? The molecules have been reduced, receiving high energy electrons from the pyruvic acid molecules that were dismantled in the Krebs Cycle. Therefore, they represent energy available to do work. These carrier molecules transport the high energy electrons and their accompanying hydrogen protons from the Krebs Cycle to the electron transport chain in the inner mitochondrial membrane.

In a number of steps utilizing enzymes on the membrane, NADH₂⁺ is oxidized to NAD⁺, and FADH₂ to FAD. The high energy electrons are transferred to ubiquinone (Q) and cytochrome c molecules, the electron carriers within the membrane. The electrons are then passed from molecule to molecule in the inner membrane of the mitochondron, losing some of their energy at each step. The final transfer involves the combining of electrons and H₂ atoms with oxygen to form water. The molecules that take part in the transport of these electrons are referred to as the electron transport chain.

The process can be summarized as follows: the electrons that are delivered to the electron transport system provide energy to "pump" hydrogen protons across the inner mitochondrial membrane to the outer compartment. This high concentration of hydrogen protons produces a free energy potential that can do work. That is, the hydrogen protons tend to move down the concentration gradient from the outer compartment to the inner compartment.

However, the only path that the protons have is through enzyme complexes within the inner membrane. The protons therefore pass through the channel lined with enzymes. The free energy of the hydrogen protons is used to form ATP by phosphorylation, bonding phosphate to ADP in an enzymatically-mediated reaction. Since an electrochemical osmotic gradient supplies the energy, the entire process is referred to as chemiosmotic phosphorylation.

Once the electrons (originally from the Krebs Cycle) have yielded their energy, they combine with oxygen to form water. If the oxygen supply is cut off, the electrons and hydrogen protons cease to flow through the electron transport system. If this happens, the proton concentration gradient will not be sufficient to power the synthesis of ATP. This is why we, and other species, are not able to survive for long without oxygen!

Anaerobic Respiration

The last few sections have talked extensively about aerobic respiration. What defines it as aerobic is its use of oxygen as the terminal electron accepter. Since this is very similar to the type of respiration that humans use, our bias is obvious. Now let me fill you in on a little secret. Microbes are capable of using all sorts of other terminal electron accepters besides oxygen. Below we talk about a few examples of anaerobic respiration. The one thing that they all have in common is the use of an electron transport system in a membrane and the synthesis of ATP via ATP synthase. In both nitrate reduction and sulfate reduction there are two types of pathways, assimilatory and dissimilatory. Assimilatory pathways are methods for taking a nutrient in the soil, moving it into the cell and using it for biosynthesis of macromolecules. Dissimilatory pathways use the substrate as a place to dump electrons and generate energy. Here we examine dissimilatory pathways. Assimilatory pathways will be explained in the context of cell biosynthesis.

Nitrate reduction

Some microbes are capable of using nitrate as their terminal electron accepter. The ETS used is somewhat similar to aerobic respiration, but the terminal electron transport protein donates its electrons to nitrate instead of oxygen. Nitrate reduction in some species (the best studied being E. coli) is a two electron transfer where nitrate is reduced to nitrite. Electrons flow through the quinone pool and the cytochrome b/c₁ complex and then nitrate reductase resulting in the transport of protons across the membrane as discussed earlier for aerobic respiration.

N0₃^- + 2e^- + 2H⁺N0₂^-+ H₂0

Figure 1 - The reaction for nitrate reduction. N0₃^-, nitrate; N0₂^-, nitrite

This reaction is not particularly efficient. Nitrate does not as willingly accept electrons when compared to oxygen and the potential energy gain from reducing nitrate is less. If microbes have a choice, they will use oxygen instead of nitrate, but in environments where oxygen is limiting and nitrate is plentiful, nitrate reduction takes place.

Denitrification

Nitrite, the product of nitrate reduction, is still a highly oxidized molecule and can accept up to six more electrons before being fully reduced to nitrogen gas. Microbes exist (Paracoccus species, Pseudomonas stutzeri, Pseudomonas aeruginosa, and Rhodobacter sphaeroides are a few examples) that are able to reduce nitrate all the way to nitrogen gas. The process is carefully regulated by the microbe since some of the products of the reduction of nitrate to nitrogen gas are toxic to metabolism. This may explain the large number of genes involved in the process and the limited number of bacteria that are capable of denitrification. Below is the chemical equation for the reduction of nitrate to N₂.

N0₃^-N0₂^- NO N₂O N₂

Figure 2 - The reduction of nitrate to nitrogen gas. NO, nitric oxide; N₂O, nitrous oxide; N₂, nitrogen gas.

The advantage for the cell of carrying out a complete reduction of nitrate is two fold. The nitrate ETS serves as a place to oxidize NADH and free it to be used in catabolism of more substrate. Denitrification take eight electrons from metabolism and adds them to nitrate to form N₂ versus just two for nitrate reduction alone. Also, donation of electrons from NADH through the cytochrome b/c₁ complex and eventually to nitrous oxide (N₂O) reductase provides another opportunity to pump protons across the membrane. The figure below presents a schematic of the spacial arrangement of the denitrification enzymes in the membrane

Figure 3 - Denitrification in the membrane. NADH dehydrogenase complex (DH), nitrate reductase (NAR), nitrite reductase (NIR), NO reductase (NOR), and N₂O reductase (N₂OR)

Nitrate reduction has been extensively studied in bacteria due to its significance in the global nitrogen cycle. Denitrification removes nitrate, an accessible nitrogen source for plants, from the soil and converts it to N₂ a much less tractable source of nitrogen that most plants cannot use. This decreases soil fertility making farming more expensive. Intermediates of denitrification, nitrous oxide and nitric oxide, are gases and will sometimes escape the cell before being completely reduced. These compounds, when in the atmosphere, contribute to the greenhouse effect and exacerbate global warming. The use of high nitrate fertilizers in modern agriculture makes matters worse. For more information, there is an extensive review of denitrification available on line.

Sulfate reduction

The disimilatory reduction of sulfate seems to be a strictly anaerobic process as all the microbes capable of carrying it out only grow in environments devoid of oxygen. Sulfate (SO₄^-2 is reduced to sulfide (S^-2), typically in the form of hydrogen sulfide (H₂S). Eight electrons are add to sulfate to make sulfide

acetate + SO₄^-2 + 3H⁺ + 2CO₂ + H₂S + 2H₂O

Figure 4 - The reduction of sulfate to sulfide during growth on acetate.

The electron potential and energy yield for sulfate reduction is much lower than for nitrate or oxygen. However, there is still enough energy to allow the synthesis of ATP when the catabolic substrate used results in the formation of NADH or FADH. Substrates for sulfate reducers range from hydrogen gas to aromatic compounds such as benzoate. The most commonly utilized are acetate, lactate and other small organic acids (lactate, malate, pyruvate and ethanol are some examples). These compounds are prevalent in anaerobic environments where anaerobic catabolism of complex organic polymers such as cellulose and starch is taking place.

Biochemistry of sulfate reducers

Sulfate reducers take these growth substrates and metabolize them to acetate. The reducing power generated travels down an electron transport chain eventually reducing sulfate to hydrogen sulfide and generating energy using ATP synthase.

Figure 5 - Pathway of sulfate reduction when grown on lactate. Lactate (in blue) is oxidized to acetate (in red) and the electrons remove eventually end up reducing sulfate (in blue) to sulfide (in red). Note that the energy gained in the process by SLP - converting acetyl phosphate to acetate - is used up to activate sulfate in the first step of sulfate reduction. Energy for metabolism is only generated via an electron transport chain.

Recent work in bioremediation of anaerobic sediments has resulted in the isolation of many novel sulfate reducing species capable of metabolizing environmentally intractable compounds including TNT, PCP and benzoate. It is becoming apparent that this group of bacteria are very important in recycling carbon to CO₂ as part of the global carbon cycle in anaerobic environments. For a look at some recent research on sulfate reducing bacteria, check out the "Journal of Bacteriology"

Carbonate reduction

Several groups of microbes are capable of using carbonate (CO₂) as a terminal electron accepter. Carbonate is a poor choice to leave your electrons with due to its low reduction potential and energy yields from CO₂ reduction are low. However, carbonate is one of the most common anions in nature and its ready availability makes it a tempting target.

Several groups of microbes have evolved mechanisms to take advantage of carbonate. The most important group among these is the methanogens. Methanogens are Archaea and comprise one phylogenetic group that is very closely related. Methanogenesis seems to be highly conserved and have deeps roots in the phylogenetic tree of life. It must have evolve early on and practitioners of methanogenesis cannot mess with the genes too much, lest they die.

HC0₃^- + 4H₂ + H⁺ CH₄ + 3H₂O

Methanogens use compounds that contain very high energy electrons as their electron donors and in the process convert CO₂ to methane (CH₄). Above is shown the use of hydrogen as the source of electrons. They are the only group of microbes that produce a hydrocarbon as major end product of their metabolism.

Another group of carbonate reducing microbes are the homoacetogens. They utilize hydrogen as the electron source and use it to reduce CO₂ to acetic acid.

HC0₃^- + 4H₂ + H⁺ CH₃-COO^- + 4H₂O

Bagi Katak, Bulan Purnama Saatnya Pesta Seks

Selama ini bulan purnama identik dengan romantisme dan saat yang asyik untuk bermesraan dengan kekasih. Ternyata hal tersebut juga benar dan berlaku di dunia hean khususnya amfibi.

Para peneliti menemukan bahwa amfibi di seluruh muka bumi melakukan pesta kawin pada saat bulan purnama. Walaupun belum banyak diketahui, tetapi fenomena ini terjadi secara global. Semua spesies amfibi seperti katak, kodok, dan salamander melakukan aktivitas perkawinannya selama periode itu.

Pergerakan bulan yang tengah berada pada fase penuh umum dimanfaatkan hewan. Amfibi pun menggunakan siklus ini untuk mengumpulkan spesies katak jantan dan betina dalam waktu yang sama. Dengan demikian, potensi kesuksesan pembuahan telur dapat dimaksimalkan.

Pada 2005, ahli biologi Rachel Grant yang sedang meneliti mengenai salamander dekat sebuah telaga di wilayah Italia Tengah, tanpa sengaja melihat begitu banyak katak memenuhi jalan di bawah bulan purnama.

“Meski masih ada kemungkinan ini hanya suatu kebetulan, tapi di bulan berikut saya melewati jalan yang sama di hari senja, dan kembali menemukan sejumlah katak. Jumlahnya meningkat seiring bulan bertambah besar, mencapai puncaknya pada bulan purnama, lantas berangsur-angsur berkurang,” ujarnya.

Oleh sebab itu, Grant kembali ke lokasi tersebut pada 2006 dan 2007. Ia kemudian membandingkan data perolehannya dengan data penelitian perilaku kawin katak-katak di sebuah kolam dekat Oxford, Inggris yang dikumpulkan oleh Tim Halliday; serta data Elizabeth Chadwick dari Universitas Cardiff mengenai katak-katak dan kadal-kadal di Wales.

Hasilnya, disimpulkan terdapat 3 fase hidup pada amfibi yang dipengaruhi perputaran bulan, yakni fase pembiakan (breeding site), fase perkawinan (mating site), dan fase bertelur (spawning site). Spesies katak biasa Bufo bufo melakukan ketiga fase ini selama masa bulan purnama. Begitu pula dengan spesies katak Jawa Bufo melanostictus, yang melakukan fase perkawinannya dalam periode bulan purnama, di mana katak betina melakukan ovulasi pada saat berdekatan atau di waktu yang sama.

Sementara spesies katak Rana temporaria melakukan fase bertelur pada bulan purnama. Perkawinan kadal juga dipengaruhi siklus bulan walaupun hasil yang ditunjukkannya tidak sejelas pada katak.

“Kami kira gejala ini tersebar di seluruh dunia. Bagaimanapun, perbedaan ekologi dan cara reproduksi juga akan mempengaruhi hal ini, dan itu perlu diselidiki lebih lanjut,” ujar Grant.

Sumber Gula Baru

Secara umum, kondisi pergulaan nasional, paling tidak, memiliki tiga persoalan utama. Pertama, rendahnya harga beli gula bagi produksi petani karena rendahnya harga gula dipasaran dunia. Kedua, rendahnya produktivitas pabrik gula dan banyak yang tidak efisien. Ketiga, perkembangan industri gula nasional terus merosot. Produksi gula di Indonesia mengalami penurunan pertahunnya sebesar 2,14% atau 44.328,695 ton. Sedangkan perkembangan konsumsi gula di Indonesia meningkat dari tahun 1991/1992 sampai tahun 2000/2001 sebesar 2,03% atau 61.186 ton. Kedua faktor tersebut memicu kenaikkan trend impor gula di Indonesia per tahunnya sebesar 11,94% atau 116.535,839 ton.

Sumber utama gula di Indonesia saat ini adalah tebu (Saccharum officinale) yang sekarang produktivitasnya menurun disebabkan oleh perubahan iklim di Indonesia yang tidak menentu. Jika hanya mengandalkan produksi gula dari tebu, penurunan produksi gula akan terus turun dan impor gula akan terus meningkat. Maka dari itu, diperlukan sumber produksi gula selain tebu yang dapat menjawab tantangan masalah perikliman dan situasi produksi industri yang ada di Indonesia saat ini.

Caryota mitis Lour. (fish-tail palm) memiliki kandungan sukrosa yang sangat tinggi pada air bunganya, yaitu sebesar 83,5 %. Karena hanya memanfaatkan bunganya saja, Caryota mitis dapat dikelola sebagai tanaman perkebunan, seperti halnya kelapa sawit, yang dapat dipanen terus-menerus selama waktu reproduktif pohon tersebut. Hipotesis kami adalah air bunga (nira) pada Caryota mitis Lour. dapat digunakan sebagai sumber gula alternatif pengganti tebu.

Proses untuk mendapatkan sukrosa murni dari air bunga pohon tersebut dapat dilakukan melalui proses ekstraksi air bunga, pengendapan kotoran, pemurnian air gula & pemisahan dari kandungan senyawa lainnya, kristalisasi dan dilakukan penyimpanan untuk selanjutnya diproses menjadi kristal gula murni.

Keberhasilan introduksi sumber gula yang satu ini akan menjadi wacana baru dalam perkembangan bio-industri skala nasional sekaligus menjawab tantangan kebutuhan salah satu komoditas pangan terpenting baik di Indonesia maupun dunia.

Sumber: www.forumsains.com