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Jumat, 06 Februari 2009

DNA (DEOKSIRIBO NUCLEIC ACID)


Asam deoksiribonukleat atau DNA merupakan persenyawaan kimia yang paling penting pada makhluk hidup, yang membawa keterangan genetik dari sel khususnya atau dari makhluk hidup dalam keseluruhannya dari satu generasi ke generasi berikutnya. Semua makhluk hidup kecuali beberapa virus memiliki DNA. Di dalam sel , bagian terbesar dari DNA terdapat di dalam nukleus, terutama dalam kromosom. Molekul DNA juga ditemukan dalam mitokondria, plastida dan sentriol. Molekul DNA dari sel – sel dengan nukleus sejati mempunyai bentuk sebagai benang lurus dan tak bercabang, sedangkan pada sel – sel tanduk nukleus sejati, mitokondria dan plastida molekul DNA berbentuk lingkaran ( Suryo, 1988 ).

DNA tersusun atas basa purin dan pirimidin, fosfor dan gula deoksiribosa yang membentuk polipepetida. Setiap DNA tersusun dari 2 polipeptida yang saling berpillin. Urutan basa dan polinukleotida setiap species DNA identik dan mentranskripsi diri membentuk DNA, RNA dibentuk oleh DNA dan memiliki struktur hampir sama dengan DNA. DNA adalah singkatan dari deoksiribonucleocid acid atau asam deoksiribonukleat. DNA terdiri dari atas 2 utas benang polinukleotida yang saling berpilin (double helix = ganda berpilin). Seutas polinukleotida tersusun atas rangkaian nukleotida. Setiap nukleotida tersusun atas :
  1. Gugusan gula deoksiribosa (gula pentosa yang kehilangan satu asam oksigen)
  2. Gugusan asam fosfat yang terikat pada atom C nomor 5 dari gula
  3. gugusan basa nitrogen yang tereikat pada atom 1 dari gula

Basa nitrogen penyusun DNA terdiri dari basa purin, yaitu adenine (A) dan guanine (G), serta basa pirimidin yaitu sitosin (S), dan timin (T). ikatan gula-basa disebut nukleosida, yaitu :

  1. Ikatan A-gula disebut adenosin deoksiribonukleosida (deoksiadenosin)
  2. Ikatan G-gula disebut guanosin, deoksiribonukleosida (deoksiguanosin)
  3. Ikatan S-gula disebut sitidin deoksiribonukleosida (deoksisitidin)
  4. Ikatan T-gula disebut timidin deoksinukleosida (deoksitimidin)
    (Syamsuri,2000)

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DNA umumnya terdapat didalam kromosom dan kromosom terdapat didalam inti sel. Berartti kromosom itu membelah, demikian pula molekul DNA. Proses kelipatan molekul DNA dinamakan replikasi DNA (Suryo,1988).


Bagian terbesar dari DNA terdapat didalam kromosom. Sedikit DNA tedapat juga didalam organel seperti mitokondria dari tumbuhan dan hewan, dan dalam kloroplas dari ganggang dan tumbuhan tingkat tinggi. DNA didalam mitokondria dan kloroplast tidak ada hubunganya dengan protein histon dan bentuk molekulnya bulat seperti yang terdapat pada bakteri dan ganggang biru. Asam nukleat tersusun atas nukleotida yang bila terurai terdiri dari gula, phosfat dan basa yang mengandung nitrogen. Karena banyaknya nukleotida yang menyusun molekul DNA, maka molekul DNA merupakan suatu polinukleotida.

  1. Gula, molekul gula yang menyusun molekul DNA adalah sebuah pentosa yaitu deoksitil.
  2. Phospat, molekul phosfatnnya berupa PO4
  3. Basa, basa nitrogen menyusun molekul DNA dibedakan atas :
  • kelompok pirimidin, kelompok ini dibedakan atas basa :

sitosin (S)
Timin (T)

  • kelompok purin, kelompok ini dibedakan atas basa :
    Adenin (A)
    Guanin (G)


Dalam tahun 1953 watson crick mengemukakan bahwa kebanyakan molekul DNA mempunyai bentuk sebagai pita yang spiral dobel yang saling berpilin (‘double helix’)
Pada isolasi tumbuhan kita menggunakan EDTA, SDS yang berfungsi:
EDTA : melisiskan membran sel
SDS : melisiskan dinding sel
(Sumarjito, 1996)

Pada isolasi DNA bakteri digunakan EDTA (efien Diamin Tetra Adsetat) yang berfungsi : melisiskan selubung sel dengan menghilangkan ion Mg dan menghambat Enzim seluler yang dapat merusak DNA. SDS digunakan yang berfungsi sebagai pelisis membran dengan senyawa lipid. Nacl yang dipakai berfungsi untuk Na+ yang akan berikatan dengan gugus asam nukleat. Yang terakhir kita tambahkan lisosim yang berfungsi mendigesti senyawa polimer yang menyebabkan kelakuan dinding Sel (Brown, 1991).


Perbedaan DNA dan RNA antara lain :

  1. Bagian pentosa RNA adalah ribosa, sedangkan pentosa DNA adalah deoksiribosa.
  2. Bentuk molekul DNA adalah helix ganda. Bentuk molekul RNA bukan helix ganda, tetapi berupa rantai tunggal yang terlipat sehingga menyerupai rantai ganda.
  3. RNA mengandung basa adenine, guanine dan sitosin seperti DNA, tetapi tidak mengandung timin. Sebagai gantinya RNA sebagai urasil.dengan demikian bagian basa pirimidin RNA berbeda dengan basa pirimidin DNA.
  4. Jumlah guanin dalam molekul RNA tidak perlu sama dengan sitosin, demikian pula jumlah adenin tidak harus sama dengan urasil.
  5. Pentosa RNA yaitu ribosa dan DNA yaitu deoksiribosa mempuyai perbedaan yaitu bahwa deoksiribosa tidak memiliki satu atom oksigen pada karbon nomor-nomornya yang membuat namanya disebut reaksi.
  6. Pada umumnya molekul RNA lebih pendek dari pada DNA (Anna,1994).


Manfaat teknik isolasi antara lain :

  • Dapat dilakukan cloning terhadap tumbuhan atau hewan yang mempunyai sifat unggul
    Meningkatkan produksi dan mengembangkan kualitas produk dari berbagai usaha pertanian, kehutanan, usaha perikanan, dan peternakan.
  • Membuka peluang perubahan make-up genetik suatu organisme melalui pertukaran genetik.
  • Untuk memanipulasi gen-gen genetiknya
  • Untuk menyimpan informasi genetik
  • Usaha untuk mengatur struktur polipeptida yang terbentuk agar sesuai dengan yang dikehendaki
  • Untuk mengetahui DNA dapat melaksanakan fungsinya yaitu menyimpan dan menggandakan informasi
  • Untuk menerangkan satu sifat utama dari informasi genetik yaitu kemampuan untuk duplikasi diri sendiri (Brown,1991).
Read more / Selengkapnya...

Spektrofotometer


Metode spektrofotometri adalah metode analisis berdasarkan pengukuran absorbsi cahaya oleh senyawa yang mengalami transisi elektron saat terkena sinar dengan panjang gelombang tertentu. Spektrofotometri merupakan salah satu cabang analisis instrumental yang mempelajari interaksi antara atom atau molekul dengan radiasi elektromagnetik. Salah satu penggunaan spektrofotometri adalah dapat menentukan kandungan kimiawi dari suatu bahan. Sumber cahaya ultraviolet dan cahaya tampak apabila dilewatkan pada sampel akan memberikan informasi nilai absorbansi dengan variasi panjang gelombang.


Alat yang digunakan untuk mengukur daya serapan dinamakan spektrofotometer. Alat ini mengeluarkan cahaya pada jarak gelombang yang dipilih terlebih dahulu, lalu dipancarkan melalui sampel (selalu dilarutkan didalan satu pelarut dan diletakkan didalam kuvet), dan kecepatan cahaya yang ditransmisikan/diserap sampel tersebut diukur.


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Terdapat dua jenis spektrofotometer, yaitu spektrofotometer beralur tunggal (single beam) dan spektrofotometer beralur ganda (double beam). Secara umum, sesebuah spektrofotometer terdiri dari komponen utama yaitu sumber cahaya, monokromator (termasuk beberapa penapis, celah (slits) dan cermin), kotak sampel, alat pengesan, dan sebuah meter atau perekam.



Sumber Cahaya


Bergantung kepada panjang cahaya, maka sesebuah spektrofotometer itu dapat mengukur daya serap pada kawasan ultraviolet, dimana lampu hidrogen atau deutrium tekanan tinggi digunakan; atau dikawasan tampak yang menggunakan lampu tungsten-halogen. Yang pertama itu mengeluarkan cahaya pada panjang gelombang 200 - 340 nm, manakala yang kedua itu pada panjang gelombang 340 - 800 nm. Alat yang mempunyai kedua-dua jenis lampu mempunyai kelenturan yang lebih baik dan boleh digunakan untuk kajian kebanyakan molekul yang mempunyai kepentingan biologi.



Monokromator



Kedua lampu diatas mengeluarkan cahayan pada keseluruhan panjang gelombang. Sehingga, sebuah spektrofotometer perlulah mempunyai sebuah sistem optik yang dapat memilih cahaya monokromatik (cahaya yang mempunyai panjang gelombang tertentu). Alat modern menggunakan prisma, atau selalu menggunakan diffraction grating untuk menghasilkan cahaya pada panjang gelombang tertentu. Perlu juga diingatkan disini bahwa cahaya yang keluar dari monokromator tidaklah terdiri dari hanya satu panjang gelombang, tetapi sebaliknya diperkaya dengan panjang gelombang tersebut. Ini bermakna, kebanyakan cahaya adalah dari panjang gelombang yang tunggal, tetapi yang pada panjang gelombang lebih pendek atau lebih panjang dari itu juga ada.




Sebelum cahaya monokromatik itu sampai kepada sampel, ia akan melalui satu siri celah (slits), kanta, penapis dan cermin. Sistem optik ini memekatkan cahaya, meningkatkan kelenturan spektra dan menumpukan ia kearah sampel. Cahaya yang melintasi dari monokromator ke sampel akan menemui satu pintu atau celah. Lebarnya celah ini menentukan kecepatan cahaya yang mengenai sampel dan kelenturan spektra cahaya tersebut. Dengan menyempitkan celah, kelenturan spektra akan meningkat, tetapi banyaknya cahaya yang mengenai sampel akan berkurang. Dalam hal ini kecekapan atau kepekaan alat pengesan akan menjadi faktor penting. Sehingga lebarnya celah perlu ditentukan untuk mendapatkan keseimbangan diantara kelenturan spektra dengan kepekaan pengesan.




Kotak Sampel



Cahaya monokromatik yang telah diproses itu kemudiannya diarahkan pada kotak sampel yang boleh menempatkan beberapa jenis pemegang sel. Sampel selalu dalam bentuk larutan. Sampel diisikan kedalam kuvet yang diperbuat dari kaca, kuarza, atau lain-lain bahan lutsinar. Kuvet kaca agak murah, tetapi disebabkan ia menyerap cahaya UV, ia hanya boleh digunakan untuk panjang gelombang melebihi 340 nm. Kuvet kuarza atau silika boleh digunakan disepanjang kawasan cahaya UV dan tampak (~200 - 800 nm). Kuvet sekarang ini banyak terdapat dipasaran dibuat dari polimetakrilat (280 - 800nm) dan polistiren (350 - 800nm).



Spektrofotometer yang kurang mahal terdiri dari alat beralur-tunggal (single-beam) yang membolehkan satu kuvet dimasukkan kedalam pemegang sel pada satu masa. Alat yang lebih canggih adalah beralur-dua (double-beam) yang boleh memuatkan dua kuvet, yang satu mengandungi sampek terlarut didalam suatu pelarut (kedudukan sampel) dan yang satu lagi mengandung pelarut tulin (kedudukan rujukan/control).




Pengesan



Kecepatan cahaya yang melintasi sampel kajian bergantung kepada banyaknya cahaya yang diserap oleh sampel tersebut. Kecepatan diukur oleh pengesan peka-cahaya, selalu merupakan sebuah tabung fotogandaan (photomultiplier tube, PMT). PMT mengesan jumlah tenaga cahaya yang kecil, menguatkannya melalui lata elektron (cascade of electrons) yang dipercepat oleh dinod (dynode), dan menukarkannya menjadi isyarat elektrik yang boleh dimasukkan kedalam sebuah meter atau perekam.



Meter dan Perakam



Alat dapat memberikan bacaan daya serapan dan /atau transmitans secara terus dalam bentuk analog atau digital. Alat ini sesuai untuk pengukuran pada panjang gelombang tunggal. Sekiranga pengimbasan (scanning) daya serapan lwn. panjang gelombang (A lwn. l) diperlukan, maka sebuah perakam (recorder) perlulah dipasang.



Pada masa ini kebanyakan spektrofotometer telah dilengkapi dengan komputer berserta perisian yang canggih bagi memudahkan pengaturan acara, parameter pengukuran, terutama untuk tujuan kajian kinetika.

Read more / Selengkapnya...

Protein


Protein (akar kata proteus dari bahasa Yunani yang berarti "yang paling utama") adalah senyawa organik kompleks berbobot molekul tinggi yang merupakan polimer dari monomer-monomer asam amino yang dihubungkan satu sama lain dengan ikatan peptida. Molekul protein mengandung karbon, hidrogen, oksigen, nitrogen dan kadang kala sulfur serta fosfor. Protein berperan penting dalam struktur dan fungsi semua sel makhluk hidup dan virus. Kebanyakan protein merupakan enzim atau subunit enzim. Jenis protein lain berperan dalam fungsi struktural atau mekanis, seperti misalnya protein yang membentuk batang dan sendi sitoskeleton. Protein terlibat dalam sistem kekebalan (imun) sebagai antibodi, sistem kendali dalam bentuk hormon, sebagai komponen penyimpanan (dalam biji) dan juga dalam transportasi hara. Sebagai salah satu sumber gizi, protein berperan sebagai sumber asam amino bagi organisme yang tidak mampu membentuk asam amino tersebut (heterotrof). Protein merupakan salah satu dari biomolekul raksasa, selain polisakarida, lipid, dan polinukleotida, yang merupakan penyusun utama makhluk hidup. Selain itu, protein merupakan salah satu molekul yang paling banyak diteliti dalam biokimia. Protein ditemukan oleh Jöns Jakob Berzelius pada tahun 1838. Biosintesis protein alami sama dengan ekspresi genetik. Kode genetik yang dibawa DNA ditranskripsi menjadi RNA, yang berperan sebagai cetakan bagi translasi yang dilakukan ribosoma. Sampai tahap ini, protein masih "mentah", hanya tersusun dari asam amino protein ogenik. Melalui mekanisme pascatranslasi, terbentuklah protein yang memiliki fungsi penuh secara biologi ( "http://id.wikipedia.org/wiki/Protein" ).

Protein membentuk sebagian besar struktur di dalam sel termasuk sebagai enzim dan pigment respiratori. Protein dibentuk dari percantuman unit asas yang dikenal sebagai asam amino. Protein dapat dibagi menjadi dua jenis yaitu protein fibrous yang banyak bergantung kepada struktur sekunder dimana bentuk protein ini boleh diulang. Bentuk kedua ialah protein globular (enzim dan antibodi) yang banyak bergantung kepada interaksi struktur tertiar. Terdapat 20 jenis asam amino yang digunakan untuk membentuk rantaian polipeptida (protein) Fungsi, bentuk, ukuran dan jenis protein akan ditentukan oleh jenis, bilangan dan taburan asam amino yang terdapat di dalam struktur tersebut. Percantuman beberapa asam amino disebut tindak balas kondensasi yang ditandai dengan terjadinya pembentukan ikatan peptida dan pembentukan molekul air. Percantuman ini akan menghasilkan rantaian peptida yang lebih dikenal sebagai polipeptida yang memiliki dua ujung rantaian yang berbeda sifatnya. Di ujung yang mempunyai kumpulan amino dikenali sebagai terminal N (amino) dan ujung yang mempunyai kumpulan karboksil dikenali sebagai terminal N. Penyambungan rantai asam amino ini memerlukan tenaga yang tinggi dan ketepatan urutan asam amino dalam rantaian ini pula bergantung kepada koordinasi di antara mRNA dan tRNA. Protein yang dibentuk dengan hanya menggunakan satu polipeptida dinamakan sebagai protein monomerik dan yang dibentuk oleh beberapa polipeptida contohnya hemoglobin dikenal sebagai protein multimerik ( "http://ms.wikipedia.org/wiki/Protein" ).

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Sumber protein :

Yang diketahui dan dikomsumsi banyak orang selama ini adalah sumber protein hewani yaitu daging, ikan, ayam, telur dan susu. Protein yang berasal dari hewan ini memiliki semua asam amino esensial, hingga disebut protein lengkap. Sumber protein lainnya adalah padi-padian, biji-bijian,dan kacang-kacangan. Namun sumber protein jenis ini yang disebut protein nabati atau protein tidak lengkap, senantiasa mempunyai kekurangan satu atau lebih asam amino esensial. Sebab itu cara mengkonsumsinya harus dikombinasikan agar saling melengkapi. Perbedaan kelengkapan itu mengakibatkan ia hanya mampu memelihara jaringan tubuh, sedangkan protein hewani mampu memelihara jaringan tubuh dan menjamin pertumbuhannya. Agar asam aminonya layak disebut sebagai protein lengkap, protein nabati bisa dikomsumsi dengan sesamanya. Misalnya padi-padian (kaya dengan methionin) dengan biji-bijian (kaya dengan lisin dan triptofan). Dalam hal ini terdapat pada nasi dengan tahu atau perkedel jagung. Namun toh protein hewani tetap penting bagi tubuh dan tak dapat digantikan seratus persen oleh protein nabati. Jika dianggap terlalu mahal, cukup mengkonsumsi sehari sekali, misalnya ikan dan telur. Kelebihan protein tidak baik, karena dapat mengganggu metabolisme protein yang berada di hati. Ginjal pun akan terganggu tugasnya, karena bertugas membuang hasil metabolisme protein yang tidak terpakai. Kekurangan protein akan membuat Anda mudah merasa lelah, tekanan darah turun, dan daya tahan terhadap infeksi menurun. Pada anak-anak, selain mudah terserang penyakit kwasiorkor, juga pertumbuhan dan tingkat kecerdasannya akan terganggu( Ahreus,1970 ).

Protein merupakan molekulmakro yang mengandung nitrogen dengan bobot molekul berkisar antara 5.000 hingga 1.000.000 lebih. Protein merupakan suatu unsure selular utama, meliputi kira – kira 50% berat kering dari sel. Fungsi [rotein berkisar dari katalik, dalam hal enzim, hingga toksik dalam hal racun bakteri dan ular (Page,1985).

Protein merupakan polimer yang terdiri dari satuan asam amino yang terikat secara kovalen. Hubungan kovalen dasarnya adalah suatu ikatan amida, sederhana yang terbentuk oleh kondensasi gugus amino dari suatu asam amino dengan gugus asam karboksilat dari yang lain. Ikatan amida ini diber nama khusus : ikatan peptide (Page,1985).

Struktur susunan molekul protein :
  1. Protein Fibriler / skleroprotein : protein yang berbentukl serabut, tidak larut dalam pelarut “encer , baik garam, asam, basa ataupun alkohol. Susunan molekulnya terdiri dari Rantai molekul yang panjang, sejajar Rantai utama , tidak membentuk kristal dan bila rantai ditarik memanjang dapat kembali seperti keadaan semula. Contoh : kolagen pada tulang rawan
  2. Protein globular : protein yang berbentuk bola ( sferoprotein ), banyak terdapat dibahan pangan ( susu, telur, dan daging ). Protein ini larut dalam larutan garam dan asam encer, juga lebih mudah berubah dibawah pengaruh suhu, konsentrasi garam, pelarut asam dan basa.


Sifat-sifat protein yang penting :

  1. Ionisasi : apabila larut dalam air akan membentuk ion ( + dan - )
  2. Denaturasi : perubahan konformasi serta posisi protein sehingga aktivitasnya berkurang atau kemampuannya menunjang aktivitas organ tertentu dalam tubuh hilang → tubuh mengalami keracunan.
  3. Viskositas : tahanan yang timbul adanya gesekan antara molekul didalam zat cair yang mengalir.
  4. Kristalisasi : proses yang sering dilakukan dengan jalan penambahan garam amonium sulfat atau NaCl pada larutan dengan pengaturan pH pada titik isolistriknya.
  5. Sistim Koloid : sistem yang heterogen terdiri atas dua fase yaitu partikel kecil yang terdispersi dari medium atau pelarutnya ( Poedjiadi ,1994).

Fungsi protein :

  1. Sebagai katalis reaksi enzimatis, yaitu reaksi-raksi kimia yang terjadi dalam sisitim biologi. Contoh : pepsin, isomerase, β – galaktosidase
  2. Sebagai sarana transportasi, sejumlah protein spesifik berperan sebagai proses transport ion dan molekul-molekul kecil. Contoh : hemoglobin
  3. Sebagai koordinasi dalam pergerakan, yaitu sebagai pembantu sel dalam berkontraksi. Contoh : aktin dan miosin, tubulin dan protofilamen
  4. Sebagai pendukung mekanik / kerangka : sebagai pertahanan kekuatan kulit dan tulang. Contoh : kolagen, keratin, fibroin.
  5. Sebagai sistim kekebalan atau perlindungan yaitu pertahanan sel dalam serangan benda asing, contoh : Imuniglobin atau antibodi
  6. Penghasil dan penerus rangsangan sistim saraf . Contoh : rhodopsin
    Sebagai kontrol pertumbuhan dan diferensiasi. Contoh : protein hormon
    (Page,1985)


Protein konjugasi : protein yang mengandung senyawa lain non protein.
Protein sederhana : protein yang tidak mengandung senyawa non protein.


Mutu protein :

  1. Mutu tinggi yaitu protein yang mampu menyediakan asam amino esensial dalam suatu perbandingan yang menyamai kebutuhan manusia
  2. Mutu rendah yaitu protein yang kekurangan satu atau lebih asam amino esensial
    ( winarmo,1992 )
Read more / Selengkapnya...

PROTEIN


Protein (akar kata proteus dari bahasa Yunani yang berarti "yang paling utama") adalah senyawa organik kompleks berbobot molekul tinggi yang merupakan polimer dari monomer-monomer asam amino yang dihubungkan satu sama lain dengan ikatan peptida. Molekul protein mengandung karbon, hidrogen, oksigen, nitrogen dan kadang kala sulfur serta fosfor. Protein berperan penting dalam struktur dan fungsi semua sel makhluk hidup dan virus. Kebanyakan protein merupakan enzim atau subunit enzim. Jenis protein lain berperan dalam fungsi struktural atau mekanis, seperti misalnya protein yang membentuk batang dan sendi sitoskeleton. Protein terlibat dalam sistem kekebalan (imun) sebagai antibodi, sistem kendali dalam bentuk hormon, sebagai komponen penyimpanan (dalam biji) dan juga dalam transportasi hara. Sebagai salah satu sumber gizi, protein berperan sebagai sumber asam amino bagi organisme yang tidak mampu membentuk asam amino tersebut (heterotrof). Protein merupakan salah satu dari biomolekul raksasa, selain polisakarida, lipid, dan polinukleotida, yang merupakan penyusun utama makhluk hidup. Selain itu, protein merupakan salah satu molekul yang paling banyak diteliti dalam biokimia. Protein ditemukan oleh Jöns Jakob Berzelius pada tahun 1838. Biosintesis protein alami sama dengan ekspresi genetik. Kode genetik yang dibawa DNA ditranskripsi menjadi RNA, yang berperan sebagai cetakan bagi translasi yang dilakukan ribosoma. Sampai tahap ini, protein masih "mentah", hanya tersusun dari asam amino protein ogenik. Melalui mekanisme pascatranslasi, terbentuklah protein yang memiliki fungsi penuh secara biologi ( "http://id.wikipedia.org/wiki/Protein" ).



Protein membentuk sebagian besar struktur di dalam sel termasuk sebagai enzim dan pigment respiratori. Protein dibentuk dari percantuman unit asas yang dikenal sebagai asam amino. Protein dapat dibagi menjadi dua jenis yaitu protein fibrous yang banyak bergantung kepada struktur sekunder dimana bentuk protein ini boleh diulang. Bentuk kedua ialah protein globular (enzim dan antibodi) yang banyak bergantung kepada interaksi struktur tertiar. Terdapat 20 jenis asam amino yang digunakan untuk membentuk rantaian polipeptida (protein) Fungsi, bentuk, ukuran dan jenis protein akan ditentukan oleh jenis, bilangan dan taburan asam amino yang terdapat di dalam struktur tersebut. Percantuman beberapa asam amino disebut tindak balas kondensasi yang ditandai dengan terjadinya pembentukan ikatan peptida dan pembentukan molekul air. Percantuman ini akan menghasilkan rantaian peptida yang lebih dikenal sebagai polipeptida yang memiliki dua ujung rantaian yang berbeda sifatnya. Di ujung yang mempunyai kumpulan amino dikenali sebagai terminal N (amino) dan ujung yang mempunyai kumpulan karboksil dikenali sebagai terminal N. Penyambungan rantai asam amino ini memerlukan tenaga yang tinggi dan ketepatan urutan asam amino dalam rantaian ini pula bergantung kepada koordinasi di antara mRNA dan tRNA. Protein yang dibentuk dengan hanya menggunakan satu polipeptida dinamakan sebagai protein monomerik dan yang dibentuk oleh beberapa polipeptida contohnya hemoglobin dikenal sebagai protein multimerik. ( "http://ms.wikipedia.org/wiki/Protein" )
Read more / Selengkapnya...

Minggu, 01 Februari 2009

New Insights Into A Leading Poultry Disease And Its Risks To Human Health

When bacteria contain the DNA plasmid pAPEC-1, they produce a powerful toxin that kills other bacteria. The top spot and bottom spot both contain pAPEC-1, creating a lysis zone where no other bacteria can grow within the area. The spot in the middle of the plate contains no pAPEC-1, allowing bacteria to grow and surround the spot. (Credit: The Biodesign Institute, Arizona State University)







Biodesign Institute at Arizona State University associate research scientist Melha Mellata, a member of professor Roy Curtiss' team, is leading a USDA funded project to develop a vaccine against a leading poultry disease called avian pathogenic E. coli (APEC).
APEC is part of a large, diverse group of microbes called extra-intestinal pathogenic E. coli (ExPEC). They cause a number of complex brain, lung and urinary tract diseases in human, animals, and birds. There is also considerable concern in the scientific community that APEC strains are becoming an emergent food pathogen. The poultry products are a suspected source of a suite of ExPEC infections, including those causing human disease.
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The U.S. is the leading poultry industry in the world at an annual value of more than $50 billion, and E. coli infections are a big threat, causing millions in losses for the industry. According to the USDA, the two most common types of poultry infections are from the bacteria E. coli and Salmonella.

Antibiotics have long been the first line of defense to prevent APEC, but have lost their potency, as the bacteria have grown increasingly resistant to treatment. How these microbes cause disease is poorly understood. Mellata and colleagues in the institute's Center for Infectious Diseases and Vaccinology, led by Roy Curtiss, have been hard at work to understand the molecular tricks these bacteria use to evade a host's immune system.
Now, in a paper published in the journal PLoS One, Mellata's team has analyzed the DNA sequence of a critical genetic element of APEC that contains several genes responsible for triggering its harmful effects. In addition, by comparing these genes to a collection of human ExPEC strains, they have shown that human and avian E. coli can carry the same disease-causing elements, which may increase the human risk of infection from poultry.

"The best way to prevent this infection is to develop a vaccine," said Mellata. "Our idea is to ultimately protect both poultry and humans by finding a group of genes common against all extra-intestinal E. coli." With this new knowledge of APEC, the group hopes to pursue the development of several new vaccine candidates.
Their latest research results help narrow the genetic search for the cause of APEC infections. Previously, she had shown that a circular, 100,000 base pair long DNA segment, called a plasmid, was responsible for causing disease. Without the plasmid, APEC becomes docile, losing its disease-causing strength.

Plasmids, in an evolutionary game of high-stakes poker, are swapped freely among bacteria in order to gain the upper hand---or in the case of pathogenic E. coli, to outwit its competitors by colonizing animals and causing disease. Over time, each plasmid becomes a patchwork quilt of DNA information, containing DNA parts exchanged among billions of bacterial encounters.
Her team took advantage of the latest advances in DNA sequencing to analyze the complete 103,275 DNA chemical letters that make up the plasmid, called pAPEC-1.

The multidisciplinary effort involved expertise from several ASU researchers, including Jeff Touchman, a School of Life Science Professor specializing in bioinformatics. It also utilized MEGA4, a software program developed by the Biodesign colleague Sudhir Kumar's lab that is used by more than 50,000 scientists worldwide to trace back and compare the evolutionary history of any DNA segment.

"DNA sequencing and bioinformatics analysis are very powerful tools that contribute in fully understanding the virulence of APEC, and provide new avenues of research," said Mellata.
The ABCs of APEC

In all, the group found 31 genes important for bacterial virulence, with more than one quarter (26 percent) conserved in other species. Almost half of the proteins made by these genes (46 percent) had no similarity to proteins that have been deposited into a public gene database.

Among the disease causing parts of the plasmid pAPEC-1 are a series of genes that make up proteins responsible for trafficking nutrients in and out of bacteria, called ABC transporters, which may be used to develop vaccine candidates. In addition to nutrition, many other ABC transporters help the bacteria elude toxins a host uses to fight off the infection.

Most of the genes that cause APEC's harmful effects are responsible for iron acquisition. Iron is a key element necessary for bacterial health, and the pAPEC-1 portion uses redundant systems to acquire and then hold onto iron at all costs. Mellata speculates that only bacteria that have strategies to acquire iron sequestered by the host can survive in specific niches and consequently cause blood-borne infections, and the bacteria may need these multiple iron acquisition systems to adapt to environment changes.

To look for the presence of these APEC genes in humans, Mellata worked with a collection of one hundred human clinical samples of ExPEC strains isolated from urinary and non-urinary tract infections by Dr. James R. Johnson of the VA Medical Center at the University of Minnesota. Her team found that human and avian E. coli can carry the same disease-causing plasmids, indicating there is a risk that APEC can be transmitted, or its genetic material transmitted from poultry to humans.
These common genes could be considered as potential candidates for a vaccine.

During the course of their research, the team also discovered a finding that could have broad implications for understanding the strategies that bacteria use to trade genetic material. Plasmids are able to acquire more virulence genes or turn benign bacteria into harmful pathogens by their ability to transfer from their own host bacteria into new recipient bacteria. By analyzing the DNA sequence of plasmid pAPEC-1 and testing the mechanism of transfer of pAPEC-1, Mellata and her team have discovered a new way that plasmids use to move from one bacteria to another. This system consists of hijacking the transfer machinery of other helper plasmids present in the same bacteria.

To create a vaccine for the USDA project, the APEC genes would be shuttled into the Salmonella bacteria in the hopes of triggering a protective immune response against both Salmonella and E. coli. This double duty vaccine could protect people not only against the increased risk of APEC causing human illness, but also against the most common food-borne illness, Salmonella.

Mellata feels that now that her team has identified many of the APEC gene targets they will use, it represents the end of the beginning of their research journey to develop a vaccine that will provide improved poultry health, an economic benefit to producers and enhanced food safety.

"The problem right now is understanding the virulence of APEC as well as Salmonella to find a way that will protect against all types of the bacteria," said Mellata.
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New Disease, Comparable To BSE, Created In Laboratory Mice

Folding of the prion proteins of moose (a), mouse (b), and the moose/mouse hybrid prion protein expressed in the transgenic RL mice (c). The loop mentioned in the text is highlighted in colour. (Credit: Image courtesy of ETH Zurich)

A team composed of researchers from across the globe and including scientists from ETH Zurich and the University of Zurich has created a new disease, comparable to BSE, in laboratory mice. The team showed that exchanging just two amino acids in the structure of the prion protein is enough to trigger a disease.

The starting point of the project was the discovery by the team led by ETH Zurich Nobel prize-winner Kurt Wüthrich of a structural peculiarity in the prion protein of moose and deer.


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Kurt Wüthrich says that it all began with the resolving of the structure of the prion protein in mammals: "A small region of this protein, the region between the 166th and 175th amino acids, forms a loop close to the surface of the protein." The ETH Zurich Professor of Biophysics was awarded the Nobel Prize for Chemistry in 2002 for his fundamental discoveries in the field of protein structural analysis. "Our analyses using nuclear magnetic resonance spectroscopy (NMR) showed that this loop has an irregular shape in the prion proteins of humans, cattle, sheep and other mammals, but, astonishingly, it is precisely defined in moose and deer."

Prion disease in deer and moose not under control

The fact that up to 20 percent of all the deer and moose living wild in the USA and Canada suffer from Chronic Wasting Disease (CWD), an infectious prion disease comparable to mad cow disease (BSE), is not well known in Europe. In this disease, as in BSE and in Creutzfeldt-Jakob Disease in humans, misfolded versions of one of the body’s own proteins lead to deposits and finally to the death of nerve cells. It is assumed that heredity also plays a part in the transmission of the disease. The shape of the prion protein characteristic of moose could now give new impetus to efforts to explain CWD and other prion diseases.

Up to 100 percent of the mice with the new gene become ill

Using the conspicuous moose prion protein for further studies of prion diseases seemed the obvious thing to do. First of all, Kurt Wüthrich’s team showed that the type of amino acids at positions 170 and 174 has a decisive influence on whether the suspect loop in the prion protein adopts a rigid or a flexible shape. The researchers now took advantage of this to test the possible effects of the rigid loop in animal experiments.

The results of this study were published in the scientific journal PNAS on 6 January 2009.

In Adriano Aguzzi’s laboratory at the University Hospital Zurich, Christina Sigurdson created a prion gene in mice with two so-called point mutations which, in the living animal, manufactures the mutant form of the mouse prion protein being studied by Wüthrich’s team and containing the rigid loop of the moose prion protein instead of a flexible loop. The researchers were astonished by the fact that, over time, all the transgenic mice carrying this artificial prion protein developed a new, transmissible and fatal prion disease. The deposits which are typical of this disease and which successively damage the organ and finally destroy it accumulated in their brains, with the mice displaying the corresponding symptoms of neurological defects.

Insights still unimaginable at the start of the research

Christina Sigurdson told Science Daily that, "We also discovered that the transfer of brain tissue from mice with the altered protein into normal mice also triggers the prion disease." She says that the fact that an infectious disease can be generated by two mutations in the prion gene deliberately introduced into the mouse prion protein is of particular scientific interest. According to Sigurdson, "This new mouse model of the disease may help us to understand how the incorrectly folded protein causes nerve cell degeneration – and it helps in the search for effective treatments for prion diseases."

Kurt Wüthrich adds, "For us, it’s a marvellous story." He says it emphasizes once again the outstanding importance of basic research undertaken without any motive for short-term profit.

According to Wüthrich, "We determined the NMR structure of a prion protein, that of the mouse, for the first time twelve years ago. We introduced the NMR method to resolve protein structures 25 years ago, with the Swiss physicist Felix Bloch and the American Edward Purcell having carried out the first NMR experiments more than 60 years ago. At none of these milestones could the researchers have dreamt that subtle NMR observations on a protein molecule would lead us directly to a new form of a hitherto incompletely characterised, infectious and fatal disease."

BSE: Sounding the all clear would be out of place

Using meat and bone meal as animal feed played a central role in the BSE crisis in Switzerland. A ban on feeding meat and bone meal to ruminants had already been imposed after the first cases of "bovine spongiform encephalopathy" (BSE; "mad cow disease") in 1990. This ban was extended to cover all livestock in 2001. However, no further cases of mad cow disease have occurred for two years. For a few producers of slaughterhouse by-products (which includes meat and bone meal) this is sufficient justification to demand at least a partial relaxation of the ban on feeding meat and bone meal to animals. However, as the Swiss Federal Veterinary Office insists, sounding the all clear would be out of place. To keep BSE under control, it will probably be necessary to maintain the meat and bone meal ban for years to come.

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How Ebola Virus Avoids The Immune System

Scanning electron microscope image of Ebola virions (spaghetti-like filaments) on the surface of a tetherin-expressing cell (center). (Credit: Paul Bates, PhD, University of Pennsylvania School of Medicine)



Researchers at the University of Pennsylvania School of Medicine have likely found one reason why the Ebola virus is such a powerful, deadly, and effective virus. Using a cell culture model for Ebola virus infection, they have discovered that the virus disables a cellular protein called tetherin that normally can block the spread of virus from cell to cell.
“Tetherin represents a new class of cellular factors that possess a very different means of inhibiting viral replication,” says study author Paul Bates, PhD, Associate Professor of Microbiology at the University of Pennsylvania School of Medicine. “Tetherin is the first example of a protein that affects the virus replication cycle after the virus is fully made and prevents the virus from being able to go off and infect the next cell.” These findings appear online this week in the Proceedings of the National Academy of Sciences.

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When a cell is infected with a virus like Ebola, which is deadly to 90 percent of people infected, the cell is pirated by the virus and turned into a production factory that makes massive quantities on new virions. These virions are then released from that cell to infect other cells and promote the spreading infection.

Tetherin is one of the immune system's responses to a viral infection. If working properly, tetherin stops the infected cell from releasing the newly made virus, thus shutting down spread to other cells. However, this study shows that the Ebola virus has developed a way to disable tetherin, thus blocking the body's response and allowing the virus to spread.

“This information gives us a new way to study how tetherin works,” says Bates. "Binding of a protein produced by Ebola to tetherin apparently inactivates this cellular factor. Understanding how the Ebola protein blocks the activity of tetherin may facilitate the design of therapeutics to inhibit this interaction, allowing the cell's natural defense systems to slow down viral replication and give the animal or person a chance to mount an effective antiviral response and recover.”

Previous research had found that tetherin plays a role in the immune system's response to HIV-1, a retrovirus, and that tetherin is also disabled by HIV. These new studies reveal that human cells also use this defense against other types of viruses, such as Ebola, that are not closely related to HIV-1. “Because we see such broad classes of viruses that are affected by tetherin, it's possible that all enveloped viruses are targets of this antiviral system,” says Bates. “If so, then understanding how tetherin works and how viruses escape from the effect of tetherin will be very important.”

Rachel L. Kaletsky, Joseph R. Francica and Caroline Agrawal-Gamse of the University of Pennsylvania School of Medicine are co-authors of this study. This work was funded by the Public Health Service Grants and the Philip Morris External Research Foundation.

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How A Brain Chemical Changes Locusts From Harmless Grasshoppers To Swarming Pests

Scientists have uncovered the underlying biological reason why locusts form migrating swarms. Their findings, reported in today's edition of Science, could be used in the future to prevent the plagues which devastate crops (notably in developing countries), affecting the livelihood of one in ten people across the globe.

This is a portrait shot of an adult solitarious phase locust. (Credit: Image copyright Tom Fayle)

A collaboration between a team of scientists in Cambridge and Oxford, UK and Sydney, Australia has identified an increase in the chemical serotonin in specific parts of the insects' nervous system as initiating the key changes in behaviour that cause them to swarm.
Desert Locusts are one of the most devastating insect pests, affecting 20% of the world's land surface. Vast swarms containing billions of locusts stretching over many square kilometres periodically devastated parts of the USA at the time of the settlement of the West, and continue to inflict severe economic hardship on parts of Africa and China. In November 2008 swarms six kilometres (3.7 miles) long plagued Australia.
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Locusts belong to the grasshopper family but unlike their harmless relatives they have the unusual ability to live in either a solitary or a gregarious state, with the genetic instructions for both packaged within a single genome.

Locusts originate from barren regions that see only occasional transient rainfalls. While unforgiving conditions prevail, locusts eke out a living as solitary individuals with a strong aversion to mingling with other locusts. When the rains come, the amount and quality of vegetation expands and the locusts can breed in large numbers.

In deserts, however, the rains are not sustained and food soon becomes more and more sparse. Thus large numbers of locusts are funnelled into dwindling patches of remaining vegetation where they are forced into close contact with each other. This crowding triggers a dramatic and rapid change in the locusts' behaviour: they become very mobile and they actively seek the company of other locusts. This new behaviour keeps the crowd together while the insects acquire distinctly different colours and large muscles that equip them for prolonged flights in swarms.

As Steve Rogers from Cambridge University emphasises: "The gregarious phase is a strategy born of desperation and driven by hunger, and swarming is a response to find pastures new".

Solitary and gregarious locusts are so different in looks and behaviour that they were thought to be separate species until 1921. But the realisation that crowding triggers swarming posed a new problem: how can the mere presence of other locusts have such a dramatic effect? The new research, which was funded by the Biotechnology and Biological Sciences Research Council, the Natural Sciences and Engineering Research Council of Canada and the Royal Society, solved this 90 year old question by identifying an increase in the chemical serotonin in specific parts of the locust's nervous system as launching the fundamental changes in behaviour that lead to the gregarious phase.

In the laboratory, solitary locusts can be turned into gregarious ones in just two hours simply by tickling their hind legs to simulate the jostling that locusts experience in a crowd. This period coincides with a threefold but transient (less than 24 hours) increase in the amount of serotonin in the thoracic region of the nervous system. Experiments were then designed to show that serotonin is indeed the causal link between the experience of being in a crowd and the change in behaviour.

First, locusts were injected with specific chemicals that block the action of serotonin on its receptors: when these locusts were exposed to the same gregarizing stimuli, they did not become gregarious. Second, chemicals that block the production of serotonin had the same effect. Third, when injected with serotonin or chemicals that mimic serotonin, locusts turned gregarious even in the absence of other locusts. Finally, chemicals that increased the natural synthesis of serotonin enhanced gregarization when locusts were exposed to the tickling stimuli. This indicates that it is the synthesis of serotonin that is driven by these specific stimuli and in turn changes the behaviour.

Dr Michael Anstey, an author of the paper from the University of Oxford, said: "Up until now, whilst we knew the stimuli that cause locusts' amazing 'Jekyll and Hyde'-style transformation, nobody had been able to identify the changes in the nervous system that turn antisocial locusts into monstrous swarms. The question of how locusts transform their behaviour in this way has puzzled scientists for almost 90 years, now we finally have the evidence to provide an answer."

Dr Swidbert Ott, from Cambridge University, one of the co-authors of the article, said: "Serotonin profoundly influences how we humans behave and interact, so to find that the same chemical in the brain is what causes a normally shy antisocial insect to gang up in huge groups is amazing."

Professor Malcolm Burrows, also from Cambridge University: "We hope that this greater understanding of the mechanisms causing such a big change in behaviour will help in the control of this pest, and more broadly help in understanding the widespread changes in behavioural traits of animals."

Professor Steve Simpson of Oxford and Sydney Universities said: "No other biological system is understood from nerve cells to populations in such detail or to such effect: locusts offer an exemplar of the how to span molecules to ecosystems – one of the greatest challenges in modern science."

Locust Facts:

  • Locusts are grasshoppers that swarm. Of the 8,000 known species of grasshoppers throughout the world only about 12 are swarm-forming locusts.
  • An adult Desert Locust is 2-2.5 inches long and weighs 0.05-0.07 oz.
  • A Desert Locust adult can consume roughly its own weight in fresh food per day.
  • They are prodigious fliers, covering 60 miles in 5-8 hours.
  • The two phases are so different in appearance and behavior that they were thought to be separate species until 1921.
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Chemists Shed Light On Health Benefits Of Garlic

A Queen's-led team has discovered the reason why garlic is so good for us.

Garlic. Chemists have discovered the reason why garlic is so good for us. (Credit: iStockphoto/Jorge Farres Sanchez)



Researchers have widely believed that the organic compound, allicin – which gives garlic its aroma and flavour – acts as the world's most powerful antioxidant. But until now it hasn't been clear how allicin works, or how it stacks up compared to more common antioxidants such as Vitamin E and coenzyme Q10, which stop the damaging effects of radicals.
"We didn't understand how garlic could contain such an efficient antioxidant, since it didn't have a substantial amount of the types of compounds usually responsible for high antioxidant activity in plants, such as the flavanoids found in green tea or grapes," says Chemistry professor Derek Pratt, who led the study. "If allicin was indeed responsible for this activity in garlic, we wanted to find out how it worked."



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The research team questioned the ability of allicin to trap damaging radicals so effectively, and considered the possibility that a decomposition product of allicin may instead be responsible. Through experiments with synthetically-produced allicin, they found that an acid produced when the compound decomposes rapidly reacts with radicals.

Their findings are published in the January 2009 issue of the international chemistry journal Angewandte Chemie.

"Basically the allicin compound has to decompose in order to generate a potent antioxidant," explains Dr. Pratt, who is Canada Research Chair in Free Radical Chemistry. "The reaction between the sulfenic acid and radicals is as fast as it can get, limited only by the time it takes for the two molecules to come into contact. No one has ever seen compounds, natural or synthetic, react this quickly as antioxidants."
The researcher is confident that a link exists between the reactivity of the sulfenic acid and the medicinal benefits of garlic. "While garlic has been used as a herbal medicine for centuries and there are many garlic supplements on the market, until now there has been no convincing explanation as to why garlic is beneficial," says Dr. Pratt. "I think we have taken the first step in uncovering a fundamental chemical mechanism which may explain garlic's medicinal benefits."
Along with onions, leeks and shallots, garlic is a species in the family Alliaceae. All of these other plants contain a compound that is very similar to allicin, but they do not have the same medicinal properties. Dr. Pratt and his colleagues believe that this is due to a slower rate of decomposition of the allicin analogs in the onions, leaks and shallots, which leads to a lower level of sulfenic acid available to react as antioxidants with radicals.
The study was funded by the Natural Sciences and Engineering Research Council of Canada (NSERC) and the Ontario Ministry of Innovation. Other members of the research team are Queen's Chemistry post-doctoral researcher Vipraja Vaidya and Keith Ingold, from the National Research Council of Canada.
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