PROTEIN, SINTESIS PROTEIN DAN METABOLISMENY A

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PROTEIN, SINTESIS

PROTEIN DAN METABOLISMENY

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BLOK 6 TAHUN 2021

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TUJUAN BELAJAR

• Mampu mengetahui dan memahami asam amino, protein, struktur protein

• Mampu menjelaskan dan memahami konsep Dogma Molekular (Replikasi, Transkripsi, dan Translasi)

• Dapat menjelaskan mekanisme sintesis protein

• Dapat menjelaskan metabolism protein

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Protein

Makromolekul yang terdiri dari > 100 asam

amino yang dihubungkan dengan ikatan peptida.

Polipeptida : kurang dari 100 asam amino

Berperan penting dalam berbagai fungsi fisiologis dalam tubuh manusia

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Asam Amino

Mempunyai gugus asam (-COOH) dan gugus amino (–NH²) , sehingga dapat bersifat asam atau basa.

Hidrolisis sempurna protein akan menghasilkan 20 macam asam amino. DNA mengkode 20

macam asam amino.

Mempunyai atom C asimetris, mengakibatkan adanya D dan L isomer. Asam amino dalam tubuh manusia ada dalam bentuk L-asam amino.

Atom C yang mengikat gugus asam (-COOH) dan gugus amino (–NH2) disebut C-alpha,

berikutnya B-beta, C-gamma dst.

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Penamaan asam amino dapat disingkat dengan

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satu huruf atau 3 huruf

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Non-polar and hydrophobic

Polar and hydrophilic

Neutral Basic Acid

Chemical properties of amino acids

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Macam-macam asam amino

Rantai R-nya berupa rantai alifatis : glisin, alanin, valin, leusin, isoleusin

Rantai R-nya mengikat gugus –OH : serin, treonin, tirosin

Rantai R-nya mengikat S : sistein dan metionin Rantai R-nya mengikat gugus asam atau

amidanya : aspartat, asparagin, asam glutamat, glutamin

Rantai R-nya mengikat gugus basa : arginin, lisin, hidroksilisin, histidin

Rantai R-nya mengikat cincin aromatis : histidin, fenilalanin, tirosin, triptofan,

Asam amino : prolin dan hidroksi prolin

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Asam amino esensiil : asam amino yang

diperlukan tetapi tidak dapat dapat disintesis

oleh tubuh (valin, leusin, isoleusin, lisin, treonin, fenilalanin, triptofan dan metionin).

Asam amino semi esensiil : asam amino yang dapat disintesis tubuh, tapi tidak cukup untuk mendukung pertumbuhan anak-anak (arginin dan hisitidin).

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Di dalam tubuh manusia terdapat asam amino yang penting, tetapi tidak ikut menyusun

protein (asam amino non-proteinogenik).

Misalnya :

1. Sitrulin yang berperan dalam siklus urea.

2. GABA (gamma-amino butyric acid) berperan sebagai neurotransmitter

3. Homosistein berperan dalam metabolisme asam folat

4. Karnitin sebagai transporter lipid dalam sel Asam amino proteinogenik : asam amino yang menyusun protein tubuh manusia (20 macam).

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Protein

Diet _Digesti,

Absorpsi Asam

Amino

Protein Diet dan Sintesis

Protein

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• Limiting amino acid (asam amino pembatas):

asam amino yang terdapat dalam jumlah paling sedikit dalam suatu bahan makanan dibandingkan dengan kebutuhan.

• Asam amino pembatas diantaranya adalah Lisin → gandum

Metionine → kacang dan polong2-an

Triptofan → jagung (gelatin tdk mengandung triptofan)

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Peptid

Polimerisasi asam L-alpha amino oleh ikatan

a

peptida merupakan strukutur dasar protein.

Apabila asam amino < 100 disebut polipeptida;

apabila asam amino > 100 disebut protein.

Polipeptida pada bidang kesehatan:

hormon : insulin, TRH

antibiotik : valinomisin, gramisidin Avaksin : peptida virus

antitumor : bleomisin Glutation

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Ikatan Peptida

dipeptida : 2 residu asam amino, 1 ikatan peptida

tripeptida : 3 residu asam asam amino, 2 ikatan peptida

penulisan dengan 3 atau 1 huruf Glu-Ala-Lys-Gly-Tyr-Ala

E A K G Y A

adanya ikatan peptida dapat ditunjukkan dengan reaksi biuret

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Protei n

Klasifika si

Berdasar bentuk molekul

Protein fibrosa : bentuk memanjang, sumbu panjang : pendek > 10. Contoh : kolagen, keratin, fibrin, miosin

Protein globuler : bentuk membulat, sumbu panjang : pendek 3:1 atau 4:1. Contoh :

albumin, globulin, insulin, enzim

Struktur menentukan fungsi protein

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Berdasar elemen penyusunnya

Protein sederhana : bila dihidrolisis sempurna akan menghasilkan asam amino saja. Contoh : albumin, globulin, glutelin, prolamin, histon

dan protamin

Protein terkonjugasi : mengandung gugus non- protein (gugus prostetis). Contoh :

nukleoprotein, glikoprotein, lipoprotein, fosfoprotein, metaloprotein, kromoprotein Berdasar kelarutannya

albumin : larut dalam air dan larutan garam globulin : larut dalam larutan

garam

protamin : larut dalam etanol 70 80%

histon : larut dalam larutan garam

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Berdasar fungsinya Katalisis : enzim

Kontraksi : aktin, miosin

Regulasi gena : histon, faktor transkripsi Hormon : insulin

Proteksi : fibrin, imunoglobulin Pengaturan : kalmodulin

Struktural : kolagen, elastin, keratin

Transport : albumin, hemoglobin, transferin Biosignal : reseptor hormon

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Struktur Protein

Struktur protein primer

Struktur rantai polipeptida yang berupa urutan asam amino yang dihubungkan dengan ikatan peptida

Struktur protein sekunder

Terbentuknya alpha-helix atau beta-sheet, beta-bends, loops dan coils karena adanya interaksi-interaksi kimia

Interaksi kimia yang menentukan struktur sekunder yaitu ikatan hidrogen, interaksi

hidrophobik, interaksi elektrostatik, interaksi van der Waals

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Struktur protein tersier

Struktur protein yang melipat (folding) menjadi struktur 3 dimensi

Struktur protein kuartener

Beberapa rantai polipeptida/protein yang bergabung menjadi satu. Tiap

polipeptida/protein disebut dengan subunit, bisa sama (homo) atau berbeda (hetero)

Protein yang terdiri dari 2 subunit yang sama disebut homodimer, bila subunit berlainan

disebut heterodimer.

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STRUCTURE OF EUCARYOTIC CELLS

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mitochondria cell membrane lysosomes

Golgi

rEPR (ribosomes) sEPR

centrosome nucleolus

nucleus

cytoplasm

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NUKLEUS

• Pusat simpanan informasi dalam sel

• Informasi ditulis dalam bentuk nukleotida

• Nukleotida :

 Basa nitrogen

 Gula 5 karbon (pentosa): Deoksiribosa (DNA) atau ribosa (RNA)

 dan Fosfat

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Watson and Crick DNA

 Double helix

 Bases in the inside

 Sugar-phosphat backbone on the outside

 Two strands run in opposite direction

 Bases are paired by hidrogen bonds (A-T, G-C)

Figure 4-3 Molecular Biology of the Cell (© Garland Science 2008)

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• Informasi di dalam nukleus dibagi ke dalam buku berupa “kromosom” (molekul DNA yg dapat diamati di dalam sel selama mitosis)

• Buku dibagi mjd beberapa bagian/chapter berupa “gen”.

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SINTESIS PROTEIN

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INTI SEL SITOPLASMA

L O K A S I

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DOGMA MOLEKULAR

gene expression?

-

Transkripsi : sintesis RNA dari DNA

template

- Translasi : formasi sebuah protein

(rangkaian asam

amino) dari RNA

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SINTESIS PROTEIN

37 DNA RNA PROTEIN

P R O S E S

Transkripsi Transformas i

Transkripsi terjadi di dalam inti,

sedangkan translasi/transformasi

terjadi di sitoplasma

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• Proses dimana molekul DNA dikopi menjadi rantai komplementer RNA (messenger RNA=mRNA)

38 • Proses pengkodean mRNA menjadi protein dengan menggunakan beberapa jenis RNA

TRANSFORMASI

TRANSKRIPSI

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DNA REPLICATION

• Semiconservative process

• Each parental

strands serves as a template

• Central enzyme DNA polymerase

• Catalyze joining of

deoxyribonucleas e 5’ triphosphat (dNTP)

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DNA POLYMERASE

E. coli

• 3 types of polymerase

• Polymerase I repair of DNA damage

• Polymerase II unknown

• Polymerase III replication

Eukariot

• 5 types of polymerase

• , ,   most active in dividing cells

 replication

•   located in mitocondria replication in mitocondria

•   active in nondividing and dividing cells  repairing of DNA damage

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PROPERTIES OF DNA POLYMERASE

Critical implications for DNA replication

• Synthesize DNA only in 5’ to 3’ direction adding a dNTP to the 3’ hydroxyl group of a growing chain

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DNA SYNTHESIS

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ORIGIN OF REPLICATION

• Unique sequence of DNA

• Serves as a specific binding site for proteins that initiate the replication process

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ORIGIN OF REPLICATION

• Bacterial & viral genome  single ORI

• E.coli 4x10⁶bp  1 ORI  30 min

• Mamm 3x10⁹ bp  1 ORI  30,000 min (3 weeks)

• Complex structure  rate of replication  10x lower

• Mamm replication few hours multiple ORI

• Mammalian genome  30,000 ORI

• Specific sequence (+ 100 bp)  Autonomously Replicating Sequence (ARS)

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ORIGIN OF REPLICATION

• ARS  11 bp highly conserved sequence binding site of Origin Replication Complex

(ORC)  initiate DNA replication

• 1 ORI  2 replication forks  DNA being actively replicated

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STEPS OF REPLICATION

1. Binding of an initiator protein (ORC) to ARS 2. Unwind the origin DNA

3. Recruit the other protein

• Helicase

• Single stranded DNA-binding protein Unwinding and exposing the template DNA

• Brace and sliding-clamp protein

Maintain association of polymerase with its template

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PROTEIN IN

REPLICATION FORK

• Helicase

Catalyze the unwinding of parental DNA

Ahead of the replication fork

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SINGLE-STRANDED DNA-BINDING PROTEIN

Stabilize the unwound template DNA

Keep it in an extended single-stranded state

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TOPOISOMERASE

Parental DNA unwind  DNA ahead is forced to rotate

Catalyze the reversible breakage and rejoining DNA strands

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PROTEINS IN REPLICATION FORK

• Accessory protein:

• Sliding-clamps protein  Proliferating Cell Nuclear Antigen (PCNA) 

bind to adjacent brace protein, forming a ring around the template DNA

Maintain the association of the polymerase with its template  allowing uninterrupted synthesis of DNA

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Figure 5-18c Molecular Biology of the Cell (© Garland Science 2008)

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THE REPLICATION FORKS

• Each fork  2 parental strands of DNA  2 new daughter strands

• Facts:

• 2 parental strands run in opposite direction (antiparallel)  continuous synthesis :

• 1strand be synthesize 5’ to 3’ direction

• 1strand be synthesize 3’ to 5’ direction

• DNA polymerase only catalyze polymerization 5’ to 3’ direction

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THE REPLICATION FORK

• 1 strand is synthesized continuously  leading strand

• 1 strand is formed from small, discontinuous pieces lagging strand

• Small pieces of newly synthesized DNA  Okazaki fragments

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SYNTHESIZE OF LAGGING STRAND

• FACT !!

• DNA polymerase requires a primer  cannot initiate synthesis de novo

• How is the synthesis of Okazaki fragments initiate?

• Short fragment of RNA  serve as primers synthesis of RNA can initiate de novo ^ primase synthesizes

short fragments of RNA

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INITIATION OF LAGGING STRAND

• Primase + polymerase α polymerase α-primase complex  initiate

synthesis of RNA de novo complement to the

lagging strand template

 RNA primer

• DNA polymerase  add a new

deoxyribonucleotide only to a preformed primer strand that is hydrogen- bonded to the template  Okazaki fragment

• Contain RNA-DNA joint

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• Continuous lagging strand  RNA primers 87 removed  replaced with DNA

• RNA removal:

▫RNase H : degrades the RNA strand of RNA-DNA hybrid

▫Polymerase δ  as an exonuclease : hydrolyze DNA (or RNA) in 3’ to 5’or 5’ to 3’ direction

5’ to 3’ exonuclease  remove ribonucleotide from 5’ end of Okazaki  replaced with dNTP

• Joining gap  DNA ligase

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TELOMERE

• DNA polymerase  extend primers 5’ to 3’ direction 

unable to copy the extreme 5’ end special mechanisms are required to replicate terminal sequence

• Terminal sequence (telomere)  tandem repeats of simple sequence DNA  replicate by unique enzyme  telomerase

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TELOMERASE

• Capable to maintain telomeres  catalyzing telomere synthesis in the absence of DNA

template

• A reverse transcriptase  synthesize DNA from RNA template

• Carries its own template RNA  complement to the telomere

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TRANSKRIPSI

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TRANSCRIPTION

• Process of copying DNA to RNA

• Differs from DNA synthesis in that only one strand of DNA, the template strand, is used to make mRNA

• Does not need a primer to start

• Can involve multiple RNA polymerases

• Divided into 3 stages

• Initiation

• Elongation

• Termination

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TRANSCRIPTION: THE FINAL PRODUCT

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TRANSLASI

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TRNA

• Is in a clover shaped structure

• Brings the amino acids to the mRNA

• Has an anticodon loop to recognise the codons in the mRNA (by Watson-Crick base pairing)

• Is responsible for the specificity of the codon recognition

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TRNA CHARGING

• Aminoacylation is the process of adding an aminoacyl group to a compound.

• It produces tRNA molecules with their CCA 3' ends covalently linked to an amino acid

• Each tRNA is aminoacylated(or charged) with a specific amino acid by an aminoacyl tRNA synthase.

• There is normally a single aminoacyl tRNA synthetase for each amino acid, despite the fact that there can be more than one tRNA, and more than one anticodon, for an

amino acid.

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PROCESS OF TRANSLATION

• Initiation

• Recognition and specificity

• Elongation

• Termination

• Recognition of STOP codons

• Usage of release factors

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mRNA

attaches to small

ribosomal subunit

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TRANSLATION - OUTLINE

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TRANSLATION.

MRNA USED TO MAKE POLYPEPTIDE CHAIN (PROTEIN)

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•First the mRNA attaches itself to a ribosome (to the small subunit).

•Six bases of the mRNA are exposed.

•A complementary tRNA molecule with its attached amino acid (methionine) base pairs via its anticodon UAC with the AUG on the mRNA in the first

position P.

•Another tRNA base pairs with the other three mRNA bases in the ribosome at position A.

•The enzyme peptidyl transferase forms a peptide bond between the two amino acids.

•The first tRNA (without its amino acid) leaves the ribosome.

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TRANSLATION 2

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The ribosome moves along the mRNA to the next codon (three bases).

The second tRNA molecule moves into position P.

Another tRNA molecule pairs with the mRNA in position A bringing its amino acid.

A growing polypeptide is formed in this way until a stop codon is reached.

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END OF TRANSLATION

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A stop codon on the mRNA is reached and this signals the ribosome to leave the mRNA. A newly synthesised protein is now complete!