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SOAL FORMATIF FKUI 2010 1. Elemen yang selalu terdapat dalam protein adalah C, H, O, N.

Analisis unsur : selalu mengandung C,H,O,N,S Mengapa selalu mengandung S?? kalo C,H,O,N si masuk akal juga…. H | COOH-C-NH | R Jawaban : SALAH 2. Protein adalah homoppoimer dari asam amino Definisi dari protein: Definisi KIMIA:

Protein adalah heteropolimer dari asam-asam amino yang terikat satu sama lain dengan ikatan peptida

Definisi BIOLOGIS: • Definisi biologis : Protein adalah senyawa yang merupakan hasil ekspresi informasi yang terkandung dalam gen

Definisi BIOKIMIA:

Definisi Biokimia : Protein adalah heterobiopolimer , dibuat oleh sel sebagai hasil ekspresi informasi dalam gen, tersusun dari asam-asam amino yang terikat satu sama lain oleh ikatan peptida

3. Asam  amino butirat adalah asam amino yang menyusun protein.

4. Asam aspartat adalah asam amino esensial. Asam amino essensial: Valiant-Pheny-Try-His-Theory-of-Meteor-Lysis-using-Selenoida-Iso-Leusine • • • • • • • • • • Valine Phenylalanine Tryptophan Histidine Threonine/Tyrosine Methionine Lysine Selenocysteine Isoleucine Leucine

5. Asam amino L-sitrulin tidak pernah menyusun protein karena tidak punya kodon. Although citrulline is not coded for by DNA directly, several proteins are known to contain citrulline as a result of a posttranslational modification. These citrulline residues are generated by a family of enzymes called peptidylarginine deiminases (PADs), which convert arginine into citrulline in a process called citrullination or deimination. Proteins that normally contain citrulline residues include myelin basic protein (MBP), filaggrin, and several histone proteins, whereas other proteins, such as fibrin and vimentin are susceptible to citrullination during cell death and tissue inflammation. Patients with rheumatoid arthritis often have detectable antibodies against proteins containing citrulline. Although the origin of this immune response is not known, detection of antibodies reactive with citrulline (anti-citrullinated protein antibodies) containing proteins or peptides is now becoming an important help in the diagnosis of rheumatoid arthritis.[3] In recent studies, citrulline has been found to relax blood vessels.[4] TRUE

6. Untuk dapat berfungsi secara maksimal, protein memerlukan pH dan suhu tertentu. TRUE •

Di luar pH optimum, aktivitas biologis protein selalu < Hal yang sama bagi to : to yg → protein aktif maks : to optimum. Di luar to optimum, aktivitas biologis suatu protein selalu <

7. Struktur sekunder berupa simpai disebabkan oleh terbentuknya ikatan S-S intra rantai polipeptida.

Heliks-@ Ikatan hidrogen (H) antara –CO- suatu ikatan peptida dengan –NH- ikatan pptd 3-4 aa ke depan atau ke belakang → heliks-α

Beta SHEET

Ikatan H antara –CO- & -NH- terbentuk antara peptida berhadapan

Lipatan/tekukan/Bending AA PROLIN Loop atau simpai O/ ikatan –S-S- terbentuk sbg hsl oksidasi 2 aa sistein dlm 1 rantai protein (1 ggs –SH /sistein) Sulur sembarang/RANDOM COIL saling tolak antara aa dengan R bermuatan sama (sama-sama asam atau basa) 8. Umumnya protein globular adalah protein regulator. TRUE Protein globular umumnya berfungsi sebagai protein regulator contoh protein globular: enzim, transporter, caraka 1 (mediator), pertahanan, reseptor

Protein fibriller umumnya berfungsi sebagai protein structural: keratin-α dan keratin-β (lembar-β), kolagen, elastin, bagian molekul myosin 9. Menurut Beadle dan Tatum, 1 gen menentukan 1 enzim, atau lebih tepatnya terdapat 1 protein. Beadle & Tatum (1946) : mutan Neurospora crassa tidak mampu meragikan roti → cacad enzim menyertai cacad gen → one gene one enzyme (protein) REMEMBER THAT ENZYME IS ALWAYS A PROTEIN!!

10. Sel melaksanakan sejumlah besar jenis reaksi kiia setiap saat secara teratur. there are something within cell, enable a large number of chemical reactions occurred in a highly coordinated manner, in a mild environtment condition and often produce various compounds with very complicated structure Enable large number of chemical reaction in a highly coordinated manner TRUE 11. Sebagian besar enzim seperti umumnya protein berada dan berfungsi dalam sel. Most enzyme, as most other protein, are synthesized, rest and work within a cell TRUE 12. Enzim pencernaan adalah enzim ektrasel. Definition of Extracellular enzyme: An enzyme, such as a digestive enzyme, that functions outside the cell from which it originates. Also called exoenzyme.

13. Enzim pencernaan termasuk kelas hidrolase. TRUE

14. Asam pantotenat diperlukan sebaga prekursor koenzim A yang diperlukan enzim untuk metabolisme asam lemak. TRUE Pantothenic acid, also called vitamin B5 (a B vitamin), is a water-soluble vitamin required to sustain life (essential nutrient). Pantothenic acid is needed to form coenzyme-A (CoA), and is critical in the metabolism and synthesis of carbohydrates, proteins, and fats. In chemical structure, it is the amide between D-pantoate and beta-alanine. Its name is derived from the Greek pantothen (πάντοθεν) meaning "from everywhere" and small quantities of pantothenic acid are found in nearly every food, with high amounts in whole-grain cereals, legumes, eggs, meat, and royal jelly. It is commonly found as its alcohol analog, the provitamin panthenol, and as calcium pantothenate. Pantothenic acid is an ingredient in some hair and skin care products 15. Enzim tidak mengubah nilai Km, enzim hanya mempercepat tercapainya bentuk peralihan. TRUE
 In an other words, it means that the presence of an enzyme will not, or even more

exactly, will never change the K value of any reaction  The role of E, therefore, is to lead S to its transition form 16. Dalam bentuk peralihan, substrat berada dalam keadaan yang sangat stabil. FALSE Transition State & Transition Form  To explain to problem, let we see the following spontaneous reaction : A→B  Indeed, the reaction occurs in the following manner : A ⇌ A’→B
 A’ is the transition form of A with the general characteristics :

- Has a very short life (µsecond or <<) - Need certain energy input (despite its spontaneity) Has a relatively unstable structure - In this condition, A’ becomes a metastable molecule

- Like other metastable systems, a very little change can push A’ into another very stable molecule, B. Then we find the 2nd half reaction : A’→ B. - If we take into account the role of A’, then in the overall reaction we will eliminate the A’ from the overall reaction, as if A’ is never exist, exactly as the ES case, therefore as the role of E itself 17. Bentuk kurva hubungan [S] dengan kerja reaksi kimia pada enzim dikenal sebagai kurva Michaelis-Menten ditemukan dalam seluruh sistem yang mempunya saturasi. TRUE v= V[S]/Km+[S] relate the concentration of substrate to rate of reaction of an enzyme, it is found in all system which has saturation 18. Sejumlah protein termasuk enzim memerlukan Ca atau Zn untuk memantapkan struktur 3D sehingga dapat berfungsi.  Cofactor’s functions : 1.As an enzyme stabilizer : Ca, Zn 2.Involve in reduction-oxidation (redox) reaction. In this case, the bounded metal can accept and release electron : Cu, Fe and Mn 3.Stabilize coenzyme or substrate : Mg 4.Make environment suitable for E:K,Na 19. Km adalah nilai K reaksi disosiasi ES, gambaran afinitas, dan juga [S] yang menyebabkan kecepatan reaksi tepat = setengah kecepatan maksimum. Km is where the v of the reaction is half of the V max 20. K disosiasi HbO2 > K disosiasi HbCO. TRUE ingat bahwa Kdis lebih kecil maka Afinitas lebih besar…. Kita ketahui bahwa afinitas HbCO lebih besar daripada HbO2 - bahayanya di lapangan parker di tempat terutup dapat menyebabkan keracunan CO sehingga berbahaya 21. Molekul enzim "memaksa" substrat untuk teregang menjadi bentuk transisi dalam suhu biasa.

TRUE Salah satu spesialisasi enzim adalah dapat membentuk substratproduk dalam suatu keadaan yang normal SUHU BIASA 22. Hb hanya akan mengikat O2 bila besi dalam hem berada sebagai Fe2+ TRUE Hb hanya dapat mengikat O2 dalam keadaan terreduksi FE2+ Facts about Hb you would like to know::
 Memberi warna merah Hem:Fe-porfirin

 Porfirin dibntk o/ 4 cincin pirol  Fe di tgh cincin, bntk ikatan koordinasi dg N pirol merah pada darah o/ pigmen Hem : Fe-porfirin 23. Imunoglobulin utama dalam serum adalah IgG. TRUE Immunoglobulin G (IgG) is a monomeric immunoglobulin, built of two heavy chains γ and two light chains. Each IgG has two antigen binding sites. It is the most abundant immunoglobulin and is approximately equally distributed in blood and in tissue liquids, constituting 75% of serum immunoglobulins in humans.[1] IgG molecules are synthesized and secreted by plasma B cells.

24. Pada sel prokariotik DNA juga dijumpai dalam mitokondria. Does prokaryote generally have Mitochondria? I don’t think so FALSE 25. Komponen asam nukleat adalah gugus fosfat, gula ribosa, dan basa nitrogen. Nucleic acid is divided into two types which are: DNA and RNA… DNA consist of Deoxyribose sugar,phosphate and nitrogen base RNA consist of ribose sugar,phosphate and nitrogen base

FALSE 26. ATP (adenosin tri fosfat) adalah molekul nukleosida .FALSE ATP is a NUCLEOTIDE Adenosine-5'-triphosphate (ATP) is a multifunctional nucleotide used in cells as a coenzyme. It is often called the "molecular unit of currency" of intracellular energy transfer.[1] ATP transports chemical energy within cells for metabolism. It is produced by photophosphorylation and cellular respiration and used by enzymes and structural proteins in many cellular processes, including biosynthetic reactions, motility, and cell division.[2] One molecule of ATP contains three phosphate groups, and it is produced by ATP synthase from inorganic phosphate and adenosine diphosphate (ADP) or adenosine monophosphate (AMP). Metabolic processes that use ATP as an energy source convert it back into its precursors. ATP is therefore continuously recycled in organisms, with the human body turning over its own weight in ATP each day.[3] 27. Perbedaan antara DNA dan RNA adalah kemampuannya dalam mempertahankan informasi genetik. TRUE ?!?!?! DNA memiliki mekanisme PROOFREADING RNA tidak meimiliki mekanisme PROOFREADING begitulah kelihatannya alasan yg baiknya 28. Informasi genetik di dalam molekul DNA dipindahkan ke molekul RNA pada saat replikasi DNA. FALSE The genetic information is transferred to RNA molecule in the process of TRANSCRIPTION The picture:

29. Perpindahan informasi genetik terjadi pada proses mitosis. False Prophase I which happened in MEIOSIS During prophase I, DNA is exchanged between homologous chromosomes in a process called homologous recombination. This often results in chromosomal crossover. The new combinations of DNA created during crossover are a significant source of genetic variation, and may result in beneficial new combinations of alleles. The paired and replicated chromosomes are called bivalents or tetrads, which have two chromosomes and four chromatids, with one chromosome coming from each parent. At this stage, non-sister chromatids may cross-over at points called chiasmata (plural; singular chiasma). 30. Kesalahan pada proses transkripsi gen dapat diperbaiki. False Look at the table, PROOFREADING

31. Kesalahan pada proses transkripsi gen dapat menyebabkan mutasi gen. TRUE hmmm kesalahan transkripsi Kesalahan RNA yg ditraskripsii  Protein yg ditranslasi MUTASI 32. Proses translasi terjadi di dalam ribosom. TRUE Lihat lagi :

33. Protein-protein mitokondria disintesis pada REK. False protein protein mitkondria disintesis di sitosol 34. Perubahan &#61537;&#61485;glukosa menjadi &#61538;&#61485;galaktosa adalah contoh mutarotasi. Mutarotation: is the change in the optical rotation that occurs by epimerization (that is the change in the equilibrium between two epimers, when the corresponding stereocenters interconvert). Cyclic sugars show mutarotation as α and β anomeric forms are interconvert.[1] The optical rotation of the solution depends on the optical rotation of each anomer and their ratio in the solution.

H

OH C

H C

O

HO

H C

H C OH HO C H H C OH O H C CH2OH

H C OH HO C H H C OH H C OH CH2OH

H C OH HO C H H C OH O H C CH2OH
35.

Senyawa yang mempunyai isomer optik dapat memutar bidang cahaya terpolarisasi. A chiral molecule is a type of molecule that lacks an internal plane of symmetry and has a nonsuperimposable mirror image. The feature that is most often the cause of chirality in molecules is the presence of an asymmetric carbon atom.[1][2] TRUE 36. Laktosa termasuk gula pereduksi karena tersusun dari glukosa dan galaktosa yang terikat dengan ikatan glikosidik &#61538;-1,4. Lactose is: • Also called milk sugar.

Composed of galactose and glucose linked by a β -1,4-glycosidic bond FALSE WHY.. BECAUSE LACTOSE IS NOT A REDUCING SUGAR Remember: Glucose + fructose sucrose

37. Persamaan antara amilopektin dan glikogen adalah dalam hal percabangan pada ikatan &#61538;-1,4 glikosidik. Amylose Unbranched (spiral) 300-400 glucose Glycosidic @(1,4) I2 : DEEP BLUE Amylopectin Branched 3000 glucose Glycosidic @(1,4) branch: @(1,6) I2: Purplish RED

Glycogen is similar to amylopectin but is even more branched Function in energy storage in muscle tissue and fiber Many branch as a quick means in putting glucose into blood

38. Bakteri yang mempunyai enzim &#61537;&#61485;glukosidase akan dapat mencerna selulosa. Cellulose A linear polymer of approximately 2800 D-glucose units per molecule joined by β-1,4glycosidic bonds

Humans and other animals cannot use cellulose as food because we lack β -glucosidases, the enzymes that catalyze the hydrolysis of β-glysodic bonds. We only have α-glucosidases, hence are limited to starch and glycogen with their α-glycosidic bonds. Many bacteria, however possess β -glucosidases and can digest cellulose. Animals such as the termite and ruminants (horses and cows) can digest cellulose because their digestive systems contain such bacteria.

REMEMBER Chitin •

The major structural component of the exoskeletons of invertebrates, such as insects and crustaceans; also occurs in cell walls of algae and fungi Composed of units of N-acetyl-β-D-glucosamine joined by β-1,4-glycosidic bonds

39. Semakin panjang rantai karbon pada asam lemak maka kelarutannya semakin tinggi. Physical properties of fatty acids Chain larger  Sollubility lower  Melting point higher

40. Lemak adalah trigliserida yang berbentuk padat pada suhu ruang.

41. Asam lemak berbentuk cis lebih berbahaya dibandingkan bentuk trans. Hmmmm…:) The naturally occurring fat is the CIS the changing to trans is to extend shelf life Look at the explanation: • • Hydrogenation of vegetable oils converts some of unsaturated bonds to saturated, trans conformation. Trans fatty acids extend shelf life, improve margarine, shortening.

Diet high in trans fatty acids risks heart disease, cancer

42. Salah satu sifat penting fosfolipid adalah sebagai zat pengemulsi.

• • • • •

Glycerol esterified to 2 fatty acids. Third position is phosphate Other end of phosphate can combine with other molecules to form various derivatives Amphipathic –emulsifying agents Production of cell membrane

43. Kolesterol adalah prekursor garam empedu.

Cholesterol -important constituent of cell membranes

-has a rigid ring system and a short branched hydrocarbon tail. Precursor to Bile Acids: - Act as detergents to dissolve dietary fats

- Fats can be broken better by enzymes Keeps the lipids in membrane from aggregrating: Keeps the membrane intact as a bilayer 44. Struktur primer pada DNA adalah rangkaian gula dan fosfat.

Primary structure : PHOSPATE

Secondary structure : SUGAR-PHOSPATE BACKBONE

TERTIARY STRUCTURE: Hidrogen BOND 45. Nukleotida adalah gabungan gula dan basa nitrogen, sedangkan nukelosida adalah gabungan gula, basa, dan fosfat. Nukleotida : Gula+Fosfat+Nitrogen Nukleosida:Gula+Fosfat NITROGEN GA TERMASUK YA DI NUKELOSIDA!!!! 46. Interaksi spesifik adalah terjadinya ikatan Hidrogen antara asam amino (yang berasal dari rantai samping protein) dengan basa nitrogen (yang berasal dari DNA) pada minor groove. Two types of interaction of DNA: 1. Specific interaction The formation of hydrogen bond between amino acid side chain and bases in the major groove

2. Non specific interaction The formation of ionic or hydrogen bonds with the phosphate residues in the ribose-phosphate backbone of the DNA 47. Polimorfisme pada DNA terjadi karena konformasi gula dan orientasi basa relatif terhadap gula. There are three natural forms of DNA (A, B and Z). The origin of these different forms are related to the conformation of the sugar (C2'-endo / C3'-endo) and the orientation of the base relative to the sugar (syn/anti).

48. Struktur double helix DNA terutama distabilkan oleh ikatan hidrogen antara basa nitrogen dengan fosfat. The double helix structure is mainly stabilized by hydrogen bonds between bases pairs. Since the hydrophobic bases are stacked inside and the hydrophilic ribose-phosphate chains are on the outside, Van der Waals forces and hydrophobic interactions are also deeply involved in the stabilization of the double helix 49. DNA ditranslasi dalam bentuk mRNA yang kemudian ditranskripsi menjadi protein. FALSE DNA DITRANSKIRPSI MENJADI MRNA DITRANSLASI JADI PROTEIN

50. Operon Lac akan bekerja pada kondisi konsentrasi glukosa rendah dan laktosa tersedia

51. Allolaktosa sebagai inducer akan berikatan pada suatu reseptor

52. Suatu operon terdiri dari 3 elemen, yaitu gen regulator, promotor, dan operator.  REGULATORY GENE  OPERON : The gene cluster and promoter, plus additional sequences that function together in regulation • • • Promotor Operator Structural Gene

53. Regulasi terhadap gen melalui atenuasi adalah khas untuk sel prokariotik. Attenuation regulates the termination of transcription as a function of tryptophan concentration. -At low levels of trp full length mRNA is made, at high levels transcription of the trp operon is prematurely halted. -Attenuation works by coupling transcription to translation. -Prokaryotic mRNA does not require processing and since prokaryotes have no nucleus translation of mRNA can start before transcription is complete. -Consequently regulation of gene expression via attenuation is unique to prokaryotes. 54. Operon arabinosa terhambat pada kondisi tanpa arabinosa. Activation If arabinose is present, it builds a complex: AraC + arabinose This complex is needed for RNA polymerase to bind to the promoter and transcribe the ara operon. Also for activation the binding of another structure to araI is needed: CAP + cyclic AMP So the activation depends on the presence of arabinose and cAMP.

Repression If arabinose is absent, the AraC protein assumes a different conformation. In this conformation the AraC protein binds to the araI DNA region as well as to the ara0 DNA region. This causes the DNA to form a loop, preventing transcription of the downstream ara operon elements. Sequence of the Operon: araC : araO : araI : araB : araA : araD

55. Selama siklus litik, DNA virus berintegrasi pada situs spesifik pada kromosom sel hospes. FALSE

56. Dalam kondisi pertumbuhan yang menguntungkan, protein cro akan terakumulasi yang memungkinkan sikluls litik terjadi. • If the growth conditions are very favorable, the intracellular levels of the proteases are high – The cII protein tends to be degraded

Therefore, PRE cannot be activated and the l repressor is not made

Instead, the cro protein slowly accumulates to high levels

The binding of the cro protein to OR prevents transcription of the l repressor from PRM At the same time, the cro protein allows the lytic cycle to proceed

• •

Thus, environmental conditions that are favorable for growth promote the lytic cycle – This makes sense because a sufficient supply of nutrients is necessary to synthesize new bacteriophages

57. Sigma subunit berikatan dengan DNA polimerase untuk menolong DNA polimerase menemukan promotor. A sigma factor (σ factor) is a prokaryotic transcription initiation factor that enables specific binding of RNA polymerase to gene promoters. Different sigma factors are activated in response

to different environmental conditions. Every molecule of RNA polymerase contains exactly one sigma factor subunit, which in the model bacterium Escherichia coli is one of those listed below. E. coli has at least eight sigma factors; the number of sigma factors varies between bacterial species. Sigma factors are distinguished by their characteristic molecular weights. For example, σ70 refers to the sigma factor with a molecular weight of 70 kDa. 58. Fisika molekuler adalah aplikasi hukum-hukum Fisika dasar yang mengatur struktur dan sifat-sifat molekul. TRUE 59. Elektroforesis dapat digunakan untuk mengukur pemisahan molekul. TRUE 60. Hibridisasi DNA dapat digunakan untuk menentukan identifikasi biomol. ybridization is the process of establishing a non-covalent, sequence-specific interaction between two or more complementary strands of nucleic acids into a single hybrid, which in the case of two strands is referred to as a duplex. Oligonucleotides, DNA, or RNA will bind to their complement under normal conditions, so two perfectly complementary strands will bind to each other readily. In order to reduce the diversity and obtain the most energetically preferred hybrids, a technique called annealing is used in the laboratory practice. However, due to the different molecular geometries of the nucleotides, a single inconsistency between the two strands will make binding between them less energetically favorable. Measuring the effects of base incompatibility by quantifying the rate at which two strands anneal can provide information as to the similarity in base sequence between the two strands being annealed. The hybrids may be dissociated by thermal denaturation also referred to as melting. Here, the solution of hybrids is heated to break the hydrogen bonds between nucleic bases, after which the two strands separate. In the absence of external negative factors, the processes of hybridization and melting may be repeated in succession indefinitely long, which lays the ground for polymerase chain reaction. Most commonly, the pairs of nucleic bases A=T and G≡C are formed, of which the latter is more stable.