RPKPS (RENCANA PROGRAM DAN KEGIATAN PEMBELAJARAN SEMESTER) 1.
Nama Mata Kuliah
: Enzimologi (Enzymology)
2.
Kode / SKS
: B10-3013 / 2-0 (BIO 512 / 2-0)
3.
Prasyarat
: 1. Biokimia Dasar (BIO-211) 2. Biokimia Teknik (B10-212)
4.
Status Matakuliah
: Pilihan (Elective)
5.
Deskripsi Singkat
:
Dalam mata kuliah ini akan dibahas tinjauan molekuler enzim, distribusi enzim, mekanisme dan kinetika kerja reaksi enzimatik substrat tunggal dan dua atau multisubstrat, biosintesis, isolasi dan pemurnian enzim dari jaringan dan organ, isozim dan peranan dalam metabolisme, pengendalian metabolisme oleh isozim, enzyme turn-over, aspek pemanfaatan analisis enzim dalam bidang kesehatan, pertanian dan pangan serta peran enzim dalam pengembangan bioteknologi. Mata kuliah ini disampaikan dalam bentuk tatap muka, dan perkuliahan diarahkan ke diskusi interaktif dalam
membahas
permasalahanpermasalahan
hayati
berbasis
molekuler,
pengembangan dan pemanfaatan enzim dalam berbagai bidang. 6.
Tujuan Pembelajaran
:
Matakuliah Enzimologi bertujuan untuk memberikan pengetahuan lebih luas tentang enzim sebagai biomolekul dan peran enzim dalam tubuh organisme, baik mikrobia,
tumbuhan
maupun
hewan,
sehingga
para
mahasiswa
dapat
memanfaatkannya lebih luas untuk kebutuhan manusia dan lingkungannya. Mata kuliah ini disampaikan seluruhnya dalam bahasa Inggris dengan tujuan membiasakan para mahasiswa mendengar, bertanya dan berdiskusi dalam bahasa Inggris sebagai alat komunikasi, sehingga nantinya para lulusan diharapkan lebih percaya diri apabila lulusan bermaksud bekerja atau melanjutkan pendidikan tinggi ke strata -2 atau strata-3.
7.
Materi Pembelajaran : Main Topic (Pokok Bahasan)
1.
Introduction
Sub-topic (Sub Pokok Bahasan) 1. Course description and objectives 2. Role of enzymology in modern biology 3. Application of enzymology in science and technology development
2.
Molecular Basis of Enzymes
1. Molecular structure of enzymes 2. Primary, secondary,
tertiary
and
quaternary structure 3. Structural hierarchy
of
enzyme
molecules 4. Enzyme distribution : intra
vs
extracellular; cytosolic vs membranebound; tissue and non-tissue specfic 3.
Nomenclature
and
Enzyme
Classification
1. International Biochemistry Union 2. Enzyme classification
and Enzyme
code number 3. Systematic name and trivial name 4.
Catalytic Mechanism of Enzyme Reaction
1. Molecular structure
and
catalytic
nature of enzyme reaction 2. Collision Theory and
enzyme-
substrate complex formation 3. Reversibility
and
irreversibility
in
enzyme reaction 4. Single substrate and multi-substrate enzyme
reaction,
mono-molecular
and bimolecular substrate reactions (Random,
Compulsary
Ping-Pong mechanism
ordered
or
Main Topic (Pokok Bahasan) 5.
Enzyme Kinetics
Sub-topic (Sub Pokok Bahasan) 1. Definition 2. Enzyme activity measurement 3. In-vivo vs in-vitro enzyme activity 4. Enzyme apparent
activity
and
Enzyme specific activity 5. Michaelis-Menten kinetics; Km and Vmax of enzyme kinetics 6. Determination of Km and Vmax by Double reciprocal Plot of Lineweaver Burk kinetics 7. Constitutive
vs
Induced
enzyme
activity 8. Inducibility of enzyme activity and 6.
enhanced enzyme activity 1. Intracellular, extra-cellular
Enzyme Biosynthesis
membrane-bound
and enzyme
biosynthgesis 2. Prokaryotic vs Eukaryotic enzyme biosynthesis; Organellic enzyme biosynthesis 3. Enzyme biosynthesis and growth 4. Enzyme biosynthesis regulation 7.
Enzyme Purification
Isolation
and
1. Objectives and strategy in enzyme isolation 2. Objectives and strategy in enzyme purification 3. Enzyme Recovery and Enzyme Purification-fold
Main Topic (Pokok Bahasan) 8.
Sub-topic (Sub Pokok Bahasan)
Enzyme Kinetic Regulation
1. Enzyme compartmentation 2. Metabolic regulation
and
enzyme
activity 3. Enzyme
activity
inhibition
through
additive, synergistic and concerted mechanism 4. Enzyme activity modulation 9.
Isozyme (Iso-enzyme)
1. Definition of isozymes 2. Biological role of isozymes 3. Application of isozyme analysis
10. Enzyme Turn-over
1. Definition and mechanism 2. Turn-over rate of enzymes in cell
11. Application of Enzymology
1. Enzyme analysis in agriculture metabolism and development 2. Enzyme analysis
in
health
and
medicine 3. Enzymes and food industry 4. Enzyme technology
(Enzyme
Reactor) 5. Enzymes used in Biotechnology 12. Wrap-up of Enzymology Lecture
8.
Discussion and reconfirmation
Hasil Pembelajaran (Learning outcome)
Mahasiswa memiliki kemampuan : a.
Memahami, membandingkan dan mengambil manfaat serta memanfaatkan pengetahuan tentang enzimologi untuk menjelaskan berbagai fenomena hayati lebih pada aras molekuler dalam berbagai cabang-cabang biologi dan ilmu-ilmu lain yang berlandasankan pengetahuan hayati
b.
Memanfaatkan serta memperluas pengetahuan dalam penelitian atau kajian baik di
bidang
biologi
maupun
bidang-bidang
lain
apabila
mahasiswa
yang
bersangkutan ingin melanjutkan pendidikan tinggi pada strata lebih lanjut setelah terbiasa menggunakan istilah-istilah teknis enzimologi dalam bahasa Inggris, serta berkomunikasi menggunakan bahasa Inggris sehingga nantinya tidak canggung dalam mengikuti secara aktif seminar-seminar berbahasa Inggris
9.
Rencana Kegiatan Pembelajaran Mingguan
Minggu
Main Topic
Sub-Topic
Metode Proses
Ke
(Pokok Bahasan)
(Sub- bahasan)
Pembelajaran
1
1. Introduction
1. Course description and objectives 2. Role of enzymology in modern biology 3. Application of enzymology in science and technology
Kuliah mimbar, pertanyaan dari dosen untuk memancing diskusi dua arah
development 2
2. Molecular Basis of Enzymes
1. Molecular structure of enzymes 2. Primary, secondary,
Kuliah mimbar, pertanyaan dari dosen
tertiary and quaternary
untuk
structure
memancing
3. Structural hierarchy of enzyme molecules 4. Enzyme distribution : intra
diskusi dua arah, peragaan model dan
vs extracellular; cytosolic
mahasiswa
vs membrane- bound;
mencoba
tissue and non-tissue
memanfaatkan
specfic
model, dan menggunakan transparansi gitam-putih dan berwarna
3
3. Nomenclature and Enzyme Classification
1. International Biochemistry Union
Kuliah mimbar, pertanyaan dari
2. Enzyme classification and
dosen
Enzyme code number
untuk
3. Systematic name and trivial name
memancing diskusi dua arah dengan mahasiswa
Minggu
Main Topic
Sub-Topic
Metode Proses
Ke
(Pokok Bahasan)
(Sub- bahasan)
Pembelajaran
4
4. Catalytic
1. Molecular structure and
Kuliah mimbar,
Mechanism of
catalytic nature of enzyme
pertanyaan dari
Enzyme
reaction
dosen
Reaction
2. Collision Theory and
untuk
enzyme-substrate
memancing
complex formation
diskusi dua arah
3. Reversibility and irreversibility in enzyme reaction 4. Single substrate and multi-substrate enzyme reaction, mono-molecular and bimolecular substrate reactions (Random, Compulsary ordered or Ping-Pong mechanism 5 -6
5. Enzyme Kinetics
Kuliah mimbar, 1.
Definition
pertanyaan dari
2.
Enzyme activity
dosen untuk
measurement
memancing
In-vivo vs in-vitro enzyme
diskusi dua
activity
arah dengan
Enzyme apparent activity
mahasiswa
3. 4.
and Enzyme specific activity 5.
Michaelis-Menten kinetics; Km and Vmax of enzyme kinetics
6.
Determination of Km and Vmax by Double reciprocal Plot of Lineweaver -Burk kinetics
Minggu
Main Topic
Sub-Topic
Metode Proses
Ke
(Pokok Bahasan)
(Sub- bahasan)
Pembelajaran
7.
Constitutive vs Induced enzyme activity
8.
Inducibility of enzyme activity and enhanced enzyme activity
7
5. Enzyme
1.
Biosynthesis 2.
3.
Intracellular, extracellular
Kuliah mimbar,
and membranebound
pertanyaan dari
enzyme biosynthgesis
dosen untuk
Prokaryotic vs Eukaryotic
memancing
enzyme biosynthesis;
diskusi dua
Organellic enzyme
arah dengan
biosynthesis
mahasiswa
Enzyme biosynthesis and growth
4.
Enzyme biosynthesis regulation
8
6. Enzyme
1.
Isolation And Purification
2. 3.
Objectives and strategy in
Kuliah mimbar,
enzyme isolation
pertanyaan dari
Objectives and strategy in
dosen
enzyme purification
untuk
Enzyme Recovery and
memancing
Enzyme Purification-fold
diskusi dua arah dengan mahasiswa
Minggu
Main Topic
Sub-Topic
Metode Proses
Ke
(Pokok Bahasan)
(Sub- bahasan)
Pembelajaran
9
7. Enzyme Kinetic
1.
Regulation 2. 3.
Enzyme
Kuliah mimbar,
compartmentation
pertanyaan dari
Metabolic regulation and
dosen untuk
enzyme activity
memancing
Enzyme activity inhibition
diskusi dua
through additive,
arah dengan
synergistic and concerted
mahasiswa
mechanism 4.
Enzyme activity modulation
10-11
8. Isozyme (Isoenzyme)
1.
Definition of isozymes
Kuliah mimbar,
2.
Biological role of
pertanyaan dari
isozymes
dosen untuk
Application of isozyme
memancing
analysis
diskusi dua
3.
arah dengan mahasiswa 12
9. Enzyme Turnover
1. Definition and mechanism
Kuliah mimbar,
2. Turn-over rate of enzymes
pertanyaan dari
in cell metabolism and
dosen untuk
development
memancing diskusi dua arah dengan mahasiswa
13-14
10. Application of Enzymology
1. Enzyme analysis in agriculture 2. Enzyme analysis in health and medicine 3. Enzymes and food industry
Kuliah mimbar, pertanyaan dari dosen untuk memancing diskusi dua arah
Minggu
Main Topic
Sub-Topic
Metode Proses
Ke
(Pokok Bahasan)
(Sub- bahasan)
Pembelajaran
4. Enzyme technology (Enzyme Reactor) 5. Enzymes used in Biotechnology 15
11. Wrap-up of
Discussion and reconfirmation
Kuliah mimbar,
Enzymology
pertanyaan dari
Lecture
dosen untuk memancing diskusi dua arah dengan
16
UJIAN AKHIR
Bahan seluruh materi kuliah
mahasiswa Soal ujian
dengan fokus materi sesudah
disajikan dalam
ujian tengah semester
Bahasa Inggris, soal pilihan ganda, uraian dan perhitungan analitik, bersifat open-book
10. Penilaian : Kriteria dan Cara Evaluasi Hasil Pembelajaran Penilaian basil pembelajaran dilakukan melalui UJIAN TENGAH SEMESTER dan UJIAN AKHIR SEMESTER. Bahan ujian terdiri dari uji kognitif, uji penalaran dan uji analitik menyelesaikan soal-soal Pilihan Ganda, Soal-soal Uraian dan soal-soal analisis data sekunder. Masing-masing jenis pertanyaan / soal diberi bobot berbeda sesuai dengan jenis pertanyaan, sebagai contoh : jenis soal kognotof dengan Pilihan Ganda diberi bobot 30%, jenis uraian 40% dan jenis analisis data 30%. Ujian tengah semester berbobot 40% dan Ujian Akhir Semester berbobot 60%. Untuk melatih berfikir mahasiswa dan memahami, beberapa kali mahasiswa diberikan Problem Set untuk dikerjakan di rumah secara mandiri. Ujian-Ujian (tengah semester dan ujian akhir semester) dibuat sejalan dan pemahaman materi kuliah dan Problem Set, sehingga hal tersebut memacu mahasiswa untuk mengerjakan dan menyelesaikan tugas. Semua Problem Set dibuat dalam Bahasa Inggris.
11. Bahan, Sumber Informasi dan Referensi Bahan kuliah disusun dalam kerangka pemikiran dan pemahaman enzimologi yang terkait dengan Tujuan Instruksional Umum Matakuliah Enzimologi. Sumber materi pembelajaran diambil dari tiga sumber buku acuan, yaitu :
1. Price, N.C. and L. Stevens (1984), Fundamentals of Enzymology, Oxford, New York
2. Segel, I.H. (1976), Biochemical Calculations, How to Solve Mathematical Problems in General Biochemistry, 2nd ed. John Wiley & Sons, New York
3. Dixon,M. & E.W. Webb (1979), Enzymes, 3rd ed., Longman Group Limited, London
Selain ketiga sumber tersebut di atas, sumber lain juga digunakan, antara lain dari Jurnal-Jurnal Ilmiah dan dari Hasil-Hasil Penelitian. 12. A. Beberapa contoh Soal Ujian Enzymology Midterm Examination
Name:
_______________________________ April 1, 1999; 100 minute (Open Book Exam.) Student ID: __________________/Bi _____________________________________________________________________ You may answer in Indonesian or in English (you will get 10-point bonus if you answer in English) Be concise in answering the question. Write your answer in this sheet only _____________________________________________________________________ 1.
All enzymes are proteins, but not all protein molecules are enzymes. What structural characteristics make a protein molecule shows catalytic capacity ?
2.
Similar enzymes from different source (different species) may have different catalytic activity. a)
do they have similar primary structure ? Yes: __ or No: ____ (tick V of your choice)
b)
do they have similar molecular orientation in the active site and catalytic site ? Yes ___
or No _____
c)
do they have similar molecular weight ? yes: ___, or No: ___
d)
do they have similar Km value ? yes: ______ , or No: ______
e)
are they isozymes ? Yes:______ , or No: _____
3.
Give your reasons of your answer in question # 2 a) b) c) d) e)
4.
If you are going to determine the Km and Vmax value of an enzyme, which of the methods you are going to use, in vivo or in vitro ? Give reasons to your answer.
5.
Draw a Michaleis Menten curve which shows: a. two enzymes that have similar Vmax but different Km b. two enzymes that have different Vmax but similar Km
B10-512 (Enzymology Final) Examination June 23, 1999; 100 minutes (Open Book Exam.)
Student Name: _______________ Student ID: ______________ /Bi
_____________________________________________________________________ You may answer in Indonesian or in English (you will get 10-point bonus if you answer in English) Be concise in answering the question. Write your answer in this sheet only (choose 4 out 5 questions) -----------------------------------------------------------------------------------------------------------------1.
Write 5 practical application you can do with enzymes:
a. b. c. d. e. 2.
Suppose that you have isolated an enzyme and you want to know whether your enzyme is monomeric or polymeric, describe how you would run the laboratory experiment
3.
During enzyme isolation and purification, what parameters that you have to know to calculate recovery and purification fold, give description of what you are doing and explain why ?
4.
If you a purified enzyme, how do you know that your pure enzyme preparation does not contain any inhibitor ? Explain your answer
5.
How would you differentiate between non-competitive and un-competitive inhibitor?
12.B Contoh Problem Set Exercise Problem Set-1 for Enzymology A. Answer the questions according to the following: Answer A if statement no. 1, 2 and 3 are right Answer B if statement no. 1 and 3 are right Answer C if statement no. 2 and 4 are right Answer D if only statement no. 4 is right Answer E if statement no. 1, 2,3 and 4 are right 1.
2.
3.
4.
Enzymes may consist of: 1.
proteins
2.
single polypeptide chain
3.
more than one polypeptide chain
4.
metal and protein
Most enzymes are : 1.
Sensitive to pH change
2.
have Km value
3.
have Vmax value
4.
resistant to high temperature
Enzymes may have this/these characteristics: 1.
show specificity to specific substrate
2.
have more than one active site
3.
Each active has one catalytic site
4.
All those statements above are wrong
Enzyme proteins may have this/these characteristics: 1.
shows alpha helix
2.
shows parallel beta-pleated sheet
3.
shows anti-parallel-beta pleated sheet
4.
none of those
5.
6.
Enzyme protein conformation 1.
coiling of polypeptide chain in 3-dimensional space
2.
may change during catalytic event
3.
differ for each enzyme
4.
depend on primary structure
During catalytic reaction, 1.
the enzyme should bind the substrate molecule
2.
the enzyme molecule should have higher molecular weight than the substrate
7.
8.
9.
3.
there is intra-molecular straining
4.
the enzyme molecule split into product
Whenever an enzyme catalytic activity is inhibited by an inhibitor: 1.
the inhibitor always changes the Vmax
2.
the inhibitor always changes the Km
3.
the inhibitor always binds the enzyme irreversibly
4.
none of the above is right
In bimolecular substrate, the enzyme 1.
binds both substrates at the same time
2.
binds both substrates at different active site
3.
the product(s) of catalytic reaction is/are released at the same time
4.
the binding of enzyme and substrate may be random or ordered
In metabolic reactions, each reaction 1.
is catalyzed by a single enzyme
2.
is catalyzed by enzyme reversibly
3.
is under control by its product
4.
is catalyzed by enzyme having similar Vmax
10. If the catalytic reaction is as follows: D>E A>B>C F>G 1.
the quantity of product E and G will be similar
2.
the rate of E and G formation will be different
3.
the quantity of product E and G is dependent on enzyme molecular weight
4.
the production of E and G is dependent on Km value
B. True or False answer of the statement. Answer V for true statement or X for false statement. 11. Enzyme with similar Vmax should have similar Km value 12. All enzyme molecule have quaternary structure 13. All enzyme always consist of a single polypeptide chain 14. All competitive inhibitor to enzyme always binds to the enzyme active site 15. All non-competitive inhibitor binds to the enzyme irreversibly 16. In metabolic pathway, the metabolic rate is dependent on Km of certain enzyme 17. Dead-end inhibitor always binds to the enzyme irreversibly 18. Ping-pong Bi-Bi catalytic reaction is dependent on the release of the first product of the reaction 19. All enzyme requires the presence of co-enzyme 20. Concerted feedback inhibition means that both end-product are inhibitory C. Draw Lineweaver-Burk kinetic graph showing competitive. Non-competitive, uncompetitive and substrate inhibition D. A young biochemist was analyzing a novel enzyme and the kinetic data is as follows : [S]
1.5 2.0 3.0 4.0 8.0 16.0
[product] w/o inhibitor micromoles
[product] w/ inhibitor micromoles
0.21 0.25 0.28 0.33 0.40 0.44
0.08 0.10 0.12 0.13 0.16 0.18
Determine : a) Km and Vmax value b) the type of inhibitor
E. A Biochemistry graduate has done enzyme isolation and purification, and the data is as follows: Protein Steps
Enzyme
vol. of fraction
Conc.
Total
Conc.
Spec.Act.
Total.
ml
mg/ml
mg
units/ml
units/mg
unit
Recov. Purification %
fold
crude
500
10
5000
3
1) ______
2) __
3) ___
4) ______
heat
500
6
3000
2.4
5) ______
6) __
7) ___
8) ______
Fill in the value of each blank (___ )
