PROGRAM STUDI

KEDOKTERAN UNILA

BIOKIMIA I
PJ BIOKIMIA : dr. Evi Kurniawaty, M.Sc
 SCHEMA BIOKIMA I
BIOCHEMISTRY

BIO LIVING
MOLEKULES ORGANISMS

NUTRIENTS
COMPLEX SIMPLE
MOLECULES MOLECULES

POLYSACCH MONOSACCH
ENERGY

POLYNUCLEO NUCLEO TIDES

CELLS

PROTEINS AMINO ACID

EUKARYO PROKARYO
TIC TIC
LIPIDS OTHERS

COMPLEX SIMPLE
CELLS CELLS

MEMBRANES ORGANELLES DNA CYTOPLASM DNA

Introduction to Biochemistry

Biochemistry is :
The chemistry of living things (Bios means “life”). Or
The chemistry of Biological systems

Biochemistry is the study of 4M’S

1. Macro molecules
2. Membranes
3. Metabolism
4. Memory
The Aim of Biochemistry Is

To describe and explain, in molecular terms, all chemical

processes of living cells.

To Achieve this

Should be carried out by experimental approach.

In fact : Biochemistry is en experimental sciences
Note

Biochemistry is the chemistry of biological sistem.

Biological systems are complex: involving a variety of
organism, tissues cell types, sub cellular organelles and
spesific molecules.
Consequently :

We (esp.Biochemists) must simplify these systems to

define and interpret their Biochemical processes.
Some (basic) techniques of experimental Biochemistry
are a useful tool to gain the simplification and
understanding of Biological systems
Some basic techniques which are encountered frequently in
experimental Biochemistry :

1.Photometry/Colorimetry/Spectrophotometry.
2.Chromatography
3.Radio isotope tracing
4.Electrophoresis
5.Centrifugation
Organism function well, when they are organized.
It means : Anything which function,is organized.
Events which occur in them are directed according to
A PATTERN ; NOT RANDOMLY. (e.g : the
function of a car,phone,computer,bacterium,human
body etc.
All organized systems acquire
1. Structure : the structure carries the pattern which
directs the functions.

2. Energy : energy is acquired :

a. to make the sistem work
b. to build it
c. to keep it in repair.
In organism

The energy source (Carbohidrate, Fats, or Protein) is

frequently used as part of the structure.
(and Vice-Versa)
For examples :
SUGARS are major energy source, but are also used as the
building material for plant cell walls.
FATS are oxydized to produce energy, but are part of
membranes in cells.

AMINO ACIDS also be used as an energy source, but they

are important units of the structural proteins of skin and
connective tissues.
This inter relationships make the sorting out of the structure
and function of living systems very complex and diverse.

Nevertheles UNIFYING features are common to all things

that live :
All make use of the same type of biomolecules and all use
energy.
Biochemistry is a field that draws on many disciplines such
as : physics, organic chemistry, botany, biology etc.

This multidisciplinary native allows it to use result from

many sciences to answer questions about the “molecular
nature of life processes.
Important applications of this knowledge are made in
medically related fields :

An understanding of health and disease at the molecular level

It leads to more effective treatment of illnesses of all sorts.

In fact, during the past six decades, Biochemical principles,
concepts and technologies become increasingly
important for :
1. Diagnosis/understanding of disease
2. Clinical treatment
3. Medical research.
Therefore :
It is very important that the medical study should include an
extensive study of biochemistry and demonstration of the
application of biochemistry to medicine.
The students often find difficulty to correlate biochemistry to
the other disciplines.
E.g :
Applyng the biochemical concepts to the functioning of the
body as a whole ; and thus the application of boichemical
concepts to the pathogenesis of disease.
To overcome these problems the biochemical course will be
discussed in several essential topics, namely :

1. The biochemistry of the cell metabolism.

Incl.role of subcellular organelles : peroxisome,
lysosome, nucleus, mitochondria, etc.
2. The biochemistry of the body as a whole.
Incl. Metabolism of energy, digestion and absorption of
foodstuffs, hormones, electrolytes etc.

3. Specialized metabolism in tissues of the body.incl.

Metab of blood,metab of iron, blood clotting, functions
of the kidney, the muscle,the brain,the CNS.
Lanjutan

4. Application of biochemistry to environmental hazards.

Incl.xenobiotics, chemical carcinogenesis etc

5. Biochemical basis of diagnosis of the disease and its

treatment. Incl. Principles of methods used, biochemical
genetics, immunology, principles of chemotherapy etc.
Photometry

Basic principle : if white light is passed through a solution

containing a colored compound, certain wavelengths of
light are selectively absorbed.
The resultant colored is due to the transmitted light.
Photometry is a useful tool because many compounds of
biochemical interest absorb light in the uv, visible, or near
ir ranges.
Chromatography

Chromatography encompasses a variety of techniques that

resolve solutes by differential migration during passage a
porous medium.
In these processes, various solute components are separated
as a result of differential affinity of the components : for a
stationary phase ( a solid or liquid) or for a mobile phase
(a gas or liquid)
Radio Isotop Tracing

Basic principle : introduction of some unstable radio active

isotop into a spesific biologically important molecul
population allows tracing of the passage or conversion of
that radio activelly labelled molecul species in a
biological process or reaction
Electrophoresis
Basic principle : electrophoresis encompasses all operations
in which charged molecules migrate in electric fields
through solution.
Depending upon the presence or absence of a solid or matrix
supporting media to carry the electrophoretic system,
electrophoresis operations are generally classified into
two classes : solution electrophoresis and zonal
electrophoresis.
Centrifugation

Basic principle : rotation of an object about a central axis

generates a centrifugal force upon the object.
The larger the molecule, or the faster the centrifugation, or
the larger the axis of rotation, the greater the centrifugal
force and the rate of molecular or particle sedimentation.
BIOKIMIA MOLEKULER
Biokimia molekuler

1. Mempelajari proses Biokimia pada tingkat molekuler.

2. Mempelajari struktur dan fungsi molekul kehidupan.

Ciri-ciri suatu sel hidup,antara lain :

1. Ada proses replikasi (berkembang biak)
2. Ada proses metabolisme yang efisien
3. Ada proses mutasi.
Unsur dasar organisme hidup adalah :
C, H, O dan N
Di alam terdapat dalam bentuk :
CO2, H2O, NH3.

Unsur-unsur dasar tersebut akan membentuk molekul organik

(sub unit organik, monomer) yaitu :
1. Asam amino
2. Monosakarida
3. Nukleotida.
Monomer-monomer akan berkondensasi membentuk molekul
Lebih besar (Makromolekul) yaitu :
1. Protein
2. Polisakarida
3. Asam nukleat.

Catatan :
Dari unsur-unsur dasar dibentuk pula makromolekul Lipida.
Selanjutnya : makromolekul saling berikatan (secara non
kovalen) membentuk molekul yang lebih kompleks:
Supramolekul
Supramolekul antara lain :
 Membran plasma
 Kromosom
 Aparatus golgi
 Retikulum endoplasmik,dls.

Supramolekul selanjutnya akan membangun sel.

Jadi : supramolekul merupakan unit fungsional suatu sel.

(makromolekul) PROTEIN

1. Rangkaian daripada asam-asam amino

2. Dapat berfungsi struktural :bagian daripada membran
sel.
3. Dapat berfungsi fungsional : sebagai enzim, hormon,
reseptor, transporter.
(makromolekul) POLISAKARIDA

1. Polimer Monosakarida
2. Fungsi utama : sebagai komponen struktural membran /
dinding sel dan sebagai sumber energi.
3. Yang dijumpai terbanyak dialam : amilum dan selulosa.
Keduanya merupakan rangkaian sub unit D-glukosa.
(makromolekul) LIPIDA/LEMAK

1. Definisi : Zat yang larut dalam pelarut organik

( kloroform, benzena, dls.) dan sukar atau tidak dapat
larut dalam air.
2. Rangkaian daripada hidrokarbon
3. Fungsi sebagai komponen struktural membran sel dan
sebagai sumber energi.
Nukleotida dan Asam Nukleat
Nukleotida :
Merupakan pra zat untuk molekul asam nukleat

Terdiri atas 3 senyawa, yaitu :

1. Gugus D-Ribosa
2. Gugus fosfat
3. Basa Nitrogen organik.
Nukleotida menyusun asam nukleat sebagai berikut :
1. Sebagai Back Bone : molekul ribosa dan fosfat letaknya
bergantian.
2. Molekul Basa N terikat pada gula.
3. Ujung 5’ mempunyai gugus fosfat
4. Ujung 3’ mempunyai gugus OH bebas.
5. Terdapat polaritas 5’ ke 3’.
Molekul yang termasuk asam nukleat : DNA &RNA.
Perbedaannya
DNA RNA

Molekul gula Deoksi-Ribosa Ribosa

Molekul Basa A, G, C, T A, G, C,U

Nitrogen

Bentuk untai Ganda Tunggal

Struktur kimia Basa N dalam asam nukleat ada 2 macam :

1. PURIN : 2. PIRIMIDIN :
 A ( Adenin )  C ( Sitosin )
 G ( Guanin )  T ( Timin )
 U ( Urasil )
Struktur kimia gula dalam asam nukleat ada 2 macam :
1. RIBOSA
2. 2- DEOKSIRIBOSA

Basa N + Gula, disebut : NUKLEOSIDA

Basa N + Gula + Fosfat , disebut : NUKLEOTIDA

ASAM NUKLEAT
1. 99,9 % terdapat dalam nukleus.
2. 0,1% terdapat dalam organel lain.
3. Merupakan rangkaian nukleotida yang lurus.
ASAM AMINO
Fungsi :
1. Membangun molekul protein
2. Pra zat hormon.
3. Neurotransmitter
4. Pigmen
Di alam ada 20 macam asam amino :
Ala s/d Val bersifat Hidrofobik,sisanya Hidrofilik
1. Ala ( ALANIN ) 1. Arg ( ARGININ )
2. Ile ( ISOLEUSIN ) 2. Asn ( ASPARAGIN )
3. Asp ( ASAM ASPARTAT )
3. Leu ( LEUSIN )
4. Cys ( CISTEIN )
4. Met ( METIONIN ) 5. Glu ( ASAM GLUTAMAT )
5. Phe ( FENIL ALANIN ) 6. Gln ( GLUTAMIN )
6. Pro ( PROLIN ) 7. Gly ( GLISIN )
7. Trp ( TRIPTOFAN ) 8. His ( HISTIDIN )
9. Lys ( LISIN )
8. Tyr ( TIROSIN )
10. Ser ( SERIN )
9. Val ( VALIN ) 11. Thr ( TREONIN )
MONOSAKARIDA
Sakar artinya : Gula
Biasanya terdiri dari 3 unsur : C, H, dan O
Dengan perbandingan 1:2:1
Gula dengan 6 atom C : Heksosa
Gula dengan 5 atom C : Pentosa
Gula dengan 4 atom C : Tetrosa
Gula dengan 3 atom C : Triosa
Monosakarida berikatan satu sama lain melalui IKATAN
GLIKOSIDIK, membentuk molekul yang lebih kompleks :
Disakarida,Oligosakarida, Polisakarida.
(Lebih lanjut ttg ) LEMAK

Macam macam LEMAK yang terdapat dalam tubuh :

1. Asam Lemak
2. Triasilgliserol ( TAG )/Trigliserida
3. Glisero/ Fosfolipid
4. Kolesterol
5. Sfingolipid.
 ASAM LEMAK
Adalah Asam Karboksilat dengan rantai Hidrokarbon yang
panjang sebagai rantai samping.
O
CH2 C
CH2 OH
H3C CH2

Catatan : Dalam tubuh, jumlah atom C

Antara 14 – 20, dan genap.
Ada 2 macam Asam Lemak

1. Asam Lemak Jenuh (tidak memiliki ikatan rangkap)

2. Asam Lemak Tidak Jenuh (memiliki ikatan rangkap)
Misal :Asam Palmitoleat, Asam Oleat, Asam Linolenat,
Asam Arakhidonat.
Beberapa catatan penting mengenai Lemak

1. Sumber energi
2. Penting untuk proses absorpsi vitamin-vitamin yang
larut dalam lemak
3. Mengkonsumsi lemak sangat penting agar tubuh
mendapat asam lemak ESENSIAL.
ASAM LEMAK ESENSIAL

1. Adalah asam lemak yang mengandung ikatan rangkap

pada w-6 (misal : Asam Linoleat, Asam Arakhidonat)
dan ikatan rangkap pada w-3 (misal : Asam Linolenat)
2. Ikatan rangkap pada w-6 dan pada w-3 ini tidak dapat
disintesis dalam tubuh manusia.
TAG/ TRIGLISERIDA

1. Lipid yang terbanyak dalam tubuh

2. Bukan komponen utama membran biologis
3. Sumber energi
4. Disintesis dan disimpan dalam adiposit.
GLISEROFOSFOLIPID

1. Komponen utama membran biologis

2. Misal : Fosfatidil Kolin, Fosfatidil Etanolamin, Asam
Fosfatidat, Fosfatidil Gliserol.
SFINGOLIPID

1. Komponen membran biologis.

2. Misal : Spingomielin,Serebrosida,Gangliosida.

KOLESTEROL

1. Komponen membran biologis.

2. Suatu steroid
3. Pra-zat untuk asam empedu dan hormon-hormon steroid.
(lebih lanjut ttg) DNA dan RNA

DNA : 1. Merupakan faktor genetik

2. Merupakan “Blue Print” untuk sintesis protein.
3. Merupakan unit struktural /unit kimiawi daripada
GEN.

Catatan : GEN adalah unit fungsional materi genetik.

Catatan penting lain mengenai DNA

1. Satu organisme yang sama memiliki urutan basa yang

sama pada DNA nya.
2. Komposisi basa DNA suatu organisme tidak dipengaruhi
oleh umur, status gizi, lingkungan,dls.
Jadi : urutan basa relatif stabil. (pernyataan ini tidak
100% benar. Ingat : MUTASI SEL)
3. Urutan basa DNA, merupakan informasi genetik dari
setiap organisme.
RNA

1. Berperan penting pada biosintesis protein.

2. Single stranded
3. Ada 3 jenis : yaitu : tRNA, rRNA dan mRNA.
Fungsi masing-masing jenis RNA
tRNA : Mentransfer asam amino ke ribosom (yaitu tempat
sintesis protein)
rRNA : Bersama protein, membentuk ribosom.
mRNA : Mengkode (membawa pesan informasi dari DNA)
urutan asam amino daripada molekul protein.

Catatan : Informasi ini bersifat KOMPLEMENTER. Artinya :

C pada DNA --- dikode G pada mRNA
A pada DNA --- dikode U pada mRNA
MEMBRAN SUPRAMOLEKUL

Misal : Membran plasma, dinding sel.

Merupakan suatu MEMBRAN BIOLOGIS dengan sifat

Permeabel untuk zat-zat non polar (Hidrofobik) dan
Impermeabel untuk zat-zat polar (Hidrofilik).
KARAKTERISTIK MEMBRAN BIOLOGIS

1. Terdiri dari 2 lapis molekul Lipid (bilayer) dengan

bagian ekor non polar saling berhadapan ditengah
bilayer, dan bagian polar menghadap keluar.

2. Pada kedua lapis tersebut tertanam molekul-molekul

protein globuler secara tidak teratur.
3. Protein tersebut menonjol dipermukaan luar membran
secara asimetris.
4. Maka : tonjolan molekul-molekul protein pada membran
lipid bilayer itu tampak sebagai suatu “MOZAIK”.

Molekul lipid dan protein pada membran biologis berikatan

Secara non kovalen sehingga kedua jenis molekul tersebut
Secara individual dapat bergerak bebas sepanjang bidang
Membran. Dengan demikian lapisan membran menjadi
Bersifat encer (“FLUID”).
Maka : membran biologis akan menunjukkan gambaran
“MOZAIK FLUID”
Derajat “FLUIDITAS” suatu membran bergantung kepada :
1. Komposisi Lipid
2. Suhu.

KOMPOSISI LIPID.
Lebih dominan asam lemak jenuh,maka membran lebih Kaku.
Lebih dominan asam lemak tidak jenuh maka,membran lebih
Encer.

PENGARUH SUHU
Pada suhu rendah, pergerakan lipid relatif lebih sedikit &
Lapisan bilayer menjadi lebih PADAT.
Berdasarkan atas LOKASINYA, protein Membran
Plasma dapat dibagi menjadi :
1. Protein Integral (protein intrinsik). Protein membentang
dari lapisan yang satu kelapisan yang lain.
Protein ini sulit dipisahkan dari komponen lainnya.

2. Protein perifer (protein ekstrinsik). Protein terdapat pada

permukaan membran.
Protein ini mudah dipisahkan dari komponen lainnya.
Protein membran plasma dapat berfungsi sebagai :
1. Reseptor Sinyal

2. Enzim

3. Transporter / Carrier

4. Ion Channel.
RESEPTOR SINYAL

1. Memiliki “BINDING SITE” untuk sinyal-sinyal extra

sel (LIGANDS).

2. Bila LIGANDS berikatan dengan reseptornya, maka

protein reseptor akan mentransduksi sinyal ini menjadi
suatu “MESSENGER” untuk pesan Intra Sel.
TRANSPORTER
1. Dijumpai hampir disepanjang permukaan membran.
2. Mengangkut nutrien dari luar kedalam sel.
3. Mengangkut sisa-sisa metabolisme dari dalam keluar sel.

ION CHANNEL
1. Sejumlah reseptor pada membran, memiliki hubungan
dengan ion channel.
2. Bila reseptor berikatan dgn ligand-nya, maka ion channel
akan terbuka (atau sebaliknya akan tertutup).
Mekanisme Transport Melalui Membran ada 4 cara :
1. Simple Diffusion
2. Facilitated Diffusion (Passive Transport)
3. Active Transport
4. Ion Channeling

Simple Diffusion.
Difusi suatu zat berlangsung dari daerah dengan konsentrasi
tinggi kedaerah dengan konsentrasi lebih rendah ; sampai
dicapai keseimbangan.
Contoh : H2O, O2, N2, CH4.
FACILITATED DIFFUSION (TRANSPORT PASIF).
Difusi berlangsung dengan bantuan suatu protein spesifik
(Transporter, Permease), Mengikuti gradien konsentrasi.
Contoh : Transport Glukosa melalui membran sel darah
aktif.

TRANSPORT AKTIF.
Transport melawan gradien konsentrasi, dan memerlukan
energi.
Contoh : Trnasport K+, Na+, Ca++, Laktosa.
ION CHANNELING

1. Dijumpai antara lain pada membran plasma sel-sel

neuron dan sel-sel otot.
2. Bila ada rangsangan pada sel neuron/ sel otot maka
terjadi perubahan potensial elektrik pada membran
plasma sel sehingga terjadi pembukaan atau penutupan
ion channel.
ORGANEL
Definisi : organel adalah bagian daripada sel yang diselimuti
membran.
Maka, sesuai dengan definisi,pembicaraan tentang organel
termasuk pula : Membran Sel, Sitosol, & “Cytoskeleton”.
Catatan : Cytoskeleton adalah network daripada filamen-
filemen yang mengisi ruang sitosol.
Filamen-filamen itu akan mengikat organel-organel
ditempatnya.
PERBEDAAN PROKARIOT & EUKARIOT.
PROKARIOT EUKARIOT
nukleus Tidak ada ada
Membran sel ada ada
mitokondria Tidak ada ada
E.R Tidak ada ada
ribosom ada ada
 Air

Mikro dan makromineral

AIR
Merupakan unsur yang paling dominan dalam tubuh.
( lebih dari 65% bagian tubuh terdiri dari air ).

SUMBER AIR TUBUH

1. Dari makanan dan minuman (per oral)
2. Dari hasil metabolisme dalam tubuh
3. Per enteral (infus, tranfusi, dls)
Air tubuh dibuang melalui :
1. Urine
2. Faeces
3. Paru-paru
4. Kulit.

STRUKTUR AIR
Air merupakan molekul yang POLAR : terdiri dari :
2 atom H+ dan 1 atom O-
O-

H+ H+
Molekul air berinteraksi satu sama lain melalui IKATAN
HIDROGEN
H O
H
O H
H O H
H H O
SIFAT AIR H
1. Zat yang reaktif
2. Karena merupakan molekul polar,maka ia sangat
potensial sebagai zat pelarut yang universal.
PRINSIP AIR SEBAGAI PELARUT
Air menyelimuti gugus yang bermuatan,
Sehingga interaksi antar molekul dihambat
(disebut : zat tersebut terlarut)
H O
H
O O H H

H + H H - H
O O O
H H H H
AIR BERPOTENSI SEBAGAI PELARUT
UNIVERSAL.
Sebab : air dapat berinteraksi dengan molekul-molekul
karbohidrat,lemak, dan protein melalui ikatan Hidrogen.
1. Molekul air dengan gugus Hidroksil.
misal : pada molekul karbohidrat.

R
R O H O
H H O
H
2. Molekul air dengan gugus keto.
Misal : pada molekul karbohidrat.
R H H
C O
H O H
R’ O
3. Molekul air dengan gugus karboksil.
Misal : pada molekul lemak.
H O
O
H O H
C
R H
O H H
O
H
4. Molekul air dengan gugus amino.
Misal pada molekul protein.

H
H O
H
R N
H
O
H H
Reaksi air dengan suatu zat disebut :HIDROLISIS, yang
Mengakibatkan suatu zat yang kompleks terurai menjadi zat
yang lebih sederhana.
Misal :
ENZIM
1. Sukrosa + H2O G.I. Glukosa + Fruktosa

ENZIM
2. Lemak + H2O Gliserol + Asam lemak
G.I.
ENZIM
3. Protein + H2O G.I. Asam amino
FUNGSI AIR DALAM TUBUH
1. Membuat zat-zat didalam sel menjadi dalam bentuk
terlarut, sehingga reaksi antar zat menjadi lebih mudah.

2. Tanpa air,proses metabolisme menjadi sukar/tidak

berlangsung. Jadi air merupakan katalisator.

3. Sebagai alat transport untuk membawa nutrient kedalam

jaringan,dan membawa sampah-sampah hasil
metabolisme keluar jaringan.
4. Regulator suhu tubuh.
Air bersirkulasi keseluruh tubuh, sehingga menyamakan
suhu diseluruh bagian tubuh.

5. Dengan air, zat-zat anorganik menjadi dalam bentuk ion,

sehingga lebih mudah digunakan oleh tubuh.

6. Air memiliki tegangan permukaan yang cukup tinggi

sehingga air akan mengangkat zat-zat kepermukaan.
Akibatnya : zat-zat tersebut lebih mudah
diangkut/dibuang/dicerna oleh enzim.
MINERAL
Tubuh mengandung (dalam % berat) :
Oksigen 65%
Karbon 18%
Hidrogen 10%
Nitrogen 3%
Kalsium 1,5%
Fosfor 1%
Elemen lain 1,5% (K,Na,Cl,dls)
Elemen/mineral yang penting untuk tubuh antara lain :
K,Na,Cl,Ca,P,Fe,I,F,Co.

Berdasarkan atas kebutuhannya per hari,mineral dibagi atas :

1. MAKRO MINERAL
Dibutuhkan lebih dari 100mg/hari.
Contoh : Ca,P,Na,K,Cl,Mg.
2. MIKRO MINERAL
Dibutuhkan kurang dari 100mg/hari.
Contoh : Cr,Co,Cu,I,Fe,Mn,Mo,Se,Si,Zn,F.
KALSIUM (Ca)
Merupakan unsur pada tulang dan gigi.
Turut mengatur fungsi syaraf dan otot.
Absorpsinya membutuhkan “Calcium Binding
Protein”,dikontrol oleh vit.D, Parathormon, Calcitonin,dls.

FOSFOR (P)
Merupakan unsur pada tulang, gigi, ATP, asam nukleat.
Absorpsinya dikontrol Vit.D
NATRIUM
Kation utama dalam cairan ekstra sel.
Mengatur volume plasma.
Mengatur keseimbangan asam- basa
Mengatur fungsi syaraf dan otot.
Aktivator untuk enzim Na+ / K+ -ATP ASE.

KALIUM
Kation utama dalam cairan intra sel.
Mengatur fungsi syaraf dan otot.
Aktivator untuk enzim Na+ /K+ -ATP ASE.
KLORIDA
Mengatur balans cairan tubuh dan elektrolit.
Unsur cairan dan getah lambung.

MAGNESIUM
Unsur pada tulang dan gigi.
Kofaktor untuk enzim kinase.

KOBALT
Unsur pada vitamin B12.
TEMBAGA (Cu)
Unsur pada enzim oksidase.
Berperan pada absorpsi Fe.

JODIUM
Unsur pada hormon Thyroxine & Triiodothyroxine

BESI
Unsur pada enzim-enzim yang mengandung Heme (misal :
hemoglobin, Sitokrom,dls.)
MOLIBDENUM (Mo)
Unsur pada enzim-enzim oksidase

MANGAN (Mn)
Kofaktor untuk enzim Hidrolase, Dekarboksilase,Transferase.
Berperan pada sintesis Glikoprotein & Proteoglikan.

SELENIUM (Se)
Unsur pada Glutathion Peroksidase.
SILIKON (Si)
Berperan pada kalsifikasi tulang.

SENG (Zn)
Kofaktor untuk enzim LDH, Alkalifosfatase,Karbonik
anhidrase, dls.

FLUORIDA (F)
Meningkatkan pengerasan tulang dan gigi.
ENZYMES
ENZYMES

What are Enzymes ?

They are Biological catalyst.
They act at very low concentration and increase the
rate of chemical reactions.
Most of the Enzymes (not all) are proteins. Then, it
can be destroyed by heat, by strong Acid,or by
strong Alkalies.
Enzymes convert substrates into products.
SOME OTHER POINTS OF ENZYMES
1. They are produced by living cells. But, its
activities are not depend on the cells. Then,
Enzymes can work ex vivo / in vitro.
2. The presence of non protein moieties (called :Co
Factor/Co Enzymes/Prosthetic groups) is
requiered for the activation of the enzyme.
But, some of the enzymes (e.g :Pepsin &
Tripsin) need no requierement of Co Enzyme.
Enzymes molecule consists of Apo Enzyme & non
protein moiety, Co Enzyme.

CO ENZYME
(NON PROTEIN)

APO ENZYME
(PROTEIN)

HOLO ENZYME
 Apo Enzyme : An enzyme or a part of an Enzyme
that consist of Polypeptide chains
alone, lacking required non protein
Co Factors.

 Holo Enzyme : An Enzyme that has all component

parts, including Apo Enzyme &
Co Enzyme.
An Enzyme molecule is often very much larger than
a molecule of its substrate : have molecular weights
ranging from 10.000 to milions, whereas substrate
are usually in the hunderds.

Mostly, anyone enzyme will act only no one

substrate it show specificity.
An Enzyme molecule has active group ( Functional
Group ) which attacks the substrate molecule.

This substrate molecule fit on to the enzyme at a

particular site,called : the active site or Binding site
or Catalytic site.
Functional group

One of the groups of atoms that give rise to

the characteristic reactions of organic compounds.
Active Site

The part of an enzyme in which the substrate binds

and at which the reaction takes place.
The architecture of the active site
The active site consists of a definite arrangement of
the amino acid side chains which are responsible for
the catalytic activity of the enzyme.

An enzyme molecule consists of polypeptide chains

which usually form Secondary, Tertiaty, or
Quaternary structure.
3D – Structure of enzyme molecule
“Active Site”
(Tempat Beraksinya E – S)
The interaction between enzyme & substrate can be
explained by two models.
1. Fischer Lock & Key hypothesis.
The Active site has rigid structural features
which are complementary to the substrate.

2. Koshland induced fit hypothesis

The Active site is flexible, possesing a structure
complementary to that of substrate only when
the substrate is bound to the enzyme.
1. FISHER LOCK & KEY MODEL

a b c

+
a Es - Complex
b c
E
Active site Is Riggid
2. KOSHLAND INDUCED FIT MODEL

a b c

+
a Es - Complex
b c
E

Active site Is Flexible

These models explain some aspects of enzyme
specificity.

That is :
Enzyme exhibit chemical and Stereochemical
specificity.
Enzymes Exhibit Specificity, because

 The conformation of the complex protein

molecule.

 The uniqueness of its active site

 The structural configuration of the substrate

molecule.
Chemical Specificity
Can be divided into two types of specificity
1. Group Specifity.
Enz. Act on several different but closely related
substrates.
E.G. : Alcohol Dehydrogenases catalyse the oxidation of
a variety of alcohols.
2. Absolute Specificity.
Enz. Act only one particular substrate.
E.G. : Glucokinase catalyse the transfer of phosphate
from ATP only to glucose.
 STEREOCHEMICAL SPECIFICITY.

Enz. Will act on substrate (S) with specific

stereochemical form.
The naming and the classification of enzymes.

The naming of enzymes.

The names of enzymes usually indicate the substrate
Involved (with the ending : - ASE)

The classification of enzymes.

The E.C. of I.U.B. divided enzymes into six main classes, on

the basis of the reaction catalyzed.
 The classification of enzymes
Enzyme Class Type of reaction catalyzed
1. Oxidoreductases Oxidation/Reduction reactions

2. Transferases Transfer of an atom or group between two molecules.

3. Hydrolases Hydrolysis reactions

4. Lyases Removal of a group from substrate.

5. Isomerases Isomerisate reactions.

6. Ligases The synthetic joining of two molecules coupled with

the breakdown of pyrophosphate bond in nucleotide
triphos phate.
Enzimes are affected by several factors. These are :
1. Temperature
2. pH
3. The concentration of the enzyme
4. The concentration of the substrate
5. The presence of inhibitors
6. The presence of the other factors
ENZYME CATALYZED REACTIONS

E+S ES E+P

 The first step : the formation of es – complex.

 The formation of es leads to the formation of P.
 The E is regeneration at the end of the reaction.
The effect of temperature

The rates of the enzymatic reactions increase with

increasing temperature, until the enzyme is
destroyed ( denatured ) and catalytic activity is
lost.
 The effect of pH.
o By changing of pH, the tertiary structure of the
enzyme is disrupted. Then, the enzyme denatured.
The effect of enzyme concentration
 If the amount of enzyme in a reaction is doubled,
the amount of substrate converted to product is
doubled
The effect of substrate concentration
 Doubling of the substrate concentration, doubles the
reaction rates ( while the enzyme concentration is kept
constant )
 Maximum velocity (V)

Zero-order kinetics
Phase II

Mixture of zero-and
V/2 First-order kinetics
Reaction rate

First-order kinetics
Phase I

Km
Substrate Concentration

Figure 7-2
Effect of substrate concentration on reaction rate, assuming that enzyme
concentration is constant.
The order of reaction
1. A first order reaction. Is one is proceed at a rate
proportional to the concentration of one reactant.
2. A second order reaction. --------- to the
concentration of two reactants.
3. A zero order reaction. Is one whose rate is
independent of the concentration of any of the
reactants.
Co Factors
Some enzyme (not all) need a non protein compound
in order to act. These compounds are called : Co Factors.

Two kinds of enzyme

catalyzed reactions

Without requiring Require the presence

co factors of co factors
Co factor
 Can be divided into three groups :
1. Prosthetic groups.
2. Co enzymes
3. Metal activators.
If this compound is tightly bound to the enzyme
molecule, this non protein part is called : the
prosthetic group.

If this compound is loosely bound to the

enzymes molecule, this part is called : the
co enzyme
Co Factor

Occurrence Hard to Easy to

dissociate dissociate

1.Organic Prosthetic group Co enzyme

2.Non organic Prosthetic Activators (Eg.

group(Eg.heavy Heavy metals)
metals)
Some important points of co enzymes
1. They are organic compounds required by
enzymes for catalytic activity.
2. They are often vitamins or derivatives of
vitamins.
3. Sometime they can act as catalysts in the
absence of the enzymes
4. They form an integral part of the active site of
the enzimes.
Co enzymes are often derivatives of B-complex
vitamins. B-complex vitamins :
1. Thiamine 8. Inositol
(aneurin,vit B1) 9. Choline
2. Lipoic acid 10. Para amino benzoid
3. Riboflavin (vit.B2) acid ( PABA )
4. Niacin (nicotinic ac.) 11. Folic acid
5. Pyridoxine ( vit.B6) 12. Cobamide (vit.B12)
6. Pantothenic acid 13. Carnithine.
7. Biotin
Co Enzymes Function As Group Transfer Reagents :

D-G CO.E A- G

D CO.E-G A

D : Donor
G : Group Transfer
C : Acceptor
From the structural and physiological point of view,
there is no similarity among the member of B-
complex vitamins.

The only similarity is :

Almost all of them function as the co
enzymes.
Therefore, co enzymes can be classified base on the
Group whose transfer they facilitate :
1. For transfer of groups other than hydrogen-sugar
phosphates : CoA.SH (transf.acyl group)
Thiamin pyrophosphate (--Aldehyde gr.)
Folate coenzymes (--C1 gr.)
Biotin (--CO2)
Cobamide coenzymes (--Alkyl gr.)
Lipoic acid (--Acyl gr.)
2. For transfer of Hydrogen :
NAD+, NADP+
FMN, FAD
Coenzymes Q
 Some co enzymes as derivative of B-complex
vitamins.
Co enzyme : Derivative of vitamin :
Biocytin Biotin
Cobamide Cobalamine (B12)
FH4 Folic Acid
Nicotinamide Nicotinamide
Pyridoxal phosph. Pyridoxine (B6)
Thiaminpyrophosphat Thiamin (B1)
Flavin Coenzymes Riboflavin (B2)
CoA.SH Pantothenic Acid
Lipoic Acid Lipoic Acid
NAD+ & NADP+
 Derivative of Nicotinic Acid
 Act on Ox/Red – reactions (that is on H+ and
electron transfer) on : Pyruvate metabolism, Lipid
metabolism, Glycolysis,etc.
 Mostly :
NAD act on catabolic metabolism
NADP act on anabolic metabolism.
Flavin Nucleotide (FMN & FAD)
 They are derivative of Riboflavin
 They act on oxidation – Reduction Reactions

Co enzyme A ( CoA-SH )
 Contains Pantothenic Acid
 Act on several metabolic processes :

Bio energetic metabolism, Lipid metabolism,

Carbohydrate metabolism etc.
FH4 ( Tetrahydrofolate )
 Derivatives of Folic Acid
 Acts on : single Carbon metabolism and
Erythropoesis.

TPP ( Thiamin Pyrophosphate )

 Derivatives of thiamin
 Acts on : Oxydative-Phosphorylation process on
Bioenergetic metabolism, and on HMP ( Hexose
Monophosphate ) shunt.
Cobamide
 Important co enzyme on : Erythropoesis, nucleate
synthesis and Protein synthesis.

Pyridoxal Phosphate
 Derivatives of Pyridoxine
 Acts on decarboxylation and transamination
processes.
Enzyme Assay.
We can measure the concentration of the
enzyme,indirectly, by its activity.

The amount of activity is expressed as :

The amount of substrate converted to product by a
known amount of enzyme in a known period of time.
The activity of enzyme is often expressed in
international unit ( I.U )
 It is defined as :
The amount of enzyme causing loss of one
micromole of the substrate per minute under
specified conditions.
The activity of enzyme can be expressed also in :
spesific activity.
 It is defined as :
Units of enzyme activity related to the total
protein content of the sample being assayed.
( it is expressed as : one unit/ mg protein )
Inhibitors
The effect of inhibitors on enzyme action.
There are two main classes of inhibitors of enzyme
Action :
1. Irreversible inhibitors
2. Reversible inhibitors
1. Irreversible inhibitors
When the enzyme is exposed to the inhibitor, it
forms a covalent bond which is very difficult to be
Broken. Then, the E1-complex is permanently
Inactive.
E+I EI E+P
E.G. : DIPF ( Diisopropylphosphofluoridate )
Potent nerve gas.
2. Reversible inhibitors
When the enzyme is exposed to the inhibitor, it
forms a loosely bond which easily dissociates from
the enzyme, leaving its activity unimpaired.

E+I E1 E+P
Reversible inhibitors are subdivided into two groups
1. Competitive inhibitors
2. Non Competitive inhibitors
1. Competitive inhibitors
 The inhibitors compete with the substrate for the
same active site on the enzyme molecule and
prevent binding of substrate, or put differently,
the enzyme molecule recognizes the inhibitor as a
substrate, but is unable to convert it to product.
 gambar

I S

Binding Site (For I and S)

E

Competitive Inhibition can be overcome by high

concentration of substrate sufficiently.
2. Non Competitive inhibitors
 The inhibitors bind to a site other than the
substrate binding site on the enzyme.
It result in changing the structure of the enzyme.
gambar

I S

E Binding Site For S

(Active Site)

Binding Site For I.

(Called : Allosteric Site)

Non Competitive Inhibition cannot be overcome by

increasing the substrate concentration.
Uncompetitive Inhibitors
The inhibitors bind to a site other than the substrate
binding site on the ES Complex.

E+S ES E+P
+
I

EIS

E
+
P
Kinetics of the enzyme catalized
 Kinetics is defined as :
The study of reaction rates and the factors
influencing them.
All kinetic is based on : the law of mass action
Its state : the rate of a reaction is proporsional to the
concentration of each reactant.

From the law of mass action developed the concept

of the order of reaction.
For most of the enzyme, the rate of catalysis varies
with the substrate concentration.

E+S ES E+P
The rate of the formation of the product is expressed
by : the Michaelis Menten Equation.

Vmax . S
V=
S + Km

V : observed velocity at given substrate

concentration.
Km : Michaelis constant. Expressed in units of
concentration (Mol/liter).
Vmax : the maximum velocity at saturating
concentration of substrate.
Km ( Michaelis constant ) :
A numerical value for the strength of binding of a
substrate to an enzyme.

The important of the Km.

Km is the measure of the strength of the ES
Complex :
1. A high Km indicates weak binding.
2. A low Km indicates strong binding
 It can also be interpreted as :
1. A high Km indicates the turnover number
(T.O.N) of the enzyme is high.
2. A low Km indicates the T.O.N of the enzyme is
low.

T.O.N is :
The number of substrate molecules converted into
product by an enzyme molecule in a unit time when
the enzyme is fully saturated with substrate.
In vivo regulation of the catalytic activity of the
Enzyme.
1. By allosteric interaction.
The Enzyme that catalyzes the first step in a
biosythetic pathway is inhibited by the ultimate
product.
2. By regulatory proteins ( calmodulin ). These
protein can either stimulate or inhibit.
3. By covalent modification.
Phosphorylation – Dephosphorylation.
Allosteric enzyme

Describe multi sub unit proteins in which

conformational change in one sub unit induces a
change in another sub unit.
End products repress enzyme synthesis :
High intracellular levels of a product (or a
metabolite) can block synthesis of the enzymes
involved in its own biosynthesis.(“Repression”)

Conversely,exhaustion of an intermediate will cause

the enzyme biosyntesis takes place
again.(“Derepression”)
This mechanism is called : (“Product Feedback
Repression”)
Calmodulin
 Together with Ca++, it can stimulate
phosphorylation via a Ca++/calmodulin
dependent multiprotein kinase.
Regulation of enzyme activity by phosphorylation-
dephosphorylation.
 Reversible modulation of the catalytic activity of
enzyme will take place by covalent attachement
of a phosphate group to one or more Ser, Thr or
his residues.
Example :

ATP ADP

Kinase

ENZ-Ser --OH ENZ-Ser -- O-PO3=

Phosphatase

Pi H2O
 Depending on the enzyme concerned, the
phospho- or the dephospho enzyme may be the
more active catalyst.
 Enz (S) that undergo covalent modification with
such modulation of their activity are termed :
“Interconvertible enzyme”.
Clinical Diagnosis
The possibility that enzymes can be used as
markers for disease is based on :
1. Some enzymes are found only in specific
or in a limited number or tissues.
2. Many enzymes arising from a variety of
source can be detected in plasma or
serum.
3. Therefore, an increase of any tissue
specific enzyme in the blood indicates
some kind of tissue damage.
4. Some enzymes are secreted into the
plasma and function there.(called :
functional plasma enzymes )
For this group
Injury to the organ (S) producing these enzymes will
cause a decrease or even a lost in activity.
E.g :
o Coagulation enzymes (thrombin etc)

o cholinesterase
5. Some are intracellular and function there.
(termed : “non functional plasma enzymes”)
o For this group :
they are only found in plasma in significant
quantities when cells are damaged as
aconsequent of the leaky cell membranes.
Thus; the assay of the enzyme activity in this group
will be related to the number of cells damaged.
 These enzymes are useful in clinical
diagnosis, both in the initial stage of the
disease, and during the period of recovery,
and repair.
Distribution of enzymes in tissues and serum
patterns.
 If the concentration of a particular enzyme in a
tissue is normally high, then a damage to a tissue
will cause release into plasma of a high
concentration of this enzyme
 And vice versa
 The nature of the enzyme released as the
consequence of damage depends on its
subcellular localisation.
 If the damage is minimal,only cytoplasmic
enzymes will leak out.
 If the damage is extensive, mitochondrial
enzymes will also be released.
 gambar
a b c

Slight
Damage

Severe
Damage
Cytoplasm
Mitochondria
Nucleus

Fig.39.7. Comparison of effect of slight and severe

damage on enzyme release.
(a) Glutamate dehydrogenase : (b) Glutamate – Pyruvate
transaminase : (c) Glutamate – oxaloacetate transaminase.
Patterns of activities in human organs.
Examples :
1. Glutamate dehidrogenase can be found in
liver,brain,heart,eritrhrocyte etc. But, this
enzyme is much more active in liver than in
heart or in lung.
2. Lactate dehydrogenase is found in a great
amount in muscle and in liver, but is very
minimal in lung.
Therefore :
Determination of several enzymes will be useful
to provide information about the site and extent
of pathological change.
 Gambar GLDH
38

14

12
Activity U/g organ

10

6 4.4
3.2
4 2.5

1.1
2 0.5
< 0. 01

Liver Kidney Brain Lung Heart Skeletal Erythrocyte

Muscle

Fig.39.5. Glutamate dehydrogenase activities in human organs.

 Gambar LDH
180

160

140

120
Activity U/g organ

100

80

60

40

20

Skeletal Liver Heart Kidney Lymph Pancreas Lung

nodes
Erythrocytes

Fig.39.5. Lactate dehydrogenase activities in human organs.

Example of the use of serum enzymes in diagnosis.
Enzyme Disease
Glutamate oxaloacetate Myocardial infarction
transaminase (SGOT)
Glutamate pyruvate Viral hepatitis
transaminase (SGPT)
Amylase, lipase Acute pancreatitis
Creatine kinase Muscle disease
Acid phosphatase Prostate carcinoma
Alkali phosphatase Bone disease
The fate of the plasma enzymes
Following release into the plasma, the enzymes will
be eliminated :
1. Excreted via urine (some enzymes with small
m.w, like amylase)
2. The majority of enzymes (with high m.w) will
be degraded via normal catabolic pathways at
very different rates
Half life of several plasma enzymes.
Enzyme Half life
GOT Circa 20 h
GPT Circa 50 h
GLDH Circa 18 h
LDH Circa 140 h
CPK Circa 15 h
Cholinesterase Circa 10 d
Lipase Circa 5 h
 Iso Enzymes
They are polymeric enzymes, which catalyze the
same chemical reaction, but migrate differently
on electrophoresis.
 The mechanism for the formation of iso enz. Is :
The arrangement of subunits arising from two
different genetic loci in different combinations to
form. The active polymeric enzyme.
 Enzyme isoform (isoenzyme) is an enzyme that
can exist in different forms in different tissues.
LDH
 A tetrameric enzyme
 Only two distinct subunits have been
elucidated, I.E. : H (Heart type) and
(Muscle type).
 These two subunits are combined in five
different types :
Type composition location
LDH1 HHHH Myocard& RBC
LDH2 HHHM Myocard& RBC
LDH3 HHMM Brain & Kidney
LDH4 HMMM Brain & Kidney
LDH5 MMMM Liver & Skeletal
muscle
Some enzyme which posses isoform :
 Lactate Dehydrogenase ( LDH )
 Creatine Kinase ( CK )
 Phosphofructokinase
Phosphofructokinase
 A tetrameric enzyme
 Consists of two types of subunits : M
(Muscle) and L (Liver type).

These two types are combined to form five

tetramer : M4,M3L,M2L2,ML3 & L4
Creatine Kinase (CK)
 A dimer enzyme
 Consists of two types of subunits I.E : M
(Muscle type) and B (Brain type).
These two subunits are combined in three
different types :
Type Composition Location

CK1 BB Mostly in brain

CK2 MB Only in
myocardium
CK3 MM Mostly in
skeletal muscle
 Relationship between genetic
abnormalities and the enzyme activities.
 Genetic defects could have significant
effects on the synthesis and activities of
the enzymes which will emerge to the
illnesses
Examples :
1. Deficiency of anti elastase will cause
destructive lung disease.
2. Defect of activity of antihaemophilic
factor ( factor VIII ) will cause
Haemophilia.
3. Defect of activity of tyrosine kinase will
cause a disturbance of the growth and
differentiation of the cells, which will lead
to the pathogenesis of carcinoma mammae
 Enzymes can function as therapeutic agent
Example :1. Streptokinase is applied in
thrombosis mode of action :

Streptokinase

Plasminogen Plasmin

fibrin More Soluble

Components.
2. Asparaginase is applied in Leucemia. Mode
of action :

Asparagin Asparaginase Decrease of

(Nutrition factor Asparagin
for tumour cells) concentration.

Decrease of asparagin concen. Leads to

decrease of tumour cells viability.
Another covalent modification control
(instead of phosphorylation ):
 ADP- Ribosylation
 Nucleotidylation
 Methylation
What use is the Km ?
1. It is a characteristic of an enzyme (E.G. like the
boiling point of a liquid). But note that mora
than one enzyme may have the same Km.
2. It tells us about the affinity of the enzyme for the
substrate. An enzyme which has a low Km has a
high affinity for its substrate, because it becomes
saturated (works at maximum rate) at a low
substrate concentration.
3. Enzymes with low Km (high affinity) are highly
important in metabolism : low Km values are of
the order of 10 p-6 M or event lower (10 p-7 M
or 10 p-8 M). Enzymes with high Km (low
affinity) are less important in metabolism : 10 p-
4 M or event higher.
4. When expressing enzyme activity in I.U.’s,the
measurements are made at optimum pH and at a
standard temperature. They must also be made at
saturating substrate concent. For obvious
reasons : the same enzyme could give very diff.
 Values if the measurements were made on
different parts of the Michaelis curve.
5. If an inhibitor is acting on the enzyme, its effect
upon the Km tells us something important about
its mode of action (E.G.irreversible inhibition,
reversible inhibition, competitive inhibition etc.)
 Note : not all of the enzymes are protein :
E.G : RNA molecules (I.E. L-19 RNA)
function as Ribonuklease and as RNA-
Polymerase.
L-19 RNA has characteristics as an enzyme :
1. Has a substrate spesificity (I.E. on
oligoribonucleotide)
2. Has a saturation phenomenon
3. It follows michaelis menten kinetic.