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PENGANTAR ILMU BIOKIMIA.
Oleh
H.Mohammad Hanafi,MBBS, dr, MS.
Pensiunan Dosen Ilmu Biokimia
FK UAIR
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Ilmu Biokimia :
mempelajari macam-macam molekul
yang ada di dalam sel mahluk hidup
dan organisme
dan reaksi-reaksi kimia
yang terjadi diantara molekul-molekul tersebut.
Ilmu Biokimia dapat  perkawinan
antara ilmu kimia dan ilmu biologi.
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Ilmu yang memperhatikan
(concerned) dengan ilmu kimia dasar
dari kehidupan
(the chemical basis of life)
Two notable breakthroughs in the history of biochemistry
(1) Discovery of the role of enzymes as
catalysts
(2) Identification of nucleic acids as
information molecules
Flow of information: from nucleic acids to proteins
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DNA
RNA
Protein
Manusia  organ
( otak, mata, organ-organ pencernaan,
paru, jantung, ginjal,
organ-organ reproduksi, dan lainnya)
Organ  jaringan,
Jaringan  sel
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Organism, Organ, Cell
Organism
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The Cell
The ER modifies proteins, makes macromolecules,
and transfers substances throughout the cell.
Nucleus only in
eukaryotic cells.
Contains most of the
cell's genetic material.
Ribosome translates
mRNA into a polypeptide
chain (e.g., a protein).
Mitochondrion
manufactures adenosine
triphosphate (ATP), which
is used as a source of
energy.
• circa 100 trillion (1014) cells in a human organism
• 200 different forms of cells
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Fig 1.15 (a) Eukaryotic cell (animal)
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Structure of a biological membrane
• A lipid bilayer with associated proteins
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Di dalam sel ada organel (mitokhondria dll),
supra molekul (ribosom, enzim),
makromulekul (polisakarida,
polipeptida),
building block (asam amino,
glukosa, asam lemak,
deoksinukleotida,
ribonukleotida dll)
metabolit (asam piruvat, asam sitrat,
asetoasetil-KoA, asam urat dll).
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Precursor adalah suatu
senyawa yang dianggap dapat
sebagai tanda
adanya kehidupan di suatu
planet
Bahannya yg dianalisa
adalah udara 
(H2O, N2, CO2, NH3 dan O2)
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Manusia tersusun atas :
(1)bahan organik,
protein 15%,
lipid 15%
dan karbohidrat 5%,
(2) bahan anorganik 5% berat badan.
(a) kation, Na+, K, Ca2+,
Mg2+, Fe, Zn2+, Cu2+ dll.
(b) anion Cl-, HCO3-, SO42-,
H2P2O42- dll.
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Karbohidrat
Senyawa polihidroksi aldehid
atau polihidroksi keton.
(1). Monosakarida (Cn H2n On ):
Jumlah atom CAldehid
Keton
Triose (3)
Gliserose Dihidroksi aseton
Tetrose (4)
Eritrose
Eritrulose
Pentose (5)
Ribose
Ribulose
Heksose (6) Glukose
Fruktose
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1
H
HO
H
H
2
3
4
5
6
CHO
C
OH
C
H
C
OH (linear form)
C
OH
D-glucose
CH2OH
6 CH2OH
6 CH2OH
5
H
4
OH
H
OH
3
H
O
H
H
1
2
OH
-D-glucose
OH
5
H
4
OH
H
OH
3
H
O
OH
H
1
2
H
OH
-D-glucose
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16
Disakarida { Cn (H2O)n-1 }:
Sukrose (glukose dan fruktose)
Laktose (glukose dan galaktose)
Maltose (dua glukose)
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(3). Oligosakarida ( 4 – 10 mono sakarida )
(4). Polisakarida:
homopolisakarida, amilum, glikogen,
innulin, sellulose dan lainnya
heteropolisakarida, chitin, glikoprotein dll.
Amilum :
Amilose ± 20 %
Amilopektin ± 80%
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Amilose
19
20
CH2OH
CH2OH
O
H
H
OH
H
H
OH
H
O
OH
CH2OH
H
H
OH
H
H
OH
H
H
OH
CH2OH
O
H
OH
O
H
OH
H
H
O
O
H
OH
H
H
OH
H
O
glycogen
H
1
O
6 CH2
H 5
H
4 OH
3
H
CH2OH
O
H
2
OH
H
H
1
O
CH2OH
O
H
4 OH
H
H
H
H
O
OH
O
H
OH
H
H
OH
H
OH
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Glikogen
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Lipida
Senyawa yang larut dalam pelarut nonpolar.
(A). Lipida sederhana
1.triasil gliserol
2.lilin
(B). Lipida komplek
1.fosfolipid, lesitin (lechitine)
2.serebrosida, sphingosin
3.lipoprotein
(C). Turunan lipid
1.asam lemak
2.gliserol
3.steroid
4.keton bodies
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Triasil Gliserol
Fosfolipida
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Sphingosine
Ceramide
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Numerical
Symbol
Common
Name
Structure
14:0
Myristic acid
CH3(CH2)12COOH
16:0
Palmitic
acid
CH3(CH2)14COOH
16:1D9
Palmitoleic
acid
CH3(CH2)5C=C(CH2)7COOH
18:0
Stearic acid
CH3(CH2)16COOH
18:1D9
Oleic acid
CH3(CH2)7C=C(CH2)7COOH
18:2D9,12
Linoleic acid
CH3(CH2)4C=CCH2C=C(CH2)7COOH
18:3D9,12,15
Linolenic
acid
CH3CH2C=CCH2C=CCH2C=C(CH2)7COOH
20:4D5,8,11,14
Arachidonic
acid
CH3(CH2)3(CH2C=C)4(CH2)3COOH
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Contoh asam lemak tidak jenuh:
1.asam linoleat
( ω 6, 18:2; ∆9, 12 )
2.asam linolenat
( ω 3, 18:3; ∆9, 12,15 )
3.asam arakhidonat ( ω 6, 20:4; ∆5, 8, 11, 14 )
COOH
19 12 9
9,12
Asam linoleat ( 6, 18:2,  )
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Asam amino dan Protein
Senyawa yang mengandung gugus asam dan amino :
H
α
R-C-N H3+
H3+N-C-COOH
COOH
|
R
Asam amino esensial (tikus putih) :
Arginine (Arg=R), Histidine (His=H),
Isoleucine (Ileu=I), Leucine (Leu=L),
Lysine (Lys=K), Phenylalanine (Phe=F),
Methionine (Met=M), Threonine (Thr=T),
Tryptophan (Try=W) dan Valine (Val=V).
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Asam amino yang lain :
Glycine (Gly=G), Alanine (Ala=A),
Serine (Ser=S), Tyrosine (Tyr=Y),
Cysteine (Cys=C), Aspartic acid (Asp=D),
Asparagine (Asn=N), Glutamic acid (Glu=E),
Glutamine (Gln=Q), dan Proline (Pro=P).
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Name
1-letter code
Triplet
Glycine
G
GGT,GGC,GGA,GGG
Alanine
A
GCT,GCC,GCA,GCG
Valine
V
GTT,GTC,GTA,GTG
Leucine
L
TTG,TTA,CTT,CTC,CTA,CTG
Isoleucine
I
ATT,ATC,ATA
Histidine
H
CAT,CAC
Serine
S
TCT,TCC,TCA,TCG,AGT,AGC
Threonine
T
ACT,ACC,ACA,ACG
Cysteine
C
TGT,TGC
Methionine
M
ATG
Glutamic Acid
E
GAA,GAG
Aspartic Acid
D
GAT,GAC,AAT,AAC
Lysine
K
AAA,AAG
Arginine
R
CGT,CGC,CGA,CGG,AGA,AGG
Asparagine
N
AAT,AAC
Glutamine
Q
CAA,CAG
Phenylalanine
F
TTT,TTC
Tyrosine
Y
TAT,TAC
Tryptophan
W
TGG
Proline
P
CCT,CCC,CCA,CCG
Terminator (Stop)
*
TAA,TAG,TGA
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Asam amino dapat membentuk
polipeptida (protein) dengan ikatan peptida.
Pembagian protein :
(A).Protein sederhana:
albumin, globulin, kollagen,
histon da protamin
(B).Protein terkonyugasi,
nukleoprotein, glikoprotein,
lipoprotein, metaloprotein, dan lainnya
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Protein Structure
 Primary structure is the sequence of the
amino acids in the protein.
 A change in one amino acid can alter
the biochemical behavior of the protein.
 Secondary structure is the regular
arrangement of segments of protein.
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Proteins
Protein Structure
One common secondary
structure is the -helix.
Hydrogen bonds between
N-H bonds and carbonyl
groups hold the helix in
place.
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STRUKTUR SEKUNDER :
H H O
| | ||
–N–C–C–
|
CH2
|
S
ikatan
|
disulfida
S
|
CH2
|
–N–C–C–
| | ||
H H O
*  Helix
R
|
C–C–N–
|| | |
O H H
:
:
:
: ikatan
:
: Hidrogen
:
:
H H O
| | ||
–N–C–C
|
R
* Lain2 : * LIPIT  =  - PLEATED
* KUMPARAN ACAK = RANDOM COIL
Cys
– SH
Cys
– SH
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Proteins
Protein Structure
 Tertiary structure is the three
dimensional structure of the protein.
 Shape of the protein
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STRUKTUR TERSIER :
celah
aktif
E
Dari satu untai rantai polipeptida
monomer
- Contoh :
MIOGLOBIN (MYOGLOBINE)  MONOMER
- Struktur Tersier :
- IKATAN HIDROGEN
2 YG. LEMAH
IKATAN
2
- GAYA VAN DER WAALS
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Tertiary structure of proteins
catalase enzyme
Structure solved using Xray crystallography
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STRUKTUR KUARTERNER :
T.D. SATU UNTAI RANTAI POLIPEPTIDA

 MONOMER
PROTOMER

HANYA SAMPAI STRUKTUR TERSIER
 DIMER
subunit

 TETRAMER
subunit
TERMASUK STRUKTUR
KUARTERNER
 OLIGOMER
POLIMER
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STRUKTUR KUARTERNER :
 SATU MOLEKUL T.D. > 1 RANTAI PEPTIDA
 T.D. 2 SUBUNIT ATAU LEBIH
 1 SUBUNIT ~ 1 RANTAI PEPTIDA
 DIIKAT OLEH :
IKATAN2 YG
 IKATAN HIDROGEN
LEMAH Ikatan non Kovalen
 IKATAN ELEKTROSTATIK
 KEGUNAAN :
 SUPAYA MOLEKULNYA LEBIH STABIL
 UNTUK MENDAPAT FUNGSI TERTENTU
ENZIM
CELAH AKTIF
(ACTIVE SITE)
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Nucleic Acids
 Nucleic acids carry genetic information.
 DNA (deoxyribonucleic acids) have
molecular weights around 6 - 16  106
amu and are found inside the nucleus of
the cell.
 RNA (ribonucleic acids) have molecular
weights around 20,000 to 40,000 amu
and are found in the cytoplasm outside
the nucleus of the cell.
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Nucleic acids are made up of nucleotides.
There are three important parts to a nucleic
acid:
1 phosphoric acid unit,
2 five carbon sugar (e.g. deoxyribose),
and
3 nitrogen containing organic base (e.g.
adenine).
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Nucleic Acids
• Originally isolated from nuclei
• Two types
– Deoxyribonucleic acid (DNA)
• Passed from generation to generation
• Constitute genome/chromosomes/genes
• Contains instructions for making proteins
– Ribonucleic acid (RNA)
• Function in the synthesis of proteins coded by
DNA
• Several distinct types
• Make up the genomes of some viruses
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Nucleotide structure
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Purin
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Pirimidin
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NUKLEOSIDA
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Nukleosida yang lain
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Nucleotide
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Nukleotida
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Adenosine Triphosphate (ATP)
• Nitrogenous base (adenine), sugar (ribose)
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Deoxyadenylic Acid
FG25_030.JPG
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Structure of a Polynucleotide
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Nucleic Acids
 DNA
and RNA have different sugars
(dexoyribose vs. ribose).
 There are only five bases found in DNA and
RNA:
 adenine
(A),
 guanine (G),
 cytosine (C),
 thymine (T found in DNA only), and
 uracil (U found in RNA only).
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Nitrogen-Containing Bases
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Nucleic Acids
 DNA
consists
of
two
deoxyribonucleic acid strands
wound together in a double helix.
 The
phosphate chains are
wrapped around the outside of
the DNA molecule.
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•Complementary base
pairs are formed from
bases which optimize Hbonding: T and A or C and
G.
•The complementary base
pairs are held together by
hydrogen bonding.
•During cell division, the
DNA double helix
unwinds.
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Complementary Base Pairs
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 A new strand is formed when
bases
attach to each strand of the
unwinding double helix.
 Because of the optimized
hydrogen bonding, there is
only one location for each
base.
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•Therefore, the order of bases in the
new strand is the same as the order of
bases in the original strand.
•This is how genetic information is
preserved during cell division
•DNA structure provides us with the
understanding of how protein
synthesis occurs, how viruses infect
cells, and other biological problems
occur.
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FG25_032.JPG
DNA
Double
Helix
Wassalamua’alikum Wr. Wb.
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