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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

DNA RNA Protein

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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, CellOrganism

Organ

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The ER modifies proteins, makes macromolecules, and transfers substances throughout the cell.

Ribosome translates mRNA into a polypeptide chain (e.g., a protein).

Mitochondrion manufactures adenosine triphosphate (ATP), which is used as a source of energy.

The Cell

• circa 100 trillion (1014) cells in a human organism• 200 different forms of cells

Nucleus only in eukaryotic cells. Contains most of the cell's genetic material.

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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 planetBahannya 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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KarbohidratSenyawa polihidroksi aldehid atau polihidroksi keton.

(1). Monosakarida (Cn H2n On ): Jumlah atom CAldehid KetonTriose (3) Gliserose Dihidroksi asetonTetrose (4) Eritrose EritrulosePentose (5) Ribose RibuloseHeksose (6) Glukose Fruktose

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H O

OH

H

OHH

OH

CH2OH

H

OH

H H O

OH

H

OHH

OH

CH2OH

H

H

OH

-D-glucose -D-glucose

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4

5

6

1 1

6

5

4

3 2

H

CHO

C OH

C HHO

C OHH

C OHH

CH2OH

1

5

2

3

4

6

D-glucose (linear form)

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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

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H O

OH

H

OHH

OH

CH 2OH

HO H

H

OHH

OH

CH 2OH

H

O

HH H O

OH

OHH

OH

CH 2

HH H O

H

OHH

OH

CH 2OH

H

OH

HH O

OH

OHH

OH

CH 2OH

H

O

H

O

1 4

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H O

H

OHH

OH

CH 2OH

HH H O

H

OHH

OH

CH 2OH

HH

O1

OH

3

4

5

2

glycogen

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Glikogen

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LipidaSenyawa 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 lemak2.gliserol3.steroid4.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

16:0Palmitic

acidCH3(CH2)14COOH

16:19 Palmitoleic acid

CH3(CH2)5C=C(CH2)7COOH

18:0 Stearic acid CH3(CH2)16COOH

18:19 Oleic acid CH3(CH2)7C=C(CH2)7COOH

18:29,12 Linoleic acid CH3(CH2)4C=CCH2C=C(CH2)7COOH

18:39,12,15 Linolenic acid

CH3CH2C=CCH2C=CCH2C=C(CH2)7COOH

20:45,8,11,14 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 Asam linoleat ( 6, 18:2, 9,12 )

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Asam amino dan ProteinSenyawa 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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ProteinsProteinsProtein StructureProtein 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 | S | CH2

|– N – C – C – | | || H H O

ikatandisulfida

R | C – C – N – || | | O H H : : : : : : : : H H O | | ||– N – C – C | R

ikatan Hidrogen

* Lain2 : * LIPIT = - PLEATED * KUMPARAN ACAK = RANDOM COIL

Cys– SH

Cys– SH

* Helix

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ProteinsProteinsProtein StructureProtein Structure

Tertiary structure is the three dimensional structure of the protein.

Shape of the protein

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STRUKTUR TERSIER :

E

celahaktif

Dari satu untai rantai polipeptida monomer

- Contoh : MIOGLOBIN (MYOGLOBINE) MONOMER- Struktur Tersier :

- IKATAN HIDROGEN- GAYA2 VAN DER WAALS IKATAN2 YG. LEMAH

39Structure solved using Xray crystallography

Tertiary structure of proteins

catalase enzyme

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STRUKTUR KUARTERNER :

MONOMER

PROTOMER

DIMER

TETRAMER

OLIGOMERPOLIMER

subunit

subunit

TERMASUK STRUKTURKUARTERNER

T.D. SATU UNTAI RANTAI POLIPEPTIDA

HANYA SAMPAI STRUKTUR TERSIER

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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 :

IKATAN HIDROGEN IKATAN ELEKTROSTATIK

KEGUNAAN : SUPAYA MOLEKULNYA LEBIH STABIL UNTUK MENDAPAT FUNGSI TERTENTU

ENZIM

IKATAN2 YGLEMAH

CELAH AKTIF(ACTIVE SITE)

Ikatan non Kovalen

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Nucleic AcidsNucleic 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), and3 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

• 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 structureNucleotide 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

5353

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), anduracil (U found in RNA only).

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Nitrogen-Containing Bases

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Nucleic AcidsNucleic 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 H-bonding: 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.