PENGANTAR ILMU BIOKIMIA. Oleh H.Mohammad Hanafi,MBBS, dr, MS. Pensiunan Dosen Ilmu Biokimia FK UAIR

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.

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

Manusia  organ ( otak, mata, organ-organ pencernaan, paru, jantung, ginjal, organ-organ reproduksi, dan lainnya) Organ  jaringan, Jaringan  sel

Organism, Organ, Cell Organism Organ

The Cell circa 100 trillion (1014) cells in a human organism Nucleus only in eukaryotic cells. Contains most of the cell's genetic material. 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. circa 100 trillion (1014) cells in a human organism 200 different forms of cells

Fig 1.15 (a) Eukaryotic cell (animal)

Structure of a biological membrane A lipid bilayer with associated proteins

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).

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)

Manusia tersusun atas : 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.

Senyawa polihidroksi aldehid atau polihidroksi keton. Karbohidrat Senyawa polihidroksi aldehid atau polihidroksi keton. (1). Monosakarida (Cn H2n On ): Jumlah atom C Aldehid Keton Triose (3) Gliserose Dihidroksi aseton Tetrose (4) Eritrose Eritrulose Pentose (5) Ribose Ribulose Heksose (6) Glukose Fruktose

Disakarida { Cn (H2O)n-1 }: Sukrose (glukose dan fruktose) Laktose (glukose dan galaktose) Maltose (dua glukose)

Amilum : Amilose ± 20 % Amilopektin ± 80% (3). Oligosakarida ( 4 – 10 mono sakarida ) (4). Polisakarida: homopolisakarida, amilum, glikogen, innulin, sellulose dan lainnya heteropolisakarida, chitin, glikoprotein dll. Amilum : Amilose ± 20 % Amilopektin ± 80%

Amilose

Glikogen

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

Triasil Gliserol Fosfolipida 24

Sphingosine Ceramide 25

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 26

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 )

Asam amino esensial (tikus putih) : 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).

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).

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

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

Primary structure is the sequence of the amino acids in the protein. 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.

Proteins One common secondary structure is the -helix. Protein Structure One common secondary structure is the -helix. Hydrogen bonds between N-H bonds and carbonyl groups hold the helix in place.

STRUKTUR SEKUNDER : H H O R | | || | – N – C – C – C – C – N – | | | || – N – C – C – | CH2 S H H O ikatan disulfida R | C – C – N – || | | O H H : : H H O | | || – N – C – C ikatan Hidrogen *  Helix * Lain2 : * LIPIT  =  - PLEATED * KUMPARAN ACAK = RANDOM COIL Cys – SH Cys – SH 36

Proteins Protein Structure Tertiary structure is the three dimensional structure of the protein. Shape of the protein

STRUKTUR TERSIER : Contoh : MIOGLOBIN (MYOGLOBINE)  MONOMER Dari satu untai rantai polipeptida monomer Contoh : MIOGLOBIN (MYOGLOBINE)  MONOMER Struktur Tersier : IKATAN HIDROGEN GAYA2 VAN DER WAALS IKATAN2 YG. LEMAH 38

Tertiary structure of proteins catalase enzyme Structure solved using Xray crystallography

STRUKTUR KUARTERNER :  MONOMER  DIMER  TETRAMER OLIGOMER POLIMER T.D. SATU UNTAI RANTAI POLIPEPTIDA  MONOMER PROTOMER  DIMER  TETRAMER OLIGOMER POLIMER HANYA SAMPAI STRUKTUR TERSIER subunit TERMASUK STRUKTUR KUARTERNER subunit 40

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 YG LEMAH Ikatan non Kovalen 41

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.

Nucleic acids are made up of nucleotides. There are three important parts to a nucleic acid: phosphoric acid unit, five carbon sugar (e.g. deoxyribose), and nitrogen containing organic base (e.g. adenine).

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 46

Nucleotide structure 47

Purin 48

Pirimidin 49

NUKLEOSIDA 50

Nukleosida yang lain 51

Nucleotide 52

Nukleotida 53

Adenosine Triphosphate (ATP) Nitrogenous base (adenine), sugar (ribose)

Deoxyadenylic Acid FG25_030.JPG

Structure of a Polynucleotide

Nucleic Acids adenine (A), guanine (G), cytosine (C), 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).

Nitrogen-Containing Bases

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.

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.

Complementary Base Pairs

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.

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.

FG25_032.JPG DNA Double Helix Wassalamua’alikum Wr. Wb.