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Introduction to Biochemistry: The Chemical Basis of Life

This book provides an overview of the various molecules in living organisms and the chemical reactions that occur between them. It explores the intersection of chemistry and biology, focusing on the flow of information from nucleic acids to proteins. The book also covers the structure and function of cells, including the cell nucleus and organelles such as mitochondria. Additionally, it discusses important biomolecules such as carbohydrates, lipids, and proteins, as well as their structures and roles in biological processes.

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Introduction to Biochemistry: The Chemical Basis of Life

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

  2. 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.

  3. Flow of information: from nucleic acids to proteins DNARNAProtein 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

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

  5. Organ Organism, Organ, Cell Organism

  6. The Cell 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

  7. Fig 1.15 (a) Eukaryotic cell (animal)

  8. Structure of a biological membrane • A lipid bilayer with associated proteins

  9. 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).

  10. 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)

  11. 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.

  12. 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

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

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

  15. Amilose

  16. Glikogen

  17. 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

  18. Triasil Gliserol Fosfolipida 24

  19. Sphingosine Ceramide 25

  20. 26

  21. 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 )

  22. 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).

  23. 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).

  24. 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

  25. 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.

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

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

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

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

  30. Tertiary structure of proteins catalase enzyme Structure solved using Xray crystallography

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

  32. 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

  33. 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.

  34. 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).

  35. 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

  36. Nucleotide structure 47

  37. Purin 48

  38. Pirimidin 49

  39. NUKLEOSIDA 50

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