METABOLISME NITROGEN
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What is Biochemistry ? • Biokimia kimia terapan yang mempelajari proses2 biologis pada taraf cellular dan molecular • Ilmu ini muncul pada awal abad 20 ketika para ilmuwan menggabungkan kimia, fisiologi dan biologi untuk meneliti sistem kimia kehidupan melalui: – Studi struktur dan sifat molekul complex yang ditemukan dalam material biologis – Studi cara molekul2 ini berinteraksi untuk membentuk sel, jaringan dan organisme secara keseluruhan KRT-2011
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Principles of Biochemistry • Sel (unit struktur dasar dari organisme hidup) sangat terorganisir dan sumber energi secara rutin dibutuhkan untuk mempertahankan keberadaannya • Proses kehidupan mengandung beribu-ribu chemical pathways (=jalur kimia). Pengaturan yang tepat & terintegrasi dari chemical pathways ini dibutuhkan untuk mempertahankan kehidupan) • Jalur yang penting, misal: Glycolysis ditemukan dalam semua organisme • Semua organisme menggunakan tipe molekul yang sama: carbohydrates, proteins, lipids & nucleic acids. • Instruksi untuk pertumbuhan, reproduksi dan perkembangan untuk setiap organisme di encoded dalam DNA KRT-2011
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Cells • Basic building blocks of life • Unit kehidupan terkecil dari suatu organisme • Tumbuh, reproduksi menggunakan energi, adaptasi, respon terhadap lingkungannya • Banyak yang tak terlihat dengan mata telanjang • Organisme bersel Satu atau berjuta-juta sel yang menyusun suatu organisme KRT-2011
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Nucleoid region contains the DNA •Cell membrane & cell wall • Contain ribosomes (no membrane) to make proteins in their cytoplasm
Contain 3 basic cell structures: • Nucleus • Cell Membrane • Cytoplasm with organelles KRT-2011
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Characteristic Bio-membranes and Organelles Plasma Membrane
A lipid/protein/carbohydrate complex, providing a barrier and containing transport and signaling systems.
Nucleus
Double membrane surrounding the chromosomes and the nucleolus. Pores allow specific communication with the cytoplasm. The nucleolus is a site for synthesis of RNA making up the ribosome
Mitochondrion
Surrounded by a double membrane with a series of folds called cristae. Functions in energy production through metabolism. Contains its own DNA, and is believed to have originated as a captured bacterium.
Chloroplasts (plastids)
Surrounded by a double membrane, containing stacked thylakoid membranes. Responsible for photosynthesis, the trapping of light energy for the synthesis of sugars. Contains DNA, and like mitochondria is believed to have originated as a captured bacterium. KRT-2011
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. Rough endoplasmic reticulum (RER)
A network of interconnected membranes forming channels within the cell. Covered with ribosomes (causing the "rough" appearance) which are in the process of synthesizing proteins for secretion or localization in membranes.
Ribosomes
Protein and RNA complex responsible for protein synthesis
Smooth endoplasmic reticulum (SER)
A network of interconnected membranes forming channels within the cell. A site for synthesis and metabolism of lipids. Also contains enzymes for detoxifying chemicals including drugs and pesticides.
Golgi apparatus
A series of stacked membranes. Vesicles (small membrane surrounded bags) carry materials from the RER to the Golgi apparatus. Vesicles move between the stacks while the proteins are "processed" to a mature form. Vesicles then carry newly formed membrane and secreted proteins to their final destinations including secretion or membrane localization.
Lysosymes
A membrane bound organelle that is responsible for degrading proteins and membranes in the cell, and also helps degrade materials KRT-2011 7 ingested by the cell.
Vacuoles
Membrane surrounded "bags" that contain water and storage materials in plants.
Peroxisomes or Microbodies
Produce and degrade hydrogen peroxide, a toxic compound that can be produced during metabolism.
Cell wall
Plants have a rigid cell wall in addition to their cell membranes
Cytoplasm
enclosed by the plasma membrane, liquid portion called cytosol and it houses the membranous organelles.
Cytoskeleton
Arrays of protein filaments in the cytosol. Gives the cell its shape and provides basis for movement. E.g. microtubules and microfilaments. http://www.biology.arizona.edu copyright © 1997 - 2004.. KRT-2011
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Biolog. Nanostructures Biochemistry
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How did organic complex molecules evolved from more simple molecules? CH4, H2O, NH3, HCN
? Biochemical Evolution
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How did organic complex molecules evolved from more simple molecules? • Urea disintesis melalui pemanasan senyawa anorganik ammonium cyanate (1828) • Hal ini menunjukkan bahwa senyawa yang banyak ditemukan dalam organisme hidup adapat disintesis dari substansi anorganik
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The Urey-Miller experiment (1950) Some amino acids could be produced:
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Many Important Biomolecules are Polymers • Biopolymers - macromolecules terbentuk melalui penggabungan beberapa molekul organik yang lebih kecil (monomers) • Condensation reactions penggabungan beberapa monomer (H2O dihilangkan dalam proses ini) • Residue - setiap monomer dalam satu rantai KRT-2011
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Molecular Organisation of a cell
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Water
•Sekitar 60-90 percent dari organisme berupa air
Air digunakan dalam banyak reaksi dalam tubuh Air disebut pelarut universal KRT-2011
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Bio-molecules • Sel merupakan building blocks dari jaringan, demikian juga molecules merupakan building blocks dari sel • Sel hewan dan tanaman mengandung sekitar 10, 000 macam molecules (bio-molecules) • Air menyusun 50-95% dari berat cells • Ion seperti Na+, K+ dan Ca+ sekitar 1% • Hampir semua jenis dari bio-molecules adalah organic (C, H, N, O, P, S) • Umumnya berbagai molecules mengandung C. •
Kebanyakan bio-molecules merupakan turunan dari hydrocarbons.
• Sifat kimia dari organic bio-molecules ditentukan oleh functional groups-nya. Umumnya bio-molecules lebih dari satu
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Biomolecules – Structure Anabolic
• • • • •
Building block Simple sugar Amino acid Nucleotide Fatty acid
• • • • •
Macromolecule Polysaccharide Protein (peptide) RNA or DNA Lipid
Catabolic KRT-2011
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Linking Monomers Cells link monomers by a process called dehydration synthesis (removing a molecule of water) Remove H H2O Forms
Remove OH
This process joins two sugar monomers to make a double sugar KRT-2011
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Breaking Down Polymers • Cells memecah macromolecules melalui suatu proses yang disebut hydrolysis (penambahan satu molekul air)
Air ditambahkan untuk memecah a double sugar KRT-2011
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Sugars • Carbohydrates merupakan molekul organik yang ditemukan berlimpah di alam • Awalnya disintesis dalam tanaman dari serangkaian reaksi complex yang melibatkan photosynthesis. • Basic unit –nya adalah monosaccharides. • Monosaccharides dapat membentuk molecules molekul yang lebih besar, misal: glycogen, plant starch or cellulose. Fungsi: • Penyimpanan energi dalam bentuk starch (photosynthesis in plants) or glycogen (in animals and humans). • Penyediaan energy melalui metabolism pathways and cycles. • Supply carbon untuk sintesis senyawa lain • Membentuk komponen struktural dalam cells and tissues. • Intercellular communications KRT-2011
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Monosaccharides -Polysaccharides
Glucose - Cellulose Glycosidic bonds connecting glucose residues are in red
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Fatty acids - Lipids • Merupakan monocarboxylic acid yang mengandung sejumlah atom C • Dua type: saturated (C-C sb) and unsaturated (C-C db) • Fatty acids merupakan komponen dari beberapa lipid molecules. • E,g. of lipids are triacylglycerol, steriods (cholestrol, sex hormones), fat soluble vitamins. Fungsi: • Energi cadangan dalam bentuk fat • Membrane structures • Insulation (thermal blanket) • Sintesis hormone
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Structure of a biological membrane • A lipid bilayer with associated proteins
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Nucleic Acids •Store hereditary information Mengandung informasi untuk membuat semua protein tubuh Ada dua tipe --- DNA & RNA
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Amino acids - Proteins: • Amino acids:
• Building blocks dari protein.
• R Group (side chains) menentukan sifatsifat kimia dari masing-masing amino acids. • Juga menentukan bagaimana protein folds dan fungsi biologisnya • Berfungsi sebagai transport proteins, structural proteins, enzymes, antibodies, cell receptors. KRT-2011
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Proteins as Enzymes • Banyak protein yang berperan sebagai biological catalysts or enzymes Ada ribuan enzim yang berbeda dalam tubuh Enzymes mengendalikan rate of chemical reactions dengan cara melemahkan ikatan, sehingga lowering the amount of activation energy yang diperlukan untuk reaksi Catalysator -> No not interfere with the equilibrium of reaction -> Enzymes are reusable !!!! KRT-2011
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Enzymes: • Active site - a cleft or groove in an enzyme that binds the substrates of a reaction The nature and arrangement of amino acids in the active site make it specific for only one type of substrate. (accepts just one enaniomer)
Egg white lysozyme
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Macromolecules
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Macromolecules
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Concepts of Life Kehidupan dicirikan oleh: •
Biological diversity: lichen, microbes, jellyfish, sequoias, hummingbirds, manta rays, gila monsters, & you
• Chemical unity: living systems (on earth) obey the rules of physical and organic chemistry – there are no new principles
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Life needs 3 things: (1) ENERGY, yang harus diketahui bagaimana: Extract • Transform • Utilize
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The Energetics of Life • Photosynthetic organisms menangkap energi cahaya matahari dan menggunakannya untuk mensintesis senyawa organik • Senyawa organik menyediakan energi untuk semua organisme KRT-2011
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Using toxic O2 to generate energy 2 H2O O2 + 4e- + 4H+ (photosynthesis)
Glucose + 6O2 6CO2 + 6H2O + Energy KRT-2011
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Glycolysis: the preferred way for the formation of ATP
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Life needs (2) SIMPLE MOLECULES, yang harus diketahui bagaimana:
Convert • Polymerize • Degrade
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Life needs (3) CHEMICAL MECHANISMS, to: • Memanfaatkan energy
• Mengendalikan serangkaian reaksi kimia • Mensisntesis & mendegradasi macromolecules • Mempertahankan suatu keadaan yang terusmenerus dinamis • Self-assemble complex structures • Replicate secara akurat dan efisien • Mempertahankan biochemical “order” vs outside KRT-2011
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Trick #1: Life uses chemical coupling to drive otherwise unfavorable reactions
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Trick #2: Life uses enzymes to speed up otherwise slow reactions
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How does an enzyme do it, thermodynamically?
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How does an enzyme do it, mechanistically?
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Chemical reaction types encountered in biochemical processes 1. Nucleophilic Substitution • Satu atom dari group disubstitusi untuk yang lain 2. Elimination Reactions • Double bond terbentuk ketika atom dalam satu molecule dihilangkan 3. Addition Reactions: • Dua molecules bergabung untuk membetuk satu produk tunggal A. Hydration Reactions • Air ditambahkan pada alkene alcohol (common addition pathway)
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4. Isomerization Reactions. • Melibatkan intramolecular shift dari atoms atau groups 5. Oxidation-Reduction (redox) Reactions • Terjadi bila ada transfer e- dari donor ke electron acceptor 6. Hydrolysis reactions • Cleavage of double bond by water.
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Summary of Key Concepts
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Biochemical Reactions •
Metabolism: total sum of the chemical reaction happening in a living organism (highly coordinated and purposeful activity) a. Anabolism- energy requiring biosynthetic pathways b. Catabolism- degradation of fuel molecules and the production of energy for cellular function
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Semua reaksi dikatalisis oleh enzymes
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Fungsi utama dari metabolisme adalah: a. Perolehan dan pemanfaatan energy b. Synthesis of molecules diperlukan untuk struktur dan fungsi sel (spt: protein, nucleic acid, lipid dan CHO) c. Removal of waste products
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Even though thousands of pathways sound very large and complex in a tiny cell: • The types of pathways are small • Mechanisms of biochemical pathways are simple • Reactions of central importance (for energy production & synthesis and degradation of major cell components) are relatively few in number KRT-2011
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Energy for Cells • Living cells are inherently unstable. • Constant flow of energy prevents them from becoming disorganized. • Cells obtains energy mainly by the oxidation of biomolecules (e- transferred from 1 molecule to another and in doing so they lose energy) • This energy captured by cells & used to maintain highly organized cellular structure and functions
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