Kuliah Pengantar Biokimia

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Text of Kuliah Pengantar Biokimia

  • Pengantar Biokimia*Bagian Biokimia Fakultas Kedokteran Universitas Hasanuddin MakassarDr. Marhaen Hardjo, M.Biomed, PhD

    Bagian Biokimia Fakultas Kedokteran Universitas Hasanuddin Makassar

  • What is Biochemistry ? Biochemistry is the application of chemistry to the study of biological processes at the cellular and molecular level.

    It emerged as a distinct discipline around the beginning of the 20th century when scientists combined chemistry, physiology and biology to investigate the chemistry of living systems by:

    Studying the structure and behavior of the complex molecules found in biological material and

    the ways these molecules interact to form cells, tissues and whole organism

    *

  • Principles of Biochemistry Cells (basic structural units of living organisms) are highly organized and constant source of energy is required to maintain the ordered state.

    Living processes contain thousands of chemical pathways. Precise regulation and integration of these pathways are required to maintain life

    Certain important pathways e.g. Glycolysis is found in almost all organisms.

    All organisms use the same type of molecules: carbohydrates, proteins, lipids & nucleic acids.

    Instructions for growth, reproduction and developments for each organism is encoded in their DNA

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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.

  • *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

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

  • *Organism, Organ, CellOrganism

  • *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 cellsNucleus only in eukaryotic cells. Contains most of the cell's genetic material.

  • CellsBasic building blocks of life

    Smallest living unit of an organism

    Grow, reproduce, use energy, adapt, respond to their environment

    Many cannot be seen with the naked eye

    A cell may be an entire organism or it may be one of billions of cells that make up the organism

    Basis Types of Cells

    *

  • Nucleoid region contains the DNACell membrane & cell wall Contain ribosomes (no membrane) to make proteins intheir cytoplasmContain 3 basic cell structures: Nucleus Cell Membrane Cytoplasm with organelles*

  • Two Main Types of Eukaryotic Cells*

  • Characteristic Bio-membranes and Organelles MitochondrionSurrounded by a double membrane with a series of foldscalled cristae. Functions in energy production through metabolism. Contains its own DNA, and is believed to have originated as a captured bacterium.

    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 ribosomeChloroplasts (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.

    *

  • 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 synthesisSmooth 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 ingested by the cell.

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    .

  • 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.

    CytoskeletonArrays 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.. *

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  • *Fig 1.15 (a) Eukaryotic cell (animal)

  • *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).

  • *BiochemistryBiolog. Nanostructures

  • Biochemical EvolutionCH4, H2O, NH3, HCNHow did organic complex molecules evolved from more simple molecules?*

  • *How did organic complex molecules evolved from more simple molecules?Urea was synthesized by heating the inorganic compound ammonium cyanate (1828)This showed that compounds found exclusively in living organisms could be synthesized from common inorganic substances

  • The Urey-Miller experiment (1950)Some amino acids could be produced:*

  • *Many Important Biomolecules are PolymersBiopolymers - macromolecules created by joining many smaller organic molecules (monomers)

    Condensation reactions join monomers (H2O is removed in the process)

    Residue - each monomer in a chain

  • *

  • Molecular Organisation of a cell*

  • *WaterAbout 60-90 percent of an organism is waterWater is used in most reactions in the bodyWater is called the universal solvent

  • Bio-moleculesJust like cells are building blocks of tissues likewise molecules are building blocks of cells.

    Animal and plant cells contain approximately 10, 000 kinds of molecules (bio-molecules)

    Water constitutes 50-95% of cells content by weight.

    Ions like Na+, K+ and Ca+ may account for another 1%

    Almost all other kinds of bio-molecules are organic (C, H, N, O, P, S)

    Infinite variety of molecules contain C. Most bio-molecules considered to be derived from hydrocarbons.

    The chemical properties of organic bio-molecules are determined by their functional groups. Most bio-molecules have more than one.

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  • *Biomolecules Structure Building block Simple sugar Amino acid Nucleotide Fatty acid Macromolecule Polysaccharide Protein (peptide) RNA or DNA Lipid

  • *Linking MonomersCells link monomers by a process called dehydration synthesis (removing a molecule of water)This process joins two sugar monomers to make a double sugarRemove HRemove OHH2O Forms

  • *Breaking Down PolymersCells break down macromolecules by a process called hydrolysis (adding a molecule of water)Water added to split a double sugar

  • *Macromolecules

  • *Macromolecules

  • *Concepts of Life Life is characterized by 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

  • *Life needs 3 things:

    (1) ENERGY, which it must know how to:

    Extract Transform Utilize

  • *The Energetics of LifePhotosynthetic organisms capture sunlight energy and use it to synthesize organic compounds Organic compounds provide energy for all organisms

  • Using toxic O2 to generate energy2 H2O O2 + 4e- + 4H+ (photosynthesis)Glucose + 6O2 6CO2 + 6H2O + Energy*

  • Glycolysis: the preferred way for the formation of ATP*

  • *Life needs (2) SIMPLE MOLECULES, which it must know how to:

    Convert Polymerize Degrade

  • *Life needs (3) CHEMICAL MECHANISMS, to:

    Harness energy Drive sequential chemical reactions Synthesize & degrade macromolecules Maintain a dynamic steady state Self-assemble complex structures Replicate accurately & efficiently Maintain biochemical order vs outside

  • *Trick #1: Life uses chemical coupling to drive otherwise unfavorable reactions

  • *Trick #2: Life uses enzymes to speed