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INTRODUCTION TO BIOCHEMISTRY

INTRODUCTION TO BIOCHEMISTRY. Khadijah Hanim Abdul Rahman 9 September 2013 Sem 1, 2013/2014 khadijahhanim@unimap.edu.my. COURSE OUTCOME (C0 1). CO1: Ability to differentiate basic structure, properties, functions and classification of important biomolecules. WHAT IS BIOCHEMISTRY?.

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INTRODUCTION TO BIOCHEMISTRY

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  1. INTRODUCTION TO BIOCHEMISTRY KhadijahHanim Abdul Rahman 9 September 2013 Sem 1, 2013/2014 khadijahhanim@unimap.edu.my

  2. COURSE OUTCOME (C0 1) • CO1: Ability to differentiate basic structure, properties, functions and classification of important biomolecules.

  3. WHAT IS BIOCHEMISTRY? • A combination of the words biology and chemistry. • Biology is the study of cells that form the fundamental units of all living organisms. • Whereas, chemistry is the science that deals with the composition, structure, and properties of substances and the transformations that they undergo.

  4. Biochemistry involves various enzymatic activities of biomolecules. • Biomolecules: any molecule produced by living organisms. • Biomolecules: proteins, polysaccharides, lipids and nucleic acids  polymeric molecules. • Polymeric: molecule made up from millions of repeated linked units of numerous natural and synthetic compounds.

  5. MEANING OF LIFE • What is the meaning of life? • Life is complex and dynamic – composed of carbon-based (organic) molecules • Life is organised and self-sustaining – composed of biomolecules (linked biomolecules formed polymers- macromolecules) • Life is cellular • Life is information-based – genes • Life adapts and evolves – mutations

  6. STRATEGIES IN ORIGIN OF LIFE STUDIES • TOP-DOWN APPROACH – phylogenetic(evolutionary) history of modern organisms based on the similarities and differences among organisms that are clues to their evolutionary past • BOTTOM-UP APPROACH – abiogenesis (mechanism of reconstructing and transformation of early earth into the first primitive living organisms), and analyzing biomolecules as vestigial remanants of the prebiotic world

  7. HISTORY OF LIFE • Study of history - based on geological (fossil record), biological and chemical evidence • Earth formed from a cloud of condensing cosmic dust and gas 4.5 billion years ago • Earliest organisms stromatolites (compressed layers of bacterial remains) existed 3.6 billion years ago.

  8. ABIOGENESIS Essential issues • How were simple organic molecules (sugars, amino acids, and nucleotides) formed? • How did these primordial molecules link up to form proteins and nucleic acids? • How did the first cells originate?

  9. PHASES IN ABIOGENESIS EARLY PHASE Energy in the form of light, lightning and heat promoted the formation of organic molecules from inorganic precursors CHEMICAL EVOLUTION Primitive cell-like structures enclosed by lipid precursors molecules possessed a richer diversity of organic molecules POLYMERIZATION Certain monomer molecules polymerized to form polypeptides and nucleic acids PRIMORDIAL CELL Once the protocells became enclosed in a membrane-like barrier, their evolution proceeded over time

  10. ASSUMPTIONS EXPLAINING ABIOGENESIS • The first form of life was simple in both structural and functional capabilities • The basic requirements of any form of life is the presence of one or more molecules that are able to duplicate themselves using raw materials available in their environment

  11. HYPOTHETICAL SCENARIO OF ORIGIN OF LIFE • Short RNA segments may have originally encoded short peptides • As protocells became more stable and complex form of genetic info, a reverse trascriptase started copying RNA sequences into DNA • This resulted in the role of DNA as the major info macromolecule in all modern organisms • Hence DNA is the genetic blueprint; PROTEINS, the devices that perform the tasks of all living processes; and RNA, the carrier of info used to manufacture protein.

  12. THE RNA WORLD CONCEPT • RNA was the first information molecule • It possess genetic info and also can behave as an enzyme • Formation of peptide bonds during protein synthesis is catalysed by an RNA component of ribosomes • In certain conditions in living cells, DNA can be synthesized from an RNA molecule by an enzyme reverse transcriptase

  13. THE LIVING WORLD • A protocellcould have contained only RNA to function as both genetic material and enzymes. • First protocellswere heterotrophsusing ATP as energy and carrying out a form of fermentation. Domains of Life on Earth: 3 domains • ARCHAEA: Halophiles and Thermophiles • BACTERIA: Cyanobacteria and Heterotrophic bacteria • EUKARYA: Flagellates, Fungi, Plants and Animals

  14. EARLY CELLS • Bacteria and Archaea are termed as PROKARYOTES –organisms whose DNA is not enclosed in a nucleus of the cell. • EUKARYOTIC cells are aerobic and arose 2.1 billion years ago. They contain nuclei and organelles. • PLANTS appeared on land (mud flats) during the ‘Paleozoic’ period, about 440 million years ago. They provided food for higher animals to evolve

  15. EARLY BACTERIA • PRECAMBRIAN ERA encompasses 87% of geological time scale and based on this, life began from 570 million to 4.6 billion years ago. • Early bacteria resembled archaea that live in hot springs today. • Archaeansresemble bacteria but developed separately from common ancestor nearly 4 billion years ago. They thrive under extreme conditions and are labeled as ‘extremophiles’.

  16. PROKARYOTES Prokaryotes are single-celled microorganisms characterized by: • the lack of a membrane-bound nucleus and • membrane bound organelles. There are two domains of prokaryote: • Eubacteria / Bacteria • Archaebacteria/Archaea

  17. DIFFERENCES BETWEEN BACTERIA AND ARCHAEA

  18. EUKARYOTIC CELLS • Eukaryotic cells are larger than prokaryotes. • They have a variety of internal membranes and structures, they are: • Organelles • cytoskeleton composed of microtubules, microfilaments and intermediate filaments • Eukaryotic DNA is composed of several linear bundles called chromosomes.

  19. Similarities between Eukaryotes and Prokaryotes • Both have DNA as their genetic material. • Both are membrane bound. • Both have ribosomes. • Both have similar basic metabolism. • Both amazingly diverse in forms.

  20. FEATURES OF PROKARYOTIC CELL • Has five essential structural components: • genome (DNA) • ribosomes • cell membrane • cell wall • surface layer • Structurally, a prokaryotic cell has three architectural regions: • appendages (flagella and pili) • cell envelope (capsule, cell wall , plasma membrane) • cytoplasm region (cell genome (DNA) and ribosomes.

  21. Other Important biochemical cell organelles (components) • Cytoskeleton • Cell wall • Nucleus • Cytoplasm • Ribosome • Mitochondrion • Chloroplast

  22. Functions of important biochemical cell components • Cytoskeleton: • Helps to maintain cell shape. • The primary importance of the cytoskeleton is in cell motility. • Provides a supporting structure for the internal movement of cell organelles, as well as cell locomotion and muscle fiber contraction could not take place without the cytoskeleton. • It is composed of proteinaceous fibers • Cell-wall: Every cell is enclosed in a membrane, a double layer of phospholipids (lipid bilayer) composed of peptidoglycan

  23. Nucleus: is enclosed in a double membrane and communicates with the surrounding cytosol (semi-liquid portion of cytoplasm) via numerous nuclear pores. Within the nucleus is the DNA providing the cell with its unique characteristics. • Ribosome: is the site of protein synthesis • Cytoplasm: This is a collective term for the cytosol plus the organelles suspended within the cytosol. The cytosol is full of proteins that control cell metabolism including signal transduction pathways, glycolysis, intracellular receptors, and transcription factors. • Mitochondria (membrane-bound organelles (double membrane): are power centers of the cell. The different sections in a mitochodrion are: outer membrane; intermembrane space; inner membrane (where oxidation phosphorylation takes place) and matrix (wherethe Kreb Cycle takes place)

  24. CHLOROPLAST IN PLANTS • Chloroplast: • This organelle contains the plant cell's chlorophyll responsible for the plant's green color. • Structurally it is very similar to the mitochondrion except it is larger than the mitochondrion, not folded into cristae, and not used for electron transport • It contains: • A permeable outer membrane, • A less permeable inner membrane, • Inter membrane space • A third membrane containing the light-absorbing system, the electron transport chain, and ATP synthetase, that forms a series of flattened discs, called the thylakoids

  25. Diagram of mitochondrion

  26. COMPARING PROKARYOTES AND EUKARYOTES SIZE Prokaryotes are usually much smaller than eukaryotic cells Eukaryotic cells are, on average, ten times the size of prokaryotic cells. CELL WALL Prokaryotes have cell wall composed of peptidoglycan (a single large polymer of amino acid and sugar). Cell wall of eukaryotes is not made up of this polymer. SURFACE AREA Prokaryotes have a large surface area /volume ratio giving them the advantage of having a higher metabolic and growth rate with smaller generation time as compared to the eukaryotes.

  27. Differentiating Prokaryotes and Eukaryotes SUPPORT In Eukaryotes provided by cytoskeleton; none in Prokaryotes PROTEIN SYNTHESIS In Eukaryotes (animals) Rough Endoplasmic Reticulum (Rough ER) is involved In Prokaryotes ribosomes are involved FAT SYNTHESIS In Eukaryotes – Smooth ER involved No fat synthesis in Prokaryotes

  28. 4. Differentiating Prokaryotes and Eukaryotes ENERGY PRODUCTION In Eukaryotes – chloroplasts (plants); mitochondrion (Kreb’s cycle) In Prokaryotes – chlorophyll (if present) but has no covering or chloroplast; no mitochondrion and Kreb’s cycle replaced by fermentation ENERGY DIGESTION Lysosomes involved in aging process of cell in Eukaryotes No lysosomes in Prokaryotes

  29. 5. Differentiating Prokaryotes and Eukaryotes MOVEMENT In Eukaryotes – cilia, flagella and pseudopod movement In Prokaryotes – flagella of different structure involved in locomotion REPRODUCTION - DNA control In Eukaryotes – DNA in chromosomes inside nucleus In Prokaryotes – DNA in single strand and floating freely without a nucleus

  30. SUMMARY Origin of life • A model for the origin of life proposes that organisms arose from simple organic molecules that polymerized to form more complex molecules capable of replicating themselves. • Compartmentation gave rise to cells that developed metabolic reactions for synthesizing biological molecules and generating energy.

  31. Cells • All cells are prokaryotic or eukaryotic. • Eukaryotic cells contain a variety of membrane-bound organelles. • Phylogenetic evidence groups organisms into 3 domains: archaea, bacteria, eukarya. • Natural selection determines the evolution of species.

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