Principles of Biochemistry - Topic 1 - Introduction to Cell Study PDF

Principles of Biochemistry Topic 1 Introduction to the Study of Cell 1  Introduction Course: PRINCIPLES OF BIOCHEMISTRY (BOI 103) Type: Compulsory Total Units: 4 (3 x 1 h lecture per week) Lecturers: 1. Prof. Dr. K. Sudesh Ku...

Principles of Biochemistry Topic 1 Introduction to the Study of Cell 1  Introduction Course: PRINCIPLES OF BIOCHEMISTRY (BOI 103) Type: Compulsory Total Units: 4 (3 x 1 h lecture per week) Lecturers: 1. Prof. Dr. K. Sudesh Kumar Email: [email protected] 2. Prof. Madya. Dr. Rashidah Abdul Rahim Email: [email protected] 3. Dr. Yazmin Bustami (Practical Class) Email: [email protected] 2  Objectives Introduction to cells, organelles, molecules; structure & function relationship; working of a cell Course contents are divided into 4 major sections: 1. Concept of a cell: Prokaryote, Eukaryote, Animal and Plant Cells; cellular organelles 2. Cell components (Structure & Function): Water and buffer, amino acids and protein, fatty acids and lipid, monosaccharide and carbohydrate, nucleotides and DNA, RNA, membrane and membrane transport 3  Objectives Course contents are divided into 4 major sections: 3. Enzymology: Enzyme as catalysts, enzyme kinetics, inhibitor effects, enzyme regulations, allosteric enzymes (after mid-sem break) 4. Energetics and metabolisms: Bioenergetic principles, carbohydrate metabolisms (glycolysis), TCA cycle, pentose phosphate pathway, gluconeogenesis and photosynthesis, fatty acid oxidation 4  Course Synopsis Introduction of the basic structure of a living cell and its organelles. Relation between the fundamental structure and function of cellular components. - protein, lipid, carbohydrate and nucleic acid. Principles of Biochemistry The basics of metabolism, enzymes as catalyst of metabolic pathways and energetics principles. Details on vital metabolic pathways and processes - glycolysis, fermentation of sugars, pentose phosphate pathway, gluconeogenesis, citric acid cycle, electron transport chain etc. 5  Textbooks / Main References (a) Main References: 1) Biochemistry. D. Voet & J. G. Voet. (2004) John Wiley & Sons Publisher. Third edition. 2) Biochemistry. M. K. Campbell & S. O. Farrel.(2006) Thomson Brooks/Cole Publisher. 3) J. Hardin & G. Bertoni (2018). Becker’s World of the Cell, 9th edition, Pearson Publisher (b) Additional References: 1) Concepts in Biochemistry. R. Boyer (2006) John Wiley & Sons Publisher. Third edition. 2) Cell and Molecular Biology. G. Karp (2005) John Wiley & Sons Publisher. 3) Biochemistry: The Molecular Basis of Life (2003) T. McKee & J. R. McKee. Mc Graw Hill Publisher. 6  LECTURES Introduction to cell - Prokaryotic cell - Eukaryotic cell (animal and plant) Cellular organelles Water and buffers -Physical properties and hydrogen bonds in water -Structure of water in cells -Importance of water to cells -Phosphate and bicarbonate buffers in cell 7  LECTURES Amino acid and protein - Structure and function Monosaccharide and carbohydrate - Structure and function Fatty acids and lipid - Structure and function Cell membrane - Structure and function - Membrane transport Nucleotide and nucleic acid (DNA and RNA) 8  Characteristics of Life: All Living Things 1. Have metabolic activity; ability to acquire and use energy. 2. Use homeostatic controls which respond to environmental change. 3. Show growth, development and reproduction. 4. DNA is a molecule of inheritance. 5. Have adaptive potential; heritable variation in form, function and behavior allows changes to accommodate changing environment. 6. Display diversity; variations in form, function and behavior as a result of natural selection and environmental change. 9  Levels of Organization of Life biosphere tissue ecosystem Cell: smallest community living unit population organelle multicellular molecule organism organ system atom organ subatomic particle 10  Perspectives Scientists study cells from various perspectives such as: 1. Cytology: what we learn with a microscope 2. Genetics: what we learn using genetic techniques 3. Biochemistry: what we learn through biochemical analysis 11 History 12 History 13  Chronology Biochemistry a. Before 1828 it was generally believed that living things i. not governed by physical laws ii. made of special substances b. Friedrich Wöhler synthesized urea from ammonium cyanate showed that biological materials (urea) were not special c. Louis Pasteur (1870)_living yeast was needed to make alcohol d. Eduard Buchner (1898)_extracts of yeast could make alcohol e. 1920's & 30’s i. Gustav Embden and Otto Meyerhof Embden-Meyerhof Pathway Glycolysis 14  Chronology ii. Otto Warburg Developed the Warburg apparatus Showed that mitochondria use O2 iii. Hans Krebs Krebs Cycle f. ATP recognized as energy source in cell g. Ultracentrifuge invented (1925-30) in Sweden allowed isolation of organelles 15  CLASSIFICATION: THE THREE DOMAIN SYSTEM Eukarya (eukaryotes) This system proposes that a common ancestor cell ("Cenancestor") gave rise to three different cell types, each representing a domain. The three domains are the Archaea (archaebacteria), the Bacteria (eubacteria), and the Eukarya (eukaryotes). The Eukarya are then divided into 4 kingdoms: Protists, Fungi, Animalia, and Plantae. 16  Three Domain System The Three Domain System, proposed by Woese and others, is an evolutionary model of classification based on: 1. Differences in the sequences of nucleotides in the cell's ribosomal RNAs (rRNA) 2. The cell's membrane lipid structure 3. Its sensitivity to antibiotics Comparing rRNA structure is especially useful because rRNA molecules throughout nature carry out the same function, their structure changes very little over time. Hence, similarities and differences in rRNA nucleotide sequence are useful indicators of the degree of relationship between various cells and organisms. 17 Bacteria & Archaea The Bacteria and the Eukarya have membranes composed of unbranched fatty acid chains attached to glycerol by ester linkages. The Archaea have membranes composed of branched hydrocarbon chains attached to glycerol by ether linkages. 18  Surface-to-volume ratio Prokaryotic cells are generally much smaller and more simple than eukaryotic cells. The smaller a cell, the greater its surface-to-volume ratio. A large surface-to-volume ratio, as seen in smaller prokaryotic cells, means that nutrients can easily and rapidly reach any part of the cell's interior. In the larger eukaryotic cell, the limited surface area when compared to its volume means nutrients cannot rapidly diffuse to all interior parts of the cell. That is why eukaryotic cells require a variety of specialized internal organelles to carry out metabolism, provide energy, and transport chemicals throughout the cell. Both, have to carry out the same life biochemical processes. 19  Surface-to-volume ratio Cells with a high metabolic rate are usually small. Why? 20 SEM of Bacteria Higher magnification 21  Structure of virus Nucleic acid with a protein envelope Virus: genetic parasite! Is it a cell? 22 T4 Bacteriophage: infects prokaryotes Used by scientists to introduce foreign genetic material into bacterial cells: genetic engineering/ recombinant technology 23 Adenovirus (cold) 24 Tobacco mosaic virus 25  Important terms: Definitions? Nucleus Nuclear membrane Cytoplasm Mitochondrion Plasma membrane Golgi apparatus/body Protoplasm/protoplast Cytosol Cell wall Endoplasmic reticulum (smooth & rough/granulated) Plastid Centriole Chloroplast Centrosome Nuclear plasma Ribosome Nucleolus Liposome Chromatin Vacuole 26  PROKARYOTE Bacterial cell 27 Bacterial nucleoid (EM) 28 Bacterial spore 29 Bacterial (E. coli) flagellar monotrichous lophotrichous amphitrichous peritrichous 30  Locomotor organelles Eukaryotic cell May have flagella or cilia. Flagella and cilia are organelles involved in locomotion and in eukaryotic cells consist of a distinct arrangement of sliding microtubules surrounded by a membrane. The microtubule arrangement is referred to as a 2X9+2 arrangement. Prokaryotic cell Some have flagella, each composed of a single, rotating fibril and not surrounded by a membrane. No cilia. 31 Flagella Transmission Electron Micrograph of Escherichia coli O157:H7 32 Structure of a eukaryotic cell 33 Structure of a eukaryotic cell 34 Plant Cell 35 Plant Cell (3D) 36 Scytonemia (blue-green algae) 37 Mitochondria 38 Lysosome 39 Centriole & Centrosome 40 Microfilament & Microtubule: Cytoskeleton 41 Nucleus 42  Nuclear body Eukaryotic cell a. Bounded by a nuclear membrane having pores connecting it with the endoplasmic reticulum b. Contains one or more paired, linear chromosomes composed of deoxyribonucleic acid (DNA) associated with histone proteins c. Nucleolus present. d. Nuclear body is called a nucleus Prokaryotic cell a. Not bounded by a nuclear membrane b. Usually contains one circular chromosome composed of deoxyribonucleic acid (DNA) associated with histone-like proteins. c. No nucleolus. d. Nuclear body is called a nucleoid 43 Chromosome 44  Cell division Eukaryotic cell a. By mitosis b. Sex cells in diploid organisms are produced through meiosis Prokaryotic cell a. Usually by binary fission. No mitosis. b. Organisms are haploid. No meiosis needed. 45  Nucleic acid DNA and RNA differ in three ways: DNA contains the nucleotide thymine while RNA contains uracil, DNA has the sugar deoxyribose while RNA has ribose, and DNA is normally double-stranded while RNA is single-stranded. (image: Sponk, Creative Commons 3.0) 46 *https://sciencenotes.org/dna-vs-rna-similarities-and-differences/ Endoplasmic reticulum (smooth & rough) 47 Rough endoplasmic reticulum (EM) 48  Golgi apparatus Lipid assembly, polypeptide chain modification, packaging of polypeptides for transport to other various locations in cell 49 Plasma membrane 50  Cytoplasmic membrane (cell membrane, plasma membrane) Eukaryotic cell a. Cytoplasmic membrane is a fluid phospholipid bilayer containing sterols as well as carbohydrates. b. Capable of endocytosis (phagocytosis and pinocytosis) and exocytosis. Prokaryotic cell a. Cytoplasmic membrane; is a fluid phospholipid bilayer without carbohydrates and usually lacking sterols. Many bacteria do contain sterol-like molecules called hopanoids. b. Incapable of endocytosis and exocytosis. 51 Plasma Membrane 52 Size comparison of cellular components 53 Size comparison 54 Comparison of eukaryotic and prokaryotic cells 55 *https://michelleburden.weebly.com/uploads/1/7/0/0/17006738/slide3.png Prokaryote? Eukaryote? WHY? 56