INTRODUCTION TO BIOCHEMISTRY Khadijah Hanim Abdul Rahman 8

INTRODUCTION TO BIOCHEMISTRY Khadijah Hanim Abdul Rahman 8 September 2014 Sem 1, 2014/2015 khadijahhanim@unimap. edu. my

COURSE OUTCOME (C 0 1) • CO 1: Ability to differentiate basic structure, properties, functions and classification of important biomolecules.

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.

• 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.

MEANING OF LIFE

Life is complex and dynamic - All organisms are primarily composed of organic (carbon-based) molecules that have three dimensional shapes - Their methods for sustaining biological processes are similar - Living processes (growth and development) involve thousands of chemical reactions.

Life is organized and self sustaining - Living organisms are hierarchically organized systems (each level is based on the one below) - The molecules that make up living organisms, referred to as “Biomolecules” - In multicellular organisms levels of organization: tissues, organs and organ systems - At each level of organization the whole is greater than the sum of the parts

Life is cellular - Cells differ widely in structure and function - Each is surrounded by a membrane that controls the transport of some chemical substances into and out of the cell. - The membrane mediates the response of the cell to components of the extracellular environtment. - Cells arise only from the division of existing cells.

Life is information - based - Organization requires information - Living organisms can be considered to be information-processing systems - Interacting molecules within cells, between cells and generation of future cells - Genetic information specifies the linear sequence of amino acids in proteins and how and when those proteins are synthesized

Life adapts and evolves - All life on earth has a common origin, with new forms arising from other forms - DNA mutations can be repaired or have no effect on the functioning of the organism - On rare occasions mutations may contribute to an increased ability of the organism to survive, to adapt to new circumstances and to reproduce - The interplay of environtmental change and genetic variation can lead to favorable traits and different forms of life.

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

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.

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?

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

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

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.

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

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: 1. Eubacteria / Bacteria 2. Archaebacteria/Archaea

DIFFERENCES BETWEEN BACTERIA AND ARCHAEA Eubacteria Archaeabacteria -cell walls composed of peptidoglycan - ester-linked straight-chain membrane lipids (fatty acids). - translation apparatus inhibited by antibiotics (e. g. streptomycin, tetracycline etc. ). cell walls composed of various different substances -have ether-linked branched -chain member lipids. - not affected by antibiotics

EUKARYOTIC CELLS • Eukaryotic cells are larger than prokaryotes. • They have a variety of internal membranes and structures, they are: 1. Organelles 2. cytoskeleton composed of microtubules, microfilaments and intermediate filaments • Eukaryotic DNA is composed of several linear bundles called chromosomes.

Similarities between Eukaryotes and Prokaryotes • 1. 2. 3. 4. Both have DNA as their genetic material. Both are membrane bound. Both have ribosomes. Both have similar basic metabolism. Both amazingly diverse in forms.

FEATURES OF PROKARYOTIC CELL • Has five essential structural components: 1. genome (DNA) 2. ribosomes 3. cell membrane 4. cell wall 5. surface layer • Structurally, a prokaryotic cell has three architectural regions: 1. appendages (flagella and pili) 2. cell envelope (capsule, cell wall , plasma membrane) 3. cytoplasm region (cell genome (DNA) and ribosomes.

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

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

• 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 (where the Kreb Cycle takes place)

CHLOROPLAST IN PLANTS • • 1. 2. 3. 4. 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

Diagram of mitochondrion

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.

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

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

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 floating freely without a nucleus

Biochemistry and Biotechnology

Definitions of Biotechnology Using living organisms or product of living organisms for human/surrounding benefits Biotechnology To make products or to solve problems

Example of process: Fermentation alcohol Bread • During fermentation- yeast decompose sugar to derive energy • Produce ethanol as waste • Yeast is added to make dough rise • Yeast ferments sugar releasing CO 2 – dough rise and creates holes • Alcohol produced- evaporated when baked

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.

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.