Biochemistry basics lecture 1.pdf

Lecture Objectives Know what biochemistry is and its principle. Know the components of a cell and its major types of bio-molecules. Understand how the role of cell organisation and different types of chemical reactions involved in maintaining high degree of internal order. ...

Lecture Objectives Know what biochemistry is and its principle. Know the components of a cell and its major types of bio-molecules. Understand how the role of cell organisation and different types of chemical reactions involved in maintaining high degree of internal order.  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: A. Studying the structure and behavior of the complex molecules found in biological material and B. the ways these molecules interact to form cells, tissues and whole organism  Bio-molecules Just 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. Sugars Carbohydrates most abundant organic molecule found in nature. Initially synthesized in plants from a complex series of reactions involving photosynthesis. Basic unit is monosaccharides. Monosaccharides can form larger molecules e.g. glycogen, plant starch or cellulose. Functions Store energy in the form of starch (photosynthesis in plants) or glycogen (in animals and humans). Provide energy through metabolism pathways and cycles. Supply carbon for synthesis of other compounds. Form structural components in cells and tissues. Intercellular communications Fatty acids Are monocarboxylic acid contains even number C atoms Two types: saturated (C-C sb) and unsaturated (C-C db) Fatty acids are components of several lipid molecules. E,g. of lipids are triacylglycerol, streiods (cholestrol, sex hormones), fat soluble vitamins. Functions Storage of energy in the form of fat Membrane structures Insulation (thermal blanket) Synthesis of hormones Major Classes of small Bio-molecules Building blocks of proteins. 1. Amino acids: 20 commonly occurring. Contains amino group and carboxyl group function groups (behavioral properties) R Group (side chains) determines the chemical properties of each amino acids. Also determines how the protein folds and its biological function. Individual amino acids in protein connected by peptide bond. Functions as transport proteins, structural proteins, enzymes, antibodies, cell receptors.  Introduction Cell Structure and Function 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 contains thousands of chemical rxns. Precise regulation and integration of these rxns are required to maintain life Certain important rxns E.g. Glycolysis is found in almost all organisms. All organisms use the same type of molecules: CHO, proteins, lipids & nucleic acids. Instructions for growth, reproduction and developments for each organism is encoded in their DNA Cells Basic 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 Cells May be Prokaryotic or Eukaryotic Prokaryotes include bacteria & lack a nucleus or membrane-bound structures called organelles Eukaryotes include most other cells & have a nucleus and membrane-bound organelles (plants, fungi, & animals) Nucleoid region contains the DNA Contain 3 basic cell structures: Cell membrane & cell wall Nucleus Contain ribosomes (no membrane) Cell Membrane to make proteins in Cytoplasm with organelles their cytoplasm Two Main Types of Eukaryotic Cells 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.. 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 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 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 All reactions are catalyzed by enzymes The primary functions of metabolism are: a. acquisition & utilization of energy b. Synthesis of molecules needed for cell structure and functioning (i.e. proteins, nucleic acids, lipids, & CHO c. Removal of waste products Even though thousands of rxns sound very large and complex in a tiny cell: The types of rxn are small Mechanisms o biochemical rxns are simple Reactions of central importance (for energy production & synthesis and degradation of major cell components) are relatively few in number Frequent reaction encountered in biochemical processes 1. Nucleophilic Substitution One atom of group substituted for another 2. Elimination Reactions Double bond is formed when atoms in a molecule is removed 3. Addition Reactions: Two molecules combine to form a single product. A. Hydration Reactions Water added to alkene > alcohol (common addition rxn) 4. Isomerization Reactions. Involve intramolecular shift of atoms or groups 5. Oxidation-Reduction (redox) Reactions Occur when there is a transfer of e- from a donor to an electron acceptor 6. Hydrolysis reactions Cleavage of double bond by water. 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 bio- molecules (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 How do complex structure of cells maintain high internal order? 1. Synthesis of bio-molecules 2. Transport Across Membranes - Cell membranes regulate the passage of ions and molecules from one compartment to another. 3. Cell Movement - Organised movement- most obvious characteristics of living cells. The intricate and coordinated activities required to sustain life require the movement of cell components. 4. Waste Removal - Animal cells convert food molecules into CO2, H20 & NH3. If these not disposed properly can be toxic.