Introduction to Biochemistry PDF

For Your Eyes Only INTRODUCTION to BIOCHEMISTRY LIVING THINGS - composed of lifeless molecules - these molecules conform to all the physical and chemical laws that describe the behaviour of the inanimate matter The IDENTIFYING CHARACTERISTI...

For Your Eyes Only INTRODUCTION to BIOCHEMISTRY LIVING THINGS - composed of lifeless molecules - these molecules conform to all the physical and chemical laws that describe the behaviour of the inanimate matter The IDENTIFYING CHARACTERISTICS of LIVING MATTER 1. Living organisms - complicated and highly organized - cells possess intricate internal structure containing many kinds of complex molecules 2. Each component part of a living organism have specific purpose or function - macroscopic structures - chemical compounds in the cell 3. Living organisms - capacity to extract and transform energy from the environment  build and maintain intricate structure from simple raw materials - carry out other forms of purposeful work (ex: locomotion) 4. Capacity for precise self-replication BIOCHEMISTRY and the LIVING STATE A. Question - why does living matter radically differ from non-living matter since both of them consists of inanimate molecules B. Goal of the Science of Biochemistry - determine how the collections of inanimate molecules found in living organisms interact with each other to constitute, maintain, and perpetuate the living state BIOMOLECULES A. Chemical Components of Living Organisms - organic compounds of carbon which is reduced or hydrogenated - many organic molecules also contain nitrogen B. E. coli - contains 5000 different kinds of compounds - 3000 different kinds of proteins - 1000 different kinds of nucleic acids C. Macromolecules - comprise most of the organic matter in living cells - very large molecular weights - proteins, nucleic acids, polymer substances (starch, cellulose) D. Humans - > 100,000 different kinds of proteins - none of the E. coli protein molecules is identical with any of the human molecules E. Cell Macromolecules - composed of simple, small building-block molecules strung together in long chains - thousands of different macromolecules are constructed from few simple building-block molecules  1st Axiom: There is an underlying simplicity in the molecular organization of the cell - building-block biomolecules are identical in all species  2nd Axiom: All living organisms have a common ancestor  For Your Eyes Only - each organism has its own sets of nucleic acids and proteins  3rd Axiom: The identity of each species of organisms is preserved by its possession of characteristic sets of nucleic acids and proteins - from the functional versatility of the building-block biomolecules  4th Axiom: Principle of molecular economy in living organisms - living cells contain the simplest possible molecules in the least number of different types, just sufficient to endow them the attribute of life and with specie identity, under environmental conditions in which they exist ENERGY TRANSFORMATIONS in LIVING CELLS A. 2nd Law of Thermodynamics (branch of physics dealing with energy and its transformations) - all physical and chemical processes always proceed with an increase in the disorder or randomness in the environment (entropy) B. 1st Law of Thermodynamics - energy can neither be created nor destroyed - living organisms cannot consume or use-up energy  only transform one form of energy to another 1. Ex: heat 2. Environment - source of free energy - source of raw materials  5th Axiom: Living organisms create and maintain their essential orderliness at the expense of their environment, which they cause to become more disordered and random C. In Thermodynamic Language 1. Living Organisms are Open Systems - exchange both energy and matter with their environment and transform it  not in equilibrium with the environment 2. Living Organisms are in Steady State (the Condition of an Open System) transfer rate of matter and energy transfer rate of matter and energy from the environment into the = out of the system system  the cell is a non-equilibrium open system 3. Living Cell - isothermal - no significant difference in pressure between parts of the cell - unable to use heat as a source of energy (heat can do work at constant pressure only if it passes from a zone of high temperature to zone of low temperature)  6th Axiom: Living cells function as isothermal chemical engines - energy absorbed from the environment is transformed into chemical energy to carry out chemical works at essentially constant temperature  For Your Eyes Only CHEMICAL REACTIONS in LIVING CELLS A. Enzyme Catalyzed Reactions - 100% yield - no by products 1. Specificity - one enzyme for one specific reaction - no effect on other chemical reactions  carry out many different chemical reactions simultaneously 2. Chemical Reactions - sequences of consecutive reactions - the product of the 1st reaction becomes the substrate of the 2nd reaction - connected into networks of converging or diverging pathways (linked by common intermediates) - sequential reactions makes the transfer of chemical energy possible  7th Axiom: The specificity of molecular interactions in cells results from the structural complimentarity of the interacting molecules - “lock and key” complimentarity between enzymes and substrates B. Divisions of Living Cells According to Type of Energy They Derive from the Environment 1. Photosynthetic Cell - sunlight as main source of energy - radiant energy absorbed by chlorophyll  chemical energy 2. Heterotrophic Cells - energy from highly reduced, energy-rich organic molecules - ex: glucose  CO2 + H2O C. ATP - major carrier of chemical energy - as it transfers energy to other molecule, it losses its terminal PO4 group  ADP D. ADP - discharged or energy poor - accept chemical energy by regaining PO4 group ATP  biosynthesis of cell components   ADP  energy from environment  For Your Eyes Only  8th Axiom: Consecutively linked sequences of enzyme catalyzed reactions provide the means for transferring chemical energy from energy-yielding to energy-requiring processes SELF-REGULATION of CELL REACTIONS A. Linkage of Enzyme-Catalyzed Reactions into Consecutive Sequences  regulation of metabolism with self-adjusting properties - over accumulation of an end-product of metabolism  inhibit the rate limiting step (feedback inhibition) B. Living Cells also Regulate the Synthesis of Catalysts  9th Axiom: Cells are capable of regulating their metabolic reactions and the biosynthesis of their enzymes to achieve maximum efficiency and economy SELF-REPLICATION of LIVING ORGANISMS A. 3 Features: 1. Some organisms are so immensely complex that the amount of genetic information transmitted seems out of proportion to the minute size of the cells that must carry it - genetic information is present in the chromosome coded through specific sequences of nucleotide building-blocks in a very amount of DNA  10th Axiom: The symbols in which the genetic information is coded in DNA are submolecular in dimension  For Your Eyes Only 2. Extraordinary stability of genetic information stored in DNA a. Structural Complementarity - one DNA strand serves as the template for the enzymatic replication of a structurally complimentary DNA strand b. DNA Breaks - may occur even in normal cells - quickly and automatically repaired by specific enzymes c. Errors of Mutation - infrequent - not always deleterious - may allow specie of organism to change its identity for adoption in the course of evolution 3. Genetic information is encoded in the form of a specific sequence of 4 different nucleotide building- blocks in the linear DNA molecule - the one-dimensional information of DNA is translated to 3-dimensional macromolecular and supramolecular components of living cells by translation of DNA structure into protein structure The MOLECULAR LOGIC of the LIVING STATE - a living cell is a self-assembling, self-regulating, self-replicating, isothermal open system of organic molecules operating on the principle of maximum economy of parts and processes; it promotes many consecutively linked organic reactions for the transfer of energy and for the synthesis of its own components by means of organic catalysts that it produces itself