MCB 502A-2014. Lecture #1— Introduction to Molecular Biology.Course introduction — the questions — the nature of the “scientific fact”Introduction into Molecular BiologyMolecular Biology and Physiology vs Genetics and BiochemistryBiopolymers (BPs)Ways to transfer information in and between biopolymersThe Cellular Organization of LifeThe structure and dimensions of a bacterial cell— DNA as the main information carrier of life.The biochemistry of chromosomes. The tetranucleotide structure of DNA.Gene as a unit of information multiplication and transferExperiments of Griffith: the “transforming principle”Experiments of Avery, MacLeod and MacCarty on pneumococcal transformationExperiment of Hershey and ChaseObservations of ChargaffThis is a transition year— Typically, I teach in chalk-talk style,with lots of tables and diagrams thatstudents copy from the board, and lots ofhomework.— This year is a transition for me, as Iwant to expand the coverage andexperiment with new topics withoutdropping my typical ones. Therefore, Iwill be back to the powerpoint style, withno homework assignments.— So that you have an idea about whatkind of problems to expect at the exam, Iwill append examples to the lecture texts.Course introduction-1— The objective of this course is toteach you how to think as a MolecularBiologist.— I will neither confuse you with themost recent, often still questionable,developments in the field, nor bombardyou with tons of useless information.— Rather, we will follow the logic ofselect experiments, ……so that you will see not only what isknown today, but what were the originalquestions, what were the approaches toaddress them, the ideas to explain theexperimental observations, and wherethe major contradictions persist till thisday.Course introduction-2— In fact, you will eventually realizethat the only way to maintain usefulknowledge is to keep alive the originalquestions, rather than to memorize thefacts of the field.— The idea is that thinkingexperimentalists, starting with importantquestions, will eventually produceuseful answers themselves and mayeven learn something new in theprocess.— On the other hand, without thinking,even having all the "right" answers, wemay not be able to apply them anywayin the ever changing circumstances...… or just because we are not thinking!Questions are seeds of knowledge, but the tree of knowledgegrows only through active understanding.The nature of the “scientific fact”-1— I would like to start with a briefdiscussion of the nature of the“scientific fact”.— You should get comfortable with theidea that experimental science does notproduce “facts”, — it produces onlyunderstanding, and understanding is aprocess, rather than a product.— That is, understanding exists only inthinking brains, and as soon as brainsstop thinking, understanding vanishes,like light bulb when we shut downelectricity.The nature of the “scientific fact”-2— The instrument ofunderstanding is idea, which canbe developed into a hypothesisand then into a concept andeventually into a theory.— However, even the mostadvanced theory is still only aninstrument.ideahypothesisconcepttheoryInstruments of understandingThe nature of the “scientific fact”-3— It sounds paradoxical for non-scientists, whotake scientific theories for “facts”, but a theorydoes not need to be correct to be “right”.— A theory may eventually turn out to beincorrect (either generally or in important details),but it still can be the right theory for the moment,as long as it brings order to most of the extant dataand is testable (“falsifiable”).— In this respect, you will later appreciate the aptcomparison of “scientific fact” with a red flag…… that simply marks the point at which it wasdecided to stop further experimentation.Introduction into MolecularBiology— What is Molecular Biology?— A trivial definition of Molecular Biology is“experimental study of the molecular basis of Life”.— The three important points in this definition are: 1)experimental; 2) molecular; 3) Life.— “Molecular” should be clear (it refers to the“chemical” level of organization of the matter), butwhat is “experimental” and what is “Life”?— There are several characteristics that distinguish alive matter from the dead one: (like active transport or the ability to sense), but mostof them will be shared only by a subset of life forms.Self-replication of metabolismIn fact, there are only two functionalprinciples defining life that all life forms mustperform:1) the ability to extract from the environmentand process energy (e) and matter (m),— we call it “metabolism”, or (e+m)acquisition/processing.2) the ability to produce independently-functioning and almost exact copies of itself,— we call it self-replication.Functionally, Life can be described as self-replication of metabolism.What about Evolution?— Parenthetically, not only all forms of Lifepossess metabolism and self-replication, butthey also constantly strive to excel in boththrough the process of Evolution(propagation of the fittest).— Both metabolism and reproduction wouldbe impossible if the organism cannot secureresources to maintain and perform them.— The ability to secure the needed resourcesfor metabolism in a particular environment iscalled “survival in this environment”.Survival: the ability to secureresources for growth.Evolution-2— Although the measure of survival at thelevel of organism is individual growth, theintegral measure of adaptation in this specificenvironment is the number of successfulprogeny the organism produces compared toother similar organisms.— Indeed, the only point of securing resourcesfor robust metabolism is to make efficient useof this metabolism for self-reproduction.— Thus, “survival” and “productivity”measure organism’s evolutionary success(adaptation), based on how well themetabolism is supported and how efficiently itis translated into self-replication.— Reproduction: the ability toleave progeny.Experimental science starts withgood description of the phenomenon— Molecular Biology is anexperimental science, — it understandsthe world around us throughexperimentation.— Experimentation starts with anaccurate description of a phenomenon tobe understood (usually, somethingpuzzling, not intuitively clear), …… but then goes far beyond the originaldescription by repeating the magic
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