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HLTH 101

Chapter 1Monday October 03 2005840 PM Chapter 1The Basic Molecular Themes of Life IntroductionoAll life is based on a number of basic molecular themes and the tremendous diversity in life forms we see are just variations on themoBiochemistry and molecular biology both try to understand life in molecular termsBiochemistry was the original name for this during a time when the main focus was on understanding the metabolism of food and small moleculesMolecular biology was a later name given and it focuses on the study of biological macromoleculesparticularly proteins DNA and the genetic mechanismUnity of life at the molecular leveloOn a molecular level all organisms are very similarwell at least the similarities exceed the differencesThis is because all organisms are derived from a single ancestor and so even though there has been a lot of evolution the basic principles remain the sameThis allows us to apply what we know about one organism to anotherLiving cells obey the laws of physics and chemistry the energy cycle in lifeoIntroductionWhen we build cellular systems we are making things ordered the opposite of entropy and so we need to expend energy in doing soThus a cell has greater energy than its surroundingsit wont achieve thermodynamic equilibrium until it dies and decomposesThe first law of thermodynamics states that energy can be neither created nor destroyedthe total amount of energy in the universe remains constantHowever we can transfer energy from one state to another for example cells extract the chemical energy in food to use as they see fitSee Figure 11 page 4The second law of thermodynamics states that all processes increase the total entropy of the universeEntropy is the degree of randomnessdisorder present in some systemthus as mentioned earlier a system of low entropy is at a higher energy than one of higher entropyoATP adenosine triphosphate is the universal energy currency in lifeProblem when we oxidate break down food free energy energy available to do work is released but there are so many different kinds of food and so many different processes to supply energy forSolution we use the food energy to form a universal molecule which can be used for energy by any processthis universal molecule is ATPATP is formed from and breaks down into ADP adenosine diphosphate and phosphateTypes of molecules found in living cellsoIntroductionAll biological molecules are based on a carbon atom bonded to some other guys mainly carbon hydrogen oxygen and nitrogen Other elements important to life include phosphorus sulfur and some metalionsThere are 2 categories of these biological cellular molecules small molecules and macromoleculesoSmall moleculesWater is the most prevalent of the small molecules over 70 of a cell is waterThe rest of the small molecules fall into some basic classesCarbohydrates have carbon and water in equal ratio store energyAmino acids building blocks of proteinsLipids form cell membranes store energySee Figure 12 page 5oThe macromolecular constituents of cellsMacromolecules are large structures formed by the polymerization of small units collectively known as monomersThus macromolecules are called polymersSimple polymers are the same monomer repeating thus there is no information content in themComplex polymers consist of different kinds of monomers thus there is information content in the order and type of monomersproteins and DNA are an example of thisProteinsoIntroductionThey are made up of 20 different kinds of amino acids into long chains called polypeptidesAfter they form these chains they fold into various 3D structures to differentiate themselves even moreSee Figure 13 page 6They can range from 50 amino acids in length to several thousandoCatalysis of reactions by enzyme proteins is central to the existence of lifeEnzymes are catalytic proteins which means they allow reactions to happen in an environment the cell which would otherwise not encourage them neutral pH low temperature etcThey are specificusually an enzyme only catalyzes a single reactionThey are efficienta catalyst can facilitate the conversion of thousands of molecules per secondWe have so many different kinds of enzymes because of the different ways that the amino acids can bond togetherthere are 20 different kinds and each protein can be from 502000 amino acids so there are many possibilitiesSince each polypeptide chain is coded for by a single gene and some proteins consist of multiple polypeptide chains we can have multiple genes coding for a single proteinWe can also have a single gene creating different kinds of proteins because of how the gene is splicedEvolution of proteinsoIntroductionEvolution depends on the synthesis of new kinds of proteins which give a selective advantageoDevelopment of new genesSometimes what happens is that we make two copies of an existing important gene and one of those copies gets mutatedthat way we maintain the essential function while gaining the new improved and possibly different functionoExamples of mutations which are maintained due to their advantageSickle cell anemiawhen we have it we dont get malariaThats why people can survive and carry this mutation because it gives an advantageCystic fibrosis providesprotection against choleraDiabetes in aboriginalshyperglycemia may be protective against cold temperaturesDNA deoxyribonucleic acidoIntroductionDNA is the substance of genesa complete DNA molecule is a chromosome which consists of DNA with proteins there as well to serve as structural componentsThe DNA tells the cell what order to put the amino acids in to form the proteins which will determine how the cell functionsThe monomers which make up DNA are called nucleotides and each nucleotide is made up of nitrogenous base sugar phosphate groupNitrogenous bases are adenine thymine guanine and cytosineDNA is made up 2 strands of these nucleotides which are bound together by hydrogen bondsIt is always set up so that an adenine nucleotide on one strand binds to a thymine nucleotide on the other strand and also cytosineguaninethis occurs because their shapes are complementarySee Figure 15 page 7oDNA can direct its own replicationIt is important for DNA to be able to replicate itself so that new cells can have the same genetic informationIt does this by separating its double strand and allowing enzymes to come and make new double strands out of each single onethis is called semiconservative replicationDNA directs protein synthesis through codonsevery 3 bases on a DNA strand is a codon which corresponds to a specific amino acid which is to be added onto the end of a polypeptide chainProteins are synthesized on cellular structures called ribosomesDNA is copied to mRNA messenger RNA which becomes a polypeptide assembled on the ribosome then turns into a protein via foldingAn unfolded protein is usually not even functionalFolding is facilitated by hydrogen bonds resulting from the hydrophobic amino acids on the inside of the molecule thus away from water and the hydrophilic amino acids on the surfaceMolecular recognition by proteinsoProteins are able to and indeed must combine to other molecules very specificallyThis is important for recognition of growth factors hormones substrate binding by enzymes and gene regulationoThe binding must also be reversibleand this is made possible because the binding is created by several weak ionic chemical bonds ionic bonds hydrogen bonds and van der Waals forcesIf the bonding wasnt reversible the enzyme would only be able to be used onceNoncovalent or weak chemical bondsoIn order from strongest to weakestIonic bonds are between oppositely charged ionsHydrogen bonds are dependent on partial atomic chargesVan der Waals forces are formed because of transient partial charges on atomsoFor all these bonds the atoms have to be very close togetherand so it is important that they be structurally complementary so that it fits just rightoBecause the bonds are weak they can be broken which is importantHow did it all startoIntroductionA membrane would have been crucial for the first ever living cell or else its contents would have dispersedSee Figure 18 page 11See Figure 19 page 11oThe RNA worldThe hardest part of the initial selfreplicating system would have been how its genetic system would have worked in order to bring about faithful replicationOne killer question is which came first the proteins to catalyze reactions or the nucleic acids to direct the synthesis of these proteinsRNA was an answer to this when we learned that RNA not a protein was able to catalyze certain reactionswe call the types of RNA which do this ribozymesSo maybe RNA could have been both the catalysts for the reactions AND the genetic material which directed the reactions
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