BIOCHEM handouts

8/3/2019 BIOCHEM handouts

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Evolution is the theory that all living thingshave changed in response to environmentalconditions by the natural selection of randomlyoccurring mutations, developing from the simplestforms to complex forms which are more prolificand stronger, due to their better adaptation totheir environment.

provided this insight thatestablishes a great chain connecting the distantpast to the present.At the molecular level, evolution is the historyof the emergence of more complex biomoleculesfrom simpler organic monomeric units or evenfrom inorganic counterparts.:.:::.::-.::!si:+=r:

After the spontaneous synthesis oforganic molecules, the next step in evolutionwas the formation of macromolecules. Underprebiotic conditions, macromolecules areformed spontaneously from monomericbuilding blocks as shown below.

The well knownshowed that simple components can reactabiotically (or in the absence of life) to giverise to biologically important compounds -such as components of proteins and nucleicacids.

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Spark-d ischargeapparatus type used inthe Miller and Ureyexperimentdemonstrating theformation of organiccompounds in abiotic,primitive atmosphericconditions. Water isheated in a closed systemcontaining NH3, CH4, andH,. An electric discharoeis passed throuqh themixture of gasessimulating lightning. Afterseveral days, organicmolecules including aminoacids were among theproducts collected.

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From macromolecules come supramolecularcomplexes which now become integral partsand components of living cells.

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Canpbe|, Mary K and Shawn O. Farreil 246. tuchenislry 5th ed ThonsonBroakJcde, Belmont, cALehninger, Aben d al 1 993 Pdnciples of eochemistry 2^d ed. worth Publshers, New

Of the macromolecules in present-daycells, only the nucleic acids are capable ofdirecting their own self-replication.Nucleic acids can serve as templates fortheir own synthesis as a result of specificbase pairing between complementarynucleotides,"A critical step in understandingmolecular evolution was thus reached in theearly 1980s, when it was discovered in thelaboratories of andthat RNA is capable of catalyzing a numberof chemical reactions, including thepolymerization of nucleotides. RNA is thusuniquely able both to serve as a templatefor and to catalyze its own replication.

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This trio of macromolecules - DNA, RNA andproteins - is present in all cells. The rest arepolysaccharides, water, inorganic ions and alarge array of small organic molecules.One of the important molecules of life iswhat we know as genes - but are actuallychemically, deoxyribonucleic acids (DNA)- that define biological structure and maintaincellular integrity. These genes encodeproteins that make up cellular structures

and carry out many activities in the cell,particularly catalytic activity, that increasesrates of cellular reactions producing largenumbers of complex molecules. The"decoding" or expression of coded geneticinfo in DNA into proteins is made possible byanother molecule - the ribonucleic acids(RNA).

The central dogma of molecular biologyillustrated in the figure below shows theorganizing principle in the flow of geneticinformation: DNA to RNA to protein.Gcne I Gene 2 ()ene 3

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Consequently, RNA is generally believedto have been the initial genetic system, andan early stage of chemical evolution is thoughtto have been based on self-replicating RNAmolecules a period of evolution known as theRNA world. (a)Catalyst Replicationffi+Cffi

I A catah'tic RNA dir:ects its orvn it,I r'eplication u'itlt tlre origirral :! uriclcoticle sequence irnd shape. it_Figuresfron Canpbel, Mary K. and Shawn O. Fatrel. 2@6gochenlstry 5lh ed. fhonson Brcakgcde, Belnonl, CA.

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1) MONERA - prokaryotic organisms2) PROTISTA - unicellular eukaryotes such asEuglena, Volvox, Amoeba, Paramecium3) FUNGI - yeasts, molds, mushrooms4) PLANTAE - plants5) ANIMALIA - animals

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Another approach to classification has alsobeen established - the three classificationscheme (nicknamed the "tree of life").

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The universal phylogenetic "tree of life" as determined by RNA sequencesanalyses (from the work of et. al. Proc. Nat'1. Acad. Sci. USA87:4578, 1 990). The tree is based on comparisons of the nucleotide sequence ofa ribosomal RNA subunit in the different species belonging to the three divisions.The lengths of the lines represent the numbers of evolutionary changes that haveoccurred in this molecule in each lineage. Figure from Albefts, Bruce et. al. 2002.Molecular Biology of the Cell. 4th ed. Garland Publishing, New York.

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This system has shown that some of theorganisms that were traditionally classedtogether as "bacteria" are as widelydivergent in their evolutionary origin as isany prokaryote from any eukaryote. Theprokaryotes in this scheme comprisetwo distinct groups that diverged early inhistory of life: the BACTERIA (or eubacteria= true bacteria) and the ARCHAEA (orarchaebacteria = early bacteria).

The third division or domain is EUCARYAwhich include all eukaryotes.

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Archaebacteria are sometimes calledextremophles because they are commoninhabitants of extreme environments. Itincludes three groups:1) strict anaerobes thatproduce methane from CO2 and H22) - require very high saltconcentrations3) - require hightemperatures and acid conditions forgrowth, typically B0-90oC and pH2

methafiogens

Complete genomes are being obtained for organismsfrom all the th?ee domains; some genomes have beencompletely sequenced as shown in the figure below.!FEi: !! tsAerT_{ .:*r{rrlE lrzL illPrsERIli* +F iF itiElilLtitLEOTC,E ilii{EtN

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r:Based on free energy sources, all organisms canbe classified as either chemotrophs or phototrophsas shown in the figure below.

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A lithotrophic bacterium. Beggiatoa, which lives insulfurous environments, gets its energy by oxidizing H2S andcan fix carbon even in the dark. Note the yellow deposits ofsulfur inside the cells. (Courtesy of Ralph Wwolfe; /nagefrom A|befts, Bruce et. a|.2002. Molecular Biology oftheCell. 4th ed. Garland Publishing, New York; Figure abovefrom Lehninger, Albeft et. aI.1993. Principles ofBiochemistry.2nd ed. Wotth Publishers, New York.)


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DEFINITION- basic structural and functional unit of allorganisms- a small compartment bounded by a semi-permeable membrane filled withconcentrated aqueous solution ofchemicals and non-living products ofits activities that is able to carry on

independently all the basic life functions

ilffiffiil # #ilffi i#sqi- 2. Cell Dossesses oenetic information.All the information - to build anorganism along with all itsstructures, run all its activitiesand make more of themselves -are stored and encoded in thecollection of its genes packagedinto a set of chromosomes. Theinformation is hereditary and arestored in the cell's DNA.

Based on inherited instructions on its DNA, cellsreproduce by division on which the contents of a"mother" cell, after faithfully dupticating itsgenetic material (DNA) is distributed into two"daughter" cells, usually equally.

Metabolism is the sum totof all the chemicalreactions in the cell. Thechem ica I tra nsformationsthat proceeds requireenzymes that greatlyincrease the rate at whicha chemicaI reaction occurs

The cell is complexbecause of the greatnumber of parts that ithas to maintain but all ofthese parts are put inorder and in their properplaces consistently. As aconsequence, /ess error istolerated in the natureand interactions of theparfs placed in a systemthat is regulated andcontrolled.Photo lrom Lodish, HaNey el. al.2004. MoleculatCeI Biology. 51r ed.W.L. Freeman andcompany, New York.

4. Cellacquires and utilizes energy. 5. Cellengages in metabolism.Virtually, all of the energyrequired by life on theearth's surface arrives in theform of electromagneticradiation from the sun-whichphotosynthetic cells trap bytheir light-absorbingpigments present in cellmembranes. The lightenergy is converted byphotosynthesis into chemicalenergy that is stored assucrose or starch. 6. Cellengages in mechanical activities.Dynamic, mechanicalchanges are carriedout by the cell:transport of materialsfrom place to place,assembly anddisassembly ofstructures or the cellitself moves from onesite to another.

For animal cells, energycomes in the form ofsugar glucose (usuallyfrom the degradation ofstarch or glycogen).Glucose in cells aremetabolized in such away that it's energycontent is stored in areadily available form(such as ATP).

1. Cell structure is highly complexanized structur


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7. Cell senses and responds to changes in theenvironment.

For multi-cellular organisms like plantsand animals. their cells have specialstructures called receptors that -'interact"with substances in the environment. Theinteraction is communicated to the interior ofthe cell. The cell may respond by alteringsome metabolic activities, prepare for celldivision, initiate movement or commitsuicide (apoptosis).

8. Cell is iapable of self-regulation.The complex system of cells require thatthey put proper order and organizationto all the materials that make up theirstructure and, to all their mechanicaland metabolic activities especially in theacquisition of energy to sustainthemselves and to reproduce.The requirement is satisfied byconstant regulation. The importance ofregulation is greatly magnified by itsbreakdown. The cell may lose many ofits important functions or becomesaberrant that it is transformed into anuncontrolled cell as in the case of cancercells.

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Prokaryotes from an evolutionary point ofview, are considered to be "ancestors" ofeukaryotic cells. In the current three domainclassification scheme, prokaryotes are dividedinto two major divisions: the ARCHAEA (orachaebacteria) and the BACTERIA (oreubacteria).several groups of organismsthat live in extremely

meihanogens ( prokaryotesconverting CO2 and H2 gasesinto methane gas);halcphiies (prokaryotes thatlive in extremely saltyenvironments);thermcacidcphi les (prokaryotesthat live at very hightemperatures and very low pH).

Other species under the Domain Bacteria- Frsteobacteria:

a diverse group including photosyntheticsulphur bacteria (using H2S as an electrondonor in photosynthetic pathways),mitochondria relatives, and some humanpathogens (Salmonella, Vibrio cholerae)- Cyanobacteria:

probably the first oxygenic photosyntheticorganisms, they are similar structurallyand physiologically to chloroplasts ineukaryotes.- Splrochaetes:motile and often parasitic pathogens(syphilis, Lyme disease)- Chlamydias: exclusively parasitic- Firmicules: spore-forming pathogens -Staph, TB, tetanus

it;;;;;The types of prokaryotes belonging to thedomain Bacteria includes the myeaplasma,the smallest living cells. it also includes themost complex prokaryotes - thecyanabaeteria, which has elaborate arrays ofcytoplasmic membranes serving as sites ofphotosynthesis. Aside from photosynthesis,many cyanobacteria are also capable ofnitrogen fixation - the conversion of N2 gasinto reduced forms of nitrogen such asammonia that is used by cells in the synthesis

of nitrogen- containing compounds likenucleotides and amino acids.

Prokaryotes are typified by the best-and-most-studied prokaryotic cell, Eset'seri*kia *efi"Itibosomes Il*cterial rilrosorrrr:t et'{: 3rnrillct th..rnerrkal-v


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E. coli is a usuallyharmless inhabitantof the intestinal tractof human beings andother mammals, It isabout 2pm long andapproximately 1pmin diameter. It has aprotective cell walland an inner plasmamembrane thatencloses the interiorof the cell.

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Outside the plasma membrane are thin butstrong layers of p*pticir:glycar:s (sugar polymerscross-linked by amino acids) which gives the cellshape and rigidity protecting the cell.Bacterial cells have varying cell walls withdifferent affinilies for the dye Gentian violet, whichis the basis for Gram's stain - (gram+ bacteriaretain the dye and gram- bacteria do not).

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The genome of E, coli'(A) A cluster of E coli cells. (B) A diagram of the E coli genome of493g,22Lnacleotide pairs (for E, cori strain K-12), The diagram iscircular because the DNAof E coli, like that of other procaryotes'forms a single, closed loop. Protein-coding genes are shown as yellow oorange bars, depending on the DNA strand from which they aretranscribed; genes encoding only RNA molecules are indicated by greenarrows, Some genes are transcribed from one strand of the DNA doublehelix (in a clockwise direction in this diagram), others from the otherstrand (counterclockwise). (Ar courtesy of Tony Brain and the SciencePhoto Library; B. after F' R. Blattner et al.. Science2771L453-L462/ 1997. O AAAS')

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Some bacteria have t"y!*s+**g*es - which areinvaginations of the cell membrane. Themesosomes are associated with DNA synthesisand secretion of proteins.Also, in the plasma membrane of most eubacteriare electron carrying proteins called4:.Fjli.]rhr*r***, which are important in ATPformation from ADP.The interior of the cell consists of the rrt'LGF9=${ttand the iir!{i**id region. In the DNA-freeregion of the cytoplasm are the ribosomeswhich are sites of protein synthesis. An E. colihas about 15,000 ribosomes aside fromthousands of copies of each of differentenzyrnes, metabolites, cofactors and variousinorganic ions.F** !:J*ci*+irl is the DNA-containing region. It

contains a single, circular molecule of DNA.Aside from the DNA in the nucleoid, thecytoplasm of many bacterial species havesma ller extrachromosomal, ci rcu lar DNA calledpl+er-id.s. These plasmids may conferresistance to one or more antibiotics upon thebacterial cell. They are of extreme usefulnessto the molecular biologist because they can beeasily manipulated, separated andreincorporated to cells, cut and accommodateforeign gene inserts used in the techniques ingenetic engineering.


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