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New DNA sequencing methods
No full textSekvenciranje DNA je metoda koja omogućava određivanje redoslijeda nukleotida u DNA molekuli. Metode se dijele na tri generacije, koje se razlikuju po brzini, preciznosti, propusnosti, veličini fragmenata, te načinu njihove detekcije i analize. 1977. godine razvijena je Sangerova metoda, temeljena na sekvenciranju DNA fragmenata pomoću prethodno obilježenih dideoksinukleotid trifosfata koji sprječavaju povezivanje daljnjih nukleotida i time prekidaju sintezu lanca DNA. Paralelno sa Sangerovim otkrićem, 1977. godine Maxam i Gilbert razvijaju metodu temeljenu na nasumičnom cijepanju fragmenata DNA na različitim bazama s obzirom na korišteni agens (hidrazin, dimetil sulfid i dr.). Razvojem tehnologije dolazi do pojave metoda druge generacije kao što je pirosekvenciranje u kojem prilikom polimerizacije DNA dolazi do otpuštanja pirofosfata i emitiranja fotona koji služe za detekciju fragmenata. Pojavom detekcije u stvarnom vremenu otvorene su nove mogućnosti sekvenciranja DNA, poput monomolekulskog sekvenciranja (SMRT), te sekvenciranje pomoću nanopora. Sukladno razvoju novih metoda, otkrivene su nove tehnike sekvenciranja poput 454 pirosekvenciranja, Illumina, SOLiD, te HeliScopea. Korištenje metoda sekvenciranja DNA omogućava napredak brojnih prirodnih znanosti, poput genetike, biomedicine i biokemije, ali i napredak u proučavanju raznih bolesti, kao i u razvoju novih lijekova.DNA sequencing is a method that allows determination of nucleotide order in DNA molecule. Methods are divided into three generations, which differ in speed, precision, throughput, fragment size, and detection and analysis. In 1977, Sanger et al. developed a method based on DNA sequencing by pre-labelled dideoxynucleotide triphosphates, which prevent incorporation of further nucleotides and interrupt synthesis of DNA chain. In 1977, Maxam and Gilbert developed another method based on random cleavage of fragments depending on the used agents (hydrazine, dimethyl sulfide, etc.). Advancement of technology led to the development of the second generation methods, such as pyrosequencing in which DNA polymerization results in the release of pyrophosphates and emission of photons, used for the detection of fragments. Real-time detection opens new possibilities for DNA sequencing, such as single molecule real time sequencing (SMRT) and nanopore sequencing. In accordance with the development of new methods, new sequencing techniques, such as 454 pyrosequencing, Illumina, SOLiD and HeliScope, are discovered. The use of DNA sequencing allows advancement of numerous natural sciences, such as genetics, biomedicine and biochemistry, as well as a progress in studying of various diseases and development of novel drugs
Experimental techniques in biomineralization research
No full textBiomineralizacija je interdisciplinarna znanstvena grana, na granici kemije, biologije i znanosti o materijalima. To je proces koji se zbiva u živim organizmima u svrhu nastajanja biominerala. Prisutnost biominerala je raznolika pri čemu oni imaju brojne biološke funkcije poput zaštite, magnetske orijentacije, mehaničke snage, skladištenja iona i drugo. Od 60 trenutno poznatih biominerala, otprilike 20 % su amorfni, a 80 % kristalinični minerali. Osim biominerala procesom patološke biomineralizacije mogu nastati i biominerali koji nisu korisni za organizam u kojem nastaju. U svrhu njihova istraživanja koriste se brojne eksperimentalne metode analize taloga poput termogravimetrijske analize (TGA), skenirajuće (SEM) i transmisijske elektronske (TEM) mikroskopije, mikroskopije atomskih sila (AFM), svjetlosne mikroskopije (OM), metoda molekulske spektroskopije Ramanska i infracrvena spektroskopija (IR), metode dinamičkog raspršenja svjetlosti. Uz metode analize taloga postoje i metode analize tekuće faze poput potenciometrije, ionske kromatografije i Uv-Vis spektroskopije. U ovom završnom radu opisane su eksperimentalne metode i tehnike analize krutih uzoraka te je objašnjen princip djelovanja i njihova primjena u svrhu istraživanja biomineralizacije. Svaka metoda potkrepljena je primjerom.Biomineralization is an interdisciplinary scientific branch, on the border of chemistry, biology and materials science. This is a process that takes place in living organisms for the purpose of formation of biominerals. The presence of biominerals is diverse, and they have numerous biological functions such as protection, magnetic orientation, mechanical strength, ion storage and the like. Of the 60 currently known biominerals, approximately 20 % are amorphous and 80 % crystalline minerals. The pathological biomineralization process may also produce minerals that are not useful for the organism in which they are formed. For the scientific research of biominerals many experimental methods are used. For example for the precipitate analysis thermogravimetric analysis (TGA), scanning electron microscopy (SEM), transmission electron microscopy (TEM), atomic force microscopy (AFM), molecular Raman spectroscopy, infrared spectroscopy (IR) and dynamic light scattering (DLS) are one of the used methods. Except from the methods for the precipitate analysis there are also variety of the methods used for the analysis of the liquid phase and some of them are potentiometry, ionic chromatography and UV-VIS spectroscopy. In this bachelor thesis experimental methods and techniques of analysis of the precipitate are described and application of each method in biomineralization research is explained. For each described method an example in biomineralization research is given
Preparation of cinnamic acid ester with meta and para nitro derivatives of N-aryl pyridinones
No full textU ovome završnom radu opisana je sinteza estera cimetne kiseline s meta- i para-nitro derivatima N-arilpiridinona. U prvome djelu opisana je priprava N-aril supstituiranih 3-hidroksipiridin-4-ona, spoja 1 (3-hidroksi-2-metil-1-(m-nitrofenil)piridin-4-on) i spoja 2 (3-hidroksi-2-metil-1-(p-nitrofenil)piridin-4-on). Spojevi 1 i 2 pripravljeni direktnom metodom iz maltola i određenog primarnog amina, korišteni su u drugome djelu rada kao polazni spojevi u sintezi spojeva 3 ([2-metil-1-(m-nitrofenil)piridin-4-on-3-il]-3-fenilprop-2-enoata) i 4 ([2-metil-1-(p-nitrofenil)piridin-4-on-3-il]-3-fenilprop-2-enoata). Oba esterska derivata 3,4-HP i cimetne kiseline uspješno su pripravljena Steglichovom metodom esterifikacije. Strukture sintetiziranih spojeva potvrđene su NMR spektroskopijom (, , DEPTQ).In this work preparation of cinnamic acid derivatives of N-arylpyridinones is described. In the first part of this work preparation of N-aryl substituted 3-hydroxypyridin-4-ones, compound 1 (3-hydroxy-2-methyl-1-(m-nitrophenyl)pyridin-4-one) and compound 2 (3-hydroxy-2-methyl-1-(p-nitrophenyl)pyridin-4one) is presented. These two compounds were prepared from maltol and primary amine using direct method. In the second part of this work prepared compounds (1 and 2) were used as starting compounds in the synthesis of compounds 3 ([2-methyl-1-(m-nitrophenyl)pyridin-4-on-3-yl]-3-phenylprop-2-enoate) and 4 ([2-methyl-1-(p-nitrophenyl)pyridin-4-on-3-yl]-3-phenylprop-2-enoate). For esterification of compounds 1 and 2 with cinnamic acid Steglich esterification method was used. The structures of synthesized compounds were identified by NMR spectroscopy (, , DEPTQ)
Mehanochemical synthesis of calcium oxalate from calcium nitrate
No full textOvim istraživanjem je prikazana mehanokemijska sinteza kalcijeva oksalata, bez i uz prisutnost otapala (vode), u planetarnom kugličnom mlinu. Sva istraživanja do sada su ponajviše bila usmjerena na sintezu kalcijeva oksalata otopinskom kemijom. Ovim radom nastojalo se opisati drugačiji pristup, kako bi se pridonijelo novim saznanjima o sintezi kalcijeva oksalata, ekološki osvještenijom, mehanokemijskom metodom. Konačni cilj istraživanja jest sinteza, karakterizacija te identifikacija pojedine hidratne faze, dobivene reakcijom kalcijeva nitrata tetrahidrata i natrijeva oksalata. Reakcija je praćena u ovisnosti o vremenu reakcije i brzini mljevenja. Strukturna i termička svojstva uzoraka ispitana su FT-IR spektroskopijom i termogravimetrijskom analizom (TGA). Morfološke osobine kalcijeva oksalata, kao i klasifikacija veličine čestica, određene su optičkom mikroskopijom i metodom dinamičkog raspršenja svjetlosti (DLS).The study presents the mechanochemical synthesis of calcium oxalate, without and in the presence of solvents, in a planetary ball mill. All studies so far have focused mainly on the synthesis of calcium oxalate using solution chemistry. In this paper, we described a different approach that could contribute to new findings in the field of calcium oxalate synthesis using mechanochemical approach. The ultimate goal of the research is synthesis, as well as structural characterization and identification of individual oxalate hydrate phase, gained by the synthesis of calcium salts (of the chlorides, nitrates and sulphates). The reaction is monitored depending on the duration of the synthesis, to determine if the effect of the milling velocity on the reaction exists. Structural and thermal properties of the sample were tested by FTIR spectroscopy and thermogravimetric analysis (TGA). Morphological properties of calcium oxalate as well as particle size distribution are gained by optical microscopy and dynamic light scattering (DLS)
Peroxidation of lipids: measurement methods
No full textLipidi su prirodni spojevi koji su topivi u organskim otapalima i pripadaju u skupinu estera. Grade ih zasićene ili nezasićene prirodne masne kiseline koje se sastoje od dugačkog ugljikovodičnog lanca koji sadrži paran broj ugljikovih atoma od C14 do C24. Višestruko nezasićene masne kiseline (PUFA) i monozasićene masne kiseline imaju ciskonfiguraciju dvostruke veze. Složeni lipidi su fosfolipidi i sfingolipidi koji sadrže šećere, dušične baze, alkohole i dugolančane masne kiseline. Lipidna peroksidacija je spontani proces koji uzrokuje hidroksilni radikal (OH) i sastoji se od tri faze: inicijacije, propagacije i terminacije. Produkti lipidne peroksidacije nisu stabilni i uzrokuju različite biološke efekte. Fe(II) ion je najznačajniji inicijator peroksidacije koja se odvija mehanizmom slobodnih radikala. Procesi oksidacije lipida prate se različitim metodama i mjernim tehnikama. Spektrofotometrijsko mjerenje konjugiranih UV diena jedna je od izravnih metoda određivanja hidroperoksida. Feritiocijanatna metoda je metoda kojom se određuju hidroperoksidi lipida. Specifične funkcionalne skupine i geometrijska izomerizacija masnih kiselina može se odrediti IR spektroskopijom. Lipidni peroksidi stvaraju mnogobrojne razgradne produkte: aldehide, ugljikovodike, ketone, epokside i aktivne radikale pod djelovanjem iona bakra ili željeza.Lipids are natural compounds which are soluble in organic solvents and they are esters. Lipids are made of saturated or unsaturated natural fatty acids which are made of long hydrocarbon chain with even number of carbon atoms (C14 - C24). Polyunsaturated fatty acids (PUFA) and monosaturated fatty acids have cis-configuration of double bond. Complex lipids are phospholipids and sphingolipids made of sugar, nitrogen base, alcohol and long chains of fatty acids. Lipid peroxidation is spontaneous process caused by OHradical. It consists of three steps: initiation, propagation and termination. Lipid peroxidation products are not stable and cause different biological effects. Fe(II) ion is most important initiator of peroxidation which is made by free radical mechanism. Processes of lipid oxidation are being studied with different methods and measurement techniques. Spectrophotometric measurement of conjugated UV diens is one of direct methods for hydroperoxides determination. The ferricthiocyanate method is method for estimation of lipid hydroperoxides. Specifics functional groups and geometrical isomerization of fatty acids can be determined with IR spectroscopy. Lipid peroxides, under the influence of copper and iron ions, create many products: aldehydes, hydrocarbons, ketones, epoxides and active radicals
The first law of thermodynamics
No full text1. zakon termodinamike jedan je od ključnih elemenata jedne od temeljnih teorija fizike-klasične termodinamike. Termodinamika je fenomenološka teorija, a njeni koncepti i zakoni odnose se na makroskopska svojstva termodinamičkih sustava. Tri su koncepta važna za formulaciju 1. zakona termodinamike: unutrašnja energija (U), toplina (Q) i rad (W). Izražen pomoću infinitezimalnih veličina 1. zakon termodinamike glasi: dU= đQ - đW (đW je bilo koji rad koji uzrokuje promjenu unutrašnje energije). Prema kinetičkoj teoriji i statističkoj fizici, makroskopska svojstva i zakonitosti termodinamičkih sustava su posljedica gibanja čestica i njihovog međudjelovanja. 1. zakon termodinamike je također neposredna posljedica zakona očuvanja energije. Značaj 1. zakona termodinamike za kemiju očituje se u tome što on, uz ostale zakone termodinamike, ima ključni značaj za analizu kemijskih procesa i reakcija pomoću koncepata kao što su termodinamički potencijali (npr. entalpija i Gibbs-ova slobodna energija). Na kraju smo značaj 1. zakona termodinamike za razmatranje i utvrđivanje različitih svojstava termodinamičkih sustava, kao što su uvjeti; ravnoteže, toplina kemijske reakcije, spontanost kemijske reakcije, promjena unutrašnje energije sustava, ilustrirali s nekoliko primjera.The first law of thermodynamics is one of the key concepts in fundamental physical science. Thermodynamics is the branch of physics that deals with macroscopic properties of thermodynamic systems. Three concepts are important for formulation of the first law: internal energy (U), heat (Q) and system work (W). When expressed in infinitesimmal quantities the first law of thermodynimcs states: dU=đQ - đW (đW is any work that causes change of internal energy). According to kinetic theory and statistical physics, macroscopic properties and rules of thermodynamic systems are consequence of motion and interaction of individual particles. The first law of thermodynamics is immediate consequence of the law of conservation of energy. The first law, along with other laws of thermodynamics, is of great significance in chemistry, since it has key role in analysis of chemical processes and reactions using concepts such as thermodynamic potentials (e.g. enthalpy and Gibbs free energy). Finally, the importance of the first law in analysing and determining various properties of thermodynamic systems, such as conditions of thermodynamic equilibrium, heat and spontaneity of a chemical reaction and change in internal energy of a system, was illustrated with several examples
Influence of magnetic stirring, temperature and citrate concentration on the precipitation of calcium oxalate dihydrate
No full textThis paper reports on the investigation of experimental conditions relevant for spontaneous precipitation of significant amount of pure calcium oxalate dihydrate (COD). For this purpose, the hydrodynamic and thermodynamic parameters, such as mode of agitation, temperature, supersaturation and concentration of additives (citrate ions), have been studied. The results show that in the model systems, without the citrate addition and applied mechanical stirring, calcium oxalate monohydrate (COM) was observed as dominant modification after 20 min of aging, while the magnetic stirring resulted in a formation of a mixture of COM and calcium oxalate trihydrate (COT), regardless of the temperature applied. In the mechanically stirred systems, the addition of citrate ions in the range of concentrations, 0.001 mol < < 0.012 mol , caused the formation of COM and COD mixture at all temperatures. At the same conditions and in the magnetically stirred systems formation of COD, in a mixture with COT or COM, has been observed. The highest COD content in the mechanically stirred system was obtained at 45 °C and = 0.001 mol (w = 89.5%), while in the magnetically stirred system almost pure COD was obtained at 37 °C and = 0.008 mol (w = 96.5%)
Determination of fatty acid profile in different types of oils
No full textMasne kiseline su kemijski spojevi koji imaju vrlo bitnu ulogu u ljudskom organizmu, pretežno kada se govori o čovjekovu zdravlju. Njihova građa je dobro poznata, radi se o karboksilnim kiselinama koje mogu nastati hidrolizom triacilglicerola, esterskog spoja koji se hidrolizira na tri slobodne masne kiseline čija je opća struktura prikazana u obliku RCOOH (, , ), i triol, odnosno trovalentni alkohol, glicerol. Pomoću plinske kromatografije i metodom metilnih estera masnih kiselina (eng. Fatty acid methyl ester, FAME) uspješno su određeni profili masnih kiselina iz različitih vrsta ulja. Ova analitička metoda pomaže znanstvenicima izolirati, ispitati, odrediti i dokazati spojeve koje svakodnevno konzumiramo u obliku hrane, pomaže dobro upoznati i opisati njihove nutritivne vrijednosti i iznijeti samu njihovu važnost u ishrani ljudi.Fatty acids are chemical compounds which play a very important role in the human organism, especially when it comes to human health. Their structure is very well known- they are carboxylic acids, products of hydrolysis of tryacylglycerol, an esteric compound which is hydrolyzed into three free fatty acids whose general structure is always shown as RCOOH (, , ) and triol or trivalental alcohol, glycerol. Gas chromatography and fatty acid methly ester method proved to be very helpful and have successfully determined fatty acid profiles from various types of oils. This analytical procedure is very usefull to scientists and it helps to isolate, examine, determineand prove compounds that are daily consumed in the form of food, furthermore it allows them to understand and describe nutritional vaules of fatty acids and express their importance in human's diet
Determination of omega-3 fatty acid concent in eggs using gas chromatography
No full textJaja se smatraju koncentriranim izvorom hranjivih tvari. U sastavu jaja možemo naći proteine, masti, nezasićene masne kiseline, dobar su izvor vitamina A, D, E i K, a nalazimo i željezo i fosfor. Obogaćivanjem jaja različitim nutrijentima, jaje postaje funkcionalna hrana. Istraživanjem utjecaja omega-3 masnih kiselina na zdravlje ljudi, utvrđen je niz dobrobiti pa se u današnje vrijeme brzog načina života pojavila potreba za proizvodnjom lako dostupnog izvora omega-3 masnih kiselina. U ovom radu opisan je postupak analize, rezultati i usporedba rezultata analize profila masnih kiselina jaja kokoši nesilica koje su bile hranjene hranom koja nije obogaćena omega-3 masnim kiselinama, i hranom koja je u svom sastavu imala omega-3 masne kiseline, kao bi se utvrdilo utječe li sastav hrane na povećanje sadržaja omega-3 masnih kiselina u jajima.Eggs are considered as an excellent source of nutrients. In the egg composition we can find proteins, fat, unsaturated fatty acids, vitamins A, D, E and K, as well as iron and phosphorus. By enriching eggs with different nutrients, the egg becomes functional food. Investigating the effects of omega-3 fatty acids on human health, a variety of well-being has been identified, so today's fast lifestyle has emerged the need to produce an easily accessible source of omega-3 fatty acid . This paper describes the process of analysis, results and comparison of the results of the analysis of fatty acid profile of eggs of hens that were fed with non-enriched omega-3 fatty acids food, and food that is rich in omega-3 fatty acids. The study was conductet to determined whether the composition of the food affects the increase of the omega-3 fatty acid content in the eggs
The Mechanism of Reduction of HMG-CoA Catalyzed by Human HMG-CoA Reductase
No full textRedukcijski mehanizam HMG-CoA katalizirane ljudskom HMG-CoA reduktazom ispitivan je QM/MM (ONIOM) metodom. Sustav je podijeljen na dva dijela gdje se aktivno mjesto tretiralo kvantnom mehanikom (DFT, B3LYP), a ostatak enzima s klasičnim metodama molekularne mehanike. Istraživana su tri različita modela drugog hidridnog prijelaza mehanizma s različitim protonacijskim stanjima katalitičkih amino kiselinskih ostataka. U aktivnom mjestu nalazio se NADPH kofaktor, mevaldehid substrat te glutamat, lizin, aspartat i histidin (Glu98, Lys639, Asp715 i His405). Metodom molekularne dinamike (MD) dobila se najpovoljnija konformacija početne kristalografske strukture, koja se koristila u svim daljnjim simulacijama. U prvom modelu glutamta i aspartat su bili deprotonirani, lizin je bio protoniran, a histidin dvostruko protoniran, dok je u drugom modelu histidin bio protoniran, a u trećem modelu lizin deprotoniran.Reduction mechanism of HMG-CoA catalysed by human HMG-CoA reductase has been studied with the QM/MM (ONIOM) method. The system has been partitioned in two parts where the active site was treated with quantum mechanics (DFT, B3LYP) and the rest of the enzyme with classical methods of molecular mechanics. The second hydride transfer of the catalytic mechanism have been studied through three different models with different protonation states of the catalytic residues. In the active site NADPH cofactor, mevaldehyde substrate, glutamate, lysine, aspartate and histidine (Glu559, Lys639, Asp715 i His405) were placed. Through molecular dynamics simulations the most favourable conformation of the initial crystallographic structure was obtained and used throughout all the later simulations. In the first model, glutamate and aspartame were deprotonated, lysin was protonated and histidine was doubleprotonated, whereas in the second model, histidine was protonated, and in third model lysine was deprotonated