Chemistry of Life

Standard Level Biology: Chemistry of Life Topic 3: Chemistry of LifeOrganic compounds are compounds that are contain Carbon and can be found in living organisms, Inorganic compounds are the opposite of this.The most common chemicals found in living organisms are carbon, hydrogen, oxygen and nitrogen.Other chemicals that are not quite as frequent include: sulfur (found in amino acids), calcium (co-factor to enzymes), phosphorous (phosphate group of ATP), iron (found in cytochromes) and sodium (found in membrane function).Water is found in all cells - in the cytoplasm - The hydrogen and oxygen atoms are held together by a covalent bond.Water is polar due to the slightly charged covalent bonds, attracting other polar/charged compounds. They will bond via weak hydrogen bonds.Thermal properties in water allow it to absorb or give off great amounts of heat without changing temperature greatly (specific heat capacity). Water is used as a cooling mechanism when it is evaporated through our skin as it absorbs heat before leaving our bodies (high heat of vaporisation). Cohesive properties in water are a result of the polar attraction between water molecules, water has a fast molecular motion which makes it able to manipulate other molecules. When temperatures drops below 0* C the hydrogen bonds freeze and the molecules are solidified. Cohesion also allows surface tension hence the ability for some animals to walk across water.Solvent properties allow for transportation within organisms through water. Aqueous solutions are capable of carrying molecules through solvent properties such as blood in humans.Carbohydrates come in monosaccharides (glucose, fructose, galactose), disaccharides (sucrose, lactose, maltose) and polysaccharides (starch, glycogen, cellulose). Proteins consist of amino acid chains and create enzymes and antibodies. Lipids are constructions of fatty acids and create triglycerides and phospholipids. Nucleic acids can be found in DNA and RNA.Lipids are stored as excess fat with energy in them when too much food is consumed in comparison to the amount of activity (energy used) conducted. Lipids are also heat insulators, as seen in arctic animals that consist of an extra layer of fat known as blubber.Molecules are gained through food consumption when food is digested into the building blocks necessary for molecules. The blocks are transported to body cells and bond together to form larger molecules once again. Hydrolysis is a catabolic reaction in order to create the building blocks out of larger compounds. Water is a main component in hydrolysis as it splits to bond with two separate building blocks to complete their molecular structure.Condensation is the reverse of hydrolysis, the reaction occurs to reform the larger structure of several small blocks. Water is a product of condensation.

The structure of DNA consists of 3 parts making up a nucleotide: The phosphate spine, a deoxyribose (sugar) and a nitrogenous base that comes in 4 variations (Guanine, Adenine, Cytosine and Thymine)Hence the name Deoxyribonucleic Acid. Each nucleotide is covalently bonded together with the above to create a single helical structure. It is the complementary base-pairs that make up a double-helix structure. Adenine pairs with Thymine and Cytosine with Guanine. The base-pairs are held together through hydrogen bonds (A-T 2 bonds and C-G 3 bonds). The two strands of DNA are antiparallel (aligned in opposite directions)DNA replication begins with the unzipping of the hydrogen bonds between the base pairs with the enzyme Helicase. Two DNA polymerase enzymes then attach themselves to the two strands, going in the proper direction according to the direction of synthesis (due to the anti-parallel nature of the double helix). Floating nucleotides are covalently bonded as DNA polymerase codes them according to the nitrogenous base of the strand's nucleotide while also creating hydrogen bonds between the old and new nucleotide strands. The daughter strand and the mother strand become a new double-helix, hence two new double-helices are created. This is a semi-conservative process as half of the pre-existing DNA molevule is always conserved.Protein Synthesis consists of two stages: Transcription and Translation. During Transcription Helicase unzips a particular area of the DNA helix - the location of the gene needed to code for a particular protein - helicase begins at a starting gene and a terminating gene. Once the section is unzipped RNA polymerase bonds RNA nucleotides according to the genes being transcribed off the appropriate strand of DNA. RNA is a single-strand nucleic acid and uses Uracil instead of Thymine. mRNA is created during transcription (messenger ribonucleic acid) which then travels out of the nucleus to be translated through a Ribosome. The ribosome is an organelle residing on the endoplasmic reticulum and within the cytoplasm. It is composed of two factions. The mRNA enters through the ribosome where each codon (a set of three bases) will code for a specific tRNA carrying a specific amino acid. Two tRNAs will be present on the ribosome at the same time, one will then unattach and the amino acid will bond with the amino acid of the other tRNA (which will relocate on to the now empty spot of the ribosome). This process continues until each codon has been coded for and a specific polypeptide chain has been created.Enzymes act as catalysts.The purpose of an enzyme is to decrease the amount of energy required for a chemical reaction to occur.Enzymes are tertiary proteins, which means they are both primary and secondary structured proteins where the radical groups have bonded with one another in order to create a large and complex structure with an active site.Temperature may affect the enzyme's properties. The temperature of the environment may aid in the speed of the chemical reaction as the molecular collision increases. If the temperature is too high the enzyme's structure may be altered through denaturing it which can be permanent or temporary. If it is too cold the enzyme may freeze and become inactive. The pH balance affects the amino acids within he enzyme or the negative OH ions residing in the surrounding environment of the enzyme. When the pH is basic, the OH ions bond with either the substrate or enzyme, hence blocking the active site. When the pH is too high it can lead to denaturing the protein. Most enzymes prefer a neutral pH balance - except for pepsin which resides in the stomach.The substrate concentration increase will increase the rate of reaction as enzymes will be used to their full potential. Eventually this will reach the enzymatic rate limit, due to all the active sites of the enzymes being in full use. The reaction will continue at a constant rate from there on out, at a high speed.Lactase is the enzyme that catalyzes the breaking down of the disaccharide lactose. Due to our natural lactose intolerance after a certain age, milk products are digested prior to their consumption through lactase treatment.Cellular Respiration:

Covalent bonds in glucose, amino acids or fatty acids represent stored energy in all organic molecules. There are several methods of releasing the energy.Rapid oxidisation is seen in burning wood, the release of heat and light being the energy product, which is not controlled by enzymes.Cells can break down - metabolise - organic compounds in order to release energy for reactions requiring ATP to occur within the rest of the body. The breaking of covalent bonds releases ATP, with the help of enzymes.During cellular respiration the first step that must occur is the break-down of 6C glucose into two 3C pyruvate molecules (Net gain of 2 ATP and 2NADH). This occurs within the cytoplasm of the cell.After this the pyruvates will break down into two molecules of Acetyl CoA (gain of 2 NADH). Once the molecule enters the mitochondria's cristae it will undergo the Kreb's Cycle. Going from 2C molecules --> 6C --> 5C --> 4C where the molecule awaits the next Acetyl CoA for further cyclical reaction. This process occurs twice since there are 2 pyruvate molecules that must undergo it. During this process the products are 2 ATP, 6 NADH and 2 FADH for both acetyl-CoA.Finally each end-product (besides ATP) continues to the ETC (Electron Transport Chain) which is located within the cristae of the mitochondria. The total 8 NADH and 2 FADH are dehydrogenised through three complex proteins in the chain which results in H ions on the outside of the membrane, which are then pumped back into the intracellular matrix through the protein ATP synthase in order to bond a third phosphate group to ADP making ATP - oxidative phosphorylation. Each NADH supplies enough H ions to create 3 ATP and each FADH supplies enough H ions to create 2 ATP. Thus:Glycolysis: 2 ATP, 2 NADHLink/Junction: 2 NADHKreb's: 6 NADH, 2 FADH, 2 ATPETC: each NADHx3 and FADHx2 + ATP = 38 ATP

In the case that the respiration is anaerobic (no oxygen is available), there are two possible outcomes. Either two 2C Ethanol molecules and 2CO2 is produced from the pyruvates, with only a net gain of 2 ATP. Or two 3C lactase molecules are produced in which case there is no CO2 and the aerobic pathway continues, although the organism may suffer from the lactic acid.

Photosynthesis is the act of converting energy in the form of sunlight into glucose. Autotrophs photosynthesise as they are the primary stage of any food chain and provide the next trophic levels with energy that must be digested and hydrolysed. Plant cells consist of chloroplasts in order to absorb energy through green color pigments known as chlorophyll.

Photosynthesis is the act of bonding glucose together with covalent bonds as a food source for the plant through the use of ATP. It is a two stage process:1. Light dependent reaction - chlorophyll and other pigments within the chloroplast absorb photons (light energy) and convert it to NADPH and ATP. This energy enters the thylakoid's grana membrane into Photosystem II, exciting an electron. The electron enters the ETC with the help of an electron carrier that guides it through proteins. During this process H2O is split into Oxygen and Hydrogen molecules (photolysis), as well as allowing active transport for Hydrogen protons as the stroma consists of a low concentration gradient and the lumen of a high. the Hydrogen protons have stored energy and go on to ATP synthase to power the reaction of ADP into ATP.Photosystem I will undergo a similar process, except it provides energy to NADP reductase to create NADPH from NADP.The products of the Light independent reaction are: Oxygen (from the splits H2O), ATP and NADPH. These will move on to the Light Ind. reaction.

2. Light Independent Reaction - takes place in the stroma. The phase is known as carbon fixation which occurs in the Calvin cycle. During this process ATP and NADPH which were previously formed go on to a cycles where a carbon molecule changes from 6C --> 3C --> 3C and then back to 6C. The products of this are the transformations of ATP back to ADP and NADPH back to NADP+. These molecules then return to the Lumen of the grana where as a sugar has also been created (a monosaccharide) which will supply the plant with stored energy, along with the release of O2 that has occurred in the first stage of photosynthesis.The equation for photosynthesis is: energy + 6CO2 + 6H2O --> C6H12O6 + 6O2The level of cell respiration within plants is relatively low in comparison to an animal. Since the lack of need for more ATP as plants do not consist of muscles that are constantly in motion, their need for energy is limited to chemical reactions.Photosynthesis can be measured through the CO2 uptake, O2 production or measuring the biomass of the plant involved.A changing environment may affect the reaction as light intensity, changing temperature, carbon dioxide concentration all play a role in the storage of energy. Temperature will increase the molecular collision and hence cause a faster chemical reaction although to a certain extent as enzymes may denature when exposed to great heat. Light intensity will only increase the reaction rate although there is an enzymatic limit that may be reached and hence all enzymes would be working at their maximum potential (all active sites busy). Carbon dioxide will likewise only increase the reaction rate although it too has a limit concerning the rate of light energy and temperature available - it will reach a plateau.