Introduction to Chemistry 1. Atoms make up elements which are the basic building blocks that make up matter. Atoms are made up of protons neutrons and electrons. The nucleus or center of the atom contains protons and neutrons. Electrons orbit the nucleus. Protons have a positive charge, neutrons have no charge and electrons have a negative charge. In each element, the protons equal the number of electrons so that each element has no net charge. 2. Electrons orbit the nucleus at distinct energy levels. These are called orbitals. The first energy level or first orbital can only hold up to two electrons. The subsequent energy levels or orbitals can hold up to eight electrons. When an energy level or orbital contains the maximum amount of electrons, the element is stable. 3. Diagrams of the elements can be made using the Lewis dot structure. The nucleus is in the center and the orbitals are drawn as circles surrounding the nucleus. Draw this Lewis dot structure of H, He, Li, Be, B , C, N, O, F, Ne, Na, and Mg. 4. Elements can react with one another based on the number of electrons in their outer orbitals. Each element wants to become stable. They can become stable by losing electrons, gaining electrons, or sharing electrons so that the number of electrons in their outer orbital is the maximum that it can hold. Except for hydrogen and helium, this number is eight. 5. Using the Periodic table identify which elements are metals, non-metals and inert gasses for the first twenty elements. 6. When elements react with one another they form compounds. Compounds are held together by bonds. There are two major types of bonds, ionic and covalent. Ionic bonds are formed when two or more elements lose or gain electrons forming ions such as sodium and chlorine. (NaCl) Draw the Lewis structure of salt. Some metals can react with water or HCl forming ionic bonds making different compounds for example. 2Li +2H2O→2LiOH+H2 Since Lithium can donate one electron to H+ , and one more to another H+ these can then bind together to become H2 and Li Write the reactions for Na + H2O and K + H2O. (Make sure the equations are balanced) Beryllium, Magnesium, and Calcium react with Hydrochloric acid to produce salts in the same manner as Zinc. Zn +2HCl → ZnCl2 + H2 Write these reactions 7. Covalent bonds occur when two or more elements share electrons such as methane. (CH4) Draw the Lewis structure of methane. 8. Water is a covalently bound compound. However, it can disassociate into two different ions [OH]- and [H]+ . If water has a high level of [OH]- ions, it is basic. If it has a high level of [H]+ ions, it is acidic. Write this reaction. ( Acid Base titration experiment) H2O ↔ H+ + OH9. Another important aspect of water is its polar property. Water is covalently bound. However, it shares its electrons unevenly. This makes the molecule have a side with a more negative charge and one with a more positive charge. Introduction to Organic Chemistry The introduction to chemistry in the previous study showed how elements bind to become molecules. They can form either ionic bonds or covalent bonds based upon whether they exchange electrons from their outer orbitals or share their outer orbital electrons. Examples from the previous study included sodium and chorine forming an ionic bond to form sodium chloride (salt) and carbon forming four covalent bonds with hydrogen to form methane (CH4). Hydrocarbons Carbon bonding is the basis for organic chemistry. Organic compounds are the products of living organisms. The most simple organic molecules are hydrocarbons. Hydrocarbons are binary compounds made up of carbon and hydrogen. Methane is a hydrocarbon .The next is ethane with two carbon atoms covalently bound to one another with three hydrogen atoms bound to each carbon atom. (Draw the Lewis Dot Structure of ethane) The next is propane with three carbon atoms covalently bound to each other and eight covalently hydrogen atoms. (Draw this structure) These carbon chains can increase in the same manner to become propane, butane, pentane, hexane, heptane, octane etc… It becomes difficult to draw these molecules in Lewis dot structure. Therefore, these molecules are drawn with lines indicating the bonds between the atoms. (Draw these structures in this manner.) Methane Ethane Propane Butane Alcohols The next group of organic molecules include alcohols. Alcohols are structurally similar to hydrocarbons except that one of the terminal hydrogen atoms is replaced by a hydroxyl group (oxygen with one hydrogen atom bound to it, OH). They are named according to their carbon chains with the suffix OL. (Draw these) Methanol Ethanol Propanol Butanol Sugars Another group of organic molecules are saccharides (sugars). Derived by photosynthesis, they are the form of energy that supplies the Planet. They are named according to the number of carbons in their carbon chains. The most abundant being glucose, a six carbon sugar. (i.e. a hexose) hexose Glucose Simple sugars are sweet in taste and are broken down quickly in the body to release energy. Two of the most common monosaccharides are glucose and fructose. Glucose is the primary form of sugar stored in the human body for energy. Fructose is the main sugar found in most fruits. Both glucose and fructose have the same chemical formula (C6H12O6); however, they have different structures, as shown (note: the carbon atoms that sit in the "corners" of the rings are not labeled): Glucose Fructose Disaccharides have two sugar units bonded together. For example, common table sugar is sucrose, a disaccharide that consists of a glucose unit bonded to a fructose unit: Sucrose Complex Carbohydrates Complex carbohydrates are polymers of the simple sugars. In other words, the complex carbohydrates are long chains of simple sugar units bonded together. All carbohydrates are made up of units of sugar (also called saccharide units). For this reason the complex carbohydrates are often referred to as polysaccharides. Amylose (starch) Glycogen (Photosynthesis and its products will be addressed in biology) Organic Acids A further s group of organics are organic acids. Organic acids have a functional group known as the carboxyl group (COOH) attached to the terminal carbon. Carbon with a double bond to one Oxygen and a single bond to another with Hydrogen bound to that Their names are as above with the suffix OIC. Methanoic acid Ethanoic acid Propanoic acid Butanoic acid An essential biomolecule is the Amino acid The general structure of an α-amino acid, with the amino group on the left and the carboxyl group on the right. An amino acid is a molecule containing both amine and carboxyl functional groups Amino acids are built from a central carbon bonded to four different groups 1. 2. 3. 4. hydrogen (–H), amino group (–NH2), carboxyl group (–COOH), and some side chain symbolized by “R”. In the approximately-20 amino acids found in our bodies, what varies is the side chain. Some side chains are hydrophilic while others are hydrophobic. Since these side chains stick out from the backbone of the molecule, they help determine the properties of the protein made from them. Most naturally-occurring amino acids are the l- form, whereas syntheticallyproduced amino acids give a 50:50 mixture. Notice that these molecules are mirror images of each other, thus there is no way you can rotate one molecule to make it look like the other. These molecules are particularly important in biochemistry. In the amino acids, the amino and carboxylate groups are attached to the same carbon, which is called the α–carbon. The various alpha amino acids differ in which side chain (R group) is attached to their alpha carbon. They can vary in size from just a hydrogen atom in glycine through a methyl group in alanine to a large heterocyclic group in tryptophan. Amino acids are very important in nutrition and are critical to life. One particularly important function is as the building blocks of proteins, which are linear chains of amino acids. Amino acids are also important in many other biological molecules, such as forming parts of enzymes. Proteins Proteins are about 50% of the dry weight of most cells, and are the most structurally complex macromolecules known. Each type of protein has its own unique structure and function. Polymers are any kind of large molecules made of repeating identical or similar subunits called monomers. The starch and cellulose we previously discussed are polymers of glucose, which in that case, is the monomer. Proteins are polymers of about 20 amino acids (the monomer). To form protein, the amino acids are linked by dehydration synthesis to form peptide bonds. The chain of amino acids is also known as a polypeptide. This is its primary structure. Some proteins contain only one polypeptide chain while others, such as haemoglobin, contain several polypeptide chains all twisted together. The sequence of amino acids in each polypeptide or protein is unique to that protein, so each protein has its own, unique 3-D shape or native conformation. If even one amino acid in the sequence is changed, that can potentially change the protein’s ability to function. For example, sickle cell anaemia is caused by a change in only one nucleotide in the DNA sequence that causes just one amino acid in one of the haemoglobin polypeptide molecules to be different. Because of this, the whole red blood cell ends up being deformed and unable to carry oxygen properly. As a polypeptide chain forms, it naturally twists and bends into its native conformation. One of the things that helps determine the native conformation of a protein is the side chains of all the amino acids involved. Remember some amino acid side chains are hydrophobic while others are hydrophilic. In this case, the “likes” attract: all the hydrophobic side chains (here represented by yellow beads) try to “get together” in the center of the molecule, away from the watery environment, while the hydrophilic side chains are attracted to the outside of the molecule, near the watery environment. Additionally, some of the hydrophilic side chains have groups of atoms attached that make them acidic, while others have groups attached that make them basic. Side chains with acidic ends are attracted to side chains with basic ends, and can form ionic bonds. Thus, the side chains interacting with each other help to hold the protein in its native conformation. is when a protein loses its native conformation. For example, egg white (also called albumen) contains a protein called albumin which is water-soluble. However, if heated, albumin becomes denatured and loses its ability to be watersoluble. There are several possible things that can denature proteins including changing the temperature (adding heat), changing the pH or salt concentration of the solution, or putting the protein into a hydrophobic solvent. In a hydrophobic solvent, the amino acids with hydrophobic side chains (the yellow beads) would all try to go to the outside of the molecule, and all those with hydrophilic side chains would cluster in the center of the molecule. If a protein remains water-soluble when denatured (unlike albumin), it can return to its native conformation if/when placed back into a “normal” environment. Denaturation Lipids: Fats, Oils, Waxes, etc. All Lipids are hydrophobic: They fear water. They are long chained fatty acids and make up a number of organic molecules This group of molecules includes fats, oils, waxes, phospholipids, steroids and cholesterol and other related compounds. The most important. in this study, are the phospholipids. Fats and oils are made from two kinds of molecules: glycerol (a type of alcohol with a hydroxyl group on each of its three carbons) and three fatty acids joined by dehydration synthesis. Since there are three fatty acids attached, these are known as triglycerides. The main distinction between fats and oils is whether they’re solid or liquid at room temperature this is based on differences in the type of bonds they have. The more double bonds they have the less saturated they are of hydrogen. Phospholipids Phospholipids are made from glycerol, two fatty acids, and in place of the third fatty acid a phosphate group is attached to its other end. The hydrocarbon tails of the fatty acids are still hydrophobic, but the phosphate group end of the molecule is hydrophilic because of the the charges they can interact with the dipolar nature of water. . Our cell membranes are made mostly of phospholipids arranged in a double layer with the tails from both layers “inside” (facing toward each other) and the heads facing “out” (toward the watery environment) on both surfaces. . Cell Structure Cellular Membrane Our cell membranes are made mostly of phospholipids arranged in a double layer with the tails from both layers “inside” (facing toward each other) and the heads facing “out” (toward the watery environment) on both surfaces. Phospholipid bilayers When phospholipids are suspended in water they can form a variety of structures. In all cases the hydrophilic phosphate region interacts with water and the hydrophobic fatty acid regions are excluded from water and form hydrophobic interactions. Different structures that can result when phospholipids are suspended in water are shown above. A bilayer of phospholipids forms a sphere in which water is trapped inside. The hydrophilic phosphate regions interact with the water inside and outside of the sphere. The fatty acids of the phospholipids interact and form a hydrophobic center of the bilayer. The beginning of primordial bacterium. This is the basis for the cell membrane. Within this bilayer are innermembrane proteins. These proteins can act as receptors, transport channels, or as cellular recognition sites Mi·to·chon·dri·on A spherical or elongated organelle in the cytoplasm of nearly all eukaryotic cells, containing genetic material and many enzymes important for cell metabolism, including those responsible for the conversion of food to usable energy. It consists of two membranes: an outer smooth membrane and an inner membrane arranged to form cristae. Mitochondria structure: 1) Inner membrane 2) Outer membrane 3) Crista 4) Matrix In cell biology, a mitochondrion (plural mitochondria) is a membraneenclosed organelle found in most eukaryotic cells.[1] These organelles range from 1–10 micrometers (μm) in size. Mitochondria are sometimes described as "cellular power plants" because they generate most of the cell's supply of adenosine triphosphate (ATP), used as a source of chemical energy. In addition to supplying cellular energy, mitochondria are involved in a range of other processes, such as signaling, cellular differentiation, cell death, as well as the control of the cell cycle and cell growth.[2] Mitochondria have been implicated in several human diseases, including mental disorders[3] and cardiac dysfunction,[4] and may play a role in the aging process. The word mitochondrion comes from the Greek μίτος or mitos, thread + χονδρίον or khondrion, granule. Their ancestry is not fully understood, but, according to the endosymbiotic theory, mitochondria are descended from ancient bacteria, which were engulfed by the ancestors of eukaryotic cells more than a billion years ago. Several characteristics make mitochondria unique. The number of mitochondria in a cell varies widely by organism and tissue type. Many cells have only a single mitochondrion, whereas others can contain several thousand mitochondria.[5][6] The organelle is composed of compartments that carry out specialized functions. These compartments or regions include the outer membrane, the intermembrane space, the inner membrane, and the cristae and matrix. Mitochondrial proteins vary depending on the tissues and species. In human, 615 distinct types of proteins were identified from cardiac mitochondria;[7] whereas in murinae (rats), 940 proteins encoded by distinct genes were reported.[8] The mitochondrial proteome is thought to be dynamically regulated.[9] Although most of a cell's DNA is contained in the cell nucleus, the mitochondrion has its own independent genome. Further, its DNA shows substantial similarity to bacterial genomes.[10] Energy conversion Mitochondria convert the potential energy of food molecules into ATP. The production of ATP is achieved by the Krebs cycle (see citric acid cycle), electron transport and oxidative phosphorylation. Without oxygen, these processes cannot occur. The energy from food molecules (e.g., glucose) is used to produce NADH and FADH2 molecules, via glycolysis Glycolysis Glycolysis (from glycose, an older term[1] for glucose + -lysis degradation) takes place in the cytoplasm. It is the metabolic pathway that converts glucose, C6H12O6, into pyruvate, C3H5O3-. The free energy released in this process is used to form the high energy compounds, ATP Adenosine triphosphate Molecular C10H16N5O13P3 formula . (adenosine triphosphate) and NADH (reduced nicotinamide adenine dinucleotide). Glycolysis is a sequence of ten reactions involving ten intermediate compounds (one of the steps involves two intermediates). The intermediates provide entry points to glycolysis. For example, most monosaccharides, such as fructose, glucose, and galactose, can be converted to one of these intermediates. The intermediates may also be directly useful. For example, the intermediate, dihydroxyacetone phosphate, is a source of the glycerol that combines with fatty acids to form fat (triacylglycerides). Glycolysis results in the net production of 2 ATP and 2 NADH ions. If oxygen is present, the product of glycolysis, pyruvate, can enter the citric acid cycle, where it is converted into carbon dioxide. The free energy released in that process is used to produce considerably more ATP and NADH. Under anaerobic conditions, glycolysis may be the main energy source of an organism. This is the case in many prokaryotes, in eukaryotic cells devoid of mitochondria (e.g., mature erythrocytes), and in aerobic eukaryotic cells under low-oxygen conditions (e.g., heavily-exercising muscle or fermenting yeast). Glycolysis is the archetype of a universal metabolic pathway. It occurs, with variations, in nearly all organisms, both aerobic and anaerobic. The wide occurrence of glycolysis indicates that it is one of the most ancient metabolic pathways known. The overall reaction of glycolysis is: D-Glucose Pyruvate + 2 NAD+ + 2 ADP + 2 Pi 2 + 2 NADH + 2 H+ + 2 ATP + 2 H2O For simple anaerobic fermentations, the metabolism of one molecule of glucose to two molecules of pyruvate has a net yield of two molecules of ATP. Most cells will then carry out further reactions to 'repay' the used NAD+ and produce a final product of ethanol or lactic acid. Many bacteria use inorganic compounds as hydrogen acceptors to regenerate the NAD+. Cells performing aerobic respiration synthesize much more ATP, but not as part of glycolysis. These further aerobic reactions use pyruvate and NADH + H+ from glycolysis. Eukaryotic aerobic respiration produces approximately 34 additional molecules of ATP for each glucose molecule, however most of these are produced by a vastly different mechanism to the substrate-level phosphorylation in glycolysis. The lower energy production, per glucose, of anaerobic respiration relative to aerobic respiration, results in greater flux through the pathway under hypoxic (low-oxygen) conditions, unless alternative sources of anaerobically-oxidizable substrates, such as fatty acids, are found. The Krebs cycle or the Citric acid cycle The citric acid cycle (or Krebs cycle or TCA cycle) takes place within the mitochondrial matrix. In this cycle, pyruvic acid generated from glycolysis is converted into acetyl coenzyme A (acetyl CoA) by losing a carbon dioxide molecule. It then combines with oxaloacetic acid to form citric acid, a six-carbon molecule. In total, it loses 2 CO2 molecules and 4 electrons, of which 3 are accepted by NAD+ to reduce it to NADH, and the last electron accepted by FAD+ to reduce to FADH2 in redox reactions. In the end, it regenerates oxaloacetic acid to continue the citric acid cycle. In addition, a single GTP molecule is created from the combination of GDP and a phosphate group. Since 2 pyruvic acid molecules are formed by glycolysis, each time a cell undergoes glycolysis two turns of the citric acid cycle will occur. That means that the citric acid cycle produces a total of 6 NADH, 2 FADH2, and 2 GTP molecules. Electron transport chain The electron transport chain is located in the cristae of the inner mitochondrial membrane. The NADH and FADH2 produced by the citric acid cycle in the matrix release a proton and electron to regenerate NAD+ and FAD+. The proton is pulled into the intermembrane space by the energy of the electrons going through the electron transport chain. The electron is finally accepted by oxygen in the matrix. The protons return to the mitochondrial matrix through the process of chemiosmosis through the protein ATP synthase. This energy is transferred to oxygen (O2) in several steps involving the electron transfer chain. The protein complexes in the inner membrane (NADH dehydrogenase, cytochrome c reductase, cytochrome c oxidase) that perform the transfer use the released energy to pump protons (H+) against a gradient (the concentration of protons in the intermembrane space is higher than that in the matrix). An active transport system (energy requiring) pumps the protons against their physical tendency (in the "wrong" direction) from the matrix into the intermembrane space. As the proton concentration increases in the intermembrane space, a strong diffusion gradient is built up. The only exit for these protons is through the ATP synthase complex. By transporting protons from the intermembrane space back into the matrix, the ATP synthase complex can make ATP from ADP and inorganic phosphate (Pi). This process is called chemiosmosis and is an example of facilitated diffusion. No higher resolution available Cell Nucleus Structure/function correlations The cell nucleus is a remarkable organelle because it forms the package for our genes and their controlling factors. It functions to: Store genes on chromosomes Organize chromosomes to allow cell division. Transport regulatory factors Produce messages ( messenger Ribonucleic acid or mRNA) that code for proteins Produce ribosomes in the nucleolus Organize the uncoiling of DNA to replicate key gene Diagram of an cell nucleus: 1. Nuclear envelope. 1.a. Outer membrane. 1.b. Inner membrane. 2. Nucleolus. 3. Nucleoplasm. 4. Chromatin. 4.a. Heterochromatin. 4.b. Euchromatin. 5. Ribosomes. 6. Nuclear pore. The Endoplasmic Reticulum The endoplasmic reticulum (ER) is a network of flattened sacs and branching tubules that extends throughout the cytoplasm in plant and animal cells. These sacs and tubules are all interconnected by a single continuous membrane so that the organelle has only one large, highly convoluted and complexly arranged lumen (internal space). Usually referred to as the endoplasmic reticulum cisternal space, the lumen of the organelle often takes up more than 10 percent of the total volume of a cell. The endoplasmic reticulum membrane allows molecules to be selectively transferred between the lumen and the cytoplasm, and since it is connected to the double-layered nuclear envelope, it further provides a pipeline between the nucleus and the cytoplasm. The endoplasmic reticulum manufactures, processes, and transports a wide variety of biochemical compounds for use inside and outside of the cell. Consequently, many of the proteins found in the cisternal space of the endoplasmic reticulum lumen are there only transiently as they pass on their way to other locations. Other proteins, however, are targeted to constantly remain in the lumen and are known as endoplasmic reticulum resident proteins. These special proteins, which are necessary for the endoplasmic reticulum to carry out its normal functions, contain a specialized retention signal consisting of a specific sequence of amino acids that enables them to be retained by the organelle. An example of an important endoplasmic reticulum resident protein is the chaperone protein known as BiP (formally: the chaperone immunoglobulinbinding protein), which identifies other proteins that have been improperly built or processed and keeps them from being sent to their final destinations. There are two basic kinds of endoplasmic reticulum morphologies: rough and smooth. The surface of rough endoplasmic reticulum is covered with ribosomes, giving it a bumpy appearance when viewed through the microscope. This type of endoplasmic reticulum is involved mainly with the production and processing of proteins that will be exported, or secreted, from the cell. The ribosomes assemble amino acids into protein units, which are transported for further processing. Those that reach the inside of the golgi apparatus are folded into the correct three-dimensional conformation, as designed by the blueprint. Chemicals, such as carbohydrates or sugars, are added, then the vesicles transport the completed proteins to areas of the cell where they are needed, or they are sent to the cellular membrane where they are released by exocytosis. What’s the Golgi Apparatus? First, you need to learn to pronounce it. The first three letters, G-O-L are pronounced “goal” and the last two letters, G-I, are pronounced “gee.” So Golgi is pronounced goal-gee. The Golgi Apparatus was named for Camillo Golgi, the Italian physician who discovered it. It is sometimes also called the Golgi Body, the Golgi Region or the Golgi Complex (probably just to confuse us). The Golgi Apparatus looks like a loose stack of pancakes. Plant cells contain many of these stacks, while animal cells have just a few. The Golgi takes simple molecules it gets from the Rough ER and makes them bigger. Remember the transition vesicles? Well, these little transported packages, or vesicles have their contents modified inside the Golgi apparatus. Not only do these little packages get modified, they get “addressed” for delivery to their next destination. The packages that now carry the modified contents are called secretory vesicles. You might want to look back it will make this a lot easier to understand. Here's how it works: Rough ER sends simple protein molecules to the Golgi Apparatus.. The Golgi Apparatus absorbs these transition vesicles though one side of its membrane. It then converts the simple molecules into larger ones. These larger molecules get packaged into secretion vesicles. The Golgi Apparatus then releases these secretion vesicles out of the other side of its membrane into the cytoplasm. From there, the secretion vesicles move on to the cell membrane and are released out of the cell. This helps the transition work more smoothly. In many cases, the Rough ER, the Smooth ER and the Golgi Apparatus are actually attached to one other. This helps them work easily together - even if what they do does sound pretty complicated to us Experiments for Home and Classroom On this web site, called The Virtual Cell, students are invited to take a self-guided tour of various organelles within a cell. Click on the appropriate organelle for the tour and information. Then (virtually) cut the organelle in half to see what's inside. Click on the strange pink folded thing in the upper part of the Cell diagram -- it represents the Rough ER, the Smooth ER and the Golgi Apparatus. Go to: http://www.ibiblio.org/virtualcell/tour/cell/cell.htm Diagram of secretory process from endoplasmic reticulum (orange) to Golgi apparatus (pink). Please click for full labels. The Golgi apparatus is an organelle found in most eukaryotic cells that is involved in important processing functions, including the sorting and modification of newly synthesized proteins as part of the secretory pathway; carbohydrate synthesis and modification; sulfation of certain molecules; and synthesis and transport of certain lipids. Also known as the Golgi body or Golgi complex, this cellular structure is composed of flattened membrane-bound compartments (cisternae) typically organized into stacks. It was identified in 1898, by Italian physician Camillo Golgi and named after him. It also known as dictyosome. The Golgi apparatus forms a part of the endomembrane system of eukaryotic cells. Its primary function is to process and package macromolecules such as proteins and lipids that are synthesized by the cell. It is particularly important in the processing of proteins for secretion, whether for functions outside the cell or intracellular (such as to lysosomes). The complexity and precision of the Golgi apparatus is remarkable, involving modification of substances by enzymes, proteins being labeled with signal sequences, transporting and sorting of proteins through the various functional regions of the Golgi apparatus, and so forth. And this is just one of numerous complex and finely tuned activities taking place continually in a eukaryote cell, which is also involved in production of proteins, replication of genes, production of ATP, and so forth. end of document