The chemistry and energy of life ( chapter ii)
The chemistry and energy of life ( chapter ii) BIO 1305
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This 8 page Class Notes was uploaded by Paola chaparro on Saturday September 10, 2016. The Class Notes belongs to BIO 1305 at University of Texas at El Paso taught by Horacio O. Gonzalez in Fall 2016. Since its upload, it has received 81 views. For similar materials see General Biology in PSCI at University of Texas at El Paso.
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Date Created: 09/10/16
The chemistry and energy of life ( chapter ii) It is estimated that water make the 70% of the bodies of most organisms. Living and nonliving things are composed of same element: atoms. Each atom has a positively charge nucleus while electrons are moving around it. The nucleus may contain protons and neutrons. *Protons have a positive electric charge *Neutrons does not have electric charge *Electrons have a negative electric charge. Different charges attract each other. However, charges that are alike repeal each other. For most atoms, they are neutral because has the same amount of electrons as protons. The mass of an atom or atomic mass is measure in daltons (Da). It is approximately, 1.7x 10^24 grams. However, an electron is even tinier so its mass can be ignored. Element is a pure substance made up of only one type of atoms. In living organisms, it is predictable to find out that 98% of the mass is composed by Carbon (c ), Oxygen ( o) , Hydrogen ( H), Phosphorus ( P), Nitrogen ( N ) and Sulfur (S). The Atomic Number of an element can be calculated by the numbers of protons on its nucleus. The Mass Number is predicted by adding the number of protons and neutrons founded in the nucleus of one atom. Hydrogen does not has neutrons while others, elements, have one or more neutrons. In fact, the number of protons determined/ identifies an element. Isotopes are atoms of the same element but different mass number. It has some characteristics. a) same number of protons b) different number of neutrons c) different mass number Example: As you can see, there are the same numbers of protons but different number of neutrons. (Carbon 13) Mass number= Neutrons+ Protons. We can re write the formula as this: Neutrons= Mass number Protons= 13 6= 7. Now, we can do the same with Carbon14, Neutrons= Mass number – Protons= 14 – 6= 8. By this example, you can see that each Isotope has a different number of neutrons. Bohr Model Bohr model is principal used to determinate and describe the behaviors of the atoms. In this case, the electrons decide if a chemical bond is able to form and its shape. As you can see, the Bohr model shows shells around the nucleus. In each shell, there are a maximum number of electrons. Fist shell= more than 2 electrons Second shell= more than 8 electrons. Third shell= more than 18 electrons Fourth and subsequent shells: more than 32 electrons. In fact, the farther away a shell is from the nucleus the electrons should be stronger because have more energy. Elements with atomic numbers between 6 thru 20 protons have to obey the Octet rule. This rule specifies the atoms will gain, lose, or share electrons to complete its outer most shell and obtain 8 electrons. Molecules are form when atoms share electrons. In the same time, there is what is called the chemical bond. It is an attractive force used for atoms to be together. A covalent bond: occurs when there are elements that do not have the stability point on its outer most shell, they have to share electrons. That way, the elements will became stable. Example: two chlorine atoms with 7 electrons on the outer most shell come together and share one electron to form a stability shell and become in a molecule. Covalent bonds are really strong, and it takes enough energy to destroy them. They are stable at temperatures where life is possible to exist. A single bond shares a pair of electrons H H. Double bonds shares 2 pairs of electrons. It means 4 electrons. Triple bonds shares 3 pairs. It means that shares six electrons. Methane forms when a carbon has reaction with four atoms of hydrogen. The properties of molecules are influenced by covalent bonds. They provide characteristics as length, angle and direction. For this table, I recommend to memorize all the information. Electronegativity is a force by an atomic nucleus on electrons. To have a strong electronegativity, there should be many positive charges. It means nucleuses that contain more protons are more attractive for electrons. Nonpolar covalent bond is when two atoms in a distance of 0.5 or less apart in electronegativity, they will share electrons equally. Polar Covalent bond is when electrons feel more attraction for one certain nucleus than others. Hydrogen bond is at atom formed in water. The negatively charged atom of one water molecule is attracted to the positively charged hydrogen atom of a water molecule. However a covalent bond is stronger than hydrogen bond. Hydrogen bond is essential for DNA and Proteins. Solvent: Water is able to dissolve different substances, so it is considered to be a good solvent. Also, that is why it is known as the “Universal Solvent”. In fact, to heat water, it takes too much heat energy to break the hydrogen bonds. There is needed more heat energy to change water from a liquid state to a gaseous state. Cohesion is defined as the potential of water molecules to resist coming apart under tension. Adhesion is the process where water molecules adhere on surfaces or objects. Hydrophilic is when polar molecules interact with water. At the same time, hydrophobic is also considered a non polar and does not interact very well with water. Ions are electrical charged particles that form when atoms lose or gains electrons. Cations are ions with positive (+) charged. In contradiction, negatively () charged ions are known as Anions. As you can imagine, Ionic attraction is defined as the force used to attract ions with opposite charges. In fact, Ionic attraction in salt is stronger than ions in solution. Functional groups: are small groups of atoms that have specific properties. When functional groups attached to a molecule, the chemical properties are transmitted to the molecule. Functional groups can determinate molecule shape and reactivity. Macromolecules are big and large molecules because contain a large number of atoms and formed by covalent linkages with other small molecules. There can be found four kinds of macromolecules in living organisms: proteins, carbohydrates, nucleic and lipids. Polymer is a substance with a molecular structure formed by a number of similar units bonded together. Monomer is a small molecule that can be bond with another similar molecule to form a polymer. 1) Proteins consist of the formation of large molecules composed for many amino acids and are essential for living organisms. Especially, it improves structural functions. The formation of hair, body tissues, muscles etc. 2) Carbohydrates are large molecules that include sugar, starch and cellulose. Carbohydrates can be found in foods and living tissues. Carbohydrates can be broken to release energy. 3) Nucleic Acids are substances in living cells. Especially, DNA and RNA. 4) Lipids can form large structures by using groups of smaller molecules. Those limited groups of molecules form a long chain. Polymers are form and broken down in water by two types of reactions. Condensation the water links monomers together. In other words, it is the conversion of a vapor or gas to liquid. Hydrolysis is performs when water breaks polymers. As result, there are created new monomers. Carbohydrates are groups of molecules with different sizes but with similar atomic composition (chemical properties and biological function) . Carbohydrates can store energy and release it for the use of organisms. A) transport stored energy B) Structural molecules that give some organisms their shapes C) they can work as signaling or recognition molecules that can attract some biological responses. Monosaccharides are sugar molecules, and have up to 7 carbon atoms. In addition, there are monosaccharides with five carbons and are known as pentoses. It is important to know that the DNA and RNA contain ribose and deoxyribose. Monosaccharides are bonded by condensation process. As result, the formation of glycosidic Linkages is completed. Look at the picture above. Deoxyribose and Ribose have the same number of carbons (5). However, the chemical properties and biological roles are different. At this image, you should focus to observe the blue line. That is an example of how a glycosidic linkage looks like. In other words, you can see that this this is joining two atoms The hexoses ( six) all have the same formula ( C6H1O6). Note, each number should be written under its respectively letter. Hexoses include glucose, fructose, mannose, and galactose. Disaccharide is any class of sugar that contains two monosaccharides. Oligosaccharides are made up of monosaccharides and have functions. They often bond to proteins and lipids (on the cell surface). They work as recognition signals. Polysaccharides are large polymers of monosaccharides that form chains. They are connected by glycosidic linkages. Starches are groups of polysaccharides of glucose. Glycogen is a substance found in the bodily tissues, and it stored carbohydrates. It is produced in the liver before it is send to the tissues. Cellulose is related to plants. It is the predominant component of plant cell walls. In addition, it is the most abundant carbon containing ( organic ) compound on the world. Lipids can be known as fats and oils. Lipids are hydrocarbons ( C and H atoms). So lipids are insoluble in water because their nonpolar covalent bonds. When the nonpolar hydrocarbons are too close together, a reaction occurs. It can be weak, but the Van der Waals Interactions hold them together. Lipids have different functions. 1) they store energy in the format of CC and CH bonds. 2) play important structural roles in cells. 3) it is used as fat for animal bodies, so the it can be used as thermal insulation. Triglycerides are known as the most common units of lipids and simple lipids. Triglycerides can be found in two different states: liquid or solid. Those that are found in a state of liquid at room temperature are known as oils. While those in solid state, are known as fats. They are really hydrophobic. Glycerol has three hydroxyl ( OH) groups. So it is considered to be an alcohol. Fatty acids consists on a hydrocarbon chain. Especially, glycerol occurs in fats and oils. By the same time, the synthesis of triglyceride has three condensation activities. So, the result molecule is almost nonpolar and is hydrophobic. That is the reason for why water and oil cannot be together. Saturated Fatty acids are saturated because there are not double bonds between the carbon atoms and fatty acids complete the right number of hydrogens. In other words, it represents that carbon atoms are completed full. Unsaturated Fatty acids contains one or more double bonds. Amphipathic is a molecule that can be said to be hydrophilic and hydrophobic. For example, the fatty acids are amphipathic. Phospholipids is like a lipid with two fatty acids bond to glycerol and a phosphate containing compound can be able to replace one of the fatty acids. However, the phosphate has a negative electric charge, so this is considered as hydrophilic. In the meanwhile, the two fatty acids are hydrophobic and avoid water. So, the fatty acids get together or with other hydrophobic substances. As it shown at the picture, a group of molecules thick with each other to form a wall. Of course, in this process water is excluded. Chemical reaction is the process that includes ionic structures of a substance, or atoms, to change a physical form or reaction. It can be describes that occur when atoms have too much energy to combine, or exchange with other atoms. For example look at image on the button. To perfom a chemical reaction, there is necessary energy. What is energy? In biochemistry, energy is consider as the capacity for change. The potential energy is the energy in position or state while kinetic energy implies movement. Metabolism is the total of chemical reactions ocurring within a living organism in order to survive. It occurs in a biological system. To perform a metabolic reactions, it involves energy to be stored or release it. A chemical reaction occurs when there is more energy consumed in the reactants than the energy released ( the product). It is a spontaneously process. Anabolic reactions are in charge to make simple molecules to form stronger and complex new molecules. The reactions that need energy to operate are called endergonic or endothermic. In exorgomic reactions energy is released. In the opposite side, there are catabolic reactions or catabolism and the main function of this is to break down the complex molecules into simpler ones. That way, its energy can be release. Anabolic and catabolic reactions often work together because the energy release from catabolic reactions is used for anabolic reactions. Laws of Thermodyways Energy Interacts with Matter In this section, the ways of how energy interacts with matter will be explained. The laws of thermodynamics are in continuation: The first law states: Energy is neither created nor destroyed. It means that the amount of energy before and after a transformation stay the same. The second law of thermodynamics states: Useful energy tends to decrease. It can be explain by saying that when energy is converted from one form to another, some of the energy are not longer a potential energy to do work. In addition, Entropy is a mesure of the changes or disorders of chemical reactions in a system. When in a chemical reaction entropy increases, the products are more disorder than the reactants. Reference All about rainbows, double rainbows, circular rainbows! [Digital image]. (2013, May 13). Retrieved from https://skullsinthestars.com/2013/05/13/all- about-rainbows-double-rainbows-circular-rainbows/. Amphipathic Molecules and Phospholipid Bilayers [Digital image]. (2011, May 22). Retrieved from http://www.freethought- forum.com/forum/showthread.php?t=24978&garpg=6. Covalent Bond [Digital image]. (n.d.). Retrieved from http://www.daviddarling.info/encyclopedia/C/covalent.html. Glycosidic Bond: Definition & Formation [Digital image]. (n.d.). Retrieved from http://study.com/academy/lesson/glycosidic-bond-definition-formation- quiz.html. Hillis, D. M., Sadava, D. E., Hill W. R.., & Price, M. V. (2014). Principles of life (2nd ed.). Sunderland, MA: Sinauer Associates. Overview of Atomic Structure [Digital image]. (n.d.). Retrieved from https://www.boundless.com/chemistry/textbooks/boundlesschemistrytextbook/atoms moleculesandions2/thestructureoftheatom34/overviewofatomicstructure20211405/. Lecture 01 (01082003) [ Digital image]. ( 2003, August 08 ). Retrieved from http://www.scottsmithonline.com/interests/medicalschool/biology/110a/Midterm1Materials/Note s/MyTextbookBSCI110aMT1.html. Mishra, A. (2016, July 23). Chemical Reactions and Equations [Digital image]. Retrieved from http://www.studynotestoday.com/2016/04/chemicalreactionsandequations.html. Steven, C. M. (2015). Deoxyribose vs Ribose sugars [Digital image]. Retrieved from https://www.mun.ca/biology/scarr/Deoxyribose_versus_Ribose.html. The Elements of Style [Digital image]. (2013, April). Retrieved from http://herb09.weebly.com/8rulesenglishwar/theoxygenatomelementsofstyleandthe atomicnumber8elementaryrulesofusage.
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