BIOL 110 , Ch. 2 Notes
BIOL 110 , Ch. 2 Notes BIOL 110
University of Louisiana at Lafayette
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Date Created: 09/07/16
CHAPTER 2 ATOMS, MOLECULES, AND WATER Biology o Based on the principles of chemistry and physics o All living organisms are a collection of atoms and molecules. Atoms o The smallest functional units of matter that form all chemical substances and that cannot be further broken down into other substances by ordinary chemical or physical means o Each specific type of atom forms a chemical element. Atomic mass o Protons and neutrons are nearly equal in mass, and both are more than 1,800 times the mass of an electron---table 2.1 o Atomic mass scale indicates an atom’s mass relative to the mass of other atoms o Most common form of carbon has six protons and six neutrons, is assigned an atomic mass of exactly 12. A hydrogen atom has an atomic mass of 1, indicating that it has 1/12 the mass of a carbon atom A magnesium atom, with an atomic mass of 24, has twice the mass of a carbon atom Isotopes o Multiple forms of an element that differ in the number of neutrons they contain. 12 o C contains 6 protons and 6 neutrons o 1C contains 6 protons and 8 neutrons o Atomic masses are averages of the weights of different isotopes of an element Hydrogen, oxygen, carbon, and nitrogen o Phosphorus and Sulfur; Happy Campers Need Only Pretty Skies o Typically make up about 95% of the atoms in living organisms Hydrogen and oxygen occur primarily in water Nitrogen is found in proteins Carbon is the building block of all living matter o Mineral elements - less than 1% o Trace elements - less than 0.01% Essential for normal growth and function Chemical bonds and molecules o Molecule 2 or more atoms bonded together o Molecular formula Contains chemical symbols of elements found in a molecule Subscript indicates how many of each atom are present o Compound A molecule composed of 2 or more elements 3 types of bonds o Covalent- share electrons Polar or nonpolar covalent o Hydrogen o ionic Covalent bonds o Atoms share a pair of electrons o Occurs between atoms whose outer electron shells are not full o Covalent bonds are often the strongest of all chemical bonds, because the shared electrons behave as if they belong to each atom o Can share … 1 pair of electrons – single bond H-F 2 pairs of electrons – double bond O=O 3 pairs of electrons – triple bond N= N Octet rule o Atoms are stable when their outer shell is full o For many atoms, the outer shell fills with 8 electrons o One exception is hydrogen, which fills its outer shell with 2 electrons Polar covalent bonds o When two atoms with different electronegativities form a covalent bond, the shared electrons are more likely to be in the outer shell of the atom of higher electronegativity rather than the atom of lower electronegativity o Polar covalent bonds occur because the distribution of electrons around the atoms creates a polarity, or difference in electric charge, across the molecule Water—Fig 2.10 o Classic example of polar covalent bonds o Electrons tend to be in the more electronegative oxygen atom rather than either of the less electronegative oxygen atoms o Molecule has partial negative charge region and a partial positive charge region Hydrogen bonds—Fig. 2.11c o Occurs between water molecules having polar covalent bonds (between polar molecules) o Represented as dashed or dotted lines o Collectively, can form strong bond overall Holds two strands together o Individually, weak bonds can form and break easily Substrate and enzyme bonding Ionic bonds—Fig. 2.12 o An ion is an atom or molecule that has gained or lost one or more electrons. o It now has a net electric charge o cations- net positive charge o Anions- net negative charge o Ionic bond occurs when a cation binds to an anion Chemical Reactions o Occurs when one or more substances are changed into other substances Reactants → products o Share many properties All require a source of energy (kinetic at least) Reactions in living organisms often require a catalyst (enzymes) Tend to proceed in a particular direction but will eventually reach equilibrium Occur in liquid environment - water Properties of water—Fig 2.16 o A solution is made up of the Solvent- liquid solutes- substances dissolved in solvent o Aqueous solution- water is the solvent o Ions and polar molecules will dissolve in water hydrophilic- “water-loving” o Readily dissolve in water o Ions and polar molecules hydrophobic- “water-fearing” o Do not readily dissolve in water o Nonpolar molecules like hydrocarbon Amphipathic molecule o Have both polar or ionized regions at one or more sites and nonpolar regions at other sites Solutions o Concentration The amount of a solute dissolved in a unit volume of solution 1 gram of NaCl dissolved in 1 liter of water = 1 g/L o Molarity Number of moles of a solute dissolved in 1 L of water 1 mole of a substance is the amount of the substance in grams equal to its atomic or molecular mass o 58.4 grams of NaCl in 1L of water = 1 Molar NaCl solution. (Na = 23; Cl = 35.4) = 1 mole/L NaCl solution H 2 in 3 states of matter o Solid (ice), liquid (water), and gas (water vapor) o Changes in state, such as changes between the solid, liquid, and gas states of H2O, involve an input or release of energy. o Water is extremely stable as a liquid Not just a solvent o Water has many important functions in living organisms Participates in chemical reactions. Hydrolysis or dehydration o Provides force or support o Removes toxic waste components o Evaporative cooling. – evaporation helps some animals dissipate body heat. o Cohesion and adhesion Acids are molecules that release hydrogen ions in solution o A strong acid releases more H than a weak acid + Bases lower the H concentration o Some release OH^- + o Others bind H pH o pH = -log 10[H ] o Acidic solutions are pH 6 or below o pH 7 is neutral o Alkaline solutions are pH 7 or above o Pure water ionizes slightly into H+ and OH-. It will have a [H+] = 10^- 7M The pH of a solution can affect o The shapes and functions of molecules o The rates of many chemical reactions o The ability of two molecules to bind to each other o The ability of ions or molecules to dissolve in water Buffers o Organisms usually tolerate only small changes in pH o Buffers help to keep a balanced pH + o An acid-base buffer system can shift to generate or remove H to adjust for changes in pH o Ex: In the blood if pH rises too high, carbonic acid (weak acid) will release H+ and form bicarbonate (which lowers pH). If pH gets too low, bicarbonate (weak base) will bind H+ and form carbonic acid (which raises pH). o H 2O <3----> H + + HCO 3^- Question of the day! pH buffers A. minimize fluctuations in the pH of solutions. B. are usually weak acids and bases. C. will take up H+ when acids are added to them D. will release H+ when bases are added to them E. all of these. CH. 2 Notes Word of the Day: Electronegativity: ability of an atom to pull electrons o Refers to the shrink of an atom to pull an electron towards it Why would an atom pull an electron? B/c the atom is its happiest when its outer shell is full electrons Atoms are always trying to fill this outer shell so they tend to want to react w/ other atoms So if an atoms outer shell isn't full and another atom's outer shell isn't full then they can share an electron o Chemical reactions depend on atoms interacting with each other. Some atoms want to, some don’t, some will only react with certain atoms and that affects how molecules interact Electrons: o Negative charge o Outside the nucleus of an atom Why don't all atoms have the same electronegativity? it depends on the need of the atom o o Size relative to the other one The nucleus of an atom pulls electrons for them If the atoms electronegativity are the same they are going to pull equally on each other The Bigger may have a stronger pull on the atom, but still are sharing the electrons ----the bigger atom has the higher electronegativity The charge distribution will be unequal ---the negative charges will not be spread equally around the whole molecule, but they will be closer to the one that’s on the left (the bigger atom) A molecule: two atoms that join in a bond The more electronegative atom is the one with the most electrons around it o slightly negative charge on the bigger atoms side So the weaker side becomes partially positive o o Atoms are normally neutral. they usually have the same number of protons and electrons o So a full charge hasn’t moved over, but a partial So a full charge hasn’t moved over, but a partial They share the electrons Hydrogen bond : Partial attractions between molecules that have this different charge distribution around them If the bigger atom gets EXTREMELY bigger than the other atom then they no longer share the electron and it takes it away. Now they are no longer neutral and the left is completely negative and the right is positive. And they will be attracted to each other b/c negative and positives attract and that’s called ionic bonds Atom: the smallest particle that makes up a substance whereby you cant break that down and still have that substance Element: the substance that each atom forms Protons: o In the nucleus o Positive charge o Are bigger in size than the electrons What happens if your chemicals stop interacting?? DEATH Neutrons: o Are neutral --not charged o In the nucleus About the same size as the protons o Most of the mass of the atom is located in the nucleus Atomic Mass: o The mass made by the protons and the neutrons o The more protons and neutrons the atom has, the larger the mass o We disregard the mass of the electrons bc Not every atom has neutrons Hydrogen is the only atom w/o a neutron in its most common state o o It has a single proton o A single electron orbiting around it Atomic Number: o # of protons in an atom The identity of an atom depends on its # of protons What are neutrons for? To serve as a buffer--to allow the protons to be able to hang out with them. Its in the o middle. How can a hydrogen bond atom not have one and a helium does? o Helium has two protons and like charges repel. Atomic Mass: o Adding up your number of protons and neutrons Neutrons are in equal weight to the protons Carbon has 6 protons and 6 neutrons in its normal state so it has an atomic mass of 12 The atomic mass of hydrogen since it is 1 is 12 the mass of carbon (like 12 times the mass) o This is relative masses Atomic mass Unit: (Da) Dalton o 12 protons =carbon --12C 14C means this carbon has more neutrons than the regular carbon Isotopes: o Atoms that are of the same type but have different #'s of neutrons that they have o That’s why the numbers don’t come out as whole numbers o The average is weighted ---the average reflects how abundant an atom is in nature Ex. If 12C and 14C were averaged and they have equal weight, you would get 13, but that isn't the atomic mass of carbon. Its 12.0107, but that tells us that the 12 has more weight. So there is more carbon 12 in nature than there is carbon 14. Living things are made up of atoms and elements and matter Trace Elements: o Hydrogen, Carbon, Nitrogen, Oxygen, Phosphorus --very important in DNA and proteins , Sulfur Happy Campers Need Only Pretty Skies We're made up of around 60-70% of water and most of the hydrogen and oxygen is in the water Nitrogen is in proteins , DNA Subscript: o Lets you know how many atoms in an element Compound: An element made up of 2 or more atoms o o Ex. Water Covalent: when atoms share electrons A molecule that has opposite sides. The sides differ in their partial charges. So if the electrons that are being shared don’t orbit around both atoms equally you get one of the poles of the atom to become partially negative and one of the poles to become partially positive. So you create a dipole. You have two areas of the molecule. Atoms in a polar covalent bond: o They have different electronegativities that’s why they form polar covalent bonds Non-polar: o Same electronegativity Hydrogen bond: o Partial attraction between polar molecules o Called hydrogen b/c a lot of the times, hydrogen will be involved in it If a molecule has a polar covalent bond in it, its called a polar molecule If 2 polar molecules come close enough together the partial negative is going to be attracted to the partial positive of the others Ionic: o When the electronegativites are in the molecule. Very different. One atom completely steals the electron from the other. So if one atom just steals an electron why do they even stay by each other?? o They are attracted to each other b/c they are oppositely charged. Covalent o Atoms sharing electrons o Any time 2 atoms share electrons its covalent o They share electrons because they want their outer shell to be full o Usually very strong bonds bc its like the electrons belong to both atoms o A covalent bond that shares unequally is a polar covalent bond o Can also describe the bonds based on how many electrons they share, so if there was only one pair of electrons being shared it would be a single bond and two pairs would be a double bond and three pairs is a triple bond o How many electrons an atom is willing to share depends on how many electrons it needs to fill its outer shell Octet rule o The desire to fill the outer shell o Goal: fill their outer shell with 8 electrons o Hydrogen is an exception because it is such a little bitty atom it only has one electron and one proton and so that electron is that very first shell which is its only shell and that shell is full at 2 and so it is happy if its outer shell has two o Important bc it tells us if whether or not the atom is already stable. o If it is full its happy and tells us it wont want to share electrons o Tells us if whether or not atoms will want to bond with other atoms If their outer shells are already full, they don’t want to bond at all o o Who they will bond with depends on how many electrons it needs to fill that outer shell Figure 2.7 Hydrogen has one electron in its outer shell--is happy with 2 electrons in outer shell Fluorine has 7 electrons in its outer shell---is happy when it has one more electron So when they come close enough together the two electrons will be shared between the two atoms So one of the electrons originally comes from the hydrogen and one electrons originally came form the fluorine but they're going to be shared equally by both and so they are going to be orbiting around both of the atoms However many more electrons an atom needs is how many bonds it can form----this is a covalent bond The number of electrons in the outer shell of the atom determines how many covalent bonds it can form with other atoms So hydrogen can form one Oxygen has 6 electrons in its outer shell so it needs two more so that means it can form two bonds So however many electrons an atom needs is how many bonds it can form o Ex. Hydrogen has one electron and is happy when it has 2 more electrons so it can form one bond because it needs one more electron. Electronegativity o The ability of an atom to pull electrons The shrink of an atom to pull electrons o So if you have two atoms and they are electrons but one is stronger than the other, then the stronger one is going to have the electrons around it more of the time--closer to them o This makes the stronger atom partially negative b/c electrons are negative o This leaves the weaker atom partially positive o So you create poles on the molecule---one pole is partially negative ---one pole is partially positive----on opposite sides of the molecule And the bond between those is the polar covalent bond o Water is a an example of a molecule that has polar covalent bonds so any molecule that has polar covalent bonds is called a polar molecule o Water is a polar molecule o In the case of water there are 3 atoms---1 oxygen and 2 hydrogen Hydrogen is a little bitty atom and oxygen is much larger and has a much larger electronegativity than hydrogen Hydrogen is relatively weak, oxygen is relatively strong. So when they come together and share electrons, a polar covalent bond is formed. So Oxygen is more negative The hydrogens are more positive o So when you have two hydrogens that are bonded covalently with an oxygen, the hydrogens become partially positive and the oxygens become partially negative o Its two partial negatives for the oxygen because its partially gaining two electrons because there are two hydrogens bonded to it and so each of these hydrogens and the electrons from it will be orbiting around this oxygen Water has 2 polar covalent bonds in a single molecule o B/c oxygen needs 2 electrons it will want to bond to 2 hydrogens b/c each hydrogen can provide both Oxygen is partially positive Within in a single water molecule, there are no hydrogen bonds. The bonds in the single water molecules are covalent bonds The hydrogen bonds come in when you have polar molecules come close enough together and its between the polar bonds Hydrogen bonds o Relatively weak because suppose they were to get excited all of a sudden, that bond wont hold. So these bonds are relatively weak especially if they are invisible bonds . The more of them you have, collectively they will be stronger. Individually they are weaker o There is no covalent bond, no linking, just a partial attraction o When they are close enough together they create this bond o Called this because hydrogen is involved o These bonds are also in DNA. They pull the two strands of DNA together o The time that the DNA strand has to pull away is during replication so it’s a good thing that these bonds are weak b/c if they were so strong it would be difficult to allow the DNA strand to unzip o Also true with enzymes binding to there substrates. The molecules they interact with because once an enzyme helps a reaction to occur the product needs to go away b/c you don’t want it stuck there forever There's a possibility for a single water molecule to have many hydrogen bonds around it. Because water is able to form hydrogen bonds with itself it has characteristics that make it pretty unusual like : Adhesion o The ability of water to stick to other substances Caused by water wanting to hydrogen bond w/ other polar molecules Why do the hydrogen bonds form?? b/c the poles of the molecules that gave these __ orbits on it are what's attracted to each other So if there is another polar molecule around water it will want to bond with it as well Cohesion o The ability of water to stick to itself Water wants to it self because it wants to make hydrogen bonds Water doesn’t like to stick to oils which means oils aren't polar Water forms surface tension o Ex. If you were to spill some water on a waxed table the water will form these little oval shaped beads. The reason it doesn’t just spread out is because of cohesion. It doesn’t want to stick to the wax because the wax isn't polar. It wants to stick to itself. So it sticks to itself as much as it can. So much that it forms like a force on the outside surface of the water droplets and that’s called surface tension. Ionic bonds o An ion A charged particle o If you're talking about a atom, then it’s a charged atom Cations-positively charged Anions-negatively charged o A type of bond formed between a cation and anion o Not a covalent bond so the attraction is causing the bond o The attraction btw the cation & anion is the ionic bond o Is not as strong as a covalent bond Atoms are normally neutral so they become an ion when they gain or lose an electron and would do this to satisfy the octet rule If 2 atoms nearby each other and one needs to lose and one needs to gain an electron then they would bond together and that’s an ionic bond Classic example of ionic bond is table salt o Na=sodium Has two electrons in the first shell 8 in the second shell Has one electron in outer shell o Cl=Chlorine Has 7 electrons in its outer shell o So when sodium and chlorine come together they will both fill their outer shells by the sodium losing an electron and giving it to Chlorine. So a chloride ion is formed and its going to be partially negative because it gained an electron meanwhile the sodium will be partially positive and the attraction between them will be an ionic bond Fig 2.12 The atoms that gains an electron becomes partially negative and the atom that loses an electron becomes partially positive. When salt dissolves the ionic bonds are being broken and the water is causing them to be broken So the sodium ions and chlorine ions that are being held together are being broken b/c of the water Water isn't ionic but it is polar So if water comes around these molecules and being how tiny it is, it will be able to sneak around the sodium ion and the chloride ion and this will break that bond Chemical Reactions o A set of substances that are called reactants that change into bigger substances which are called products o They have to have some energy and that is kinetic energy o Kinetic energy is motion o Need kinetic energy for the molecules to get close enough together or even collide to interact with each other o In living things, in order to stay alive, chemical reactions have to happen at a certain time and at a certain speeds o In most cases, cells wait around to come close enough to other molecules for the chemical reactions to take place We employ enzymes to speed up reactions Reactions change into products but there are times that products change into reactants Reactions tend to go in one direction The equilibrium is when the forward reactant is occurring at the same rate as …. All reactions occur in water Water has an important role in chemical reactions o Sometimes directly involved and sometimes indirectly Solvent vs. Solute o Substances that have the ability to dissolve in water is called a solute If there is an interaction with the water, then substance may dissolve Fig 2.16 Salt is an example of an ionic Salt dissolves in water b/c water molecules is going to be attracted to the ions Some substances like to interact with water--water loving ---hydrophilic---anything that is polar or ionic Others don’t---water fearing --hydrophobic ---anything not polar ---so it wont interact with water Hydrogen and carbon o Non polar--so electronegativity is equal o have very similar qualities Amphipathic o Having both hydrophobic and hydrophilic parts Solutions o Solution concentration: The amount of a solute can dissolve in a solvent mole o the amount of substance of a system which contains as many elementary entities as there are atoms in 0.012 kilogram of carbon 12; its symbol is "mol". In order to know how many grams of something you need for a mole you have to know the atomic mass If talking about a mole of an element you only need to know the atomic If talking about the mole of a compound have to know the ____???? Molecular mass??? Molarity: o When we have solutions where we're looking at the number of moles of the solute dissolved in specifically 1 liter of water So if you have one molar of solution of sodium chloride it tells you that you have 1 mole of sodium chloride. So if this was 2 molars of sodium chloride, how many moles of that would you have in liters?? Answer: 2 A mole is equal to the molecular mass So all you have to do is know what the atomic masses of sodium and chlorine and then b/c its sodium chloride, you add them together 23+35.4=58.4 o Add the molecular mass of Na(23) + Cl(35.4) to get the grams A mole of any substance will always have 6.02 x 10 ^23 particles in it, but wont have the same amount of grams. So if you’re interested in having substances with the same number of particles in it, you want to make substances of equal molarities. So if I make a 1 molar solution of sodium chloride, then there's going to be 6.02 x10^23 particles in it. H 0 in 3 States of Matter o Unusual feature b/c most small substances especially small like water wont exist in all 3 states but water does b/c of its hydrogen bonds o The difference between a gas and a liquid of the same substance is the energy o Particles move more in gas so more kinetic energy o Particles move less in liquid so less kinetic energy o Hydrogen bonding has something to do with how gas can turn into a liquid….maybe???? o You would expect there to be more hydrogen bonds in the liquid state o A lot more hydrogen bonds in the solid state o Density-number of particles in a given space o If we have ice, liquid water, and gas. Which is the most fullest? Ice and we know that because it floats in water. But everything else one the planet, if you change it into a solid its density becomes more not less. SO why is water different? There are more hydrogen bonds in the solid state than in the liquid. o Hydrogen bonds form when the water molecules are in certain distances apart and once they form they will keep the water molecules that same distance apart o The hydrogen bonds hold the molecules at the same distance apart in the solid and in liquid state of water. o This crystal formation forces the molecules to stay where they are Water isn't just a solvent o It helps you cool off o When you sweat you have water that gets formed on the surface of your skina nd when the water evaporates it changes into a gas. In order to change into a gas it has to be able to break the hydrogen bonds that are in the water. Because there are these hydrogen bonds there its going to take heat to break those hydrogen bonds enough so that it can change into a gas o The heat that’s used to break the hydrogen bonds is the heat that comes from ___? o That’s where the energy _____??? o Because water can dissolve at lot of substances it also is the thing that removes a lit of toxic wastes on our bodies o Also, b/c it likes to stick to itself and to other polar molecules ……??? o Hydrolysis:…….???? o Water interacts well with polar substances b/c of this ability there are types of reactions that can occur in water Acids are… o A substance that releases hydrogen ions o Strong acids release a lot of hydrogen ions Bases o take hydrogen ions away from the solution and can do it by directly bonding the hydrogen ions to the cell or releasing OH^- ions into the solution. o Releasing OH^- ions into the solution would motor the hydrogen ions b/c its going to bind the hydrogen ions. So OH will bind to hydrogen ions pH o In order for cells to remain alive they have to have a pH of around 7 o pH-the measure of the hydrogen ions binding to the OH^-'s Is the measure of the concentration of hydrogen ions in a solution o When you look at the concentration of hydrogen ions, they're gonna be small o If we're measuring the concentration in molar its going to be part of the molar o The number you come out with will be numbers are less than 1 o Write those numbers in scientific notation o Scale- runs from 0-14 o 6 or below --acidic o 8+---basic or alkaline o *pure water ionizes slightly into H+ and OH-. o Why is a pH of 7 considered neutral?? o It will have a [H+]=10^-7 M (same as 1x10^-7)=.0000001-- pH=7----this is smaller compared to 1 x 10^-5M= The 7 comes from the water In pure water, if you were to measure the concentration hydrogen ions in pure water, the concentration is ___to 7. o 1 x 10^-5M=.00001---decimal format This one is greater than 1 x 10^-7M pH=5 Has more hydrogen ions Is more acidic o The lower the pH, the more acidic it is o The higher the pH, the more basic/alkaline o Your stomach is so acidic because it helps begin the digestive process and kills a lot of bacteria that we take in when we eat o Even in the even in the water not all of those molecules stay as intact water molecules. Some have the ability to release hydrogen ions The pH of a solution can affect o Cells in living things have a large concentration of water in them o Substances that are either acids or bases can change the pH of a solution when they're in a living things. Therefore, the pH can affect many things in living things that have to happen o The change in a pH can affect the shape of a molecule which determines its functions o pH affects the rates of chemical reactions o Affects whether or not molecules will bond to each other or whether or not ions or molecules can dissolve o Cells have to be careful about their pH o They have to maintain in a certain range or can't function Acids and bases are going to be in cells and in organisms and they are necessary for chemical reactions to occur Buffers o Solutions that help to keep a constant pH o Living things such as ourselves have buffers o If the solution gets too acidic the substance can take those hydrogen ions out of it --this is base work o If the solution is too basic , we give back those hydrogens --this is acid work o We have buffers in our blood and our body uses it to keep our pH of our blood at around 7 o If the pH numbers are getting too high then our body acid produces ions --keeps pH where it needs to be o If pH gets too low--which means higher acidity and hydrogen ions getting too high so our body will pick up some hydrogen ions --Buffer system
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