Biology 115 Fall 2001 Campos/Saupe Atoms and Molecules I. Introduction - living things are composed of the same chemical elements as the nonliving world and obey the same physical and chemical laws - living things have unique characteristics, properties -- life - structural hierarchy to biological systems: atomic level to biosphere - to understand life: understand properties of molecules that make up living systems and reactions in which they participate understand basic concepts regarding building blocks of such molecules -- atoms II. Atoms A. General characteristics 1. All matter is composed of atoms consist of a positively charged nucleus containing one or more protons may contain one or more neutrons negatively charged electrons move around nucleus 2. Atoms and constituents have mass proton and neutron have mass of about 1 dalton (1.7 x10-24 grams) o mass of proton serves as standard unit of molecular mass measurement (atomic mass unit) mass of electron is very small -- not factored into calculation of mass of an atom 3. Atomic constituents are charged and neutral proton has charge of +1 neutron is neutral electron has charge of -1 - charge of atom depends on number of protons and electrons 4. Atoms are mostly empty space if you expand atom proportionately to the size of the largest dome in the world: o the nucleus would be the size of a grain of salt, electrons would be too small to see o remainder of this enormous atom would be empty space B. Elements 1. Elements are pure substances that contain only one type of atom -- for example, hydrogen consists solely of hydrogen atoms - more than 100 different elements are found in the universe elements arranged in a periodic table
periodic table groups the elements according to their physical and chemical properties o arranges elements left to right based on number of protons o arranges elements in columns based on similarities in their properties 2. Characteristics of an element atomic number -- number of protons in each of its atoms atomic weight (mass) -- total number of protons and neutrons in nucleus of each of its atoms, mass of atom in daltons elements have more than one atomic form, different isotopes o isotope: atoms of the same element that have different atomic weights -- same number of protons, differ in number of neutrons o in periodic table atomic mass shown is average atomic mass for a representative sample of the atoms of the element with isotopes in normally occurring ratios 3. About 98% of the mass of living organisms is made of carbon, hydrogen, nitrogen, oxygen, and sulfur. III. Chemical reactions between elements A. Electron behavior 1. Chemical reactions are changes in atomic composition of substances depend on the number and arrangement of electrons in elements involve changes in relationship of electrons with one another 2. Electrons found in orbitals -- volume of space within an atom where an electron likely to be] there are various orbitals in an atom depending on number of electrons an orbital can be occupied by at most two electrons different orbitals have different forms and characteristics in space 3. Orbitals arranged in electron shells (energy levels) around nucleus first electron shell consists of only one orbital, s orbital second electron shell made up of four orbitals, 1s, 3p subsequent shells have different number of orbitals outermost shells usually hold only eight electrons 4. The outermost electron shell determines how an atom combines with other atoms outermost shell with eight electrons -- no unpaired electrons -- atom is stable atoms of chemically reactive elements have unpaired electrons in outer shell seek to attain stability by: o sharing electrons with other atoms o gaining or losing electrons from outer shell
B. Chemical bonds - a chemical bond is an attractive force that links two atom to form a molecule - types of chemical bonds: covalent bonds hydrogen bonds ionic interactions van der Waals interactions hydrophobic interactions 1. Covalent bonds consist of shared pairs of electrons hydrogen molecule behavior of carbon -- methane molecule example covalent bonding capabilities of biologically important elements multiple covalent bonds covalent bonds are very strong 2. Polar vs. nonpolar covalent bonds -- equal vs. unequal sharing of electrons - sometimes when atoms share electrons, nucleus of one atom exerts a great attraction on the electron pair than the other nucleus -- pair tends to be closer to that atom - electronegativity -- attractive force that atom exerts on electrons nonpolar covalent bonds form when electronegativities between tow atoms about equal - - ethane polar covalent bonds form when atoms with strong electronegativity (oxygen) bond to atoms of weak electronegativity (hydrogen) - example of water (H2O) d- d+ 3. Hydrogen bonds - form between an electronegative atom and a hydrogen bonded to an electronegative atom example of hydrogen bonds between molecules: water example of hydrogen bonds within a molecule -- stabilization of protein and DNA structure - hydrogen bonds only 1/10 the strength of covalent bond -- however, when many H-bonds form they have considerable strength 4. Ionic bonds - ionic bonds are formed by electrical interactions between ions bearing opposite charges - ions form when an atom gains or loses one or more electrons when one interacting atom is much more electronegative than the other a complete transfer of one or more electrons occurs - example of NaCl
- ions can interact with other ions or with polar molecules -- basis of solubility of ions in aqueous systems 5. Hydrophilic and hydrophobic molecules - hydrophilic molecules interact with one another through their polarity induced hydrogen bonds: d- to d+ interactions - hydrophobic molecules - nonpolar molecules that interact with one another -- can't form hydrogen bonds, nonpolar molecules aggregate IV. Properties of water - water's molecular structure and capacity to form hydrogen bonds give it unusual properties significant for life A. Ice floats - ice is held in a crystalline structure by the orientation of water molecules hydrogen bonds - each molecule forms hydrogen bonds with four other molecules - these four hydrogen bonds actually increase the space water molecules take up in their solid state, so water expands as it freezes, and ice is less dense than liquid water forms an insulating layer on lakes and helps keep them from freezing solid insulation protects organisms in the cool, lower liquid layer from subfreezing temperatures B. Melting and freezing - compared to other nonmetallic substances, it takes a lot of heat to melt ice because hydrogen bonds must be broken - the opposite process, freezing, requires water to lose a great deal of heat to transform water to a solid - this property of water helps to moderate Earth's temperature C. Heating and cooling - it takes a lot of heat energy to change the temperature of liquid water because of hydrogen bonds specific heat is the number of calories needed to raise one gram of a substance 1 o C the specific heat of liquid water is 1 - this property also helps to moderate the fluctuation of Earth's temperature D. Evaporation and cooling - the heat of vaporization is the amount of heat needed to change a substance from its liquid state to its gaseous state - it requires a lot of heat to change water to a gaseous state because the hydrogen bonds of the liquid water must be broken - thus, evaporation has a cooling effect by absorbing calories evaporation is an important means for cooling large multicellular organisms a person can survive a temperature well in excess of their body, yet maintain normal body temperature by sweating and evaporating the sweat evaporation occurs less readily in high humidity, which is why hot, humid areas seem hotter at the same temperature than those places that have low humidity E. Cohesion and surface tension - water has a cohesive strength even though it is a liquid the attraction of water molecules to each other results in the transport of water from the roots to the tops of trees
water has high surface tension, which means that the surface of liquid water is relatively difficult to puncture E. Solutions - solutions are produced when substances are dissolved in water - concentration is the amount of a given substance in a given amount of solution concept of molarity - most biological substances dissolved at very low concentrations V. Acids, bases and the ph scale - acids are substances that dissolve in water and release hydrogen ions (H + ) - bases are substances that dissolve in water and release hydroxide (OH ) ions - acids donate H + ; bases accept H + 1. Strong acids completely dissociate in solution: HCl -->H + + Cl - H2SO4 --> 2H + + SO4 2-2. Weak acids partly dissociate in solution H2CO3 <--> H + + HCO3-3. Strong bases completely dissociate in water, tie up H + NaOH --> Na + + OH - 4. Weak bases do not completely dissociate in solution and as such are slower to accept H + H2CO3 <--> H + + HCO3 - NH2 + H + <--> NH3 + 5. The ph scale - the ph scale indicates the strength of a solution of an acid or base the scale is arrayed as a set of values 1 through 14 these values may be measured by electronic instruments - the ph value is defined as the negative logarithm of the hydrogen ion concentration in moles per liter (molar concentration): ph = - log10 [H + ] - a ph 7 means the concentration of hydrogen ions is 1 10 7 M -- this is 1 10 7 moles per liter of water when water is at ph 7, both the H + and OH are at a concentration of 10 7 molar when water is ph 8, it is 10 8 molar for H + and 10 6 molar for OH - thus the higher the number of the ph, the greater the OH concentration and the lower the H + concentration, and vice versa 6. Buffers - mixture of a weak acid and its corresponding base -- carbonic acid and bicarbonate ions - limit the change of ph when hydrogen ions are added or removed - concept of buffering range VI. Properties of molecules 1. Molecules range in size and molecular weight from the very smallest, H2, to the massive, such as the DNA molecule that makes up the length of a chromosome and contains millions of atoms carbon-containing molecules are called organic molecules and are common in life forms
most organic molecules also contain hydrogen and oxygen, and many contain nitrogen and phosphorus - all molecules have a specific three-dimensional shape based on bonds between atoms that form them -- orientation of bonding orbitals 2. Often talk of functional groups groups of atoms that are part of a larger molecule and have particular chemical properties -- shape, polarity, reactivity, solubility same functional group may be part of two very different molecules 3. Isomers - isomers are molecules that have the same chemical formula but different arrangements of the atoms. structural isomers differ in how atoms are joined together - butane and isobutane optical isomers are mirror images of each other - optical isomers can occur whenever a carbon has four different atoms or groups attached to it a carbon such as this is called asymmetric amino acids (except glycine) exist in two optical isomeric forms called D- and L-amino acids -- L-amino acids are those commonly found in most organisms