Lecture 2: The Chemistry of Life
In this lecture: Matter, atoms, and the periodic table Chemical bonding Ionic vs. covalent bonds Hydrogen bonds and Van der Waals forces Polarity Electronegativity
What is stuff made of? Matter Anything that takes up space and has mass (or weight) Makes up everything we see, touch, feel, and hear in the universe (Dark matter is another thing entirely)
What is matter made of? Matter is made up of elements. An element is a substance that cannot be broken down to other substances by chemical reactions Potassium, hydrogen, carbon, phosphorus Compounds are substances made of two or more elements The properties of a compound are not related to the properties of its elements
The periodic table is very carefully arranged. We shall see why soon
Matter = atoms = elements Compounds = 2+ elements
The elements of life About 20-25% of the elements are necessary to life Carbon, hydrogen, nitrogen, and oxygen make up 96% of living beings Phosphorus, calcium, potassium, and sulfur make up most of the other 4% There are some trace elements that are necessary for life, but needed in very minute amounts Zinc in DNA regulation, silicon in shell formation, iron in blood
What is matter made of? Matter is made of atoms An atom is the smallest unit of matter that still retains the properties of an element Atom means indivisible in Greek
What are atoms made of? Three subatomic particles go into an atom Proton (positive charge) Neutron (neutral/no charge) Electron (negative charge)
Neutrons and protons form the atomic nucleus Electrons form a cloud around the nucleus Neutron mass and proton mass are almost identical and are measured in daltons
A helium atom Is this what an atom really looks like?
Atomic Number and Atomic Mass Atoms of the various elements differ in number of subatomic particles An element s atomic number is the number of protons in its nucleus Atomic mass, the atom s total mass is the sum of protons plus neutrons in the nucleus
Electron positions Electrons are arranged in shells around the nucleus 2 electrons in the innermost shell, 8 in all the subsequent shells
The number of electrons an atom has is equal to the number of protons (7 positive protons + 7 negative electrons = neutral charge) Neutrons just hang out
Figure 2.9 First shell Second shell Third shell Hydrogen 1H Lithium 3Li Sodium 11Na Beryllium 4Be Magnesium 12Mg Boron 5B Aluminum 13Al Carbon 6C Silicon 14Si Nitrogen 7N Phosphorus 15P Oxygen 8O Sulfur 16S Fluorine 9F Chlorine 17Cl Neon 10Ne Argon 18Ar Helium 2He 2 He 4.00 Mass number Atomic number Element symbol Electron distribution diagram
Valence electrons Valence electrons are those in the outermost shell The chemical behavior of an atom is mostly determined by the valence electrons Elements with a full valence shell are chemically inert
Diagram of valence electrons
Let s draw a sulfur atom What is the atomic number of sulfur? How many protons? How many neutrons? How many electrons? Where do the electrons go?
Solution: A sulfur atom
Isotopes All atoms of an element have the same number of protons but may differ in number of neutrons Isotopes are two atoms of an element that differ in number of neutrons Radioactive isotopes decay spontaneously, giving off particles and energy
Radioactive decay of isotopes Half-life is the time it takes half of the isotopes in a compound to decay into normal atoms The ratio of carbon-14 to carbon-12 can be used to date biological samples
Some applications of radioactive isotopes in biological research are Dating fossils Tracing atoms through metabolic processes Diagnosing medical disorders
Summary of an atom
Chemical Bonds Atoms with incomplete valence shells (<8) want to have filled shells Atoms will bond with each other to fill their shells, forming a chemical bond
Figure 2.11-3 Hydrogen atoms (2 H) Hydrogen has one proton and one valence electron It wants two to completely fill its inner shell, and so will bond Hydrogen molecule (H 2 )
Bonding A molecule consists of two or more atoms held together by covalent bonds Four types of bonds: covalent, ionic, metallic, hydrogen (sometimes) Covalent and hydrogen most common in biology
Ionic Bonding Ionic bonding electron is donated
Ionic Bonding Atoms sometimes strip electrons from their bonding partners An example is the transfer of an electron from sodium to chlorine After the transfer of an electron, both atoms have charges A charged atom (or molecule) is called an ion
A cation is a positively charged ion An anion is a negatively charged ion An ionic bond is an attraction between an anion and a cation
Covalent Bonding Covalent bonding electron is shared
Some examples of covalent bonds
Bonding in covalent bonds A single bond is the sharing of one pair of valence electrons A double bond is the sharing of two pairs of valence electrons
Polarity in covalent bonds In a nonpolar covalent bond, the atoms share the electron equally In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule
Electronegativity Atoms in a molecule attract electrons to varying degrees Electronegativity is an atom s attraction for the electrons The more electronegative an atom, the more strongly it pulls shared electrons toward itself
Electronegativity Electronegativity increases in this direction
Weak Chemical Bonds Most of the strongest bonds in organisms are covalent bonds that form a cell s molecules Weak chemical bonds, such as ionic bonds and hydrogen bonds, are also important Weak chemical bonds reinforce shapes of large molecules and help molecules adhere to each other
Weak Chemical Bonds Hydrogen Bonds A hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom In living cells, the electronegative partners are usually oxygen or nitrogen atoms
Weak Chemical Bonds: Van der Waals force Polar molecules have hot spots of negative or positive charge where electrons are unevenly distributed Van der Waals interactions are attractions between molecules that are close together as a result of these charges This force comes from fluctuations in charge distributions between neighboring molecules, which need not be polar; their charge fluctuations naturally fall into synch, creating an attractive force.
How Geckos stick on der Waals Geckos use Van der Waals interactions between their toe hairs and a wall to stick
Chemical Reactions: making and breaking bonds The starting molecules of a chemical reaction are called reactants The final molecules of a chemical reaction are called products
Photosynthesis, a chemical reaction Plants use sunlight to create an essential building block Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen 6 CO 2 + 6 H 2 0 C 6 H 12 O 6 + 6 O 2
What do my multivitamins do in the body? The FDA officially recognizes 12 essential minerals: calcium, magnesium, zinc, selenium, copper, manganese, chromium, molybdenum, and chloride Silicon, boron, nickel, vanadium, and lead may play a biological role, but aren t essential The role of these hasn t been well defined For a lot of these, we don t know exactly what they do, so the FDA is hands-off
Biological organisms and elements Mono Lake, CA:
The Aliens of Mono Lake Mono Lake has no natural outlets Chemicals enter, but don t leave HUGE buildup of toxic waste chemicals and salt No fish, only brine shrimp can live there In December 2010 NASA announced the discovery of a bacteria that can use arsenic Arsenic is normally VERY toxic to living things!! It replaces phosphorus in biochemical reactions, but is far less stable Anything that accidentally includes arsenic (DNA, ATP, etc.) tends to break down very fast
These bacteria can stably integrate arsenic in place of phosphorus into their DNA Use large storage vacuoles to isolate arseniccontaining molecules away from important cellular machinery
Controversey 2012 scientists begin refuting NASA s findings NASA scientists fed the bacteria salts that contained trace amounts of phosphorus, which may have allowed the bacteria to live No arsenic found in the DNA after all http://www.scientificamerican.com/article.cfm?id=study-fails-to-confirm-existence
Vocabulary Matter Element Compound Atom Molecule Protons, neutrons, electrons Nucleus Atomic number Isotope Potential energy, kinetic energy Valence electrons Electron shells Electronegativity Covalent bond, ionic bond Hydrogen bond, Van der Waals force Products, reactants Polarity