Chemistry PDF

Lesson 02: Chemistry Fun. Life, like all material entities, is comprised of matter. Matter is anything that has mass and occupies space. (You can borrow a cup of matter from a neighbor.) Matter comes in varieties called elements. Nature produced 92 elements. Humans have made a few more. Elements com...

Lesson 02: Chemistry Fun. Life, like all material entities, is comprised of matter. Matter is anything that has mass and occupies space. (You can borrow a cup of matter from a neighbor.) Matter comes in varieties called elements. Nature produced 92 elements. Humans have made a few more. Elements come in a package called an atom.Think of an atom as a unit quantity (e.g., $, mg, atoms) of an element. An atom is the smallest unit of matter that retains the properties of the element. Organization of Atoms Atoms are organized with uniformity. Most atoms possess 3 kinds of subatomic particles: Proton - a particle with a positive charge + Neutron - a particle with no charge 0 Electron - a particle with a negative charge - Atoms of different elements differ by the number of protons, neutrons and electrons they possess. Elements in Human Biomass O = 65% C = 18% H = 10% N = 3% Ca = 2% P = 1% K = 0.5% S = 0.3% Na = 0.2% Cl = 0.2% Other trace elements occur in our biomass (e.g., Fe, Zn). Some elements are toxic even at trace levels (e.g., Pb, Ni). Periodic Table:Atomic Number Atomic Number (AN)= nr. of protons in an atom’s nucleus. It is a whole number found in each cell of the PTE. 1 1.008 6 12.011 11 22.989 20 40.080 H C Na Ca Hydrogen Carbon Sodium Calcium In neutral atoms, AN also tells you nr. of electrons because P = E in neutral atoms. Periodic Table: Mass Number Mass Number (MN)= mass of the atomic nucleus (P+N). It is a decimal number because it is a calculated average of all known isotopes of the element. 1 1.008 6 12.011 11 22.989 20 40.080 H C Na Ca Hydrogen Carbon Sodium Calcium You can estimate the number of neutrons of the most common isotope by subtracting the atomic number from the mass number. How many neutrons in H, C, Na, and Ca? How many neutrons in 2H, 14C, 15N, 18O? Organization of Atoms Atoms have two general regions: a core or nucleus - ‣ protons and neutrons (each - assigned 1 AMU) - - + 0 - outer cloud 0 + + - ‣ electrons (e–) (0 AMU) - 0 + 0 0 + + Because e have relatively – 0 little mass and are moving - - - - about the nucleus rapidly, they - may be depicted as a cloud. Orbitals are the specific volumes of space, within this cloud, where e– reside. Atoms (Shell Hypothesis) It is useful to depict electrons (e–) as particles within concentric energy shells around an atomic nucleus. Each shell can hold a max number of e–. Max Number of e– per shell Shell 1 Shell 2 Shell 3 2 8 8 To diagram: add e– from inner → valence shell. Unpaired valence e– have the greatest potential to bond atoms together into molecules. Atoms ‘seek’ to maximize the number e– of in their valence shells through bonding. Determine nr. of valence e–: H, C, N, O, Na, K, P, S, Cl, Ca. Types of Atoms Atoms may vary in the ratio of subatomic particles. There are 3 kinds of atoms: neutral atoms have an equal ratio of protons and electrons (P=E) and often have the same nr. of neutrons (P=E=N) ions have an unequal ratio of protons to electrons (P≠E); e.g., H+, Na+, K+, Ca2+, Cl–, etc. isotopes have an unequal ratio of protons to neutrons (P≠N); e.g., 2H, 14C, 15N, 18O, etc. ➡ isotopes undergo radioactive decay yielding energy that can be used in medical imaging  Isotopes Neutral Atom Ions 2H Deuterium H Hydrogen H+ Hydrogen Ion - - 0 + + + 3H Tritium H– Hydride Ion - - Note: most H - atoms don’t 0 + 0 possess a + neutron and violate P=N  Isotopes Neutral Atom Ions 14C Carbon 14 C Carbon Na+ Sodium Ion 18O Oxygen 18 O Oxygen Cl– Chloride Ion Ions: Cations and Anions Ions: (P ≠ E) because they have lost or gained electrons. Cations are positively charged ions (+). H+ Na+ Each + symbol is the nr. of protons in the nucleus not counterbalanced by K+ Ca2+ electrons that have been lost from the cloud to other atoms or molecules. Fe2+ NH4+ Anions are negatively charged ions (–). Each – symbol is the nr. of electrons not H– Cl– counterbalanced by protons in the nucleus because the ion gained electrons in its PO43– CO32– cloud from other atoms or molecules. Ions are Bioactive You ingest ions in your food and water as salts and minerals that are dissociated in aqueous solvents. Ions are important to you (and other biota) for: muscle contraction (Na+, K+ and Ca2+) neuron function (Na+, K+ and Ca2+) bone formation (Ca2+) oxygen transport (Fe2+) ventilation (aka breathing) homeostasis (H+) e– Form Chemical Bonds Atoms conjoin via chemical bonds to form molecules. Compounds are molecules with 2 or more elements. Electrons form the chemical bonds among Atom atoms Atom Atom ENERGY Molecule Atom Atom Atom Types of Chemical Bonds Molecules can be assembled via three types of chemical bonds: non-polar covalent, polar covalent, and ionic. All bonds maximize valence e– of the bonding atoms! Non-polar Polar Ionic Transfer Equal sharing Unequal Mechanism followed by of e– sharing of e– ionization Relative Very strong Strong Weak Strength Dissociation Moderately Not likely Highly likely in H2O likely Non-polar bonds are very common in biomolecules; require enzymes, marked change in pH or heat to break. The molecules (left) are bonded via covalent bonds. H2, O2, and CH4 are non- polar whereas H2O is polar. Why? The geometry/orientation of the atoms and their relative mass (electronegativity). The O atom is more massive and its 8 protons attract shared electrons more so than the less massive H atoms with only a single proton each. Note each type of diagram! Types of Chemical Bonds Ionic bonds: e– transfer from orbitals of one atom to another; atoms ionize with opposite charges attracting each other. Salts are bonded via ionic bonds. Association Crystallization: molecules Lattices can attract to dissolve in H2O. form a lattice. Ionic bonds dissociate Some bonds in H2O to form ions. dissociate in H2O. Types of Physical Bonds δ– y Polar molecules have regions of partial nsit O de positive (δ+) and partial negative (δ–) e– H H charge due to unequal e– distribution. δ+ δ+ A δ+ region of one molecule can attract to a δ– region of another molecule or ion forming a physical bond. When such a bond involves H atoms we call it a Hydrogen bond. H bonds are weak in isolation but strong in numbers. That is why H-bonds in liquid H2O can dissociate salts! About Chemical Reactions A chemical reaction is a process that rearranges the organization of atomic constituents of molecules. Reactant(s) react(s) to form products. Some chemical rxns are reversible. A + + double arrow Reactants Products depicts rxn reversibility. In biota, essentially all chemical reactions are catalyzed (i.e., overcome reaction inertia) by enzymes (-ase). A pathway is a series or cascade of chemical reactions involved in cellular activities and systemic functions.