Chemistry for Bio 9

Which of the following is/are properties of life? 1.Cellular structure 2.the ability to take in energy and use it 3.the ability to respond to stimuli from the environment 4.the ability to reproduce 5.All of the choices are correct.

Lecture outline Chemistry- definition, scope, and relevance to biology Classification of matter The atom and subatomic particles Chemical bonding & reactions Chemistry of water Acids, Bases, and the pH scale

Chemistry is relevant to Biological Concepts Chemistry is the study of matter and its interactions All Living things are made of matter Biolgists are interested in: – Complex biological molecules – Chemical energy – Biochemical reactions – The chemical environment

Complex biological molecules All living things are made of complex macromolecules Chemical principles rule their assembly

Chemical energy Photosynthesis creates molecules rich in energy: 6CO 2(g) + 6H 2 O (l) + hν  C 6 H 12 O 6(s) + 6O 2(g) Earth has been transformed by chemical reactions peformed by living things

Biochemical reactions All living things are collections of a vast number of chemical reactions Even the simplest living things contain impossibly complex pathways

The Chemical Environment The physical properties of water determine the fate of life on earth pH, salinity and other chemical factors influence Living things are profoundly influenced by their chemical environment

Chemical reactions performed by living things have transformed earth over billions of years of its history

Classification of matter

Mixtures can be homogeneous or heterogeneous Mixtures can vary in composition of their ingredients Compounds are defined substances with proportional amounts of ingredients: water, carbon dioxide, etc. Elements cannot be broken down into ingredients by chemical processes

Basic principles of chemistry

The periodic table is an organized display of all the elements in the universe

The Structure of the Atom Subatomic particles- protons, neutrons electrons Orbitals and the nucleus

All matter is ultimately comprised of atoms Atoms are the smallest individual unit of matter Atoms are comprised of protons, neutrons and electrons Proton: Charge= +1, Mass= 1 Neutron: Chg= 0, mass= 1 Electron: Chg = -1, mass= ~0 Mass= p + n Charge = p - e

LE 2-4a Protons Neutrons Electrons Helium atom Mass number = Protons Neutrons Electrons Carbon atom Mass number = 12 Electron cloud Nucleus 2e – 6e –

Reading the Periodic Table

Elements are defined by the number of their protons There are 92 naturally occurring elements Many others have been synthesized Atomic number = # protons Atomic mass (mass number) = protons + neutrons of an individual atom Atomic weight= Naturally occurring average of isotopes of a substance

The number of neutrons in atoms of a single element is variable Isotopes are variants of an element, differentiated by numbers of neutrons Some isotopes are stable, others are radioactive

Some isotopes are common, others rare

Many Isotopes for an element can exist; radioisotopes are radioactive

Radioisotopes can be used in medical diagnosis- Radioisotopes of iodine target the thyroid gland

How is atomic weight different from atomic mass?

The sodium atom contains 11 electrons, 11 protons, and 12 neutrons. What is the mass number (atomic mass) of sodium?

96% of human tissue is comprised of 6 elements Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorous, Sulfur (CHNOPS) 25 elements serve known functions in the body, incl. Ca, K, Na, Cl, Mg, Fe Trace elements are essential, but in small quantities

A compound 1.A) is a pure element. 2.B) is less common than a pure element. 3.C) contains two or more elements in a fixed ratio. 4.D) is exemplified by sodium. 5.E) is a solution.

Atomic structure Protons and electrons in the nucleus Electrons orbit around Bohr atom- classic model featuring electrons in “planetary” orbitals Each orbit holds a determined number of electrons (first holds two, 2 nd and 3 rd hold eight

Electron cloud model Currently accepted model of atomic structure 90% probability cloud Mostly empty space Unfilled orbitals found in unstable, reactive elements Therefore, orbitals influence bonding

Electrons in the outermost shell of an atom are called valence electrons

Intramolecular Chemical Bonds: Ionic, Covalent, and the formation of molecules

Atoms are stable when their valence shells are filled with electrons What atoms are these? How could they satisfy their valence shells?

Noble gases have a stable electron structure Their outer orbitals have a full complement of electrons Noble gases are very unreactive

Elements combine in chemical reactions to form compounds Molecules- 2 or more atoms combined in specific ways Compounds- different elements in a molecule, in exact, whole-number ratios, joined by a chemical bond 2 major kinds of intramolecular chemical bonds: Covalent (incl. polar and nonpolar) and Ionic

In ionic bonding, an atom takes an electron from another atom, forming ions LE 2-7 Transfer of electron Na Sodium atom Cl Chlorine atom Na  Sodium ion Cl  Chloride ion Sodium chloride (NaCl)

Ions Ions- Charged atoms or molecules Anion- negative ion Cation- positive ion Ionization- reaction producing ions Salt- a neutral compound comprised of ions

LE 2-7a-2 Na  Sodium ion Cl  Chloride ion Sodium chloride (NaCl)

LE 2-7b Na  Cl 

The nucleus of an atom contains 1.protons and neutrons. 2.protons and electrons. 3.only neutrons. 4.only protons. 5.only electrons.

In covalent bonding, electrons are shared Atoms form as many bonds as they have vacancies in their outermost electron orbitals Atoms are bound together by the sharing of electrons Chemical reactions often involve the exchange of covalent bonds

LE 2-6b Nitrogen (N) Atomic number = 7 Oxygen (O) Atomic number = 8

Covalent bonds hold together the macromolecules of life Living things create macromolecular products for structure: 6CO 2(g) + 6H 2 O (l) + hν  C 6 H 12 O 6(s) + 6O 2(g) Macromolecules as reactants are broken down for energy: C 6 H 12 O 6(s) + 6O 2(g)  6CO 2(g) + 6H 2 O (l) All the reactions of a living thing are called its metabolism

Many chemical reactions solely involve exchange of covalent bonding partners 

Chemical reactions performed by your body create essential molecules your body needs Beta-caroteneVitamin A (2 molecules)

Electronegativity and its effect on chemical bonds Ionic bonds, covalent bonds, and intermolecular forces

Electronegativity values can predict how atoms will bond

In covalent bonds, electrons do not always share time between bond partners equally Comparisions of electronegativity Na: 0.9 H: 2.1 C: 2.5 N: 3.0 Cl: 3.0 O: 3.5

Electronegativity = “electron greediness” Large differences in polarity of atoms in a bond creates polar molecules Relative electronegativity of Hydrogen and oxygen makes water a very polar molecule Polar- regions of positivity and negativity By Oxygen, water is (slightly) negative By Hydrogens, water is (slightly) positive

Intermolecular forces and the chemistry of water Polarity and hydrophilicity, Nonpolarity and hydrophobicity, hydrogen bonding, and the chemistry of water

Water is a “universal solvent” and dissolves many polar and ionic compounds (“like dissolves like”)

The polarity of water allows hydrogen bonding Polar regions of water molecules interact to form hydrogen bonds Hydrogen bonds: weak/temporary intermolecular forces between positive and negative regions

Other molecules can engage in H- bonding, w/ water or other substances

Hydrogen bonds hold together the two strands of a DNA double helix

Hydrogen bonding in water determine many of water’s unique properties H-bonds can form a lattice (ice) H-bonds require much energy (usually heat) to break H-bonds give water surface tension Hydrogen bond

Hydrogen Bonds help to make water cohesive, allowing water surface tension and capillary action

Capillary action allows redwoods to grow to heights over 300 feet

Just as heat breaks H-bonds, as water cools, more H-bonds form Hydrogen bond Ice Hydrogen bonds are stable Liquid water Hydrogen bonds constantly break and re-form Because H-bonds have a fixed distance, the crystal lattice of water makes ice less dense

Hydrogen bonds require energy to break- water has a high specific heat Water’s high specific heat allows evaporative cooling -and makes sweating an effective cooling mechanism

Due to water’s high specific heat, proximity to water has a stabilizing effect on regional temperature

Nonpolar molecules are mostly neutral C: 2.5, H: 2.1 Very few positive or negative regions, if any Hydrocarbons- compounds solely made of hydrogen and carbon, e.g. fats, oils, & gas Nonpolar substances are hydrophobic and do not mix well with water

Acids, bases, and the pH scale

Since ions do not share electrons, they may separate in solution

Water also forms ions sometimes H 2 O ↔ H + + OH - Spontaneously happens to water molecules 1/ 10 7 water molecules are ionized in distilled water In dH 2 O, [H + ]= [OH - ]

Because Oxygen is much more electronegative than Hydrogen, water can occasionally Ionize H 2 O  H + + OH - Also called dissociation Ions quickly reform into water: – H + + OH -  H 2 O Approx 1 in 10,000,000 water molecules is dissociated at any given time (that is, )

Other substances ionize Usually ionic compounds Many ionize completely Salt: NaCl  Na + + Cl - Hydrochloric acid: HCl  H + + Cl - Sodium Hydroxide:NaOH  Na + + OH - Substances which ionize can affect the pH of a water solution

pH is a measure of acidity/basicity pH = -log [H + ] (logarithmic scale) pH 1  6.9: acid pH 7.1  14: base Acids donate [H + ] to water- cause burns Bases remove [H + ] from water (or donate [OH - ] to water) – often have a slimy feel Strong acids & bases are ~equally nasty Proteins are sensitive to small changes in pH

LE 2-15 Acidic solution OH  HH HH HH HH HH HH HH HH HH HH HH HH HH Increasingly ACIDIC (Higher concentration of H  ) Neutral solution OH  HH HH Basic solution NEUTRAL  H        pH scale Lemon juice, gastric juice Grapefruit juice, soft drink Tomato juice Human urine Pure water Human blood Seawater Milk of magnesia Household ammonia Household bleach Oven cleaner Increasingly BASIC (Lower concentration of H  )

Acid rain pollution can cause tremendous ecological damage SO 2 (g)+ H 2 O  SO 2 ·H 2 O SO 2 ·H 2 O  H + +HSO 3 - HSO 3 -  H + +SO 3 2-

Mechanism of acid rain

More effects of acid rain

Buffers can help control changes in pH

The Relationships between Two Different Drinking Water Fluoride Levels, Dental Fluorosis and Bone Mineral Density of Children S.R. Grobler*, A.J. Louw, U.M.E. Chikte, R.J. Rossouw and T.J. van W. Kotze Oral and Dental Research Institute, Faculty of Dentistry, University of the Western Cape, Republic of South Africa Abstract: This field study included the whole population of children aged 10–15 years (77 from a 0.19 mg/L F area; 89 from a 3.00 mg/L F area), with similar nutritional, dietary habits and similar ethnic and socioeconomic status. The fluoride concentration in the drinking water, the bone mineral content, the bone density and the degree of dental fluorosis were determined. The left radius was measured for bone width, bone mineral content, and bone mineral density. The mean fluorosis score was 1.3 in the low fluoride area and 3.6 in high fluoride area. More than half the children in the low fluoride area had no fluorosis (scores 0 and 1) while only 5% in the high fluoride area had none. Severe fluorosis (30%) was only observed in the high fluoride area. The Wilcoxon Rank Sum Test indicated that fluorosis levels differed significantly (p < 0.05) between the two areas. No relationships were found between dental fluorosis and bone width or between fluorosis and bone mineral density in the two areas (Spearment Rank correlations). A significant positive correlation was found in the high fluoride area between bone mineral density over age. In the and year age groups in the high fluoride area, girls had higher bone mineral densities. However, a significant negative correlation (p<0.02) was found in low fluoride area (0.19 mg/L F) over age.

Water's surface tension and heat storage capacity is accounted for by its 1. orbitals. 2.weight. 3.hydrogen bonds. 4.mass. 5.size.