Review of Chemistry and the Properties of Water

Quick Comments on Ch 1  The reading guides are designed to help you focus your attention in the chapter. They are NOT the end goal. The goal is that you use the text to learn the subject matter.  Khan academy  Bozeman science  The Vocab included in the chapter is all review, so you need to know it. If any of it is new to you, then please spend some time with it.  Ex: Emergent properties, eukaryote, +/- feedback, domain, falsifiable hypothesis  Levels of organization memorized  Aspects of a controlled experiment  What is the control group?  Impossible to hold all variables constant except for one when you are out in the field…so we use “constants” to cancel out the effects of unknown variables

Chapter 2

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 Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

◦Dating fossils ◦Tracing atoms through metabolic processes ◦Diagnosing medical disorders Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings Some applications of radioactive isotopes in biological research are:

Fig. 2-6 TECHNIQUE RESULTS Compounds including radioactive tracer (bright blue) Incubators °C15°C20°C 25°C 30°C 35°C 40°C45°C50°C Human cells Human cells are incubated with compounds used to make DNA. One compound is labeled with 3 H. The cells are placed in test tubes; their DNA is isolated; and unused labeled compounds are removed. DNA (old and new) The test tubes are placed in a scintillation counter. Counts per minute (  1,000) Optimum temperature for DNA synthesis Temperature (ºC)

Fig. 2-6a Compounds including radioactive tracer (bright blue) Human cells Incubators ºC 45ºC40ºC 25ºC 30ºC 35ºC 15ºC 20ºC 10ºC Human cells are incubated with compounds used to make DNA. One compound is labeled with 3 H. 1 2 The cells are placed in test tubes; their DNA is isolated; and unused labeled compounds are removed. DNA (old and new) TECHNIQUE

Fig. 2-6b TECHNIQUE The test tubes are placed in a scintillation counter. 3

Fig. 2-6a Compounds including radioactive tracer (bright blue) Human cells Incubators ºC 45ºC40ºC 25ºC 30ºC 35ºC 15ºC 20ºC 10ºC Human cells are incubated with compounds used to make DNA. One compound is labeled with 3 H. 1 2 The cells are placed in test tubes; their DNA is isolated; and unused labeled compounds are removed. DNA (old and new) TECHNIQUE

Fig. 2-6c RESULTS Counts per minute (  1,000) Temperature (ºC) Optimum temperature for DNA synthesis

Fig. 2-12c (c) Water (H 2 O) Name and Molecular Formula Electron- distribution Diagram Lewis Dot Structure and Structural Formula Space- filling Model

Fig. 2-12d (d) Methane (CH 4 ) Name and Molecular Formula Electron- distribution Diagram Lewis Dot Structure and Structural Formula Space- filling Model

Fig NaCl Na Cl Na Sodium atom Chlorine atom Cl Na + Sodium ion (a cation) Cl – Chloride ion (an anion) Sodium chloride (NaCl)

A cation is a An anion is a negatively charged ion positively charged ion An ionic bond is an attraction between an anion and a cation Animation: Ionic Bonds Animation: Ionic Bonds Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Compounds formed by ionic bonds are called ionic compounds, or salts Salts, such as sodium chloride (table salt), are often found in nature as crystals Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Fig Na + Cl –

Fig    ++ ++    ++ ++ ++ Water (H 2 O) Ammonia (NH 3 ) Hydrogen bond

Fig (a) Structures of endorphin and morphine (b) Binding to endorphin receptors Natural endorphin Endorphin receptors Morphine Brain cell Morphine Natural endorphin Key Carbon Hydrogen Nitrogen Sulfur Oxygen

Fig. 2-UN7

Comments on Chapter 3 Water is polar, and therefore is the key to life Use white boards to explain polarity at your tables List and explain the 4 emergent properties that arise because water is polar.  Cohesion  High specific heat  Moderation of earth’s temp  Evaporation is a cooling process  Expansion upon freezing  Almost universal solvent  Hydrophilic and hydrophobic

Fig. 3-UN4 Liquid water: transient hydrogen bonds Ice: stable hydro- gen bonds

Fig. 3-7 Cl – Na Cl – – – – – – – – – Na + – – – +

Fig. 3-8ab (b) Lysozyme molecule (purple) in an aqueous environment (a) Lysozyme molecule in a nonaqueous environment

Concept 3.3: Acidic and basic conditions affect living organisms A hydrogen atom in a hydrogen bond between two water molecules can shift from one to the other: ◦The hydrogen atom leaves its electron behind and is transferred as a proton, or hydrogen ion (H + ) ◦The molecule with the extra proton is now a hydronium ion (H 3 O + ), though it is often represented as H + ◦The molecule that lost the proton is now a hydroxide ion (OH – ) Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Acidic solutions have pH values less than 7 Basic solutions have pH values greater than 7 Most biological fluids have pH values in the range of 6 to 8 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

The pH Scale In any aqueous solution at 25°C the product of H + and OH – is constant and can be written as [H + ][OH – ] = 10 –14 The pH of a solution is defined by the negative logarithm of H + concentration, written as pH = –log [H + ] For a neutral aqueous solution [H + ] is 10 –7 = –(–7) = 7 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

pH Calculations 1. How many times more acidic is a pH of 3 vs. a pH of 5? 2. Explain the difference between a pH of 8 and a pH of 12 in terms of H+ concentration. 3.. What is the hydronium ion concentration of an acid with a pH of 3? What does this number really mean?

Buffers The internal pH of most living cells must remain close to pH 7 Buffers are substances that minimize changes in concentrations of H + and OH – in a solution Most buffers consist of an acid-base pair that reversibly combines with H + Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Acetic acid Buffer system in blood Exercise produces high CO2 and H+ in blood and muscles from the metabolism of glucose If O2 supply is depleted, lactic acid is produced (sore muscles) CO2 and lactic acid both decrease the pH of blood. Below pH 7.4 is acidosis, death at pH 6.8 So….buffer systems come in handy Solution will contain BOTH the weak acid and its corresponding base H2CO3 = carbonic acid. Forms from H2 + CO2 If the solution is too basic, it needs more H+, so carbonic acid donates a proton If solution is too acidic, it needs less H+, so HCO3- accepts the H+, reducing the H3O+ content