Bozeman Biology – Chemical Basis of Life Biochemistry: Atomic And Molecular Structure (This chapter is a review of physical science- we will be going through this chapter very quickly. If you have any questions. . . . ASK. Bozeman Biology – Chemical Basis of Life

Element A pure substance that is composed of only one type of atom; There are 92 natural elements Ex: Sodium (Na), Chlorine (Cl), Hydrogen (H), Lead (Pb)

Copyright Pearson Prentice Hall Atoms Basic unit of matter; smallest particle of element with all properties of that element Copyright Pearson Prentice Hall

Copyright Pearson Prentice Hall Placed side by side, 100 million atoms would make a row only about 1 centimeter long. Atoms contain subatomic particles that are even smaller. Copyright Pearson Prentice Hall

Copyright Pearson Prentice Hall The subatomic particles that make up atoms are protons neutrons electrons Copyright Pearson Prentice Hall

Copyright Pearson Prentice Hall Protons (+): positively charged particles in the nucleus Neutrons (0): neutral particles (no charge) in the nucleus Electrons (-): negatively charged particles outside the nucleus Helium atoms contain protons, neutrons, and electrons. The positively charged protons and uncharged neutrons are bound together in the dense nucleus, while the negatively charged electrons move in the space around the nucleus. Copyright Pearson Prentice Hall

Isotopes atom of same element w/ different number of neutrons (e.g., carbon-12, carbon-13, carbon-14)

Protons + Neutrons = Atomic Mass Drawing An Atom 1) All the mass of an atom is in the center or nucleus. 2) The mass of an atom can be calculated by adding the number of protons and the number neutrons. Ex: 6 C 12 (Atomic Mass) Protons + Neutrons = Atomic Mass

Atomic Number = The # of Protons Where can I find the number of protons? Ex: 6 (atomic number) C 12 Atomic Number = The # of Protons

Atomic Mass – Atomic Number = The # of Neutrons How do I find the number of neutrons? Ex: 6 C 12 12 – 6 = 6 Neutrons Atomic Mass – Atomic Number = The # of Neutrons

Copyright Pearson Prentice Hall Chemical Compounds A chemical compound is a substance formed by the chemical combination of two or more elements in definite proportions. Copyright Pearson Prentice Hall

Examples of Chemical Compounds Water H2O Table salt NaCl Carbon dioxide CO2 Sugar C6H12O6

Characteristics of Compounds Always formed from a specific combination of elements 2. Always formed in a fixed ratio Ex: H3O does not = water Ex: CO4 does not = carbon dioxide

Characteristics of Compounds Compounds are chemically and physically different from the elements they are made from: Ex: Water (H2O) has different properties than hydrogen (H) or oxygen (O)

Copyright Pearson Prentice Hall Chemical Bonds The atoms in compounds are held together by chemical bonds. The electrons that are available to form bonds are called valence electrons. Copyright Pearson Prentice Hall

Bozeman Biology – Chemical Bonds: Covalent and Ionic Bonds The main types of chemical bonds are: Ionic bonds Covalent bonds Bozeman Biology – Chemical Bonds: Covalent and Ionic Bonds Copyright Pearson Prentice Hall

Copyright Pearson Prentice Hall Ionic Bonds force of attraction between oppositely charged ions (atoms that gain or lose electrons); electrons are transferred (e.g., NaCl) Copyright Pearson Prentice Hall

Copyright Pearson Prentice Hall The chemical bond in which electrons are transferred from one atom to another is called an ionic bond. The compound sodium chloride forms when sodium loses its valence electron to chlorine. Copyright Pearson Prentice Hall

Copyright Pearson Prentice Hall Covalent Bonds chemical bond formed when 2 atoms combine by sharing electrons (e.g., H2O) Copyright Pearson Prentice Hall

Copyright Pearson Prentice Hall The structure that results when atoms are joined together by covalent bonds is called a molecule. Copyright Pearson Prentice Hall

Copyright Pearson Prentice Hall One more bond type…Van der Waals Forces When molecules are close together, a slight attraction can develop between the oppositely charged regions of nearby molecules. Copyright Pearson Prentice Hall

Properties of Water! Properties of Water Bozeman Biology Water as a Polar Molecule

Properties of water Six emergent properties of water contribute to Earth’s fitness for life Cohesion/Adhesion Surface tension Temperature Moderation High specific heat Evaporative cooling Universal solvent http://www.sumanasinc.com/webcontent/animations/content/propertiesofwater/water.html

Why do we study water properties in biology class? About 2/3 of the mass of a cell is water! Most life-sustaining reactions occur in water solutions

Water Molecule 2 atoms of hydrogen linked by covalent bonds to 1 atom oxygen (H2O) Polar Molecule: has positive hydrogen end and negative oxygen end

Water is Polar Polarity: The electrons are unevenly distributed between the Oxygen and the two Hydrogen atoms. Oxygen has 8 protons. Each hydrogen has 1.

Water is Polar The atom with more protons (Oxygen) pulls electrons away from the atom(s) A diagram of what’s happening:

Water forms Hydrogen Bonds Hydrogen Bonds: Form due to attraction between water molecules. Not as strong as ionic/covalent bonds

Water forms Hydrogen Bonds Water can form up to 4 hydrogen bonds at once A diagram of what’s going on:

Hydrogen Bonds Exist Between Water Molecules http://www.northland.cc.mn. us/biology/biology1111/animat ions/hydrogenbonds.html

Water is Cohesive Cohesion: Water molecules are drawn tightly together (on the surface of a lake or a pond, this forms a film, which is called surface tension) Explains why: Water beads on a surface (like the lab table) Insects can walk on water http://www.youtube.com/watch?v=RphuMEUY3Og http://news.nationalgeographic.com/news/2003/08/0806_030806_skeeters.html

A Cool Example of Cohesion / Surface Tension: Water Strider Insect http://www.youtube.com/watch?v=RphuMEUY3Og http://news.nationalgeographic.com/news/2003/08/0806_030806_skeeters.html

Water is Adhesive = Adhesion = Water adheres (sticks) to different surfaces Ex: Measuring water in a graduated cylinder Water adheres (sticks) to the glass more than it adheres to itself. That’s why there is a dip in the water when you read the volume

Cohesion Adhesion Ex: Water Bubble Ex: Water and Paper Towels Cohesion Video

Water can undergo Capillary Action Capillary Action= Water can flow up a tube, against gravity Ex: Plants absorbing water through their roots

Water is an Excellent Solvent Water often found as part of a mixture called a solution Solution: one substance (solute) dissolves into another (solvent); water is called the “universal solvent” Why is this important in humans? Salt (NaCl) in Water

What does ice look like at the molecular level?

Water is Less Dense as a Solid Which is ice and which is water? 1

Water is Less Dense as a Solid Ice 1

States of Matter Liquid Gas Solid

Water has a High Heat Capacity Water absorbs a lot of heat from the air without having a large temperature change So…lakes and oceans often stabilize air temperatures Water absorbs heat when it evaporates; this is why sweating helps us cool down!

So why does it take so much heat to increase the temperature of water?! You have to break the hydrogen bonds between water molecules first!

Water is less dense in its solid form Water is less dense in its solid form than it is in its liquid form (Ice floats!) Why might it be a bad thing for ice to sink in a pond?

Water: The Essential Substance for Life

Water Has a Neutral pH pH: measure of how acidic or basic a solution is scale is 0 to 14 If pH = 7, then substance is neutral (not acid or base)

Water Has a Neutral pH acid: forms hydrogen ions (H) in water; pH is less than 7 base: forms hydroxide ions (OH) in water; pH is greater than 7

Hydrophilic and Hydrophobic Substances A hydrophobic substance Does not have a liking for water Nonpolar lipids A hydrophilic substance Has a liking for water Polar or ionic Carbohydrates, salts

Acids and Bases Dissociation of water molecules leads to acidic and basic conditions that affect living organisms Organisms must maintain homeostasis in the pH of their internal and external environments

Effects of Changes in pH Water can dissociate Into hydronium ions (H+ or H3O+) and hydroxide (OH-) ions Changes in the concentration of these ions Can have a great affect on pH in living organisms H Hydronium ion (H3O+) Hydroxide ion (OH–) + – Figure on p. 53 of water dissociating

Acids, Bases and pH H2O  H+ + OH- One water molecule in 550 million naturally dissociates into a Hydrogen Ion (H+) and a Hydroxide Ion (OH-) Hydrogen Ion Hydroxide Ion Acid Base H2O  H+ + OH-

Acid / Base Reactions pH level determines rate & types of reactions that can take place buffer: weak acid or base that can react with a strong acid or base to prevent sudden changes in pH Buffers help maintain a constant pH.  A change in pH in living cells could denature proteins, DNA and other important molecules resulting in the death of the cells.

Acids and Bases An acid- (sour) Is any substance that increases the hydrogen ion (H+) concentration of a solution A base- (bitter/slippery) Is any substance that reduces the hydrogen ion concentration of a solution (more OH- ions)

The pH Scale Scale goes from 0-14 with 7 neutral The pH of a solution Is determined by the relative concentration of hydrogen ions Difference of 10X in hydrogen ion concentration between any two pH values Each pH unit represents a factor of 10X change in concentration pH 3 is 10 x 10 x 10 (1000) stronger than a pH of 6 Acids have a higher number of H+ ions than a base Acids produce H+ ion in solution Bases produce OH- ions in solution

The pH scale and pH values of various aqueous solutions Increasingly Acidic [H+] > [OH–] Increasingly Basic [H+] < [OH–] Neutral [H+] = [OH–] Oven cleaner 1 2 3 4 5 6 7 8 9 10 11 12 13 14 pH Scale Battery acid Digestive (stomach) juice, lemon juice Vinegar, beer, wine, cola Tomato juice Black coffee Rainwater Urine Pure water Human blood Seawater Milk of magnesia Household ammonia Household bleach Figure 3.8

Example: For a neutral solution: [H+] is 10-7 or - log 10-7 or - (-7)

Acids: pH <7 etc. Bases: pH >7 etc. Each pH unit is a 10x change in H+

Comment [H+] + [OH-] = 14 Therefore, if you know the concentration of one ion, you can easily calculate the other.

Buffers The internal pH of most living cells Buffers Must remain close to pH 7 Buffers Are substances that minimize changes in the concentrations of hydrogen and hydroxide ions in a solution Consist of an acid-base pair that reversibly combines with hydrogen ions Made by organisms

The Threat of Acid Precipitation Refers to rain, snow, or fog with a pH lower than pH 5.6 Is caused primarily by the mixing of different pollutants with water in the air

Acid Rain

Acid Rain

Bozeman Biology – Acids, Bases and pH Acid precipitation Can damage life in Earth’s ecosystems 1 2 3 4 5 6 7 8 9 10 11 12 13 14 More acidic Acid rain Normal rain More basic Figure 3.9 Acids, Bases and pH Bozeman Biology – Acids, Bases and pH