Essential Chemistry in Biology Mrs. Norris Topics Discussed in these notes Matter, Elements and Compounds Periodic Table of the Elements: Metals vs. Nonmetals Atomic Structure Chemical Bonding: Ionic vs. Covalent Bonding Chemical Reactions and Chemical Equations The Structure of Water Water as a Solvent The Importance of Water to Living Things Acids, Bases and pH Self-test/Review Questions

BASIC CHEMISTRY Organisms and all other things in the universe consist of matter Matter: Elements and Compounds Matter is anything that occupies space and has mass Matter is composed of chemical elements and compounds Elements: substances that cannot be broken down into other substances There are 92 naturally occurring elements on Earth What are compounds? Examples?

Periodic table of the elements Location of.... Metals? Nonmetals?

25 Elements are essential to life C, H, O, N: 96% of the weight of the human body

Some Elements React to Form Compounds Elements can combine chemically to form compounds Compounds contain two or more elements chemically combined in a fixed ratio Examples of Compounds: Table salt (sodium chloride): NaCl Water: H2O Glucose: C6H12O6

Each element consists of one kind of atom Atom: smallest unit of matter that retains the properties of an element Each element consists of one kind of atom (a) Hydrogen atom (b) Carbon atom (c) Oxygen atom Proton Neutron Electron First shell Second shell Atomic nucleus Fig. 2.02

The subatomic particles of an atom Atomic Structure The subatomic particles of an atom Electron  Negative charge Proton • Participates in chemical reactions  Positive charge  Determines element • Outer-shell electrons determine chemical behavior Neutron  No charge  Determines isotope Nucleus • Consists of neutrons and protons

Atomic Number: number of protons Elements differ in the number of subatomic particles in their atoms Atomic Number: number of protons determines which element it is Mass number sum of the number of protons and neutrons

Chemical Properties of Atoms Electrons Located outside the nucleus of an atom in specific electron shells (energy levels) The number of electrons in the outermost shell determines the chemical properties of an atom

Atoms of the four elements most abundant in life First electron shell: can hold 2 electrons Outermost electron shell: can hold 8 electrons Electron Hydrogen (H) Atomic number = 1 Carbon (C) Atomic number = 6 Nitrogen (N) Atomic number = 7 Oxygen (O) Atomic number = 8

Orbital Diagrams of the First 18 Elements 1st Shell 2nd Shell 3rd Shell 2 8 8

Chemical Bonding and Molecules Chemical reactions: Atoms give up or acquire electrons in order to complete their outer shells Result in atoms staying close together to form molecules Chemical bonds hold molecules together Ionic Bonds Covalent bonds

Ionic Bonds: form between metals and nonmetals When an atom loses or gains electrons, it becomes electrically charged Charged atoms are called ions Ionic bonds are formed between oppositely charged ions Sodium atom (Na) Chlorine atom (Cl) Complete outer shells Sodium ion (Na) Chloride ion (Cl) Sodium chloride (NaCl)

Atoms: electrically neutral Ions: Electrically charged (a) Hydrogen atom (H) (b) Hydrogen ion (H+) 1 electron No electron 1 proton 1 proton No net electrical charge (c) Sodium atom (Na) (d) Sodium ion (Na+) 11 electrons 10 electrons 11 protons 11 protons No net electrical charge Fig. 2.03

Covalent Bonds: form between nonmetallic atoms A covalent bond forms when two atoms share one or more pairs of outer-shell electrons

Covalent bonding in water Water molecule (H2O) Oxygen atom with unfilled shell Full shell with 8 electrons – Slightly negative Covalent bond (shared pair of electron) + + Slightly positive Full shells with 2 electrons each Hydrogen atoms with unfilled shells Fig. 2.04a

Chemical Reactions Cells constantly rearrange molecules by breaking existing chemical bonds and forming new ones Such changes in the chemical composition of matter are called chemical reactions Hydrogen gas Oxygen gas Water Reactants Products

Chemical Equations: symbolize chemical reactions Reactants: on the left side of the equation the starting materials Products: on the right side of the equation the ending materials (the stuff produces) Law of Conservation of Mass Chemical reactions do not create or destroy matter—they only rearrange it!

The abundance of water is a major reason Earth is habitable WATER AND LIFE The abundance of water is a major reason Earth is habitable Modern life still remains tied to water Your cells are composed of 70%–95% water

The Structure of Water The water molecule: two hydrogen atoms joined to one oxygen atom by single covalent bonds H H O

Water: a polar molecule The electrons of the covalent bonds are shared unequally between oxygen and hydrogen unequal sharing of electrons makes water a polar molecule hydrogen atoms: partially positive (d ) Why? oxygen atom: partially negative (d -) Why? (d ) (d ) (d )

The Structure of Water The polarity of water results in weak electrical attractions between neighboring water molecules These interactions are called hydrogen bonds () Hydrogen bond () () () () () () () (b)

Water’s Life-Supporting Properties The polarity of water molecules and the hydrogen bonding that results explain most of water’s life-supporting properties Versatility of water as a solvent Water’s cohesive nature Water’s ability to moderate temperature Floating ice

Water as the Solvent of Life A solution is a liquid consisting of two or more substances evenly mixed The dissolving agent is called the solvent The dissolved substance is called the solute Salt crystal Ion in solution

Dissolving of Sodium Chloride (NaCl) in Water Salt Electrical attraction Water molecules dissolve NaCl, breaking ionic bond Water Water molecules (H2O) Hydrogen bonds Edge of one salt crystal Ionic bond

Water molecules stick together as a result of hydrogen bonding The Cohesion of Water Water molecules stick together as a result of hydrogen bonding This is called cohesion Cohesion is vital for water transport in plants Microscopic tubes

Surface tension is the measure of how difficult it is to stretch or break the surface of a liquid Hydrogen bonds give water an unusually high surface tension Figure 2.13

Water Moderates Temperature Because of hydrogen bonding, water has a strong resistance to temperature change Water can absorb and store large amounts of heat while only changing a few degrees in temperature Earth’s Oceans cause temperatures to stay within limits that permit life

constantly break and re-form The density of ice is lower than liquid water This is why ice floats Hydrogen bond Ice Liquid water Stable hydrogen bonds Hydrogen bonds constantly break and re-form

The Biological Significance of Ice Floating When water molecules get cold, they move apart, forming ice A chunk of ice has fewer molecules than an equal volume of liquid water Since ice floats, ponds, lakes, and even the oceans do not freeze solid Marine life could not survive if bodies of water froze solid

Acids, Bases, and pH Acid Base A chemical compound that donates H+ ions to solutions Base A compound that accepts H+ ions and removes them from solution

The pH scale is used to describe the acidity of a solution Oven cleaner Household bleach Household ammonia Acidic: pH < 7 H+ > OH- Basic: pH > 7 H+ < OH- Neutral: pH = 7 H+ = OH- Basic solution Milk of magnesia Seawater Human blood Pure water Neutral solution Urine Tomato juice Grapefruit juice Lemon juice; gastric juice Acidic solution

CheckPoint Which of the following are compounds? Elements?: C6H12O6, CH4, O2, Cl2, HCl, MgCl2, Fe, Ca, Ne, NaI, I What is the difference between an atom and an ion? Give examples of each to support your response. Which subatomic particle determines the identity of an atom? Which subatomic particle determines the chemical properties of an atom? Explain the difference between an ionic and covalent bond in terms of what happens to the electrons in the outer shell of the participating atoms.

Chemical Reactions and Enzymes

Chemical Reactions A chemical reaction is a process that changes one set of chemicals into another set of chemicals. The elements or compounds that enter into a chemical reaction are known as the reactants. The elements or compounds produced by a chemical reaction are known as products.

Energy in Reactions Chemical reactions can either release energy or absorb energy. An exergonic reaction releases energy and will often occur spontaneously. An endogonic reaction absorbs energy and will not occur spontaneously.

Activation energy is the energy required to get a chemical reaction started. Burning glucose (sugar): an exergonic reaction high high activation energy needed to ignite glucose glucose activation energy from light captured by photosynthesis glucose + O2 energy content of molecules energy content of molecules net energy captured by synthesizing glucose energy released by burning glucose Figure :6-2 Title: Energy relations in exergonic and endergonic reactions Caption: (a) An exergonic (downhill) reaction, such as the burning of sugar, proceeds from high-energy reactants (here, glucose) to low-energy products (CO2 and H2O). The energy difference between the chemical bonds of the reactants and products is released as heat. To start the reaction, however, an initial input of energy—the activation energy—is required. (b) An endergonic (uphill) reaction, such as photosynthesis, proceeds from low-energy reactants (CO2 and H2O) to high-energy products (glucose) and therefore requires a net input of energy, in this case from sunlight. Question In addition to heat and sunlight, what are some other potential sources of activation energy? CO2 + H2O CO2 + H2O low low progress of reaction progress of reaction Photosynthesis: an endergonic reaction

Enzymes speed up chemical reactions that take place in cells. Copyright Pearson Prentice Hall

“on” or “off” keys (binding proteins) Regulation of Enzyme Activity allosteric regulator molecule Allosteric inhibition pH Temperature “on” or “off” keys (binding proteins) Up: Enzyme “off” Down: Enzyme “on” Competitive inhibition Enzyme structure active site substrate enzyme allosteric regulatory site Figure :6-11 Title: Enzyme regulation by allosteric regulation and competitive inhibition Caption: (a) Many enzymes have an active site and an allosteric regulatory site on different parts of the molecule. (b) When enzymes are inhibited by allosteric regulation, binding by a regulator molecule alters the active site so the enzyme is less compatible with its substrate. (c) During competitive inhibition, a molecule somewhat similar to the substrate fits into the active site and blocks entry of the substrate. Competitive- key Fits lock, but wont Open door Up: Enzyme “off”

Enzymes are proteins that act as biological catalyst A Catalyst is a substance that speeds of the rate of a chemical reaction high activation energy without catalyst activation energy with catalyst energy content of molecules reactants Figure :6-8 Title: Catalysts lower activation energy, increasing the rate of reactions Caption: A high activation energy (black curve) means that reactant molecules must collide very forcefully in order to react. Only very fast-moving molecules will collide hard enough to react, so reactions with high activation energies proceed slowly at low temperatures, where most molecules move relatively slowly. Catalysts lower the activation energy of a reaction (red curve), so a much higher proportion of molecules move fast enough to react when they collide. Therefore, the reaction proceeds much more rapidly. Question Can a catalyst make a non-spontaneous reaction occur spontaneously? Enzymes are proteins that act as biological catalyst products low progress of reaction

Enzymes provide a site where reactants can be brought together and aligned properly to react. - the reactants of an enzyme catalyzed reaction.

substrates active site of enzyme enzyme Figure :6-9 Title: The cycle of enzyme–substrate interactions Caption: Question How would you modify reaction conditions if you wanted to increase the rate at which an enzyme-catalyzed reaction produced its product?

“on” or “off” keys (binding proteins) Regulation of Enzyme Activity allosteric regulator molecule Allosteric inhibition pH Temperature “on” or “off” keys (binding proteins) Up: Enzyme “off” Down: Enzyme “on” Competitive inhibition Enzyme structure active site substrate enzyme allosteric regulatory site Figure :6-11 Title: Enzyme regulation by allosteric regulation and competitive inhibition Caption: (a) Many enzymes have an active site and an allosteric regulatory site on different parts of the molecule. (b) When enzymes are inhibited by allosteric regulation, binding by a regulator molecule alters the active site so the enzyme is less compatible with its substrate. (c) During competitive inhibition, a molecule somewhat similar to the substrate fits into the active site and blocks entry of the substrate. Competitive- key Fits lock, but wont Open door Up: Enzyme “off”