C.+Biochemistry+(2-3)

__**Chapter 2- The Chemical Context of Life**__

**Target I**
- The elements important to living things include Carbon, Nitrogen, Oxygen, Hydrogen, Phosphorus, Sulfur, Calcium, Potassium. 25/92 natural elements are essential to life - Trace elements are also required by organisms to sustain life, but are required in minute quantities. Trace elements include Iron and Iodine. (All of the elements in the diagram are important to sustain life, but the elements making up less than 0.01 % would be the trace elements) - Elements- Ex. Sodium (Na) and Chlorine (Cl) - Compounds (2 or more different elements bonded together) - Ex. Sodium Chloride (NaCl) - Molecules (Any 2 elements bonded, do not have to be different)- Ex. O2 - All compounds are molecules but not all molecules are compounds - Polar- atom or molecule has a positive or negative charge - Non-polar- atom or molecule has a neutral charge
 * 1) State elements important to living things. Identify trace elements.**
 * 2) Differentiate between elements, compounds, and molecules.**
 * 3) Identify the basic principles of atomic structure and how they determine the behavior of an element**
 * 4) Given a specific element identify: # protons, # neutrons, # electrons, atomic weight, atomic mass**



**5) Identify and distinguish between ionic and covalent bonds. Rank these in order of** **strength. Explain the behavior of valence electrons in each.** 1. The lone valence electron of a sodium atom is transferred to join the 7 valence electrons of a chlorine atom. 2. Each resulting ion has a completed valence shell. An ionic bond can form between the oppositely charged ions. An ionic bond is the attraction between oppositely charged atoms, or ions. It can form between any two oppositely charged ions, and the two ions do not need to have gotten their charge from electron transfer with each other.
 * Electron transfer and ionic bonding **

- (a) Two hydrogen atoms form a single bond - (b) Two oxygen atoms form a double bond by sharing two pairs of electrons - (c) Two hydrogen and one oxygen molecules are joined by covalent bond - (d) Four hydrogen atoms complete the valence shell of one carbon atom
 * Covalent Bonds **

A covalent bond is formed between two atoms when they share a pair of valence electrons. The number of electrons need to complete an atom’s valence shell generally determines the number of bonds that the atom will form.

-In organisms, most of the strongest chemical bonds are covalent bonds

**6) Identify and distinguish between hydrogen bonds and van der Waals interactions. Rank these in order of strength. Explain the behavior of valence electrons in each intermolecular interaction. ** Explanation and animation of hydrogen bonds: [|Hydrogen Bonds]

-Hydrogen bond: Bond formed when a hydrogen bond covalently bonded to one electronegative atom is also attracted to another electronegative atom -Stronger than van der Waals interactions

-Van der Waals interactions: weak interactions that occur when randomly moving electrons accumulate and cause regions of positive and negative charge in a molecule that enable atoms and molecules to stick to each other -Only occur when atoms and molecules are very close together -Give non-polar molecules a temporary difference in charge

**7) Distinguish between polar and non-polar molecules by examining elements present in** **each molecule.** Explanation of non-polar and polar molecules:
 * [|Non-polar and Polar Molecules]**

-Non-polar molecules occur when there is no polarity in the bonds (equal sharing of electrons) or because of the symmetrical arrangement of polar bonds -Ex of symmetrical arrangement: l -Polar molecules occur when the two ends of the molecules have opposite charges because of polar covalent bonds (uneven distribution of electrons)

<span style="display: block; font-family: 'times new roman',times,serif; font-size: 120%; text-align: justify;">**8) Relate polarity of a molecule to electronegativity of elements within a molecule.** -Electronegativity: Attraction of an atom for the electrons of a covalent bond -Greater electronegativity means it will pull shared electrons more closely -The bigger the difference in electronegativity of 2 atoms, the more polar the bonds -Ex: Bonds between the hydrogen and oxygen atoms of a water molecule are quite polar because oxygen is one of the most electronegative of all the element and attracts electrons more strongly than hydrogen.

Ex: water is a polar molecule due to its shape; this polarity contributes to many of water's functions. -The shape of an enzyme attributes to what proteins is can break down. The Lock and Key model is a perfect example of how shape relates to strucure.
 * 9) Explain how molecular size and shape relates to specificity and function in organisms.**
 * -**The shape of a molecule is a key feature that deterimes polarity.The polarity of a molecule has a direct effect on the type of reactions that it can go through.
 * 10) Explain bond-making, bond-breaking, and atomic rearrangement in the context of a chemical reaction.**

-Bond-breaking in biology is catalyzed using enzymes. Enzymes break down bonds that exist between proteins, or helps bonds connect between two different molecules. -There are two different types of enzyme reactions: the Lock and Key model and the induced fit model. -By breaking bonds or making bonds, enzymes change the rearrangement of the molecules



__<span style="font-family: 'Times New Roman','serif'; font-size: 16px;">Review of Chapter 2, Target 5-8 __ <span style="font-family: 'times new roman','serif'; font-size: 16px; line-height: 0px; overflow: hidden;">

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[|Quia Quiz for Chapter 2 Review]

=__**(TARGET II-MASTERY OF WATER CHEMISTRY AND PH)**__= __**<span style="font-family: 'Times New Roman','serif'; font-size: 16px;">CHAPTER 3- **__** Water Chemistry and pH ** //**1)Draw the chemical structure of water with its partial charges and describe polarity.**// -Covalent Bond: Sharing of one or more electrons between atoms -Water is a polar covalent bond. Polar covalent bond=electrons not shared equally because one atom is more electronegative -oxygen is more electronegative, electrons more attracted to oxygen. Electrons spend more time around oxygen. -Hydrogen, each 1 electron. -The 2 Hydrogen atom's charge is (+) because each of its electrons spend more time with the oxygen atom. -Oxygen atom's charge is (-) because electrons more attracted to it. media type="youtube" key="KiZJOTt3Dl0" width="425" height="350"

//**2)Relate the structure of water to hydrogen bonding between water molecules.**// -Water=polar molecule because 2 ends of molecule have opposite charges. -Since oxygen more electronegative, electrons more attracted to it, its charge is (-). -Since hydrogen's electrons more attracted to oxygen atom, hydrogen atom's charge is (+). -Hydrogen bonds=hydrogen atom covalently bonded to 1 electronegative atom is attracted to another electronegative atom. -Hydrogen(gray) attracted to 1 oxygen atom(red) is also attracted to another oxygen atom since hydrogen is (+) and oxygen is (-).

media type="youtube" key="wZ9CCj4X28Q" width="425" height="350" (skip to 1:17)

//**3). Identify and discuss the 4 unique qualities of water. Provide an example of each property as it relates to living organisms.**// 1. Cohesion:hydrogen bonds holding substances together. -allow water to go upwards in plants and evaporate through leaves -water evaporate from leaf, H-bonds cause water molecules to tug on molecules further down=upward pull of water Adhesion:clinging of 1 substance to another -water cling to leaves wall. Also counters gravity.

2. Moderation of Temperature -Water has a very high specific heat. -Very hard to boil because lots of heat needed to break apart hydrogen bonds for water molecules to move faster -high amount of energy require to evaporate water -good because organism made of mainly water, resist change in temperature. Also stabilize marine life bc constant ocean temp.

3. Insulation of bodies of water by floating ice -Ice is less dense than water so it floats -water freezes because molecules dont move fast enough to break h-bonds -h bonds keeps molecules further away, so ice is less dense. hydrogen bonds of ice. molecules further apart. lower density hydrogen bonds of water. molecules closer together. higher density. -good because insulates liquid below

4. The Solvent of Life -Solvent=dissolving agent -water is a very versatile solvent -It breaks the bonds of solute by separating and shielding atoms from e/o -forms hydration shell: spheres of water molecule around dissolved ion. hydration shell pic media type="youtube" key="ctkgD_UuX90" width="425" height="350"

HYDROPHILIC water loving polar:one element more electronegative than other can dissolve in water or colloid: suspension of fine particles in water form H-bonds water is polar so it prefers polar molecules
 * 4). Describe properties/characteristics of molecules that are hydrophobic and hydrophilic.**

HYDROPHOBIC water fearing nonpolar: elements equally electronegative. repel water can't form H-bond fats,oil water doesn't bond well with nonpolar molecules. media type="youtube" key="5oEsZ3a01g0" width="425" height="350" only part of video, if want to watch full, have to go here and purchase http://www.mindbites.com/lesson/3950-biology-hydrophilic-hydrophobic-substances[|link]

More practice on questions 1-4 - Acids are found lower in the pH scale, while bases are found higher in the pH scale. A pH of 7 is considered to be a neutral solution.
 * 5) Explain the pH scale in terms of the mathematical relationship between H+ concentration and OH- concentration. Re****late the terms acid, base, and neutral to the 0-14 scale.**



[|Acids, bases, and pH scale mini quiz]

Buffers are solutions whose pH doesn't change much when moderate amounts of acids or bases are added. Properties of acids Properties of bases include: [|VIDEO: Properties of bases and acids: Start at 1:35 for overview of basic properties]
 * 6) Describe properties of acids, bases, and buffers**
 * React with most metals to form hydrogen gas
 * Taste sour
 * Feel sticky
 * Usually gases or liquids
 * Feel "slippery" (The slippery feeling is caused because your skin dissolves a little when you touch them.)
 * Taste bitter
 * React with oils and greases (that's why bases are used as drain and window cleaners)
 * Frequently solids

[|Tiny Properties Quiz]