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Chapter 2 Notes: The Chemistry of Life. I. Levels of Chemical Organization. A. Atom -The functional unit of an element 1. Nucleus- The central core of an atom a. Proton- atomic particle with a positive charge b. Neutron- atomic particle with a neutral charge.

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I levels of chemical organization
I. Levels of Chemical Organization

A. Atom-The functional unit of an element

1. Nucleus-The central core of an atom

a. Proton- atomic particle with a positive charge

b. Neutron-atomic particle with a neutral charge


Http www intcul tohoku ac jp yamaguch jpg systemic room supplement sft profile atomic structure gif
http://www.intcul.tohoku.ac.jp/~yamaguch/JPG/systemic_room_supplement/sft_profile/atomic_structure.gifhttp://www.intcul.tohoku.ac.jp/~yamaguch/JPG/systemic_room_supplement/sft_profile/atomic_structure.gif


c. Atomic number-http://www.intcul.tohoku.ac.jp/~yamaguch/JPG/systemic_room_supplement/sft_profile/atomic_structure.gifequal to the number of protons in the nucleus; it determines identity

#protons = atomic #

d. Atomic mass-equal to the number of neutrons plus the number of protons

#protons + #neutrons = atomic mass


20http://www.intcul.tohoku.ac.jp/~yamaguch/JPG/systemic_room_supplement/sft_profile/atomic_structure.gif

Ca

Calcium

40.08

Atomic Number

Element Symbol

Element Name

Atomic Mass


2. http://www.intcul.tohoku.ac.jp/~yamaguch/JPG/systemic_room_supplement/sft_profile/atomic_structure.gifEnergy levels-the regions surrounding the atomic nucleus that contains electrons. Sometimes these are nicknamed shells.

a. Electron-atomic particle with a negative charge In a neutral atom the number of protons equals the number of electrons.

b. Each energy level contains one or more sublevels (s,p,d,f) with one or more orbitals. Each orbital can only hold 2 electrons.

c. Valence shell-the outermost energy level. This “shell” can only hold 8 electrons. The number of electrons (e-) in the valence shell determines the bonding behavior of the atom. “Valence electrons”-# e- in the outer shell

d. Energy increases with distance from the nucleus.


B elements molecules
B. Elements & Moleculeshttp://www.intcul.tohoku.ac.jp/~yamaguch/JPG/systemic_room_supplement/sft_profile/atomic_structure.gif

1. Element-a pure substance made of only 1 type of atom; it cannot be broken down without losing its chemical properties.

2. Molecule-two or more atoms bonded together in a group

a. Elemental-two or more atoms of the same element bonded together

b. Compound-molecules with two or more different elements

3. 96% of the human body is composed of:

a. oxygen c. hydrogen

b. carbon d. nitrogen

There are 20 other common elements (see p.23)


4 formulas consist of
4. Formulas http://www.intcul.tohoku.ac.jp/~yamaguch/JPG/systemic_room_supplement/sft_profile/atomic_structure.gifconsist of:

  • Symbols-for each element

    b. Subscripts-after the symbol indicate the # of atoms of the element

    c. Coefficients- in front of the formula show how many molecules


Ii chemical bonding
II. Chemical Bondinghttp://www.intcul.tohoku.ac.jp/~yamaguch/JPG/systemic_room_supplement/sft_profile/atomic_structure.gif

  • Why atoms bond

    All atoms want to be stable and have a full valence shell.

    Atoms will gain, lose or share electrons to achieve stability.


B ionic bonding the electrons are donated
B. Ionic Bonding-the electrons are “ http://www.intcul.tohoku.ac.jp/~yamaguch/JPG/systemic_room_supplement/sft_profile/atomic_structure.gifdonated “

1. Ions form when an atom gains or loses electrons in the outer energy level to become stable

http://iss.cet.edu/electricity/pages/images/B/b11_5.jpg


  • Positive ionshttp://www.intcul.tohoku.ac.jp/~yamaguch/JPG/systemic_room_supplement/sft_profile/atomic_structure.gif

    form when an atom loses one or more electrons. The number of protons now is greater than the number of electrons-so now the charge is

    +

    We show that an atom is a positive ion by placing a superscript positive sign and the number if greater than one. i.e. Na+ or Ca2+


b. http://www.intcul.tohoku.ac.jp/~yamaguch/JPG/systemic_room_supplement/sft_profile/atomic_structure.gifNegative ions

form when an atom gains one or more electrons. The number of electrons is now greater than the number of protons so now the charge is

-

We show that an atom is a negative ion by placing a superscript negative sign and the number if greater than one. i.e. Cl- or O2-


2. Once the atoms become charged ions there is an electrical attraction between oppositely charged particles and an ionic bond has formed.

http://lc.brooklyn.cuny.edu/smarttutor/core3_21/images/nature/9.a.Ionicbond-nacl.gif


Water is a polar molecule. Although the overall charge is neutral, it has a relatively positive side and a relatively negative side


3. An electrolyte is an ionic molecule that dissociates or breaks apart in water to form ions.

http://itl.chem.ufl.edu/2041_f97/lectures/g_003.GIF


C. Covalent bonding-when atoms share electrons to fill up their outer shells to become stable instead of gaining or losing them. To share their energy levels must overlap.

Thus they form a close bond and usually do not dissociate in water.



Iii inorganic chemistry
III. Inorganic Chemistry

A. Organic molecules contain C-C covalent bonds and/or C-H covalent bonds.

B. Inorganic molecules do not.


C water the most abundant compound in the body
C. Water-the most abundant compound in the body.

  • Solvent-a liquid substance in which other compounds are dissolved.

    Water is the primary solvent of the body and is in and around all cells.

    Solute-a substance that dissolves in a solvent.

    When water is the solvent for a mixture that mixture is called an aqueous solution.



  • 2. http://www.prevor.com/EN/autres/lec_chimie/solvatation/Image88.gifChemical reactions-interactions among molecules in which atoms regroup into new combinations. Water is often involved in the chemical reactions of the body.

    a. dehydration synthesis-when 2 or

    more smaller reactants combine to

    form a larger product after losing H and

    O atoms which in turn form water.


http://io.uwinnipeg.ca/~simmons/cm1503/Image71.gifhttp://www.prevor.com/EN/autres/lec_chimie/solvatation/Image88.gif


b. http://www.prevor.com/EN/autres/lec_chimie/solvatation/Image88.gifhydrolysis-when water disrupts the bonds in large molecules causing them to be broken down into smaller molecules.

Not the same as dissociation; water is added to the subunits of the molecule


http://fig.cox.miami.edu/~cmallery/150/protein/c8.8x13.hydrolysis.sucrose.jpghttp://fig.cox.miami.edu/~cmallery/150/protein/c8.8x13.hydrolysis.sucrose.jpg


c. Chemical reactions always involve a transfer of http://fig.cox.miami.edu/~cmallery/150/protein/c8.8x13.hydrolysis.sucrose.jpgenergy. Energy is stored when bonds are formed and is released when bonds are broken.


D chemical equations
d. Chemical equationshttp://fig.cox.miami.edu/~cmallery/150/protein/c8.8x13.hydrolysis.sucrose.jpg

K+ + Cl- KCl

reactants product

H2O H+ + OH-

Means reaction occurs in both directions


D acids bases and salts
D. Acids, Bases, and Saltshttp://fig.cox.miami.edu/~cmallery/150/protein/c8.8x13.hydrolysis.sucrose.jpg

  • Acids and bases are chemical opposites. Both dissociate in water but release different types of ions. Water molecules continuously dissociate in a reversible reaction that produces hydrogen ions (H+) and hydroxide ions (OH-). In pure water the ratio of H+ to OH- is equal.

    H2O H+ + OH-


2. http://fig.cox.miami.edu/~cmallery/150/protein/c8.8x13.hydrolysis.sucrose.jpgAcids-substances that release H+ ions when it dissociates in an aqueous solution. The concentration of H+ is then higher than OH-.

3. Bases-substances that release OH- ions when it dissociates in an aqueous solution. The concentration of OH- is then higher than H+.



4. The pH scale measures http://www.brooklyn.cuny.edu/bc/ahp/SDKC/Chem/graphics/dissociation.gifacidity and alkalinity. When the amount of H+ and OH- ions are equal (as in pure water) the pH is 7 which means neutral. It is neither an acid or a base. pH values above 7 are basic or alkaline (litmus paper turns blue). pH values below 7 are acidic (litmus paper turns red).


http://upload.wikimedia.org/wikipedia/commons/thumb/4/46/PH_scale.png/639px-PH_scale.pnghttp://upload.wikimedia.org/wikipedia/commons/thumb/4/46/PH_scale.png/639px-PH_scale.png


  • 5. A http://upload.wikimedia.org/wikipedia/commons/thumb/4/46/PH_scale.png/639px-PH_scale.pngsalt is a chemical compound that forms when an acid and a base are combined. When acids and bases are mixed they form both salts and water. This is called neutralization.

  • 6. The acid-base balance in the body must be maintained. Buffers are chemical systems that absorb excess acids or bases to maintain a relatively stable pH. This helps the body maintain

    homeostasis.


Iv organic chemistry there are 4 major types of organic compounds in the body
IV. Organic Chemistry-there are 4 major types of organic compounds in the body.

  • Carbohydrates

  • Proteins

  • Lipids

  • Nucleic acids


A carbohydrates sugars and complex carbohydrates
A. compounds in the body.Carbohydrates-sugars and complex carbohydrates.

1. Contain carbon, hydrogen, and oxygen

2. Carbohydrates are made up of six-carbon subunits called monosaccharides (i.e. glucose C6H12O6). These single sugars are the primary source of energy for the body’s cells.


Glucose molecule
Glucose molecule compounds in the body.

  • http://davidpaultorres.com/images/glucose.jpg



3. compounds in the body.Disaccharide- a double sugar made of 2 monosaccharide units (i.e. sucrose or table sugar and lactose or milk sugar)



4. http://courses.cm.utexas.edu/jrobertus/ch339k/overheads-2/ch9_common%20disaccharides.jpgPolysaccharides- complex carbohydrate made up of many monosaccharide units. Polysaccharides are broken down into single sugars to be used by cells or are converted to glycogen and stored for later use.



B. Lipids-includes http://courses.cm.utexas.edu/jrobertus/ch339k/overheads-2/ch9_common%20disaccharides.jpgfats (solid at room temp.) and oils (liquids at room temp.) Lipids are the most concentrated source of energy. They are not soluble in water.

1. Triglycerides are composed of 1 glycerol unit and 3 fatty acids. They store energy for later use.

http://content.answers.com/main/content/wp/en-commons/thumb/6/62/250px-Trimyristin-3D-vdW.png


2. http://courses.cm.utexas.edu/jrobertus/ch339k/overheads-2/ch9_common%20disaccharides.jpgPhospholipids are composed of 1 glycerol unit and 1 phosphate group (these together form the head) and 2 fatty acids (which forms the tail). Phospholipids are the primary component of cell membranes. The head attracts water (inside or outside of the cell) and the tail repels water. Cell membranes are composed of 2 layers of phospholipids called a phospholipid bilayer.


3. http://courses.cm.utexas.edu/jrobertus/ch339k/overheads-2/ch9_common%20disaccharides.jpgCholesterol-these lipids have a steroid structure and are found in cell membranes to add stability. They are also converted to steroid hormones by the body.




C proteins macromolecules that contain carbon oxygen and nitrogen
C. http://www.dmacc.edu/Instructors/rbwollaston/Biology_I/images/cholesterol_molecule.gifProteins-macromolecules that contain carbon, oxygen, and nitrogen.

1. Amino acid-the basic unit and “alphabet” of proteins. There are 20 common amino acids. They form strands with each amino acid joined to the next by a peptide bond (a type of covalent bond). The strands may coil and fold-each protein has a particular shape. Each type of protein has a particular number and sequence of amino acids.

2. With proteins shape determines function. If the protein loses its shape (due to changes in temperature or pH, radiation, hazardous chemicals) it then loses its function.


3. http://www.dmacc.edu/Instructors/rbwollaston/Biology_I/images/cholesterol_molecule.gifStructural proteins- form the structures of the body. For example collagen is fibrous and holds many tissues together. Keratin forms the tough, waterproof fibers of the outer layer of the skin.

4. Functional proteins-participate in chemical processes. Examples include: hormones, cell membrane channels, cell membrane receptors, and enzymes.

Enzymes-are catalysts-they help chemical reactions take place. One way is described by the lock and key model-each enzyme fits a particular molecule that it acts on as a key fits into a lock.

5. Proteins can combine with other organic molecules to form mixed molecules such as glycoproteins or lipoproteins.


D. Nucleic Acids-form http://www.dmacc.edu/Instructors/rbwollaston/Biology_I/images/cholesterol_molecule.gifDNA or RNA and direct the overall structure and function of the body by controlling the formation of structural and functional proteins.



  • They are composed of:http://www.phschool.com/science/biology_place/biocoach/images/transcription/dvsrna.gif

    i. A sugar (ribose or deoxyribose)

    ii. A phosphate group

    iii. A nitrogen base (adenine, thymine, uracil, guanine, cytosine)

http://www.biologie.uni-hamburg.de/b-online/library/cat-removed/nuct.gif


2. DNA http://www.phschool.com/science/biology_place/biocoach/images/transcription/dvsrna.gif(deoxyribonucleic acid)-is the cell’s “master code” for making proteins. It has deoxyribose as the sugar unit and adenine, thymine, cytosine & guanine. (noturacil) as the bases. It forms a double helix shape.



3. RNA http://images.encarta.msn.com/xrefmedia/aencmed/targets/illus/ilt/T039731A.gif(ribonucleic acid) is the “working copy” of a gene. It has ribose as its sugar unit and adenine, uracil, cytosine & guanine(not thymine) as the bases.



  • Adapted from http://images.encarta.msn.com/xrefmedia/aencmed/targets/illus/ilt/T039731A.gifThe Human Body in Health and Disease. Thibodeau, Gary A. & Patton, Kevin T. Mosby, 2005


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