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Why are C, H, O, and N chemically re-active and can interact with one another?

-They are all Chemically reactive since they require an addition of electrons to complete their orbitals
-The stable covalent bonds are relatively weak, making and breaking in living systems is possible, generating new types of molecules and also energy.


Why are these Abundant Elements used
in living systems

for Complexity and Diversity


Unique properties of Water:

1-It Clings to itself (Capillary force---transpiration)
2- High Heat of Vaporation (can cool down by evaporation)
3- Forms a solid less dense then its liquid---bodies of water can thaw
4- High Specific heat- water is a relatively stable environment (takes alot to change the temp)
5-It is a GOOD SOLVENT-(many compounds can dissolve in water, breaking apart ionic bonds between molecules/atoms.



Sharing of electrons between 2 atoms
-vary in strength based on # of electrons being shared

-2-sp linear 180 degrees
-3-sp2 trigonal planar 120 degrees
-4- sp3 tetrahedral 109.5 degrees



Transfer of Electrons
-Can be weakened by interactions with water and other charged molecules.

Ionic Electrostatic Interactions are important in biologica systems, since its easy to make and break the interactions between the enzyme (-) and the substrate (+)


Why is it important that water is a polar molecule , to the cell function and life?

-Excellent Solvent
-Allows ease of movement through biological membranes
-Takes place in many chemical reactions
-thermal properties are suitable to support life


Explain why cellular pH and ionic conditions must be maintained at constant values.



How do Ionic bonds contribute to macro-molecular interactions.?



Discuss the relative strengths of covalent, ionic, hydrogen, and van der Waals bonding.



Compare the stability of covalent and ionic bonds in an aqueous environment.



Explain the difference between a polar and nonpolar covalent bond:

*The Distribution of electrons is UNEQUAL between the atoms
*They are Hydrophillic (soluble in water)
*The positive charge is concentrated towards one end.
*The distribution of electrons is EQUAL between the atoms
*They are hydrophobic, and insoluble in water


Why is a polar covalent bond important in molecular interactions?



Name polymers formed from glucose, amino acids, and nucleotides.



Explain how two monosaccharides can be joined together to form a disaccharide, and polysaccharide.



List the ways in which different polysaccharides can be generated



Draw a generalized carbohydrate



Identify the different "parts" of a triglyceride and phospholipid.



Explain what is meant by amphipathic molecule:



Explain the concept of a protein domain and provide an example:



Draw a tri-peptide and show both peptide bonds..



Explain the molecular interactions involved in generating an alpha- helix within a polypeptide chain. (B-sheet)



Explain how the sequence of AA's determine the 3'D structure of a protein:



Explain how a phospholipid is both polar and nonpolar:

The phospholipid bilayer in cell membranes is both polar and nonpolar. The heads, which face the outside and inside of the cell, are polar. Thus they form hydrogen bonds with the water outside of the cell and the cytoplasm inside the cell. They are called "hydrophilic," which means they love water. The tails are on the inside of the bilayer and are nonpolar. They are hydrophobic, which literally means they are scared of water.


Provide an explanation for why lipids will form a micelle or bilayer in water:



Explain how glucose can generate polymers (poly saccharides) with different chemical properties.



Provide a model for how proteins function.



Draw a phosphodiester bond between two nucleotides



Name the pyrimidines and purine bases.

-PYRIMIDINES: {cing tut lived in a pyramid]
*Cytosine and Thymine (C and T)
-PURINE: "Pure things are All Good"
*Adenine and Guanine (A and G)


Name the 4 general classes of amino acid and discuss how each contributes to the tertiary structure of a protein.

-Disulfide bonds are formed by oxidation of the sulfhydryl groups on cysteine. Different protein chains or loops within a single chain are held together by the strong covalent disulfide bonds.

-Hydrogen bonding between "side chains" occurs in a variety of circumstances. The most usual cases are between two alcohols, an alcohol and an acid, two acids, or an alcohol and an amine or amide

-Salt bridges result from the neutralization of an acid and amine on side chains. The final interaction is ionic between the positive ammonium group and the negative acid group. Any combination of the various acidic or amine amino acid side chains will have this effect.

-The hydrophobic interactions of non-polar side chains are believed to contribute significantly to the stabilizing of the tertiary structures in proteins. This interaction is really just an application of the solubility rule that "likes dissolve likes". The non-polar groups mutually repel water and other polar groups and results in a net attraction of the non-polar groups for each other


Based on structure, explain how the R-groups associated with an alpha helix could have functional importance.

The alpha helix structure allows the R-groups to attach on the outside. These hanging R-groups will determine how it will interact with surrounding functional groups.