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BIOL 112 Study Guide - Van Der Waals Force, Electron Transport Chain, Citric Acid Cycle


Department
Biology
Course Code
BIOL 112
Professor
Joseph Dent

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BIOL-112 Condensed Notes
R. O’Loghlin
Bonding
Covalent Bonds
o When an atom has an orbital with only one electron in it, it becomes reactive, wanting
to fill the space
o Strongest bonds
o Made up of 2 electrons, one from each atom
o The electrons are shared between the two atoms, not always equally, but shared
Hydrogen Bond
o Electrostatic interaction between partial negative charge of an atom and the partial
positive charge of another atom
o Both must be involved in polar covalent bonds
o Only occurs between Hydrogen and Oxygen or Nitrogen, or (more rare) Carbon and
Oxygen
Ionic Bond
o Occur between elements on the far left and far right of the periodic table
o Ionic bonds in biology aren’t as strong as the ones in chemistry due to the biological
ones usually being individual bonds such as those in the interior of proteins in the
absence of water
Polar molecules tend to be hydrophilic, and dissolve in water
Nonpolar molecules are hydrophobic, and are generally made up of c-c or c-h bonds
Hydrophobic interactions
o Water forces nonpolar molecules together, because doing so minimizes their disruptive
effects on the h-bonded water network
o Fairly weak
Van der Waal’s interaction
o Nonpolar molecules are also attracted to eachother via weak attractions caused by
transient dipoles (temporary)
o Strength increases with increasing molecular weight
In order of decreasing strength:
o Covalent bond (50-110 kcal/mol)
o H-bond and Ionic Bond (Both 3-7 kcal/mol)
o Hydrophobic interaction (1-2 kcal/mol)
o Van der Waals interaction (1 kcal/mol)

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Acids & Bases
Acids release/donate ions in solution
o Strong acids completely disassociate in solution
Bases accept in solution, or you could say that they release 
o A strong base completely disassociates in solution
Buffers
o Make the overall solution resistant to pH change
o Can make a buffer out of a solution of a weak acid and its conjugate base, or a weak
base and its conjugate acid
o Law of Mass Action
The rate of any given chemical reaction is proportional to the concentration of
the reactants
Functional Groups
Carboxyl group
o Carboxylic acids
o COOH (with double bond between C and one O)
o Acetic Acid
Amino group
o Amines
o NH2
o Methylamine
Hydroxyl group
o Alcohols
o OH
o Ethanol
Carbonyl Group
o CO
o Aldehyde if the carbonyl group is at the end of the molecule
Acetaldehyde
o Ketone if it is in the interior
Acetone
o Phosphate group
Organic phosphates
-PO4
ATP
o Sulfhydryl Group
Thiols
-SH
Mercaptoethanol

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Large Molecules
Macromolecules are made the same way in all living things, and are present in all organisms in
roughly the same proportions
Proteins, nucleic acids, and lipids can form polymers of multiple molecules
o Reaction is called polymerization
o Condensation reaction releases a molecule of water for each bond formed
o Depolymerisation involved hydrolysis, consuming a water molecules to break a bond
Isomers
o Molecules that have the same chemical formula, but different atomic arrangements
o Structural isomers
A group is attached to different carbon atoms
o Optical Isomers
A group is attached in a different way to the same carbon atom
Optical isomers are non-superimposable mirror images of eachother
Occur whenever a carbon has four DIFFERENT atoms or groups attached to it
Sugars
o Carbohydrates (sugars) act as energy storage and building blocks for other molecules
o Serve a structural components
o Monosaccharides
A single sugar such as glucose
o Disaccharides
2 Sugars such as sucrose
o Polysaccharides
Many sugars
o General carbohydrate formula is CH2O
o Glucose has two ring forms
Alpha and Beta glucose
Optical isomer caused by four different groups being bonded to carbons 2-5
DNA
o Contains genetic information
o Transcribed to RNA, which makes proteins
o Nucleotides have additional functions as signalling molecules and energy transducers
Phosphate groups
o Joined to the C5 hydroxyl of the ribose sugar
Nitrogenous Bases
o Purines
Adenine
Guanine
o Pyrimidines
Thymine
Cytosine
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