Chemical and Physical Foundations Section Flashcards
Chromatography
the separation of a mixture by passing it in solution or suspension or as a vapor (as in gas chromatography) through a medium in which the components move at different rates.
- The solute concentration will affect the size of the spots on the paper chromatogram, not the average migration rate.
- Thickness of the paper affects the amount that each component can be fully separated, not the relative migration rates of components.
- stationary phase will be an immobilized surface, not a solution.
- migration rate may depend on hydrogen bonding
amino acids
a group of organic molecules (organic is primarily made of carbon molecules) that consist of a basic amino group (NH2-), an acidic carboxyl group (-COOH) and an organic R group (side chain that Is unique to each amino acid). Each amino acid contains a central (alpha) carbon.
non polar amino acids
They are hydrophobic, in water, they will bury their side chains on the inside. (polarity is based on the side chain)
Nonpolar= alanine, valine, leucine, glycine, isoleucine, methionine, tryptophan, phenylalanine, proline
polar, uncharged amino acids
serine, cysteine, asparagine, glutamine, threonine, tyrosine.
must have at least one atom (N, S, O) with electron pairs available for hydrogen bonding to water and other molecules.
acidic amino acids
Aspartic and glutamic acid
Each has a carboxylic acid on it side chain which gives it electron donating properties. At a physiological pH, these amino acids will ionize, giving them a charge of -1. The ionic forms are aspartate and glutamate.
basic amino acids
arginine, histidine, and lysine. Each side chain is basic- meaning it can accept a proton
in dehydration reaction
-OH is lost from the carboxyl group and an H is lost from the amino group. This will take a molecule of H2O and leave an amide linking two amino acids.
Carbocation intermediate
SN1, E1, and alkene addition reactions will have a carbocation intermediate.
carbocation intermediate from Alkene addition
adding strong acid to an alkene gets us a carbocation
strong acid
any acid that ionizes completely in a solution. That means, a great number of hydrogen ions or protons will dissociate. Strong acids are able to conduct electricity.
HClO3, HBr, HCl, HI, HNO3, HCLO4, H2SO4
Good nucleophile
A good base is usually a good nucleophile. So, strong bases — substances with negatively charged O, N, and C atoms — are strong nucleophiles. Examples are: RO⁻, OH⁻, RLi, RC≡C:⁻, and NH₂⁻. Some strong bases are poor nucleophiles because of steric hindrance.
SN1 reaction
The SN1 reaction is a substitution reaction in organic chemistry. “SN” stands for “nucleophilic substitution”, and the “1” says that the rate-determining step is unimolecular. Thus, the rate equation is often shown as having first-order dependence on electrophile and zero-order dependence on nucleophile
The SN1 reaction mechanism involves an intermediate carbocation that is formed by loss of the leaving group. A nucleophile can react with the planar carbocation from either side, leading to the inversion or retention of the configuration at the site of the substitution.
Electrophile
In chemistry, an electrophile is a chemical species that forms bonds with nucleophiles by accepting an electron pair. Because electrophiles accept electrons, they are Lewis acids.
Good Electrophiles
Good electrophiles typically contain weak polar or polarizable bonds. This means that electrons can favor one side of a bond over the other, creating dipoles.
carbon-centric
Organic chemistry is carbon-centric. Carbon is the key atom in these reactions and carbon atoms do some very predictable things- like many four bonds.
Cis and Trans Isomers
cis isomer has two groups on the same side. Trans isomer has two groups on opposite sides.
Non polar molecule identification
Non polar molecules will be made up of one element. For example, N2, O2, Cl2, and noble gases are non polar. Containing only carbon and hydrogen is non polar. Does the molecule have symmetry?
CO2 is non polar, for example. I-Br is also non polar because the electronegativity difference between the atoms is not great along the bond.
Polar molecule identification
If hydrogen is directly attached to N, O, F, it is polar. Ex, water, CH3OH (presence of alcohol), CH3COOH, if molecule lacks symmetry and the bond is polar then it will be a polar molecule.
stereospecific
A reaction in which the stereochemistry of the reactants controls the outcome of the reaction. In general, one stereoisomer of certain reactant produces one stereoisomer of a certain product, whereas a different stereoisomer of the same reactant produces a different stereoisomer of the same product. You wouldn’t end up with a mixture of cis and trans alkenes in the product.
aldehyde
Carbon atom shares a double bond with oxygen, a single bond with H, and a single bond with R. Derived from alcohols.
H-C-R
=O (the equal sign should be vertical). That is the carbonyl group.
Carboxyl group
Same as Aldehyde except for there is an O where the H would’ve been. A carboxyl group can react with an amine to form a peptide bond.
amine group
Contain basic nitrogen atom with a lone pair. These form peptide bonds. The conjugate base of an amine is also called an amide (like the bond that is made when a peptide is formed).
amine group
Contain basic nitrogen atom with a lone pair. These form peptide bonds. The conjugate base of an amine is also called an amide (like the bond that is made when a peptide is formed).
alkyl
contains only carbon and hydrogen atoms in a chain. Ex: CH3.