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Organic Chemistry II
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Biological Molecules
Spectra
Separations and Purifications
Organic Chemistry II
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Biological Molecules
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Carbohydrates
Amino acids and proteins
Lipids
Phophorous containing compounds
Biological Moleculescarbohydrates
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Polyhydroxy aldehyde or ketone
Empirical formula often (CH2O)n
Many contain N, P, or S
Monosaccharide (1 unit), oligosaccharide (2-10), polysaccharides
(10+)
Glucose and Fructose most common on MCAT
Carbohydratesnomenclature, classification, and
common names
Named according to the number of carbons they possess and existence as
polyhydroxy aldehydes (Aldoses) or polyhydroxy ketones (Ketoses)
#
Carbons
Category Name
Relevant examples
3
Triose
Glyceraldehyde,
Dihydroxyacetone
4
Tetrose
Erythrose
5
Pentose. Furanoses
(bent ring)
Ribose, Ribulose,
Xylulose
6
Hexose,
Pyranoses (chair)
Glucose,
Galactose,
Mannose, Fructose
7
Heptose
Sedoheptulose
Carbohydratesnomenclature, classification, and
common names
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Common disaccharides and polysaccharides
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Sucrose: glucose + fructose (α 1,4)
Maltose: glucose + glucose (α 1,4)
Cellulose: (glucose)n (β 1,4)
Lactose: galactose + glucose (β 1,4)
Amylose: (glucose)n (α 1,4)
Amylopectin (plants): branched glucose chains (α 1,4)
 Branching (α 1,6)
Glycogen (animals): branched glucose chains (α 1,4)
 Branching (α 1,6)
Carbohydratesabsolute configuration
The last chiral center in an aldose chain
(farthest from the aldehyde group) was
chosen by Fischer as the D / L designator
site
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D: if the hydroxyl group in the projection
formula points right
L: left directed hydroxyl group (the mirror
image) then represented the L-family.

Absolute configuration, which is different
from d/l (dextra/levarotary +/-) relative
configuration based on rotation of light.

D sugars are the natural form we can
assimilate following digestion. (Refer
to the highest numbered chiral carbon)
How many stereoisomers exist for
a molecule of D-glucose?
A.
B.
C.
D.
4
16
32
64
D-glucose
Carbohydrates
Epimers and Anomers

Epimers- A diastereoisomer that has the opposite configuration at only
one of two or more stereogenic centers.

Ex/ Mannose and α-glucose
α-D-Glucose

Mannose
Anomers- a type of epimer. cyclic stereoisomers of sugars that differ
only in their configuration at the hemiacetal (anomeric) carbon.

Ex/ α-glucose and β-glucose
α-D-Glucose
β-D-Glucose
CarbohydratesCyclic structure and conformations
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Many simple sugars can
exist in a chain form or a
ring form.
The ring form is favored in
aqueous solutions
Alcohol group on the chiral
carbon furthest from the
carbonyl carbon may act
as a nucleophile attacking
the carbonyl carbon
Forms hemiacetals in
aldoses and hemiketals in
ketoses
Hemiacetal and Hemiketal
Formation
Carbohydrateshydrolysis of the glycoside linkage
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Hydrolysis of starch involves the cleavage of the acetal functional
groups with the addition of a molecule of water for each glycoside
linkage
Hydroxyl group reacts with anomeric carbon
Produces many molecules of glucose
Carbohydrateshydrolysis of the glycoside linkage
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This is done by the enzymes called glycosidases or amylases which
are found in saliva.
These enzymes work only on alpha glycoside linkages and do not
attack beta linkages. Such beta linkages are found in cellulose.
Amino Acids and Proteins

Amino acids are the basic structural units of proteins
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They contain an amino group, carboxyl group, a H
atom, and a distinct R group (side chain)
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AA have acidic and basic properties (zwitterions can
be both proton acceptors and donors)
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Most exist as zwitterions at physiological pH
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Because they are dipolar (+ and – charges) they
have unique isoelectric points, but there is no net
charge on the molecule
AA and Proteinsabsolute configuration at the a position
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Amino acids have a chiral carbon (except
glycine), are all L stereo-isomers.
Amino acid general structure

Amino acids in solution
Low pH
High pH
Amino Acids
Titrations and Isoelectric Point (pI)
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
Isoelectric point of a protein is the pH at which the
amino acid exist as a zwitterion
Amino acids essentially exist as diprotic acids at low
pH, and their titration curves resemble those of
diprotic acids.
AA and Proteins-classification
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Polar side groups- hydrophilic
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
Face aqueous solution
Nonpolar side groups- hydrophobic
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Face interior of protein
Polar
Nonpolar
Asparagine
Alanine
Cysteine
Glycine
Glutamine
Isoleucine
Serine
Leucine
Threonine
Methionine
Tyrosine
Phenylalanine
Proline
Tryptophan
Valine
Acidic
Aspartic
Acid
Glutamic Acid
Basic
Arginine
Lysine
Histidine
Amino Acids
Titrations and Isoelectric Point (pI)

A.
B.
C.
D.
Amino acids can be separated by placing them in
an electric field such as is the case in gel
electrophoresis. If a solution of amino acids at pH
8 underwent electrophoresis, which of the
following would most likely move the furthest
towards the anode?
Arginine
Glutamate
Histidine
Lysine
AA and Proteins-reactions
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Peptide linkage (formation of an amide): This is the
covalent bond that joins amino acids together. Formed
by a condensation reaction involving the formation of
water (Dehydration synthesis)
It is formed between the alpha-amino group of one
amino acid and the alpha-carboxyl group of another
amino acid
The peptide bond is rigid due to resonance and partial
C=N character.
+

+ Water
AA and Proteins-reactions
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Hydrolysis: the reverse reaction
Peptides and proteins chains have direction because the chains
have different ends, an alpha-amino end and an alpha-carboxyl
end
By convention the amino end is taken as the beginning of a chain
An amino acid sequence is written starting from the N-terminal
amino end
Thus the tripeptide gly-ala-leu is not the same as leu-ala-gly
because the former has gly at the N-terminal and leu at the Cterminal whereas the latter has leu at the N-terminal and gly at
the C-terminal. Chemically, in the former gly has a free amino
group, and in the latter leu has a free amino group.
+ Water

+
AA and proteins-general
principles
1o structure: the amino acid sequence of a protein written from
the amino to the carboxy terminus.
2o structure: certain common repeating structures found in
proteins: alpha-helix and beta-pleated sheet
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Tertiary structure: the full 3D folded structure of the
protein
Quaternary Structure: protein polymers, e.g.
hemoglobin in is made of 4 proteins, 2 alpha globins
and 2 beta globins
Which structure of a polypeptide
is most likely affected by the
double bond nature of the peptide
bond?
A.
B.
C.
D.
Primary
Secondary
Tertiary
Quarternary
Lipids
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Lipids have hydrophobic (long hydrocarbon tails) and
hydrophilic (charged heads) ends
Lipid bi-layers
(phospholipids)
make up cell
membranes
Molecules with
polar and non-polar
groups are called
amphipathic
http://kvhs.nbed.nb.ca/gallant/biology/phospholipid.jpg
Lipids
Free Fatty Acids
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Fatty acids- long carbon chain with carboxylic
acid end.
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Serve as hormones and messengers- eicosanoids
Components of cell membranes
Fuel for body
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Stored as triacylglycerols

Store more than twice the energy of carbohydrates and
proteins
Triacyl Glycerols (fats and
oils)
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Glycerol backbone with three carboxylic acid derivatives
http://www.oliveoilsource.com/images/triglyceride.jpg
Triacyl Glycerols (fats and
oils)
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Saturated: no double bonds; i.e. saturated with hydrogen
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Unsaturated: has double bonds. Double bonds can be cis or trans and
are bent. The more unsaturated means more irregular structure and a
lower MP
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Shorter chains also have a lower MP (fewer vDW interactions)
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Lipases and phospholipases are enzymes that break up lipids
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Treatment with NaOH (saponification) breaks the fat into glycerol and
fatty acids. Soap used to be made this way
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The Ca2+ ion in water, known as hard water, cross links the head
groups causing the soap scum

Natural glyceraldehydes are always D
The salts of fatty acids are used
as soaps because the salts:
A.
B.
C.
D.
have a polar region and a nonpolar region
and are thus insoluble in water.
have a polar region and a nonpolar region
and are thus help organic materials become
water soluble.
are exclusively polar and thus dissolve in
aqueous solutions.
are exclusively nonpolar and thus dissolve
organic materials.
passage 28
Steroids
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Steroids have a four ring
structure
Cholesterol, a steroid
derivative, is essential to fluid
nature of the cell membrane
Cholesterol decreases the
melting point and increases the
boiling point.
Bacteria do not make steroids.
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/steroid_3.gif
http://www.ems.psu.edu/~radovic/cholesterol.gif
Terpenes
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Terpenes are widespread in nature, mainly
in plants as constituents of essential oils.
The building block is the
hydrocarbon isoprene
Terpene hydrocarbons have molecular
formulas (C5H8)n
Examples camphor, menthol, vitamin A1.
Phosphorus Compounds
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ATP, ADP, TTP, GTP, CTP, UTP, Insecticides,
phosphatidyl choline, protein phosphorylation, cell
signaling
There is a large amount of energy stored in
phosphoric acid bonds, so it is used for energy
storage
P-O-P is the phosphoric
anhydride bond (high
energy). C-O-P is the
phosphoester bond.
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/ATP.html
Phosphorous Compounds
passage 31
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Wittig reaction: is an important method for the
formation of alkenes
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The double bond forms specifically at the
location of the original aldehyde or ketone
Spectra, Separations, and
Purifications
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Spectra
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Absorption spectroscopy
Mass spectroscopy
NMR spectroscopy
Extraction
Separations and Purifications
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Distillation
Chromatography
Recrystallization
IR -Absorption
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wave number = 1/l; 4000-625 cmDetects functional groups: polar bonds stretch at
characteristic frequencies
Divide IR (4000 to 4000 into 4 regions)
 4000-2500: N-H, C-H, O-H
 2500-2000: Triple bonds (CtbC, CtbN)
 2000-1500: Double bonds (C=O, C=C, C=N)
 1500-400: Fingerprint region (most complex region of IR)
IR -Absorption
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When a compound is exposed to infrared
radiation, the polar bonds stretch and contract in
a vibrating motion.
Different bonds vibrate at different frequencies
In IR Spec, the frequency of IR light is slowly
changed and frequencies of absorption are
recorded
No dipole moment = no energy is absorbed
UV -Absorption
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

Detects conjugated C=C
Changes in energy of molecular orbitals. When pi electron of conjugated
system is displaced, energy is absorbed
Increase 30-40 nm for each additional C=C, increase 5 nm for each
additional alkyl group
Conjugated
Isolated
Visible-Absorption
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Visible region: 8+ double bonds, usually
conjugated
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Beta carotene, 11 C=C, max absorbance at 497
nm, looks orange
Effects of structural changes on absorption

indicators
Mass Spectrometry -Emission
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
Molecules ionized by collision with high energy e- (dislodging a
valence e-, and yielding a cation), causing some of the molecules
to fragment, (some +, -, and neutral).
Passage of charged fragments through magnetic field then sorts
them according to their mass.
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m/z- mass:charge. z is usually one, so m/z gives mass of + charged
ions.
Tallest peak (100%)- base peak, fragment in highest concentration.
Unfragmented ion- parent peak, M+ (molecular ion)
The peak furthest downfield is the unfragmented cation. The sample
passes through a magnetic field and detects the mass/charge (m/e)
ratio
determines molecular weight
NMR: nuclear magnetic
resonance
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

•
Can tell the protons and their environment.
Nuclei align with a magnetic field.
Bombarded with electromagnetic energy.
Resonance frequency, the nuclei turn against the
magnetic field.
Shielding: e- environment of the
proton
• Integral value: # of equivalent
protons
• Spin-spin splitting: peaks splits
into n+1. n is the number of
adjacent, different protons
NMR: nuclear magnetic
resonance
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Nuclei with odd atomic/mass number exhibit nuclear spin
When placed in external magnetic field, nuclei aligns its own field
with or against the external field (with = lower E, against = higher
E).
When the nucleus is irradiated with photons, it can absorb energy
and flip its orientation in the magnetic field => Resonance.
Electromagnetic radiation is held constant while magnetic field
strength varies.
Shielding- EWG shield less and shift the peak downstream, EDG
shield more and shift the peak upstream.
Aldehyde protons have a distinctive shift at 9.5ppm
NMR
Electron withdrawing = shift downstream
Electron donating = shift upstream
Integral Values = ?
http://www.cem.msu.edu/~reusch/VirtualText/Spectrpy/nmr/nmr1.htm#nmr1
Separations and Purifications

Extraction: distribution of solute between two immiscible
solvents. Solvents dissolve impurities and move them
to aqueous layer for removal. Products remain in the
organic layer. Like dissolves like.
 Add strong acid: protonates amines and bases to make
them polar
 Add weak base: deprotonates strong acids to make
them non-reactive
 Add strong base: deprotonates any remaining acids
* Dilute acids make organic bases soluble in water
* Dilute bases make organic acids soluble in water.
http://orgchem.colorado.edu/hndbksupport
Separations and Purifications

Distillation: Purification based on
boiling points

Lower boiling point will distill first

Raoult’s law: PA = XAPAO
compounds in a mixture combine to boil off together at an
intermediate boiling point

Azeotrope: A liquid mixture of two or more substances that
retains the same composition in the vapor state as in the liquid
state when distilled or partially evaporated under a certain
pressure.
http://www.tiscali.co.uk/reference/encyclopaedia/hutchinson/m0020819.html
Simple vs. Fractional
Distillation


Simple distillation- separates components by
differences in BP of entire sample. Raoult’s Law
Fractional distillation- initial sample of distillate is
continuously redistilled, thus at each point the
sample boils at a lower and lower temperature,
ultimately approaching the boiling point of the pure
substance with the lower boiling point.

Accomplished by the use of fractional distillation column,
packed with a suitable material which subjects a mixture to
repeating vaporization-condensation cycles until a pure
substance emerges.
Separations and Purificationschromatography

Column chromatography:

Add analyte to the top of the column (stationary phase)

Liquid solvent (eluent, mobile phase) is passed over the
column

Different interactions with the column (based on size,
polarity, etc.) leads to separation

Components are collected as the solvent drips from the
column
Why does an increasing salt gradient release
molecules from an ion-exchange column?
A.
B.
C.
D.
It increases the molecular weight of the molecules,
causing them to move through the column faster.
It decreases the strength of the charge interactions
between the molecules and the stationery phase.
It increases the charge differences between the
negatively and positively charged molecules.
It fills the porous beads, thereby excluding
entrance by the molecules into the column.
Separations and Purificationschromatography

Gas-liquid chromatography:

The sample is vaporized and injected into the
head of the chromatographic column

The sample is transported through the column by
the flow of an inert, gaseous mobile phase

The column itself contains a liquid stationary
phase which is adsorbed on to the surface of an
inert solid
Separations and Purificationschromatography
Paper chromatography:

A sheet of paper is the inert phase

Analyze complex mixtures, such as ink, by separating
them into the chemicals from which they are made

Degree of retention of a component is called the
retardation factor
(Rf) = distance migrated by an analyte (Da)
distance migrated by the solvent (Ds)

Separations and Purificationschromatography
Paper chromatography:

A sheet of paper is the inert phase

Analyze complex mixtures, such as ink, by separating
them into the chemicals from which they are made

Degree of retention of a component is called the
retardation factor
(Rf) = distance migrated by an analyte (Da)
distance migrated by the solvent (Ds)

Thin-layer chromatography:



an adsorption chromatography in which samples are
separated based on the interaction between a thin layer
of adsorbent and a selected solvent
same principles apply as in paper chromatography
http://www.agsci.ubc.ca/fnh/courses/food302/chromato/schromato03.htm
Separations and Purificationschromatography
Passages 29 and 32

Recrystaliztation:

Impurities stay in solution and the pure product
crystallizes

Solvent choice, is most important. Solvent should
dissolve product at high temperature and have high
affinity for impurities at low temperature or no affinity at
all at high temperature

According to the adage "like dissolves like," a solvent
that has a similar polarity to the solute being dissolved
will usually dissolve the substance very well.