Mcat Organic Chemistry Lecture 4

Front 1

Fatty acids

Back 1

long carbon chains with a carboxylic acid end

3 functions:
1. hormones and intracellular messengers
2. components of phospholipids and glycolipids of cell membranes
3. act as fuel for body, stored in form of tryacylglycerols which can be hydrolyzed to form glycerol and corresponding fatty acids

carbonyl C is assigned #1
C next to carbonyl is a-C (alpha-C)
C at opposite end of chain is w-carbon (omega carbon)

pKa = 4.5, exist in anion form in cellular environment

C chains can be saturated or unsaturated

amphipathic molecules, nonpolar

enter Krebs cycle 2 C at a time

Front 2

lipolysis

Back 2

hydrolysis of tryacylglycerols into glycerols and corresponding fatty acids

reverse of esterification

tryacylglycerols can be cleaved by addition of NaOH

Front 3

saponification

Back 3

tryacylglycerols can be cleaved by addition of NaOH

production of soap

Front 4

triacylglycerols

Back 4

form in which fatty acids are stored in adipose cells (fat cells)

lipolysis takes place inside adipose cells

Front 5

Krebs cycle

Back 5

acetyl CoA (2C) enters Krebs cycle for further oxidation by condensation with oxaloacetate

Front 6

Amino acids

Back 6

building blocks of proteins

single proteins consists of 1 or more chains of amino acids strung end to end by peptide bonds

Front 7

peptide bonds

Back 7

holds amino acids end to end to form chain, resulting in proteins

N is comfortable with 4 bonds and O is comfortable with partial negative charge, thus electrons delocalize creating resonance that results in partial double bond character of peptide bond

prevents bond from rotating freely

affects secondary and tertiary structure of polypeptide

Front 8

polypeptide

Back 8

chain of multiple amino acids, held together end to end by peptide bonds, forming proteins

secondary and tertiary structure affected by double bond characteristic of peptide bonds

Front 9

amide

Back 9

functional group created by peptide bond

an amine connected to a carbonyl C

formed via condensation of 2 amino acids

reverse reaction is hydrolysis of peptide bond

N-C=O

Front 10

a-amino acids

Back 10

alpha amino acids

amino acids used by body

amine group attached to C which is alpha to carbonyl C (similar to a-H of ketones and aldehydes)

Front 11

Side chains

Back 11

R groups on amino acids

each amino acids differs only in R groups, which have different chemical properties, divided into 4 categories:
1. acidic (polar)
2. basic (polar)
3. polar
4. nonpolar

20 a-amino acids
10 essential amino acids

Front 12

Acidic Amino acids

Back 12

polar, side chain contains carboxylic acid

isoelectric point below pH 7

1. aspartic acid
2. glutamic acid

Front 13

Basic Amino acids

Back 13

polar, side chain contains amines

isoelectric point above pH 7

HAL:
1. histidine
2. arginine
3. lysine

Front 14

Polar amino acids

Back 14

hydrophilic

will turn to face an aqueous solution, such as cytosol

affect protein's tertiary structure

1. valine
2. isoleucine
3. proline
4. methionine
5. alanine
6. leucine
7. tryptophan
8. phenylalanine
9. glycine

Front 15

Nonpolar amino acids

Back 15

hydrophobic

will turn away from aqueous solution, such as cytosol

affect protein's tertiary structure

1. serine
2. threonine
3. cysteine
4. tyrosine
5. glutamine
6. asparagine

Front 16

3 forms in which amino acids exist:

Back 16

1. low pH, acidic, positive charge on N
2. pH 7, neutral, negative charge on O of OH and positive charge on N, zwitterion (dipolar ion)
3. high pH, basic, negative charge on O of OH and H removed from N (no charge)

Front 17

isoelectric point (pI)

Back 17

when all protons (H+) have been removed from all carboxylic acids from amino acid

pH where the population has no net charge and max # of species are zwitterions

more acidic the side chain, the lower pI

the more basic the side chain, the greater pI

Front 18

Carbohydrates

Back 18

carbon and water

for each C atom there exists 2 H

Cn(H2O)n

most common: glucose or fructose

named for # of C they posses:
3 C = triose
4 C = terose
5 C = pentose
6 C = hexose
7 C = keptose

labeled D or L depending on chirality:
D = OH on highest # chiral C points to R on fischer projection
L = OH on highest # chiral C points to L on fischer projection

Front 19

Hexoses

Back 19

6 C carbohydrates

ex:
1. glucose (aldehyde)
2. fructose (ketone)

Front 20

aldoses

Back 20

polyhydroxyaldehydes

ex:
glucose

Front 21

ketoses

Back 21

polyhydroxyke-tones

ex:
fructose

Front 22

aldohexose

Back 22

carbohydrates, polyhydroxyaldehydes, aldehydes, with 6C

ex:
glucose

Front 23

anomeric C

Back 23

only C attached to 2 O because its OH may point upwards or downwards on ring resulting in alpha or beta anomer

in carbohydrate, OH on chiral C farthest from carbonyl may act as nucleophile and attack carbonyl, resulting in nucleophilic addition to aldehyde or ketone, forming hemiacetal, creating ring structure

C 1 is called anomeric C

Front 24

carbohydrate cyclic ring structure nomenclature

Back 24

named according to # of ring members (including O)

5 member ring = furanose
6 member ring = pyranose

ex: glucose ring = glucopyranose

names of reducing sugars end in "ose" = hemiacetals

names of nonreducing sugars end in "oside" = acetals (reducing blocking agents)

Front 25

Sucrose

Back 25

1,1' glycosidic linkage: glucose and fructose

linkage is alpha with respect to glucose

linkage is beta with respect to fructose

Front 26

Maltose

Back 26

alpha - 1,4' glucosidic linkage: 2 glucose molecules

Front 27

lactose

Back 27

beta- 1,4' galactosidic linkage: galactose and glucose

Front 28

cellulose

Back 28

beta- 1,4' glucosidic linkage: chain of glucose molecules

Front 29

amylose

Back 29

alpha- 1,4' glucosidic linkage: chain of glucose molecules

Front 30

amylopectin

Back 30

alpha- 1,4' glucosidic linkage: branched chain of glucose molecules with alpha- 1,6' glucosidic linkages formed the branches

Front 31

glycogen

Back 31

alpha- 1,4' glucosidic linkage: branched chain of glucose molecules with alpha- 1,6' glucosidic linkages forming the branches

Front 32

Lab techniques

Back 32

1. spectroscopy
2. spectrometry
3. separations

Front 33

Spectroscopy

Back 33

1. nuclear magnetic resonance (NMR)
2. infrared spectroscopy (IR)
3. ultraviolet spectroscopy (UV)

Front 34

Spectrometry

Back 34

1. Mass spectrometry (Mass Spec)

Front 35

Separations

Back 35

1. Chromatography
2. Distillation
3. Crystallization
4. Extraction

Front 36

Nuclear Magnetic Resonance (NMR)

Back 36

observes nuclear spin exhibited by nuclei (hydrogen) with odd atomic # or odd mass #

frequency of electromagnetic radiation is held constant, while magnetic field strength is varied

protons with a compound absorb electromagnetic energy of same frequency at different magnetic field strengths

Front 37

NMR spectrum

Back 37

graph of magnetic field strengths absorbed by H of a specific compound at a single frequency

field strength is measured in parts per million (ppm) and increases from left (downfield) to right (upfield)

upfield is peak at 0 ppm due to reference compound

each peak represents chemically equivalent hydrogens

splitting of peaks is created by "neighboring hydrogens"

Front 38

chemical shift

Back 38

difference between resonance frequency of chemically shifted H and resonance frequency of H on reference compound (tetramethylsilane)

enantiotropic H are repesented by same peak in NMR spectrum and have same chemical shift

Front 39

area under peak of NMR spectrum

Back 39

represents # of H represented by peak

the more chemically equivalent H, the greater the are

tallest peak doesn't correspond to greatest area

Front 40

integral trace

Back 40

line drawn above peaks that rises each time goes over a peak

rise of integral trace is proportional to # chemically equivalent H in peak beneath it

ratio of H from 1 peak to another can be determine, but not exact # of H

Front 41

electron shielding

Back 41

H with less shielding have peak downfield (left), electron withdrawing groups

H with more shielding have peak upfield (right), electron donating groups

Front 42

Splitting

Back 42

spin-spin splitting

results from neighboring H that are not chemically equivalent

# of peaks due to splitting = n + 1
n: # of neighboring H that are not chemically equivalent

Front 43

neighboring hydrogens

Back 43

H that is on an atom adjacent to atom to which H is connected

Front 44

NMR steps:

Back 44

1. identify chemically equivalent H
2. identity and count neighboring H that are not chemically equivalent, use n+1 to figure out splitting for chemically equivalent H
3. if necessary, identify electron withdrawing/donating groups near chemically equivalent H

aldehyde protons = 9.5 ppm

C-13 is only C isotope to register on NMR (ignore splitting)

Front 45

Infrared radiation

Back 45

when exposed to IR, polar bonds within compound stretch and contract in vibration motion

different bonds vibrate at different frequencies

Front 46

IR spectroscopy

Back 46

IR slowly changes frequency of infrared light shining upon a compound and record frequencies of absorption in reciprocal centimeters (cm^-1 = number of cycles per cm)

if a bond has no dipole moment, IR does not cause vibration and no energy is absorbed

Front 47

IR spectrum

Back 47

predictable section: 1600 - 3500 cm^-1 region

C=O: sharp dip, 1700 cm^-1
O-H: broad dip, 3200-3600 cm^-1

1. Carboxylic acid: O-H (2500-3500), C=O (1710)
2. Aldehyde: saturated C-H (2800-3000), aldehyde C-H (2700, 2800), C=O (1710)
3. alcohol: O-H (3300), saturated C-H (2800-3000)
4. Amine: N-H (short, 3300), saturated C-H (2800-3000)
5. Nitrile: saturated C-H (2800-3000), C triple bond N (2200)
6. Amides: N-H (long, 3300), saturated C-H (2800-3000), C=O (1710)

greater mass = lower frequencies
stiffer bonds = higher frequencies

Front 48

fingerprint region

Back 48

2 compounds do not have exactly same IR spectrum

region where complex vibrations that distinguish 1 compound from similar compound are found (600-1400)

unique to all compounds

Front 49

Ultraviolet light

Back 49

wavelength between 200 and 400 nm

shorter and much higher energy level than infrared light

Front 50

ultraviolet spectroscopy (UV)

Back 50

detects conjugated double bonds (double bonds separated by one single bond) by comparing intensities of 2 beam of light from same monochromatic light source

difference in radiant energy between sample and solvent is recorded as UV spectrum of sample compound

Front 51

UV spectrum

Back 51

UV starts around 217nm with butadiene

30 to 40nm increase for each additional conjugated double bond

5nm increase for each additional alkyl group

isolated double bonds do not increase absorption wavelength

carbonyls, C=O, also absorb light in UV region

Front 52

Visible spectrum

Back 52

if compound has 8 or more double bonds, its absorbance moves into visible spectrum

Front 53

complementary color

Back 53

beta-carotene (11 conjugated bonds) absorbs at 497nm (blue-green light), giving complementary color of red-orange

Front 54

Mass Spectrometry

Back 54

gives the MW and molecular formula

molecules of sample are bombarded with electrons, causing them to break apart and to ionize

largest ion is size of original molecule minus 1 electron

ions are accelerated through magnetic field and resulting force deflects ions around curved path

magnetic field strength is altered to allow passage of different size ions through flight tube

computer records # of ions at different magnetic field strengths as peaks on chart

Front 55

mass to charge ratio

Back 55

m/z ratio of ion

establishes radius of curvature of the ion's path

most ions have charge of +1

Front 56

Base peak

Back 56

largest peak on mass spec graph

Front 57

parent peak

Back 57

peak made by molecular ion that didn't fragment

all the way on right of spectrum

Front 58

Chromatography

Back 58

resolution (separation) of mixture by passing it over/through matrix that absorbs different compounds with different affinities, altering the rate at which they lose contact with the resolving matrix

mobile phase: solution into which mixture is dissolved
resolving matrix: solid surface
stationary phase: compounds from mixture absorbed by surface

compounds with greater affinity for surface move more slowly

more polar compounds move more slowly because of greater affinity for stationary phase

results in establishment of separate and distinct layers, 1 pertaining to each component mixture

Front 59

Different types of chromatography

Back 59

Solid to liquid:
1. column chromatography
2. paper chromatography
3. thin layer chromatography

gas to liquid:
1. gas chromatography

Front 60

Column chromatography

Back 60

solution containing mixture is dripped down a column containing solid phase (glass beads)

more polar compounds travel more slowly, separating compounds

compound are collected as elutes with solvent, dripping out of bottom of column

Front 61

paper chromatography

Back 61

sample is spotted onto paper, one end of paper is placed in solvent, solvent moves up paper via capillary action and dissolves sample as it passes over it

more polar components move slowly because they are attracted to polar paper

less polar components move more quickly

results in series of colored spots representing different components of sample with most polar near bottom and least polar near top

Front 62

Rf factor

Back 62

can be determined for each component

divide distance traveled component by distance traveled by solvent

nonpolar components have Rf factors close to 1

polar components have Rf factors lower than 1

always between 0 and 1

Front 63

thin layer chromatography (TLC)

Back 63

similar to paper chromatography except coated glass or plastic plate is used instead of paper

results are visualized via iodine vapor chamber

Front 64

gas chromatography

Back 64

liquid phase is stationary phase

mixture dissolved into heated carrier gas (He or N) and passes over liquid phase bound to column

compounds in mixture equilibrate with liquid phase at different rates and elute as individual components

Front 65

Distillation

Back 65

separation based upon vapor pressure

solution with 2 volatile liquids with boiling points that differ by 20 degrees or more may be separated by slow boiling

compound with lower boiling point (higher vapor pressure) will boil off and be captured and condensed in cool tube

Front 66

fractional distillation

Back 66

more precise method of distillation

vapor runs through glass beads allowing compound with higher boiling point to condense and fall back into solution

Front 67

Crystallization

Back 67

based upon principle that pure substances form crystals more easily than impure substances

very inefficient method of separation, very difficult to arrive at pure substance

crystallization of salts is an exothermic process

ex:
iceberg = pure water (no salt)

Front 68

Extraction

Back 68

based upon solubility due to similar polarities

likes dissolve likes

1. organic mixture on top of aqueous layer (different polarities)
2. add strong acid and shake. acid protonates bases like amines in organic layer, making them polar. polar amine dissolve in aq layer and are drainer off
3. add weak base. base deprotonates only strong acids like carboxylic acids, making them polar. polar carboxylic acids dissolve in aq layer and drain off.
4. add strong base. strong base reacts with rest of acids (weak acids). acids dissolve in aq layer and drain off.