3. General Chemistry of Carbon
Carbon is a non-metal chemical
element.
A covalent bond is a chemical bond
that involves the sharing of electron
pairs between atoms.
4. General Chemistry of Carbon
Carbon atomic number =
6 Protons
6 Electrons
6 Neutrons
Group IV
Four valence electrons
5. Atomic Theory of Carbon
Ground state electronic configuration of
carbon is:
1s22s22p2
[He] 2s22p2 1S2
2S2
2P2
Nucleus
16. Molecular Formulas
For example, glucose
Symbols for carbon, hydrogen, and
oxygen are C, H, and O respectively
Molecular formula for glucose is C6H12O6
17. Structural Formulas
Show arrangement of atoms:
How atoms are bonded,
In which order they are bonded
Whether single, double or triple bonds are
used
19. Condensed Formulas
Show:
Groups of atoms in a molecule
The sequential relationships of these group of
atoms to each other with or without showing
covalent bonds
23. Organic Chemistry:
Carbon Atom
1. Structural
Classifications
2. Atomic Theory
3. Dipoles &
Resonance
4. Isomers
5. Functional Groups
6. Organic Reactions
24. Organic Chemistry
The chemistry of compounds which contain
carbon.
Carbon forms more compounds than any other
element, except hydrogen.
25. Organic Chemistry Major Concepts
1. Structural Classifications
2. Hybridization
3. Charges of Organic Molecules
4. Dipoles & Dipolar Resonance
5. Isomers
6. Functional Groups
7. Organic Reactions
26. Structural Classification of Carbon
Atoms
Three main classifications are:
1. Primary Carbons
2. Secondary Carbons
3. Tertiary Carbons
4. Quaternary Carbons
27. Primary Carbons
Denoted as 1° carbons.
Also called terminal or end carbon atoms.
Found at the ends of a straight chains or the
branches.
Covalently bonded to one carbon atom.
CH3 – CH2 – CH3
29. Tertiary Carbons
Denoted as 3° carbons.
Covalently bonded to three other carbon
atoms.
CH3 – CH – CH3
|
CH3
30. Quaternary Carbons
Denoted as 4° carbons.
Covalently bonded to four other carbon
atoms. CH3
|
CH3 – C – CH3
|
CH3
31. Definitions
Valence Bond Theory:
Electrons in a covalent bond reside in a region
in which there is overlap of individual atomic
orbitals.
For example, the covalent bond in molecular
methane (CH4) requires the overlap of valence
electrons:
33. Definitions
Valence Shell Electron Pair Repulsion (VSEPR)
Electron pairs arrange themselves around an
atom in order to minimize repulsions between
pairs.
Carbon has a valence of four and must have a
tetrahedral geometry.
In methane, each carbon atom must have a
bond angle of 109.5⁰. This is the largest bond
angle that can be attained between all four
bonding pairs at once.
38. Hybridizations
In sp3 hybridization, an electron is promoted
from a 2s orbital into a p orbital.
The 2s orbital and three 2p orbitals form four
hybrid orbitals (sp3).
Ground state: 1s2 2s2 2Px
1 2Py
1 2Pz
0
Excited state: 1s2 2s1 2Px
1 2Py
1 2Pz
1
39. Hybridizations
The overlap of each hybrid orbital with a
hydrogen atom results in a sigma bond ( σ
bond).
Only one σ bond can exist between two atoms.
42. Hybridizations
In sp2 hybridization, the 2s orbital and two of
the 2p orbitals form three hybrid orbitals (sp2).
The Pz orbital of each carbon atom remains
unhybridized.
These unhybridized Pz orbitals overlap with
one another to form a π-bond.
45. Hybridizations
In sp hybridization, the 2s orbital and one 2p
orbital form two hybrid orbitals (sp).
The triple bond is actually one σ bond and
two π bonds.
48. Definitions
Dipole:
The measure of net molecular polarity.
Formula: the magnitude of the charge Q times
the distance r between the charges.
μ = Q × r
The larger the difference in electronegativities
of the bonded atoms, the larger the dipole
moment.
49. Definitions
Resonance:
Part of the Valence Bond Theory
Describes the delocalization of electrons within
molecules.
Used when Lewis structures for a single
molecule cannot describe the actual bond
lengths between atoms.
Structures are not isomers of the target
molecule, since they only differ by the position
of delocalized electrons.
50. Definitions
Resonance Hybrid:
The net sum of valid resonance structures.
Several structures represent the
overall delocalization of electrons within the
molecule.
A molecule that has several resonance
structures is more stable than one with fewer.
51. Definitions
Hyperconjugation:
The interaction of the electrons in a sigma
bond (usually C–H or C–C) with an adjacent
empty (or partially filled) non-bonding p-orbital,
antibonding π orbital, or filled π orbital.
Only electrons in bonds that are β to the
positively charged carbon can stabilize a
carbocation by hyperconjugation.
58. Hyperconjugation
A.K.A "no bond resonance".
The delocalization of σ-electrons or lone pair of
electrons into adjacent π-orbital or p-orbital.
Overlapping of σ-bonding orbital or the orbital
containing a lone pair with adjacent π-orbital or
p-orbital.
An α- carbon next to the π bond, carbocation or
free radical should be sp3 hybridized with at least
one hydrogen atom bonded to it.
59. Hyperconjugation
Other hydrogens on the methyl group also
participate due to free rotation of the C-C
bond.
There is NO bond between an α-carbon and
one of the hydrogen atoms.
The hydrogen atom is completely detached
from the structure.
The C-C bond acquires some double bond
character and C=C acquires some single
bond character.
73. Definitions
Chiral Molecules - when a molecule and its
mirror image cannot completely overlap.
They are non-superimposable mirror images
of one another.
Dextrorotatory (R, +) - a compound whose
solution rotates the plane of polarized light to
the right (when looking toward the source of
light).
74. Definitions
Levorotatory (S, -) - a compound whose
solution rotates the plane of polarized light to
the left (when looking toward the source of
light).
Racemic Mixture - a mixture of equal
amounts of optical isomers. Because the
two isomers rotate the plane of polarized
light by the same angle in opposite
directions, they cancel each other out and
have no net effect.
75. Determining L (S, -) or D (R, +)
configuration
1. Rank the four substituents according to the
atomic numbers of the atoms bonded
directly to the double bonded carbons,
from highest (1) to lowest (4).
76. Determining L (S, -) or D (R, +)
configuration
2. If two substituents have the same ranking:
Look at the next atoms in their substituent
chains.
List the atoms that are two bonds away
from the chiral center according to their
atomic number, from highest to lowest.
Assign the lower number to the
substituent that has the atom with the
higher atomic number.
77. Determining L (S) or D (R)
configuration
If it is still the same atom for both
substituents, continue down the list until a
difference is found and assign a ranking
in the same manner.
3. If a substituent has a double or triple
bonds in its chain, it is counted as two or
three bonds to the same atom.
78. Determining L (S, -) or D (R, +)
configuration
4. Determine whether the ranking defines a
clockwise or counterclockwise direction.
If clockwise, the projection is an R
configuration.
If counterclockwise, it is an S configuration.
89. Functional Groups
Organic molecules may have functional
groups attached.
A functional group is a group of atoms of a
particular arrangement that gives the entire
molecule certain chemical characteristics.
Functional groups are named according to
the composition of the group.
90. Functional Groups
Organic chemists use the letter "R" to indicate
an organic molecule.
The "R" can be any organic molecule.
91. Hydrocarbons
The simplest organic compounds.
Contain only carbon and hydrogen,
Can be straight-chain, branched chain, or cyclic
molecules.
Carbon tends to form four bonds in a tetrahedral
geometry.
93. Hydrocarbons
Aromatic - Aromatic hydrocarbons contain a set
of covalently bound atoms with specific
characteristics:
A delocalized conjugated π system, with the
common arrangement of alternating single and
double bonds
96. Alkanes
Saturated hydrocarbons.
Are hydrocarbons which contain only single
bonds.
All alkanes are insoluble in water, but dissolve
in organic solvents.
Density, viscosity, melting point & boiling
points increase as the molecular weight/size of
the hydrocarbon increases.
97. Alkanes
Contain single covalent bonds.
Have the same structural formula:
Cn H2n+2
All carbons have single bonds therefore the
molecular geometry is tetrahedral.
98. Alkanes
The names of alkanes start with the name of the
alkane but end with the suffix –ane.
99. Alkanes
Each atom in an alkane uses all its 4 valence
electrons in forming single bonds with other
atoms.
Alkyl groups may be used as substituents for
hydrogens.
100. Alkanes
Alkyl groups form the branches of straight chain
hydrocarbons.
Can have more than one alkyl group for hydrogens.
For multiple substituents of the same type, use the
following prefixes:
di-
tri-
tetra-
penta-
hexa-
102. Alkanes
Other functional groups can be used as
substituents.
More than one substituent requires a prefix.
Any hydrogen can be substituted by:
1. Halogens
2. Alcohols
3. Amines
4. Nitriles
5. Thiols
6. Aldehydes
7. Ketones
103. Alkanes
Any carbon can be substituted by:
Carboxylic Acids
Esters
Amides
Thioesters
Addition of other atoms:
Ethers
Thioethers
Disulfides
105. Cycloalkanes
Saturated hydrocarbons.
Form one or more rings fused together.
A single carbon in a ring may have two hydrogen
atoms.
Are insoluble in water, but dissolve in organic
solvents.
Have higher boiling points, melting points, and
densities than alkanes.
106. Cycloalkanes
All have the same general formula:
CnH2n
The carbon atoms in cycloalkanes are sp3
hybridized.
Each atom in a cycloalkane uses all its 4 valence
electrons in forming covalent bonds with other
atoms.
107. Cycloalkanes
Can have more than one alkyl group to make
straight chains.
For multiple alkyl groups of the same type, use
prefixes.
108. Cycloalkanes
Many functional groups can be used as substituents.
More than one substituent requires a prefix.
Any hydrogen or carbon atom can be substituted by:
114. Alkenes
Also known as olefins.
Are unsaturated hydrocarbons and are generally
very reactive.
Are insoluble in water, but dissolve in organic
solvents.
Ethene, propene and butene are gases at room
temperature. The remaining are liquids.
Boiling points increases with molecular mass
(chain length). The higher the molecular mass,
the higher the boiling point.
115. Alkenes
Are hydrocarbons which contain one or more
double bonds.
Double bonds are:
Have the same structural formula:
CnH2n
116. Alkenes
The main centers are the carbons of the
double bond.
The geometry of each carbon in the center is
trigonal planar.
This portion of the molecule is flat, with bond
angles of 120 degrees.
118. Alkenes
The carbon-carbon double bond does not
rotate.
Substituents groups on the molecule are
locked on either one side of the molecule or
opposite each other.
119. Alkenes
The names of alkenes start with the name of the
alkane but end with the suffix –ene.
For alkenes above propene, the position of the
double bond must be specified in the name.
120. Alkenes
Can have more than one alkyl group to form
branches.
For more than one alkyl group, use prefixes.
121. Alkenes
Many functional groups can be used as substituents.
More than one substituent requires a prefix.
Any hydrogen or carbon atom can be substituted by:
122. Alkenes
For multiple double bonds, use the following prefixes:
di-
tri-
tetra-
penta-
hexa-
123. Alkenes
A diene is a hydrocarbon chain that has two
double bonds that may or may not be adjacent
to each other.
127. Alkynes
Also known as acetylenes.
Are unsaturated hydrocarbons and are
generally very reactive.
Are insoluble in water; but quite soluble in
organic solvents of low polarity (e.g. ligroin,
ether, benzene, carbon tetrachloride, etc.).
Alkynes of four or fewer carbon atoms are
gases. The rest are liquids.
Their boiling points increase with increasing
number of carbons.
128. Alkynes
Are hydrocarbons which contain one or more
triple bonds.
Triple bonds are:
Have the same structural formula:
CnH2n-2
129. Alkynes
The main centers are the carbons of the triple
bond.
The geometry of the center is linear.
This portion of the molecule is linear, with
bond angles of 180 degrees.
131. Alkynes
The names of alkynes start with the name of the
alkane but end with the suffix –yne.
For alkynes above propyne, the position of the
triple bond must be specified in the name.
132. Alkynes
Many functional groups can be used as substituents.
Only one substituent is allowed.
Any hydrogen or carbon atom can be substituted by:
133. Alkynes
For multiple double bonds, use the following prefixes:
di-
tri-
tetra-
penta-
hexa-
136. Aromatics
Coplanar structures, with all the contributing atoms in the
same plane.
Are arranged in one or more rings.
Benzene rings are not a common motif.
The three general requirements for a compound to be
aromatic are:
The compound must be cyclic.
Each element within the ring must have a p-orbital that
is perpendicular to the ring, hence the molecule is
planar.
The compound must follow Hückel's Rule.
137. Aromatics
The number of π delocalized electrons must
follow Hückel's Rule.
number of π electrons = 4n + 2
where n = 0, 1, 2, 3, and so on
The number of π delocalized electrons is an
even number, but not a multiple of 4 to be an
aromatic compound.
138. Aromatics
The most common examples of aromatic
hydrocarbons are organic compounds, which
contain one or more benzene rings.
Benzene
140. Aromatics
Each atom in benzene uses all its 4 valence
electrons in forming covalent bonds with other
atoms.
Other functional groups can be used as
substituents.
More than one substituent requires a prefix.
142. Aromatics
When two substituents are attached to the benzene
ring:
Ortho, meta, or para can be used to indicate
where the two substituents are on the benzene
ring.
Three classifications:
ortho- (o-): position 1, 2-
meta- (m): posotion 1, 3-
para- (p): position 1, 4-
155. Haloalkanes
The alkyl halides have the general form
where the R in the general form is typically an alkyl
group with a halogen replacing one of the
hydrogens.
X is written as:
F = fluoro
Cl = chloro
Br = bromo
I = iodo
157. Haloalkanes
There can be multiple substitutions of halogens
for hydrogens, and also variations where
alkenes, alkynes or aromatics are involved.
158. C – O Bonds Organic
Compounds
1. Alcohols
2. Ethers
160. Alcohols
Are organic compounds containing a hydroxyl
group, -OH, substituted for a hydrogen atom.
The center of the alcohol functional group is the
oxygen.
Have two lone pairs of electrons on the oxygen.
This forces the molecular geometry on the
alcohol oxygen to be BENT. This portion of the
molecule is flat, with bond angles of 109
degrees.
161. Alcohols
Are organic compounds containing a hydroxyl
group, -OH, substituted for a hydrogen atom.
The names of alcohols start with the name of the
alkane but end with the suffix –ol.
Can have more than one hydroxyl group for
hydrogens, and also variations where alkenes,
alkynes or aromatics are involved.
Use a prefix for multiple hydroxyl groups.
162. Alcohols
Are classified according to the number of
carbon atoms attached directly to the carbon
containing the hydroxyl group.
164. Ethers
Are compounds with the general formula:
The center of the ether functional group is the
oxygen.
Have two lone pairs of electrons on the oxygen.
This forces the molecular geometry on the ether
oxygen to be BENT. This portion of the molecule
is flat, with bond angles of 109 degrees.
170. Thiols
Are sometimes called sulfides.
Are organic compounds containing a sulfhydryl
group, -SH, substituted for a hydrogen atom.
Are the sulfur analogue of alcohols. Sulfur takes
the place of oxygen in the hydroxyl group of an
alcohol.
Are stronger acids than alcohols.
The –SH functional group itself is referred to as
either a thiol group or a sulfhydryl group.
171. Thiols
The center of the thiol functional group is the
sulfur.
Have two lone pairs of electrons on the sulfur.
This forces the molecular geometry on the thiol
sulfur to be BENT. The C–S–H angles approach
90°.
172. Thiols
Classified according to the number of carbon
atoms bonded directly to the carbon containing
the thiol group.
The names of thiols start with the name of the
alkyl but end with the suffix –thiol.
173. Thiols
Can have more than one sulfhydryl group, and
also variations where alkenes, alkynes or
aromatics are involved.
Use a prefix for multiple thiol groups.
176. Thioethers
Are sometimes called sulfides.
Are compounds with the general formula:
The center of the thioether functional group is the
sulfur.
A thioether is similar to an ether except that it
contains a sulfur atom in place of the oxygen.
177. Thioethers
Have two lone pairs of electrons on the sulfur.
This forces the molecular geometry on the
thioether sulfur to be BENT.
This portion of the molecule is flat, with bond
angles of 90 degrees.
90⁰
181. Disulfides
Another class of sulfur containing molecules
that have important biological implications.
Have the generic formula:
Are products from the oxidation of two thiols.
182. Disulfides
The center of a disulfide functional group has two
sulfur atoms single bonded to each other and to
two different carbon atoms.
Have two lone pairs of electrons on each sulfur.
This forces the molecular geometry on the
thioether sulfur to be BENT.
183. Disulfides
Are named by naming the R groups attached
to the sulfur atoms followed by the suffix -
disulfide.
Dimethyldisulfide
189. Amines
Are organic compounds that contain nitrogen
and are basic.
The general form of an amine is:
R represents an alkyl group, but either or both
of the hydrogens may be replaced by other
groups and still retain its class as an amine.
190. Amines
The center of the amine functional group is the
nitrogen.
Have one lone pair of electrons on the nitrogen in
addition to the single bonds.
This forces the molecular geometry on the amine
nitrogen to be trigonal pyramid.
This portion of the molecule is not flat, with bond
angles of 109 degrees.
191. Amines
The common names for simple aliphatic
amines consist of the alkyl group followed by
the suffix -amine.
The amino group (-NH2) is named as a
substituent in more complicated amines, such
as those that incorporate other functional
groups or in which the alkyl groups cannot be
simply named.
192. Amines
Are classified according to the number of
carbon atoms bonded directly to the nitrogen
atom.
196. Nitriles
Are organic compounds that have a
functional group.
Have one lone pair of electrons on the nitrogen
in addition to one triple bond with a carbon atom.
This forces the molecular geometry on the cyano
nitrogen to be linear.
197. Nitriles
The common names for simple nitriles consist of
the alkane/alkyl followed by the suffix -nitrile.
The cyano group (−C≡N) is also used
interchangeably.
201. Aldehydes
Are compounds containing a carbonyl group with
a hydrogen attached at end and an organic
group of carbons at the other side.
The center of the aldehyde functional group is
the carbon double bond oxygen.
202. Aldehydes
Have two lone pairs of electrons on the oxygen.
With three atoms attached to this carbon, the
molecular geometry is trigonal planar.
This portion of the molecule is flat, with bond
angles of 120 degrees.
207. Ketones
Are compounds containing a carbonyl group
with two hydrocarbon groups attached to it.
The center of the ketone functional group is
the carbon double bond oxygen.
208. Ketones
Have two lone pairs of electrons on the oxygen.
With three atoms attached to this carbon, the
molecular geometry is trigonal planar.
This portion of the molecule is flat, with bond
angles of 120 degrees.
209. Ketones
IUPAC name includes the prefix from the alkyl
group and the suffix -one.
For more than one ketone group, use a prefix.
213. Carboxyl Derivatives
Are derivatives of carboxylic acids.
Can be distinguished from aldehydes and
ketones by the presence of a group
containing an electronegative heteroatom -
usually oxygen, nitrogen, or sulfur – bonded
directly to the carbonyl carbon.
214. Carboxyl Derivatives
Have two sides:
1. The carbonyl group attach to an alkyl
group. This is called an acyl group.
2. The heteroatom-containing group, refer to
as the ‘acyl X' group
216. Carboxylic Acids
Are important intermediate products for the
production of esters and amides.
Are hydrocarbon derivatives for which the
functional group is the carboxyl group.
The center of the acid functional group is the
carbon double bonded to an oxygen and single
bonded to a hydroxyl group.
217. Carboxylic Acids
Each oxygen atom has a pair of lone electrons.
With three atoms attached to this carbon, the
molecular geometry is trigonal planar. This
portion of the molecule is flat, with bond angles of
120 degrees.
An additional molecular geometry is centered on
the oxygen of the - OH group. This is bent.
218. Carboxylic Acids
In the IUPAC system, the –e ending in alkane
is removed from the name of the parent chain
and is replaced -anoic acid for the COOH
acidic bond system.
219. Carboxylic Acids
Cyclic carboxylic acids that are saturated are
called cycloalkane carboxylic acids.
Dicarboxylic acids are known as alkanedioic
acids.
224. Esters
Are compounds with the general formula:
The center of the ester functional group is the
carbon double bonded to an oxygen and single
bonded to an oxygen attached to an alkyl group.
225. Esters
Each oxygen atom has a pair of lone electrons.
With three atoms attached to this carbon, the
molecular geometry is trigonal planar. This
portion of the molecule is flat, with bond angles
of 120 degrees.
An additional molecular geometry is centered
on the oxygen with all single bonds. This is
bent.
226. Esters
Complex esters are more frequently named
using the systematic IUPAC name, based on the
name for the alkyl group followed by the suffix –
oate.
Cyclic esters are called lactones.
231. Amides
Also known as an acid amide.
Are formed when carboxylic acids react with
amines.
Are nitrogen-containing organic compounds with
the general formula
232. Amides
The center of the amide functional group is the
carbon double bonded to oxygen and single
bonded to nitrogen.
Classified according to the number of carbons
attached directly to the nitrogen atom:
233. Amides
The oxygen atom has two lone pair of electrons.
The nitrogen atom has one pair of lone electrons.
With three atoms attached to this carbon, the
molecular geometry is trigonal planar. This
portion of the molecule is flat, with bond angles
of 120 degrees.
234. Amides
The molecular geometry centered on the
nitrogen is bent and also flat as an extension of
the trigonal planar geometry.
235. Amides
In the IUPAC system:
For primary amides, the –e is removed from the
alkane name and the suffix -amide is added.
236. Amides
For 2⁰ and 3⁰ amides, alkyl groups attached to
the nitrogen are named as substituents.
The letter N is used to indicate they are attached
to the nitrogen.
For more than one of the same substituent
groups, use a prefix.
244. Thioesters
Are the product of esterification between a
carboxylic acid and a thiol.
Are compounds with the functional group:
The center of the thioester functional group is
the carbon double bonded to an oxygen and
single bonded to sulfur attached to an alkyl
group or hydrogen.
245. Thioesters
The oxygen and sulfur atoms, each, have two
sets of lone pairs electrons.
With three atoms attached to this carbon, the
molecular geometry is trigonal planar. This
portion of the molecule is flat, with bond angles
of 120 degrees.
246. Thioesters
The molecular geometry centered on the
sulfur is bent and also flat as an extension of
the trigonal planar geometry.
247. Thioesters
In the IUPAC system, the name consist of the alkyl
group followed by the alkane with the suffix –thioate
or –carbothioate
Alkyl groups attached to the sulfur are named as
substituents. The letter S is used to indicate they
are attached to the sulfur.
S-Methyl ethanethioate
(IUPAC)
248. Thioesters
For common names, the name consist of the alkyl
group followed by the prefix “thio” before the
common name with the suffix –ate or -carboxylate.
Alkyl groups attached to the sulfur are named as
substituents. The letter S is used to indicate they are
attached to the sulfur.
S-PENTACHLOROPHENYL PENTACHLORO-1,3-
BUTADIENE-1-THIOCARBOXYLATE
264. Lewis acid-base definition: transfer of electron
pair from a base to an acid
Definitions
265. Nucleophiles
Are attracted to a positively charged cations or
atoms with partially positive dipole.
Share or transfer its electrons with an
electrophile during a reaction.
266. Nucleophiles
Can be negatively charged anions, neutral
ions, molecules with a lone pair of electrons or
at least one π bond.
Because nucleophiles donate electrons, they
are by definition Lewis bases.
269. Electrophiles
Atoms that are positively charged, carry a
partially positive dipole, or does not have an
octet of electrons.
Attracted to electrons of nucleophiles in a
chemical reaction.
Because electrophiles accept electrons, they
are Lewis acids.
276. Addition Reactions
The components of an organic molecule A–B
are added to the carbon atoms in a C=C
bonds.
Involve the conversion of a π bond into 2 σ
bonds.
General form: A + B → C
278. Addition Reactions
Alcohols are often produced by addition
reactions.
Initial attack by the π bond of an alkene on a
Hδ+ of H3O+ produces a carbocation.
The carbocation then undergoes nucleophilic
attack by a lone pair of electrons from H2O.
This is followed by elimination of H+ to form
the alcohol.
280. Addition Reactions
With symmetrical alkenes, addition of
hydroxyl group produces one type of alcohol.
281. Addition Reactions
With unsymmetrical alkenes, addition of
hydroxyl group produces different types of
alcohols depending on the location of the
double bond
+
283. Elimination Reactions
The removal or “elimination” of adjacent
atoms from a molecule.
Two σ bonds are lost, replaced by a new π
bond.
The dehydration reaction of alcohols to
generate alkene proceeds by heating the
alcohols in the presence of a strong acid,
such as sulfuric or phosphoric acid, at high
temperatures.
284. Elimination Reactions
The required range of reaction temperature
decreases with increasing substitution of the
hydroxyl carbon:
1° alcohols: 170° - 180°C
2° alcohols: 100°– 140 °C
3° alcohols: 25°– 80°C
285. Elimination Reactions
If the reaction is not sufficiently heated, the
alcohols do not produce alkenes, but they
react with one another to form ethers
(Williamson Ether Synthesis).
289. Elimination Reactions
In dehydration reactions of alcohols, hydride
or alkyl shifts relocate the carbocation to a
more stable position.
The dehydrated products are a mixture of
alkenes, with and without carbocation
rearrangement.
290. Elimination Reactions
Hydride or alkyl shifts are the result of
hyperconjugation. The interaction between the
filled orbitals of neighboring carbons and the singly
occupied p orbital in the carbocation stabilizes the
positive charge in carbocation.
The tertiary cation is more stable than a secondary
cation, which is more stable than a primary cation.
293. Substitution Reactions
Nucleophilic substitution reactions.
An electronegative atom is replaced by
another more electronegative atom, called a
stronger nucleophile.
The stronger nucleophile must possess a pair
of electrons and have a greater affinity for the
electropositive carbon atom than the original
electronegative atom.
A σ bond is replaced by another σ bond .
296. Rearrangement Reactions
Are isomerisation reactions.
An organic molecule changes structure.
Constitutional change in carbon skeleton.
Reaction may involve changes in bond type.
General form: A → B
298. Condensation Reactions
Two molecules combine to form one single
molecule with the loss of a small molecule.
When this small molecule is water, it is known
as a dehydration reaction.
Other possible small molecules lost include
hydrogen chloride, methanol, or acetic acid.
299. Condensation Reactions
When two separate molecules react, their
condensation is termed intermolecular.
The condensation of two amino acids to form
a peptide bond (red) with expulsion of water
(blue).
300. Condensation Reactions
When a condensation is performed between
different parts of the same molecule, the
reaction is termed intramolecular
condensation.
In some cases this leads to ring formation.
302. Esterification Reactions
Esters are obtained by refluxing a carboxylic
acid with an alcohol in the presence of an
acid catalyst.
The reaction is driven to completion by using
an excess of either the alcohol or the
carboxylic acid, or by removing the water as
it forms.
Alcohol reactivity order : CH3OH > 1o > 2o >
3o (steric effects).
303. Esterification Reactions
A carboxylic acid and an alcohol react
together under acidic conditions to form
an ester and lose water.
304. Esterification Reactions
Esters can also be made from other
carboxylic acid derivatives, especially acyl
halides and anhydrides, by reacting them
with the appropriate alcohol in the presence
of a weak base.
If a compound contains both hydroxy- and
carboxylic acid groups, then cyclic esters or
lactones can form via an intramolecular
reaction. Reactions that form 5- or 6-
membered rings are particularly favorable.
306. Hydrolysis
A reaction in which water is a reactant, and
becomes part of the reaction product.
A number of organic compounds undergo
hydrolysis with water, such as amides, esters,
halogenoalkanes and acyl halides.
307. Hydrolysis
Reactions require a catalyst.
The catalyst is either an acid (H+ ions) or alkali
(OH- ions).
Hydrolysis might involve refluxing in the
presence of dilute hydrochloric acid or sodium
hydroxide solution.
308. Hydrolysis
In the overall reaction, a bond in an organic
molecule is broken.
A water molecule also breaks into ions.
The -OH group from water is added to one
end of the organic molecule and the
remaining H atom is added to the other.
309. Hydrolysis of an Ester:
The addition of a strong acid, such as dilute
hydrochloric acid, is required to free the carboxylic
acid molecule.
In the base-catalyzed, the carboxylic acid molecule
loses a proton to a hydroxide ion.
310. Hydrolysis of Amides & Nitriles:
Amide acid catalyzed - HCl
Nitrile acid catalyzed – HCl or H2SO4
313. Summary of Hydrolysis Reactions
1. The hydrolysis of a primary amide:
RCONH2 + H2O → RCOOH + NH3
2. The hydrolysis of a secondary amide:
RCONHR' + H2O → RCOOH + R'NH2
314. Summary of Hydrolysis Reactions
3. The hydrolysis of an ester:
RCOOR' + H2O → RCOOH + R'OH
4. The hydrolysis of a halogenoalkane:
RBr + H2O → ROH + H+ + Br-
316. Definitions
Oxidation-Reduction reactions:
Involve changes in oxidation state at one or more
atoms.
Can often be identified by changes in the number
of oxygen atoms at a particular position in the
hydrocarbon skeleton or in the number of bonds
between carbon and oxygen at that position.
It is not consider an oxidation or reduction
reaction:
Addition or loss of H+
, H2O, HX.
317. Definitions
Oxidation:
The oxidation state increases
Loss of H2
Loss of a C-H bond
Addition of O or O2
Formation of a C-O bond or equivalent (C-Cl,
CΞN, C-S)
Addition of X2 (halogens)
318. Definitions
Reduction:
The oxidation state decreases
Addition of H2 or H-
Formation of a C-H bond
Loss of O or O2
Loss of a C-O bond or equivalent
Loss of X2.
An increase in the number of hydrogen atoms in a
hydrocarbon is often an indication of a reduction.
319. Oxidation States
Carbon oxidation states are assigned on the basis
of the electronegativity of attached atoms.
For each bond to a more electronegative atom
give +1.
For each bond to a less electronegative atom
(even H) give –1.
For each bond to carbon give 0.
323. Assign oxidation states to all atoms in the
following structure:
C
HO C
H
C
C
O
H
H
H
H
H
H
324. Assign oxidation states to all atoms in the
following structure:
-2 C
+1HO +3 C
H
+1
C-2
-3
C
-2
O
+1H
+1
H
H
H+1
H+1
H+1
+1
-2
325. 1) Identify if the following reactions are
oxidation-reduction reactions.
2) For any that are, identify the atoms that are oxidized
and reduced.
Br I+ NaI + NaBr
+ H2
OH
+K-O
O
+ KMnO4 + MnO2 + H2O
Problem
326. Problem
No, both Br and I are more electronegative than C
-2
+ H2
Yes, the carbon atoms are reduced, the H2 molecule is oxidized
329. REDOX Reactions of Alcohols
Alcohols can undergo either oxidation or reduction
type reactions.
Oxidation is a loss of electrons.
Reduction is a gain of electrons.
330. Oxidation of Alcohols
1⁰ and 2⁰ alcohols are easily oxidized by a variety
of reagents.
The most common reagents used:
Pyridinium chlorochromate (PCC)
Potassium permanganate
Thermal dehydrogenation
331. Oxidation of Alcohols
The most common reagent used for oxidation of 2⁰
alcohols to ketones is chromic acid, H2CrO4.
3⁰ alcohols are resistant to oxidation because they
have no hydrogen atoms attached to the oxygen
bearing carbon (carbinol carbon).
332. Oxidation of 1⁰ Alcohols
1⁰ alcohols are easily oxidized just like 2⁰ alcohols.
The product of oxidation is an aldehyde.
The aldehyde is easily oxidized to an acid as a result
of “over-oxidation”.
A reagent that selectively oxidizes a 1⁰ alcohol to an
aldehyde is pyridinium chlorochromate, PCC.
333. Oxidation of 2⁰ Alcohols
The alcohol and chromic acid produce a chromate
ester, which then reductively eliminates the Cr
species.
The Cr is reduced (VI IV), the alcohol is
oxidized to a ketone.
335. Reduction of Alcohols
Normally an alcohol cannot be directly reduced to
an alkane in one step.
The –OH group is a poor leaving group and
hydride displacement cannot happen.
Instead, the hydroxyl group is easily converted
into other groups that are better leaving groups, and
allow reaction to move forward.
336. Reduction of Alcohols
Commons reagents are tosyl chloride and lithium
aluminum hydride (LiAlH4).
The reaction involves the formation of a tosylate.
The tosylates can undergo either substitution or
elimination reactions.
337. Reduction of Alcohols
The tosylate reduces to cyclohexane very easily
with lithium aluminum hydride.
347. Definitions
Biochemistry is the study of chemical
compounds and reactions which occur in
living organisms.
It overlaps extensively with organic chemistry
since most compounds in living cells contain
carbon.
Biochemistry involves the study of
carbohydrates, lipids, proteins and nucleic
acids, which are the types of molecules
involved in the chemistry of living organisms.
348. Definitions
Hydrogen bonds – ionic and hydrophilic
interactions between a polar or ionic molecules
and water.
350. Macromolecules
All living things contain these organic
molecules: carbohydrates, lipids, proteins,
and nucleic acids.
These organic molecules are often called
macromolecules.
They may be very large, containing thousands
of carbon and hydrogen atoms and bonded to
other smaller molecules.
They are classified as polar, ionic or non-polar
molecules.
351. Macromolecules
Polar and ionic molecules have either full or
partially (dipole) positive or negative charges.
They are attracted to water molecules.
They are said to be hydrophilic because
they interact with (dissolve in) water by
forming hydrogen bonds.
352. Macromolecules
Nonpolar molecules are neutral (NO dipole).
They are NOT attracted to water or polar
molecules.
They are hydrophobic because they DO
NOT dissolve in water or form hydrogen
bonds.
354. Macromolecules
Portions of macromolecules may be
hydrophobic and other portions of the same
molecule may be hydrophilic.
The chains may be branched or form rings.
356. Functional Groups
Some functional groups are polar and others can
ionize.
For example, if the hydrogen ion is removed from
the COOH group, the oxygen will retain both of
the electrons and will have a negative charge.
The hydrogen that is removed leaves behind its
electron and is now a hydrogen ion (proton,
cation, H+).
357. Functional Groups
If polar or ionizing functional groups are attached
to hydrophobic molecules, the molecule may
become hydrophilic due to the functional group.
Some ionizing functional groups are: -CO2H, -OH,
R2-C=O, and -NH2.
370. Organic Reactions Classes:
1. Group Transfer
2. REDOX
3. Eliminations,
Isomerizations,
Rearrangements
4. C-C Bond Making &
Breaking
5. Hydrolysis
371. Group Transfer Reactions
Nucleophilic Substitution
Transfer an electrophile from one nucleophile
to another.
Commonly transferred groups:
1. Acyl
2. Phosphoryl
3. Glycosyl
4. Amino
376. REDOX Reactions
Involve the loss or gain of electrons.
C-H bond cleavage with the loss of electrons.
Use of electron acceptors:
NAD+
FAD+
NADP+
Coenzyme Q
Fe centers in Cytochrome C
377. REDOX Reactions
Electrons are highly reactive and do not exist
on their own in cells.
If oxidation occurs to one molecule in the cell,
reduction must immediately to another
molecule.
386. Elimination Reactions: Dehydration
Enzyme catalyzed reactions.
Two Types of Enzyme-Catalysis:
1. Acid: Protonation of OH group
2. Base: Abstraction of a proton
388. Other Dehydration Reactions
Condensation reactions.
Involved in the assembly of all four types of
macromolecules.
An H atom is removed from a functional
group on one molecule, and an OH group is
removed from another molecule.
Products: a larger molecule + water
396. Rearrangement Reactions
Breaking and reforming C-C bonds to
rearrange carbon atoms in the backbone of a
molecule.
Useful in oxidation of odd number of carbon
atoms fatty acids and several amino acids.
398. C-C bond Breaking & Making
Reactions
Addition of a nucleophilic carbanion to an
electrophilic carbon atom.
Most common electrophilic carbon atoms are
sp2 hybridized carbonyl carbon atoms:
1. Aldehydes
2. Ketones
3. Esters
4. Carbon Dioxide
399. C-C bond Breaking & Making
Reactions
1. Condensation
Aldol
Claisen Ester
Other Condensations Reactions:
o Amino Acids
o Saccharides
o Fatty Acids
2. Decarboxylations
406. Hydrolysis
Involved in the breakdown of macromolecules
into their monomers.
Water is added to break the bonds between
monomers.
H from the water is added to one molecule,
and the OH group is added to the adjacent
monomer.
Covalent bond between monomers breaks to
form two smaller molecules.
416. Carbohydrates
Compounds which provide energy to living
cells.
Made up of carbon, hydrogen and oxygen
with a ratio of two hydrogens for every
oxygen atom.
The name carbohydrate means "watered
carbon" or carbon with attached water
molecules.
Are used directly to supply energy to living
organisms.
417. Carbohydrates
Many carbohydrates have empirical formuli
which would imply about equal numbers of
carbon and water molecules.
The general formula for carbohydrates is
(CH2O)n.
The names of most sugars end with the
letters -ose.
The pentose sugars ribose and deoxyribose
are important in the structure of nucleic acids
like DNA and RNA.
418. Carbohydrates
Three key classification schemes for sugars are:
1. Monosaccharides
2. Disaccharides
3. Polysaccharides
419. Monosaccharides
Simple sugars, having 3 to 7 carbon atoms.
Are linear molecules but in aqueous solution they
form a ring form structure.
In aqueous solution, monosaccharides with five or
more C atoms form cyclic ring structures.
These 6-membered ring compounds are called
pyranoses.
These rings form due to a general reaction that
occurs between alcohols and aldehydes or ketones
to form derivatives called hemiacetals or
hemiketals.
421. Monosaccharides
May form several types of stereoisomers since
they share the same molecular formula.
Four Classes of Stereoisomers:
1. Diastereomers
2. Enantiomers
3. Epimers
4. Anomers
427. Monosaccharides: Anomers
Stereoisomers that differ in the configuration around the
anomeric carbon.
Two types of anomers are: α or β.
In hemiacetals, the anomeric carbon is at position 1.
430. Disaccharides
Glycosides
Formed from two monosaccharides.
The -OH of one monosaccharide condenses with
the intramolecular hemiacetal of another
monosaccharide, forming a glycosidic bond.
Glycosidic bonds can be: α or β.
440. Trehalose
Found in bacteria, yeast, invertebrates,
mushrooms and seaweed.
Glycosidic Linkages:
Protects organisms from extreme temperatures
and drying out.
441. Trehalose
Is used:
As a preservative for foods and to minimize
harsh flavors and odors.
As a moisturizer in cosmetics.
As an natural sweetener for diabetics.
Antioxidant to stabilize proteins and lipids in
neurodegenerative diseases like Alzheimer's
and Huntington's Disease.
To protect organs for transplants.
442. Trehalose
Is:
Involved in the regulation of developmental
and metabolic processes in plants.
The major transport sugar in shrimp, insects
and plants.
The major carbohydrate energy storage
molecule used by insects for flight.
443. Trehalose
In plants, synthesis is carried out by trehalose
phosphate synthase and trehalose
phosphatase:
446. Polyssacharides
Ten or more monosaccharides bonded together
to form long chains.
The chains are typically contain hundreds of
monosaccharaides.
Can have one, two or many different types of
monosaccharides.
1. Homopolysaccharides
2. Heteropolysaccharides
449. Cellulose & Chitin
Are polysaccharides with 1500 glucose rings
chain together.
Function is support and protection.
The monomers of cellulose and chitin are
bonded together in such a way that the
molecule is straight and unbranched.
The molecule remains straight because every
other glucose is twisted to an upside-down
position compared to the two monomers on
each side.
450. Cellulose & Chitin
Humans and most animals do not have the
necessary enzymes needed to break the
linkages of cellulose or chitin.
Some bacteria and some fungi produce
enzymes that digest cellulose.
Some animals have microorganisms in their gut
that digest cellulose for them.
Fiber is cellulose, an important component of
the human diet.
451. Cellulose
Is composed of beta-glucose monomers.
Cellulose fibers are composed of long parallel
chains of these molecules.
The chains are attached to each other by
hydrogen bonds between the hydroxyl groups
of adjacent molecules.
The cell walls of plants are composed of
cellulose.
453. Chitin
The cell walls of fungi and the exoskeleton of
arthropods are composed of chitin.
The glucose monomers of chitin have a side
chain containing nitrogen.
455. Glycogen
Animals and some bacteria store extra
carbohydrates as glycogen.
In animals, glycogen is stored in the liver and
muscle cells.
Between meals, the liver breaks down
glycogen to glucose in order to keep the
concentration of glucoses in the blood stable.
After meals, as glucose levels in the blood
rise, glucose is removed from the blood and
stored as glycogen.
457. Glycogen
Homopolymer of glucose.
Two types of glycosidic linkage:
α–(1, 4) for straight chains
α–(1, 6) for branched chains, occurring every
8-10 residues.
458. Glycogen
Glycogen is a very compact structure that
results from the coiling of the polymer chains.
This compactness allows large amounts of
carbon energy to be stored in a small volume,
with little effect on cellular osmolarity.
459. Starches
Starch and glycogen are composed of 300 –
1000 alpha-glucose units join together.
It is a polysaccharide which plants use to
store energy for later use.
Starches are smaller than cellulose units, and
can be more readily used for energy.
460. Starches
Foods such as potatoes, rice, corn and wheat
contain starch granules which are important energy
sources for humans.
The human digestive process breaks down the
starches into glucose units with the aid of enzymes,
and those glucose molecules can circulate in the
blood stream as an energy source.
461. Starches
Amylopectin is:
1. A form of starch that is very similar to
glycogen.
2. Branched but have less branches than
glycogen.
Amylose is:
A form of starch that is unbranched.
469. Definitions
Peptide - a short chain of amino acids bonded
together.
Oligopeptide- a short chain of at least 2 amino
acids and up to 20 amino acids long.
Polypeptide - a longer chain of many amino
acids, typically 50 or more.
Proteins - consist of one or more polypeptides,
subunits, chains or domains.
470. Proteins
Are the building materials for living cells, appearing in
the structures inside the cell and within the cell
membrane. About 75% of the dry weight of our bodies.
They contain carbon, hydrogen, oxygen, nitrogen,
sulfur and phosphorus.
Protein molecules are often very large and are made
up of hundreds to thousands of amino acid units.
471. Proteins
Functions:
Transport oxygen (Hb)
Build tissue (Muscle)
Copy DNA for cell replication
Support the body as structural proteins
Components of cell membranes (receptors, membrane
transport, antigens)
Control metabolic reactions as regulatory proteins called
enzymes
472. Proteins
Functions:
Hormones
Storage (egg whites of birds, reptiles; seeds)
Protection (antibodies)
Toxins (botulism, diphtheria)
Some proteins are in solution in the blood and other body
fluids.
Others are solids that make up the framework of tissue,
bone and hair.
473. Proteins
Proteins can be characterized as extremely long-
chain polyamides. The amides contain nitrogen,
and nitrogen composes about 16% of the protein
atomic content.
In the cell, the DNA directs or provides the
master blueprint for creating proteins, using
transcription of information to mRNA and then
translation to actually create proteins.
474. Proteins
Proteins are synthesized via condensation of amino
acids under the influence of enzyme catalysts.
The 20 amino acids are combined in different ways to
make up the 100,000 or so different proteins in the
human body.
The amino acid units in a protein molecule are held
together by peptide bonds, and form chains called
polypeptide chains.
476. Proteins
During translation, the protein goes through
several different structural stages:
1. Primary
2. Secondary
3. Tertiary
4. Quaternary
Final structures may undergo post-
translational modifications based on their
determined function.
478. Proteins: Primary Structure
The sequence of amino acids in the
polypeptide chain.
The sequence of the R groups determines
the folding of the protein.
A change of a single amino acid can alter the
function of the protein.
Sickle cell anemia - caused by a change of
one amino acid from glutamine to valine.
480. Proteins: Secondary Structure
Folding and coiling due to H bond formation between
carboxyl and amino groups of non-adjacent amino
acid.
R groups are NOT involved.
This bonding produces two common kinds of shapes
seen in protein molecules- coils, called alpha helices,
and beta sheets.
A single polypeptide may contain many of these
helices and sheets.
482. Proteins: Tertiary Structure
The overall 3-dimensional shape of the
polypeptide chain.
Hydrophobic interactions with water
molecules are important in creating and
stabilizing the structure of proteins.
Hydrophobic (nonpolar) amino acids
aggregate to produce areas of the protein
that are out of contact with water molecules.
483. Proteins: Tertiary Structure
Hydrophilic (polar and ionized) amino acids form
hydrogen bonds with water molecules.
Hydrogen bonds and ionic bonds form between
R groups to help shape the polypeptide chain.
Disulfide bonds are covalent bonds between
sulfur atoms in the R groups of two different
amino acids. These bonds are very important in
maintaining the tertiary structure of some
proteins.
485. Proteins: Tertiary Structure
The shape of a protein is typically described as
being globular or fibrous.
Globular proteins contain both coils and sheets.
Fibrous proteins are elongated molecules in
which either α-helices or β-pleated sheets are
the dominant structures.
487. Proteins: Quaternary Structure
Relationship among multiple polypeptide chains
forming one protein structure.
Contain two or more tertiary structures that
associate to form a single protein.
The overall 3-D structure is due to interactions
between polypeptide chains after synthesis:
1. Hydrophobic & hydrophilic interactions
2. H- bonds
3. Ionic interactions
4. Disulfide bonds
489. Proteins: Enzymes
Some proteins are structural, but some are
control proteins called enzymes.
These enzymes can be used in the synthesis
of proteins, including their own synthesis.
Each protein, including enzymes, is made
according to a pattern of nucleotides along a
segment of the DNA called a "gene".
A single living cell contains thousands of
enzymes.
491. Proteins: Enzymes
Speed up the rate of chemical reactions.
Proteins are able to function as enzymes due
to their shape.
Enzyme molecules are shaped like the
reactants, allowing the reactants to bind closely
with the enzyme.
492. Proteins: Enzymes
Have a small a pocket located on the 3-D
surface of the folded protein.
This is the binding site, where the substrate
binds and chemical reactions take place .
493. The binding site matches the shape of the
substrate molecules.
The enzyme is then able to hold the substrate
molecules in the correct orientation for the
chemical reaction to proceed.
The enzyme itself does not participate in the
reaction and is not changed by the reaction.
Proteins: Enzymes
494. Other Kinds of Proteins
Simple proteins contain only amino acids.
Conjugated proteins contain other kinds of
molecules.
Three key classes of conjugated proteins:
1. Glycoproteins (carbohydrates)
2. Nucleoproteins (nucleic acids)
3. Lipoproteins (lipids)
497. Amino Acids
Are organic compounds.
Each has a carboxyl group and an amino group
attached to the same carbon atom, called the
alpha carbon.
Amino acids have the general form:
498. Amino Acids
There are 20 amino acids which make up the
proteins, distinguished by the R-group.
The structure of the R-group determines the
chemical properties of the amino acid.
Types of chemical properties:
1. Polar Charged
2. Nonpolar
3. Electrically Charged
499. Amino Acids: Polar Uncharged
Are hydrophilic and can form hydrogen
bonds.
1. Serine
2. Threonine
3. Glutamine
4. Asparagine
5. Tyrosine
6. Cysteine
500. Amino Acids: Nonpolar
Are hydrophobic and are usually found in the
center of the protein.
Also found in proteins which are associated
with cell membranes.
1. Glycine
2. Alanine
3. Valine
4. Leucine
5. Isoleucine
6. Methionine
7. Phenylalanine
8. Tryptophan
9. Proline
501. Amino Acids: Electrically Charged
Have electrical charges that can change
depending on the pH.
1. Aspartic Acid
2. Glutamic Acid
3. Lysine
4. Arginine
5. Histidine
502. Amino Acids: Chemical Properties
The simplest amino acid is glycine. It fits in
tight spaces in the 3-D structure of proteins. It
contain hydrogen as an R group.
Cysteine can form covalent disulfide bonds in
3⁰ and 4⁰ structures.
Proline has a unique structure and causes
kinks in the protein chains.
503. Amino Acids
Amino acids are the structural elements from which
proteins are built.
When amino acids bond to each other, it makes an
amide bond.
This bond is formed as a result of a condensation
reaction between the amino group of one amino
acid and the carboxyl group of another.
504. Amino Acids
Amino acids can have either left-handed or
right-handed molecular symmetry.
The most common are left-handed amino acids.
These are the building blocks of proteins.
505. Amino Acids
The human body can synthesize all of the
amino acids necessary to build proteins, except
for the ten called the “essential amino acids”.
An adequate diet must contain these essential
amino acids.
Typically, they are supplied by meat and dairy
products, but if those are not consumed, some
care must be applied to ensuring an adequate
supply.
506. Amino Acids: Non-essential
The 10 amino acids that we can produce are:
alanine, asparagine, aspartic acid, cysteine,
glutamic acid, glutamine, glycine, proline,
serine and tyrosine.
Tyrosine is produced from phenylalanine, so
if the diet is deficient in phenylalanine,
tyrosine will be required as well.
507. Amino Acids: Essential
The essential amino acids are: arginine (required
for growing children), histidine, isoleucine, leucine,
lysine, methionine, phenylalanine, threonine,
tryptophan, and valine.
Humans do not have all the enzymes required for
the biosynthesis of essential amino acids.
508. Amino Acids
The failure to obtain enough of any of the 10
essential amino acids has serious health
implications and can result in degradation of the
body's proteins.
Muscle and other protein structures may be
degraded to obtain the one amino acid that is
needed.
The human body does not store excess amino
acids for later use. The amino acids must be
obtained from food daily.
512. Nucleic Acids
Control the processes of heredity:
Transcription
Translation
Cell Replication
The key nucleic acids are:
DNA (deoxyribonucleic acid)
RNA (ribonucleic acid)
513. Nucleic Acids
Nuclei acid consist of a long chain of units
called nucleotides.
Nucleotides are the basic structural units of
nucleic acids
The nucleotides are made up of a phosphate
group, a pentose sugar, and a nitrogen base.
518. Nucleic Acids
The larger bases adenine and guanine are
purines which differ in the kinds of atoms that
are attached to their double ring.
The other bases (cytosine, uracil, and
thymine) are pyrimidines, which differ in the
atoms attached to their single ring.
The resulting DNA (deoxyribonucleic acid)
contains no uracil, and RNA(ribonucleic acid)
does not contain any thymine.
519. DNA
Stores information regarding the sequence of
amino acids in each of the body’s proteins.
Is the master blueprint for the production of
proteins and cell replication.
In protein synthesis, serves as a pattern for
mRNA synthesis, in a process called
transcription.
mRNA contains all the DNA information to
manufacture a protein, in a process called
translation.
520. DNA Structure
Is a double helix.
The bases may be attached in any order.
This gives the vast number of possibilities of
arrangements, making the genetic code
diverse.
The bases are only attached by hydrogen
bonds to their complementary base. This
arrangement makes possible the separation
of the strands and the replication of the DNA
double helix.
522. DNA Structure
Antiparallel
1. The end of a single strand that has the
phosphate group is called the 5’ end. The
other end is the 3’ end.
2. The two strands of a DNA molecule run in
opposite directions.
524. DNA Structure
Complimentary base pairing
A-T
G-C
Two hydrogen bonds hold adenine to thymine.
Three hydrogen bonds hold cytosine to
guanine.
526. RNA
Is directly involved in the synthesis of proteins
in a process called "translation".
mRNA itself is directed synthesized from DNA
in a process called transcription.
mRNA is the template for the synthesis of all
proteins.
RNA has many forms, but the three most
important are messenger RNA (mRNA),
transfer RNA (tRNA) and ribosomal RNA
(rRNA).
529. mRNA
The anti-sense strand is used as a template to
produce a single strand of mRNA.
The sequence of bases on a segment of DNA called
a gene is copied to a strand of mRNA with the
assistance of RNA polymerase.
The bases in the mRNA strand are complimentary to
the bases in DNA.
530. mRNA
The mRNA contains three-letter codes, called
a codon. It is the code for one amino acid.
The sequence of codes in DNA therefore
determines the sequence of amino acids in
the protein.
531. mRNA
The mRNA has regions called introns and exons.
Introns are not a part of the pattern for the protein
to be synthesized, so those segments are
excised from the mRNA.
Exons are the only segments present before the
mRNA's are released from the nucleus.
These pattern for protein synthesis is then read
and translated into the language of amino acids
for protein synthesis with the help of tRNA.
533. tRNA
Is directly involved in the translation of the sequence
of nucleotides in mRNA with rRNA.
The synthesis of tRNA itself is directed by the DNA
in the cell that provides a pattern for the production
of mRNA by "transcription".
When mRNA reaches rRNA to be translated, tRNA
molecules with all the required amino acids must be
present for the process to proceed.
Since most proteins use all twenty amino acids, all
must be available, attached to appropriate tRNA
molecules.
534. tRNA
Is commonly called a cloverleaf form.
Binds an amino acid at one end opposite to
the anticodon on the other end.
This anticodon will bind to a codon consisting
of three nitrogenous bases which specify an
amino acid according to the genetic code.
535. tRNA
The many types of tRNA have roughly the
same size and shape, varying from about 73
to 93 nucleotides.
Besides the usual bases A, U, G, and C, all
have a significant number of modified bases,
which are formed by modification after the
transcription.
536. tRNA
Letter Code Modified Bases
I Inocine
mI methylinosine
mG methylguanosine
m2G dimethylguanosine
Psi Pseudouridine
D Dihydrouridine
537. tRNA
All tRNAs have sequences of nucleotides that
are complementary to other parts of the
molecule and base-pair to form the five arms
of the tRNA.
Four of the arms are fairly consistent, but the
variable arm can range from 4 to 21
nucleotides.
539. rRNA
Associates with a set of proteins to form
ribosomes.
Physically moves an mRNA molecule and
catalyze the assembly of amino acids into
protein chains.
Binds tRNAs and various accessory
molecules necessary for protein synthesis.
Ribosomes are composed of a large and
small subunit, each of which contains its own
rRNA molecule or molecules.
541. Translation
Translation is the whole process by which the
base sequence of an mRNA is used to bring and
join amino acids in a polypeptide.
The three types of RNA participate in this
essential protein-synthesizing pathway in all
cells.
543. ATP
Adenosine triphosphate is a nucleotide that is
used in energetic reactions for temporary energy
storage.
Energy is stored in the phosphate bonds of ATP.
The cells use the energy stored in ATP by
breaking one of the phosphate bonds, producing
ADP.
549. Lipids
Fats, oils, waxes, and sterols are collectively
known as lipids.
Fats contain only carbon, hydrogen, and
oxygen.
550. Lipids
Are insoluble in water but soluble in nonpolar
solvents.
Are also an important component of cell
membranes.
Used for long-term energy storage.
One gram of fat stores more than twice as
much energy as one gram of carbohydrate.
552. Phospholipids
Contain:
Phosphate group on third -OH group of
glycerol.
Two fatty acids.
Have a polar head, which increases
hydrophilicity.
553. Phospholipids
Arrange themselves into double-layered
membranes with the water-soluble phosphate
ends on the outside and the fatty acid facing
the inside.
Cell membranes are not rigid or stiff since
phospholipids are in constant motion as they
move with the surrounding water molecules
and slide past one another.
557. Steroids: Cholesterol
Cholesterol is a vital component of the cell
membranes and used by cells to synthesize
other steroids.
High cholesterol levels are associated with
heart disease and the formation of plaques
which obstruct blood vessels.
High blood levels of cholesterol bound to a
carrier molecule called a low-density
lipoprotein (LDL) are associated with the
formation of the plaques in arteries.
559. Steroids: Cholesterol
Cholesterol bound to high-density lipoproteins
tends to be metabolized or excreted and is
often referred to as "good cholesterol".
560. Glycerides
Fats and oils are composed of fatty acids and
glycerol.
Fatty acids have a long hydrocarbon chain with
a carboxyl group.
The chains of fatty acids usually contain 16 to 18
carbons.
Fats are nonpolar and therefore they do not
dissolve in water.
561. Glycerides
Fats are generally classified as esters of fatty
acids and glycerol.
There can be one to three ester linkages of fatty
acid chains to the glycerol, leading to the
classification as:
1. Monoglycerides
2. Diglycerides
3. Triglycerides
564. Saturated Fatty Acids
Have no double bonds between the carbons in
its fatty acid chains.
Animal fats are more highly saturated than
vegetable fats.
Highly saturated fats are usually solid at room
temperature.
565. Unsaturated Fatty Acids
Also called “polyunsaturated fat”.
Contain at least one to several double bonds
between the carbons in its fatty acid chains.
Each double bonds produces a "bend" in the
molecule.
Molecules with many bends cannot be packed
as closely together, so these fats are less dense.
566. Unsaturated Fatty Acids
Usually these fatty acid are oils.
Most oils are of vegetable origin.
Triglycerides composed of unsaturated fatty
acids melt at lower temperatures than those with
saturated fatty acids.
567. Unsaturated Fatty Acids
Trans fat is the common name for a type of
unsaturated fat with trans-isomer fatty acids.
Most trans fats consumed today are created
industrially by partial hydrogenation of plant oils.
The goal of partial hydrogenation is to add hydrogen
atoms to cis-unsaturated fats, making them more
saturated.
568. Unsaturated Fatty Acids
These saturated fats have a higher melting point,
which makes them attractive for baking and extends
their shelf-life.
Trans fats are not essential in the diet and have
been linked with rises in levels of "bad" LDL
cholesterol and lowering levels of "good" HDL
cholesterol.
570. Triglycerides
Are made up of a glycerol molecule with three
fatty acid molecules attached to it.
Glycerol contains 3 carbons and 3 hydroxyl
groups.
It reacts with 3 fatty acids to form a triglyceride
or fat molecule.
The naturally occurring fatty acids always have
an even number of carbon atoms.
572. Waxes
Are composed of a long-chain fatty acid
bonded to a long-chain alcohol
They form protective coverings for plants and
animals (plant surface, animal ears).
573. Summary of Lipids
Monomer: Fatty acid
Functional group(s):
Carboxyl
Cholesterol Fused Rings
Ester
Polymers: many – depending on the type of
lipid
Phospholipid, Steroid, Triglycerides, Waxes
