General Chemistry Review
Part I
General Chemistry:
Carbon Atom
1. Atomic Theory
2. Covalent Bonding
3. Chemical Formulas
General Chemistry of Carbon
 Carbon is a non-metal chemical
element.
 A covalent bond is a chemical bond
that involves t...
General Chemistry of Carbon
 Carbon atomic number =
 6 Protons
6 Electrons
6 Neutrons
 Group IV
Four valence electro...
Atomic Theory of Carbon
Ground state electronic configuration of
carbon is:
1s22s22p2
[He] 2s22p2 1S2
2S2
2P2
Nucleus
Electronic Configuration
1
2
3
4
5
6
7
C
Atomic Theory of Carbon
 Carbon atom ground state configuration:
1s2 2s2 2Px
1 2Py
1 2Pz
0
Covalent Bonding
Carbon can covalently bond with other elements:
 Hydrogen
 Oxygen
 Nitrogen
 Sulfur
 Halogens
Covalent Bonding
 Carbon only forms single, double or triple
bonds with other carbon atoms
Covalent Bonding
 Carbon only forms single bonds with hydrogen
and/or halogens atoms
Covalent Bonding
 Carbon may form single bonds with
nitrogen, oxygen and sulfur
Covalent Bonding
 Carbon may also form double bonds with
nitrogen, oxygen and sulfur
Covalent Bonding
 Carbon may also form triple bonds with
nitrogen, sulfur and oxygen
Chemical Formulas
 Three classes are:
1. Molecular
2. Structural
3. Condensed
Molecular Formulas
Show:
 The types of atoms present
 The numbers of each atom present in a
molecule
Molecular Formulas
For example, glucose
 Symbols for carbon, hydrogen, and
oxygen are C, H, and O respectively
 Molecula...
Structural Formulas
Show arrangement of atoms:
 How atoms are bonded,
 In which order they are bonded
 Whether single, ...
Structural Formulas: Examples
Condensed Formulas
Show:
 Groups of atoms in a molecule
 The sequential relationships of these group of
atoms to each ot...
Condensed Formulas: Examples
Condensed Formulas: Examples
Organic Chemistry
Review
Part II
Organic Chemistry:
Carbon Atom
1. Structural
Classifications
2. Atomic Theory
3. Dipoles &
Resonance
4. Isomers
5. Functio...
Organic Chemistry
 The chemistry of compounds which contain
carbon.
 Carbon forms more compounds than any other
element,...
Organic Chemistry Major Concepts
1. Structural Classifications
2. Hybridization
3. Charges of Organic Molecules
4. Dipoles...
Structural Classification of Carbon
Atoms
Three main classifications are:
1. Primary Carbons
2. Secondary Carbons
3. Terti...
Primary Carbons
 Denoted as 1° carbons.
 Also called terminal or end carbon atoms.
 Found at the ends of a straight cha...
Secondary Carbons
 Denoted as 2° carbons.
 Covalently bonded to two other carbon
atoms.
CH3 – CH2 – CH3
Tertiary Carbons
 Denoted as 3° carbons.
 Covalently bonded to three other carbon
atoms.
CH3 – CH – CH3
|
CH3
Quaternary Carbons
 Denoted as 4° carbons.
 Covalently bonded to four other carbon
atoms. CH3
|
CH3 – C – CH3
|
CH3
Definitions
Valence Bond Theory:
 Electrons in a covalent bond reside in a region
in which there is overlap of individual...
Definitions
 Types of valence bond theory overlap:
Definitions
Valence Shell Electron Pair Repulsion (VSEPR)
 Electron pairs arrange themselves around an
atom in order to m...
Definitions
Hybridization:
 Atomic orbitals modify themselves to meet
VESPR geometry and valence bond theory.
 Three typ...
Hybridization: Valence Bond
Theory
Hybridization: VSEPR Geometry
Hybridizations
Hybridizations
 In sp3 hybridization, an electron is promoted
from a 2s orbital into a p orbital.
 The 2s orbital and th...
Hybridizations
 The overlap of each hybrid orbital with a
hydrogen atom results in a sigma bond ( σ
bond).
 Only one σ b...
Hybridizations
sp3 hybridization of methane:
Hybridizations
sp3 hybridization of ethane:
Hybridizations
 In sp2 hybridization, the 2s orbital and two of
the 2p orbitals form three hybrid orbitals (sp2).
 The P...
Hybridizations
sp2 hybridization of ethene:
Hybridizations
sp2 hybridization and bond rotation:
Hybridizations
 In sp hybridization, the 2s orbital and one 2p
orbital form two hybrid orbitals (sp).
 The triple bond i...
Hybridizations
 sp hybridization of ethyne:
No free rotation
Charges in Organic Molecules
Definitions
Dipole:
 The measure of net molecular polarity.
 Formula: the magnitude of the charge Q times
the distance r...
Definitions
Resonance:
 Part of the Valence Bond Theory
 Describes the delocalization of electrons within
molecules.
 U...
Definitions
Resonance Hybrid:
 The net sum of valid resonance structures.
 Several structures represent the
overall delo...
Definitions
Hyperconjugation:
 The interaction of the electrons in a sigma
bond (usually C–H or C–C) with an adjacent
emp...
Carbon Atom Dipoles
 Carbon- Halogen Bonds
Carbon Atom Dipoles
 C-O, C-S and C-N Covalent Bonds:
δ+
δ+ δ-
δ-
Dipolar Resonance
Dipolar Resonance
Dipolar Resonance
Dipolar Resonance
Hyperconjugation
 A.K.A "no bond resonance".
 The delocalization of σ-electrons or lone pair of
electrons into adjacent ...
Hyperconjugation
 Other hydrogens on the methyl group also
participate due to free rotation of the C-C
bond.
 There is N...
Hyperconjugation
Hyperconjugation: Examples
Hyperconjugation: Examples
Hyperconjugation: Examples
Isomers
Compounds that have:
 The same molecular formula.
 Similar or different types of structural
formulas.
 Differen...
Isomers:
Two main classes are:
1. Structural or constitutional
2. Stereoisomers
Structural Isomers
 Also known as constitutional isomers
Stereoisomers
a. Configurational
 Geometric or Diastereomers
 Optical or Enantiomers
b. Conformational or Rotamers
Diastereomers
Geometric Isomers: Examples
Geometric Isomers: Examples
Optical Isomers
Definitions
 Chiral Molecules - when a molecule and its
mirror image cannot completely overlap.
They are non-superimposab...
Definitions
 Levorotatory (S, -) - a compound whose
solution rotates the plane of polarized light to
the left (when looki...
Determining L (S, -) or D (R, +)
configuration
1. Rank the four substituents according to the
atomic numbers of the atoms ...
Determining L (S, -) or D (R, +)
configuration
2. If two substituents have the same ranking:
 Look at the next atoms in t...
Determining L (S) or D (R)
configuration
 If it is still the same atom for both
substituents, continue down the list unti...
Determining L (S, -) or D (R, +)
configuration
4. Determine whether the ranking defines a
clockwise or counterclockwise di...
Determining L (S, -) or D (R, +)
configuration
L (S, -) Configuration
 A common optical isomer for amino acids in
Biochemistry
Optical Isomers: Examples
Summary of Isomers
Summary of Isomers
Conformational Isomers
 Also known as Rotamers
 Stereoisomers that can be interconverted
by the rotation of atoms about ...
Conformational Isomers
Rotamers: Examples
Functional Groups
1. Hydrocarbons
2. Derivatives of Hydrocarbons
Functional Groups
 Organic molecules may have functional
groups attached.
 A functional group is a group of atoms of a
p...
Functional Groups
 Organic chemists use the letter "R" to indicate
an organic molecule.
 The "R" can be any organic mole...
Hydrocarbons
 The simplest organic compounds.
 Contain only carbon and hydrogen,
 Can be straight-chain, branched chain...
Hydrocarbons
 Two classifications:
1. Aliphatics
2. Aromatics
 Aliphatic - hydrocarbons which do not contain an
aromatic...
Hydrocarbons
 Aromatic - Aromatic hydrocarbons contain a set
of covalently bound atoms with specific
characteristics:
 A...
Aliphatics
1. Alkanes
2. Cycloalkanes
3. Alkenes
4. Alkynes
Alkanes
IUPAC ending is …ane
Alkanes
 Saturated hydrocarbons.
 Are hydrocarbons which contain only single
bonds.
 All alkanes are insoluble in water...
Alkanes
 Contain single covalent bonds.
 Have the same structural formula:
Cn H2n+2
 All carbons have single bonds ther...
Alkanes
 The names of alkanes start with the name of the
alkane but end with the suffix –ane.
Alkanes
 Each atom in an alkane uses all its 4 valence
electrons in forming single bonds with other
atoms.
 Alkyl groups...
Alkanes
 Alkyl groups form the branches of straight chain
hydrocarbons.
 Can have more than one alkyl group for hydrogen...
Alkanes
Alkanes
 Other functional groups can be used as
substituents.
 More than one substituent requires a prefix.
 Any hydrog...
Alkanes
 Any carbon can be substituted by:
 Carboxylic Acids
 Esters
 Amides
 Thioesters
 Addition of other atoms:
...
Cycloalkanes
the prefix cyclo- and the ending
…ane
Cycloalkanes
 Saturated hydrocarbons.
 Form one or more rings fused together.
 A single carbon in a ring may have two h...
Cycloalkanes
 All have the same general formula:
CnH2n
 The carbon atoms in cycloalkanes are sp3
hybridized.
 Each atom...
Cycloalkanes
 Can have more than one alkyl group to make
straight chains.
 For multiple alkyl groups of the same type, u...
Cycloalkanes
 Many functional groups can be used as substituents.
 More than one substituent requires a prefix.
 Any hy...
Cycloalkanes
 The names follow those of the alkanes with the
prefix cyclo- .
Cycloalkanes
Cycloalkanes
Cycloalkanes
Alkenes
IUPAC ending is …ene
Alkenes
 Also known as olefins.
 Are unsaturated hydrocarbons and are generally
very reactive.
 Are insoluble in water,...
Alkenes
 Are hydrocarbons which contain one or more
double bonds.
 Double bonds are:
 Have the same structural formula:...
Alkenes
 The main centers are the carbons of the
double bond.
 The geometry of each carbon in the center is
trigonal pla...
Alkenes
All the alkenes with 4 or more carbon atoms in
them show structural isomerism.
Alkenes
 The carbon-carbon double bond does not
rotate.
 Substituents groups on the molecule are
locked on either one si...
Alkenes
 The names of alkenes start with the name of the
alkane but end with the suffix –ene.
 For alkenes above propene...
Alkenes
 Can have more than one alkyl group to form
branches.
 For more than one alkyl group, use prefixes.
Alkenes
 Many functional groups can be used as substituents.
 More than one substituent requires a prefix.
 Any hydroge...
Alkenes
 For multiple double bonds, use the following prefixes:
 di-
 tri-
 tetra-
 penta-
 hexa-
Alkenes
 A diene is a hydrocarbon chain that has two
double bonds that may or may not be adjacent
to each other.
Alkenes: Examples
Alkenes: Examples
Alkynes
IUPAC ending is …yne
Alkynes
 Also known as acetylenes.
 Are unsaturated hydrocarbons and are
generally very reactive.
 Are insoluble in wat...
Alkynes
 Are hydrocarbons which contain one or more
triple bonds.
 Triple bonds are:
 Have the same structural formula:...
Alkynes
 The main centers are the carbons of the triple
bond.
 The geometry of the center is linear.
 This portion of t...
Alkynes
All the alkynes with 4 or more carbon atoms in
them show structural isomerism.
Alkynes
 The names of alkynes start with the name of the
alkane but end with the suffix –yne.
 For alkynes above propyne...
Alkynes
 Many functional groups can be used as substituents.
 Only one substituent is allowed.
 Any hydrogen or carbon ...
Alkynes
 For multiple double bonds, use the following prefixes:
 di-
 tri-
 tetra-
 penta-
 hexa-
Alkynes: Examples
Aromatics
Structures that meet Huckel’s Rule
Aromatics
 Coplanar structures, with all the contributing atoms in the
same plane.
 Are arranged in one or more rings.
...
Aromatics
 The number of π delocalized electrons must
follow Hückel's Rule.
number of π electrons = 4n + 2
where n = 0, 1...
Aromatics
 The most common examples of aromatic
hydrocarbons are organic compounds, which
contain one or more benzene rin...
Aromatics
 Benzene follows Huckel’s Rule:
Aromatics
 Each atom in benzene uses all its 4 valence
electrons in forming covalent bonds with other
atoms.
 Other func...
Aromatics
 Any hydrogen or carbon atom can be substituted
by:
Aromatics
When two substituents are attached to the benzene
ring:
 Ortho, meta, or para can be used to indicate
where the...
Aromatics
Aromatics: Examples
o-dihydroxybenzene,
m-dihydroxybenzene,
p-dihydroxybenzene
Aromatics: Examples
Aromatics: Examples
Aromatics: Examples
Aromatics: Examples
Summary of Hydrocarbon
Summary of Hydrocarbon
Summary of Hydrocarbon
Derivatives of Hydrocarbons
Are formed when there is a substitution of
a functional group at one or more carbon
atoms.
Derivatives of Hydrocarbons
1. Prefixes
2. Haloalkanes
3. Alcohols
4. Ethers
5. Amines
6. Nitriles
7. Thiols
8. Thioethers...
Prefixes
For multiple substituents of the same
type, use the following prefixes:
 di-
 tri-
 tetra-
 penta-
 hexa-
Haloalkanes
 The alkyl halides have the general form
where the R in the general form is typically an alkyl
group with a h...
Haloalkanes
 Classify according to the number of carbons
bonded directly to the alkyl halide.
Haloalkanes
 There can be multiple substitutions of halogens
for hydrogens, and also variations where
alkenes, alkynes or...
C – O Bonds Organic
Compounds
1. Alcohols
2. Ethers
Alcohols
IUPAC ending is …ol
Alcohols
 Are organic compounds containing a hydroxyl
group, -OH, substituted for a hydrogen atom.
 The center of the al...
Alcohols
 Are organic compounds containing a hydroxyl
group, -OH, substituted for a hydrogen atom.
 The names of alcohol...
Alcohols
 Are classified according to the number of
carbon atoms attached directly to the carbon
containing the hydroxyl ...
Ethers
… “oxy”….IUPAC ending ….ane
Ethers
 Are compounds with the general formula:
 The center of the ether functional group is the
oxygen.
 Have two lone...
Ethers: Examples
Ethers: Examples
Summary of Alcohols & Ethers
C - S Bonds Organic
Compounds
1. Thiols
2. Thioethers
3. Disulfides
Thiols
IUPAC ending…thiols
Thiols
 Are sometimes called sulfides.
 Are organic compounds containing a sulfhydryl
group, -SH, substituted for a hydr...
Thiols
 The center of the thiol functional group is the
sulfur.
 Have two lone pairs of electrons on the sulfur.
 This ...
Thiols
 Classified according to the number of carbon
atoms bonded directly to the carbon containing
the thiol group.
 Th...
Thiols
 Can have more than one sulfhydryl group, and
also variations where alkenes, alkynes or
aromatics are involved.
 ...
Thiols: Examples
Thioethers
IUPAC ending….sulfide
Thioethers
 Are sometimes called sulfides.
 Are compounds with the general formula:
 The center of the thioether functi...
Thioethers
 Have two lone pairs of electrons on the sulfur.
 This forces the molecular geometry on the
thioether sulfur ...
Thioethers: Examples
Thioethers: Examples
Disulfides
IUPAC ending…..disulfide
Disulfides
 Another class of sulfur containing molecules
that have important biological implications.
 Have the generic ...
Disulfides
 The center of a disulfide functional group has two
sulfur atoms single bonded to each other and to
two differ...
Disulfides
 Are named by naming the R groups attached
to the sulfur atoms followed by the suffix -
disulfide.
Dimethyldis...
Disulfides: Examples
Disulfides: Examples
Disulfides: Examples
Carbon and Nitrogen
Organic Compounds
1. Amines
2. Nitriles
Amines
1. IUPAC ending ….amine
2. Prefix is …amino
Amines
 Are organic compounds that contain nitrogen
and are basic.
 The general form of an amine is:
 R represents an a...
Amines
 The center of the amine functional group is the
nitrogen.
 Have one lone pair of electrons on the nitrogen in
ad...
Amines
 The common names for simple aliphatic
amines consist of the alkyl group followed by
the suffix -amine.
 The amin...
Amines
 Are classified according to the number of
carbon atoms bonded directly to the nitrogen
atom.
Amines: Examples
Amines: Examples
Nitriles
1. IUPAC ending is …..nitrile
2. Prefix is …..cyano
Nitriles
 Are organic compounds that have a
functional group.
 Have one lone pair of electrons on the nitrogen
in additi...
Nitriles
 The common names for simple nitriles consist of
the alkane/alkyl followed by the suffix -nitrile.
 The cyano g...
Nitriles: Examples
Carbonyl Organic
Compounds
1. Aldehydes
2. Ketones
Aldehydes (CHO)
IUPAC ending is …al
Aldehydes
 Are compounds containing a carbonyl group with
a hydrogen attached at end and an organic
group of carbons at t...
Aldehydes
 Have two lone pairs of electrons on the oxygen.
 With three atoms attached to this carbon, the
molecular geom...
Aldehydes
 IUPAC name includes the prefix from the alkyl
groups and the suffix –al.
Aldehydes
 IUPAC name for cyclic aldehydes includes the
prefix cyclo and the suffix carbaldehyde.
Aldehydes: Examples
Ketones
IUPAC ending is …one
Ketones
 Are compounds containing a carbonyl group
with two hydrocarbon groups attached to it.
 The center of the ketone...
Ketones
 Have two lone pairs of electrons on the oxygen.
 With three atoms attached to this carbon, the
molecular geomet...
Ketones
 IUPAC name includes the prefix from the alkyl
group and the suffix -one.
 For more than one ketone group, use a...
Ketones: Examples
Summary of Aldehydes & Ketones
Carboxyl Derivatives
1. Carboxylic Acids
2. Esters
3. Amides
4. Thioesters
Carboxyl Derivatives
 Are derivatives of carboxylic acids.
 Can be distinguished from aldehydes and
ketones by the prese...
Carboxyl Derivatives
 Have two sides:
1. The carbonyl group attach to an alkyl
group. This is called an acyl group.
2. Th...
Carboxylic Acids
IUPAC ending is …oic acid
Carboxylic Acids
 Are important intermediate products for the
production of esters and amides.
 Are hydrocarbon derivati...
Carboxylic Acids
 Each oxygen atom has a pair of lone electrons.
 With three atoms attached to this carbon, the
molecula...
Carboxylic Acids
 In the IUPAC system, the –e ending in alkane
is removed from the name of the parent chain
and is replac...
Carboxylic Acids
 Cyclic carboxylic acids that are saturated are
called cycloalkane carboxylic acids.
 Dicarboxylic acid...
Carboxylic Acids
Carboxylic Acids: Examples
Carboxylic Acids: Examples
Esters
IUPAC ending …oate
Esters
 Are compounds with the general formula:
 The center of the ester functional group is the
carbon double bonded to...
Esters
 Each oxygen atom has a pair of lone electrons.
 With three atoms attached to this carbon, the
molecular geometry...
Esters
 Complex esters are more frequently named
using the systematic IUPAC name, based on the
name for the alkyl group f...
Esters: Examples
Esters: Examples
Esters: Examples
Amides
IUPAC ending is …amide
Amides
 Also known as an acid amide.
 Are formed when carboxylic acids react with
amines.
 Are nitrogen-containing orga...
Amides
 The center of the amide functional group is the
carbon double bonded to oxygen and single
bonded to nitrogen.
 C...
Amides
 The oxygen atom has two lone pair of electrons.
 The nitrogen atom has one pair of lone electrons.
 With three ...
Amides
 The molecular geometry centered on the
nitrogen is bent and also flat as an extension of
the trigonal planar geom...
Amides
In the IUPAC system:
 For primary amides, the –e is removed from the
alkane name and the suffix -amide is added.
Amides
 For 2⁰ and 3⁰ amides, alkyl groups attached to
the nitrogen are named as substituents.
 The letter N is used to ...
Amides
Amides
Amides: Example
Amides: Example
Amides: Example
Amides: Example
Thioesters
1. IUPAC ending….-thioate or -
carbothioate
2. Prefix….thio & ending….-ate or -
carboxylate
Thioesters
 Are the product of esterification between a
carboxylic acid and a thiol.
 Are compounds with the functional ...
Thioesters
 The oxygen and sulfur atoms, each, have two
sets of lone pairs electrons.
 With three atoms attached to this...
Thioesters
 The molecular geometry centered on the
sulfur is bent and also flat as an extension of
the trigonal planar ge...
Thioesters
 In the IUPAC system, the name consist of the alkyl
group followed by the alkane with the suffix –thioate
or –...
Thioesters
 For common names, the name consist of the alkyl
group followed by the prefix “thio” before the
common name wi...
Thioesters: Examples
Thioesters: Examples
Summary of Carboxyl Derivatives
Summary of Functional Groups
Organic Reactions
1. Chemical Bonds
2. Non-polar Reactions
3. Polar Reactions
4. Classifications
Chemical Bonds in
Reactions
1. Bond Breaking
2. Bond Forming
Chemical Bond Breaking
 Polar reactions involve heterolytic bond cleavage
 Radical reactions involve homolytic bond clea...
Chemical Bond Making
Non-polar Reactions
Free Radicals Formation
Free Radicals
 Are neutral and electron-deficient.
 They do not meet the octet rule.
 Examples:
Free Radicals
 Stability of free radicals:
Free Radicals
 React to complete its valence shell.
General Form:
Non-polar Reactions
Non-polar Reactions
 Termination step:
Polar Reactions
1. Nucleophiles
2. Electrophiles
 Lewis acid-base definition: transfer of electron
pair from a base to an acid
Definitions
Nucleophiles
 Are attracted to a positively charged cations or
atoms with partially positive dipole.
 Share or transfer ...
Nucleophiles
 Can be negatively charged anions, neutral
ions, molecules with a lone pair of electrons or
at least one π b...
Nucleophiles: Examples
Nucleophiles: Examples
Electrophiles
 Atoms that are positively charged, carry a
partially positive dipole, or does not have an
octet of electro...
Electrophiles
 H+
 NO+
 HCl
 Alkyl halides
 Acyl halides
 Cl2
 Br2
 Organic peracids
 Carbenes
 Radicals
 BH3
...
Polar Reactions
 Nucleophiles – transfers electrons to an
electrophilic atom
 Electrophiles - accept electrons from a
nu...
Polar Reactions
General Form:
 Products never exceed the octet rule.
Polar Reactions
 The nucleophilic site can be neutral or
negatively charged.
Polar Reactions
 The electrophilic site can be neutral or
positively charged.
Organic Reactions
1. Addition
2. Elimination
3. Substitution
4. Rearrangement
5. Condensation
6. Esterification
7. Hydroly...
Addition Reactions
 The components of an organic molecule A–B
are added to the carbon atoms in a C=C
bonds.
 Involve the...
Addition Reactions
 Symmetrical alkenes produce one product.
 Unsymmetrical alkenes produce racemic mixtures.
Addition Reactions
 Alcohols are often produced by addition
reactions.
 Initial attack by the π bond of an alkene on a
H...
Addition Reactions
Addition Reactions
 With symmetrical alkenes, addition of
hydroxyl group produces one type of alcohol.
Addition Reactions
 With unsymmetrical alkenes, addition of
hydroxyl group produces different types of
alcohols depending...
Addition Reactions
Formation of hemiketals & hemiacetals:
 Reactions between an acohol and either a
ketone or aldehyde.
Elimination Reactions
 The removal or “elimination” of adjacent
atoms from a molecule.
 Two σ bonds are lost, replaced b...
Elimination Reactions
 The required range of reaction temperature
decreases with increasing substitution of the
hydroxyl ...
Elimination Reactions
 If the reaction is not sufficiently heated, the
alcohols do not produce alkenes, but they
react wi...
Elimination Reactions
General form: A → B + C
Elimination Reactions
 1⁰ Alcohols
Elimination Reactions
 2⁰ Alcohols
Elimination Reactions
 In dehydration reactions of alcohols, hydride
or alkyl shifts relocate the carbocation to a
more s...
Elimination Reactions
 Hydride or alkyl shifts are the result of
hyperconjugation. The interaction between the
filled orb...
Elimination Reactions
 Hydride shift:
Elimination Reactions
 Alkyl shift:
Substitution Reactions
 Nucleophilic substitution reactions.
 An electronegative atom is replaced by
another more electr...
Substitution Reactions
General form: A + B → C + D
 Non-polar reactions:
Substitution Reactions
 Polar reactions:
Rearrangement Reactions
 Are isomerisation reactions.
 An organic molecule changes structure.
 Constitutional change in...
Rearrangement Reactions
Condensation Reactions
 Two molecules combine to form one single
molecule with the loss of a small molecule.
 When this ...
Condensation Reactions
 When two separate molecules react, their
condensation is termed intermolecular.
 The condensatio...
Condensation Reactions
 When a condensation is performed between
different parts of the same molecule, the
reaction is te...
Condensation Reactions
Esterification Reactions
 Esters are obtained by refluxing a carboxylic
acid with an alcohol in the presence of an
acid c...
Esterification Reactions
 A carboxylic acid and an alcohol react
together under acidic conditions to form
an ester and lo...
Esterification Reactions
 Esters can also be made from other
carboxylic acid derivatives, especially acyl
halides and anh...
Esterification Reactions
Pericyclic esters
Hydrolysis
 A reaction in which water is a reactant, and
becomes part of the reaction product.
 A number of organic comp...
Hydrolysis
 Reactions require a catalyst.
 The catalyst is either an acid (H+ ions) or alkali
(OH- ions).
 Hydrolysis m...
Hydrolysis
 In the overall reaction, a bond in an organic
molecule is broken.
 A water molecule also breaks into ions.
...
Hydrolysis of an Ester:
 The addition of a strong acid, such as dilute
hydrochloric acid, is required to free the carboxy...
Hydrolysis of Amides & Nitriles:
 Amide acid catalyzed - HCl
 Nitrile acid catalyzed – HCl or H2SO4
Hydrolysis of Halogenalkanes:
Hydrolysis of Aromatics
Summary of Hydrolysis Reactions
1. The hydrolysis of a primary amide:
RCONH2 + H2O → RCOOH + NH3
2. The hydrolysis of a se...
Summary of Hydrolysis Reactions
3. The hydrolysis of an ester:
RCOOR' + H2O → RCOOH + R'OH
4. The hydrolysis of a halogeno...
Reduction & Oxidation
(REDOX) Reactions
1. Oxidation States
2. Oxidations
3. Reductions
Definitions
Oxidation-Reduction reactions:
 Involve changes in oxidation state at one or more
atoms.
 Can often be ident...
Definitions
 Oxidation:
 The oxidation state increases
 Loss of H2
 Loss of a C-H bond
 Addition of O or O2
 Formati...
Definitions
 Reduction:
 The oxidation state decreases
 Addition of H2 or H-
 Formation of a C-H bond
 Loss of O or O...
Oxidation States
 Carbon oxidation states are assigned on the basis
of the electronegativity of attached atoms.
 For eac...
Oxidation States
Oxidation States
 In nitrogen-containing compounds, the
number of carbon–nitrogen bonds changes
with the oxidation state ...
Oxidation States
Assign oxidation states to all atoms in the
following structure:
C
HO C
H
C
C
O
H
H
H
H
H
H
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) Identify if the following reactions are
oxidation-reduction reactions.
2) For any that are, identify the atoms that are...
Problem
No, both Br and I are more electronegative than C
-2
+ H2
Yes, the carbon atoms are reduced, the H2 molecule is ox...
Problem
Summary of Oxidation States
REDOX Reactions of Alcohols
 Alcohols can undergo either oxidation or reduction
type reactions.
 Oxidation is a loss of ...
Oxidation of Alcohols
 1⁰ and 2⁰ alcohols are easily oxidized by a variety
of reagents.
 The most common reagents used:
...
Oxidation of Alcohols
 The most common reagent used for oxidation of 2⁰
alcohols to ketones is chromic acid, H2CrO4.
 3⁰...
Oxidation of 1⁰ Alcohols
 1⁰ alcohols are easily oxidized just like 2⁰ alcohols.
 The product of oxidation is an aldehyd...
Oxidation of 2⁰ Alcohols
 The alcohol and chromic acid produce a chromate
ester, which then reductively eliminates the Cr...
Summary of Oxidation of Alcohols
Reduction of Alcohols
 Normally an alcohol cannot be directly reduced to
an alkane in one step.
 The –OH group is a poor...
Reduction of Alcohols
 Commons reagents are tosyl chloride and lithium
aluminum hydride (LiAlH4).
 The reaction involves...
Reduction of Alcohols
 The tosylate reduces to cyclohexane very easily
with lithium aluminum hydride.
Reduction of Carboxylic Acids
 Carboxylic acids are reduced to 1⁰ alcohols.
Reduction of Esters
 Esters are reduced to 1⁰ alcohols.
Reduction of Amides
 Amides are reduced to 1⁰, 2⁰, or 3⁰ amines.
Reduction of Aldehydes
 Aldehydes and ketones are reduced to 1⁰ and
2⁰ alcohols respectively.
Summary REDOX Reactions
Combustion Reactions
 The reaction of an organic molecule with
oxygen to form carbon dioxide, heat/energy
and water.
Combustion Reactions
 Alkanes:
 Alkenes:
 Alcohols
Introduction to
Biochemistry
Part III – Foundations of Organic
Chemistry in Biochemistry
Biochemistry
1. Macromolecules
2. Functional
Groups
3. Organic
Reactions
4. Carbohydrates
Definitions
 Biochemistry is the study of chemical
compounds and reactions which occur in
living organisms.
 It overlaps...
Definitions
 Hydrogen bonds – ionic and hydrophilic
interactions between a polar or ionic molecules
and water.
Definitions
 Hydrophobic interactions - tendency of
nonpolar substances to aggregate in aqueous
solution and exclude wate...
Macromolecules
 All living things contain these organic
molecules: carbohydrates, lipids, proteins,
and nucleic acids.
 ...
Macromolecules
 Polar and ionic molecules have either full or
partially (dipole) positive or negative charges.
 They are...
Macromolecules
 Nonpolar molecules are neutral (NO dipole).
 They are NOT attracted to water or polar
molecules.
 They ...
Macromolecules
 Nonpolar molecules are hydrophobic.
 Polar and ionic molecules are hydrophilic.
Macromolecules
 Portions of macromolecules may be
hydrophobic and other portions of the same
molecule may be hydrophilic....
Functional Groups in
Biochemistry
1. Hydrocarbons
2. Aromatics
3. Common Functional Groups
Functional Groups
 Some functional groups are polar and others can
ionize.
 For example, if the hydrogen ion is removed ...
Functional Groups
 If polar or ionizing functional groups are attached
to hydrophobic molecules, the molecule may
become ...
Hydrocarbons
Cycloalkanes
Cycloalkanes
Cycloalkanes
Aromatic Compounds
Aromatic Compounds
Aromatic Compounds
Aromatic Compounds
Common Functional Groups
Common Functional Groups
Summary of Functional Groups
Summary of Functional Groups
 Important bond linkages in Biochemistry:
Organic Reactions Classes:
1. Group Transfer
2. REDOX
3. Eliminations,
Isomerizations,
Rearrangements
4. C-C Bond Making &...
Group Transfer Reactions
 Nucleophilic Substitution
 Transfer an electrophile from one nucleophile
to another.
 Commonl...
Group Transfer Reactions: Acyl Group
Acylation Reactions
Group Transfer Reactions: Phosphoryl
Group
Phsophorylation Reaction
Group Transfer Reactions: Glycosyl
Group
Glycosylation Reactions
Group Transfer Reactions: Amino
Group
Transamination Reactions
REDOX Reactions
 Involve the loss or gain of electrons.
 C-H bond cleavage with the loss of electrons.
 Use of electron...
REDOX Reactions
 Electrons are highly reactive and do not exist
on their own in cells.
 If oxidation occurs to one molec...
REDOX Reactions
REDOX Reactions
REDOX Reactions
REDOX Reactions
Elimination Reactions
 Formation of alkenes
 Products are:
 Trans (anti) – Major
 Cis (syn)
 Elimination of:
 Water
...
Elimination Reactions
 Types of Mechanisms:
1. Concerted
2. Carbocation Formation: C-O bond breakage
3. Carbanion Formati...
Elimination Reactions: Concerted
& Carbocation
Elimination Reactions: Carbanion
Elimination Reactions: Dehydration
 Enzyme catalyzed reactions.
 Two Types of Enzyme-Catalysis:
1. Acid: Protonation of ...
Elimination Reactions: Dehydradation
Other Dehydration Reactions
 Condensation reactions.
 Involved in the assembly of all four types of
macromolecules.
 An...
Condensation of Amino Acids
Condensation of Saccharides
Condensation of Fatty Acids
Elimination Reactions: Deaminations
Elimination Reactions: Deaminations
Isomerization Reactions
 Relocation of a = bond.
 Intramolecular shift of a proton.
 Most common are base catalyzed rea...
Isomerization Reactions
Rearrangement Reactions
 Breaking and reforming C-C bonds to
rearrange carbon atoms in the backbone of a
molecule.
 Usef...
Rearrangement Reactions
C-C bond Breaking & Making
Reactions
 Addition of a nucleophilic carbanion to an
electrophilic carbon atom.
 Most common...
C-C bond Breaking & Making
Reactions
1. Condensation
 Aldol
 Claisen Ester
 Other Condensations Reactions:
o Amino Acid...
Condensation Reactions: Aldol
Condensation Reactions: Claisen
Esters
Decarboxylation Reactions
 Removes a carboxyl group
 Releases carbon dioxide.
Decarboxylation Reactions
Decarboxylation Reactions: Citric
Cycle
Decarboxylation Reactions:
Precursors of the Citric Cycle
Hydrolysis
 Involved in the breakdown of macromolecules
into their monomers.
 Water is added to break the bonds between
...
Hydrolysis of Proteins
Hydrolysis of Polysaccharides
Hydrolysis of Fats
Synthesis of Common Functional Groups
Synthesis of Common Functional Groups
Biochemistry: The
Chemistry of the Human
Body
Part IV - Macromolecules
Macromolecules
 Many of the common macromolecules are
synthesized from monomers.
Carbohydrates
1. Monosaccharides
2. Disaccharides
3. Polysaccharides
Carbohydrates
 Compounds which provide energy to living
cells.
 Made up of carbon, hydrogen and oxygen
with a ratio of t...
Carbohydrates
 Many carbohydrates have empirical formuli
which would imply about equal numbers of
carbon and water molecu...
Carbohydrates
 Three key classification schemes for sugars are:
1. Monosaccharides
2. Disaccharides
3. Polysaccharides
Monosaccharides
 Simple sugars, having 3 to 7 carbon atoms.
 Are linear molecules but in aqueous solution they
form a ri...
Monosaccharides
Monosaccharides
 May form several types of stereoisomers since
they share the same molecular formula.
 Four Classes of S...
Monosaccharides: Isomers
Monosaccharides: Diastereomers
 Stereoisomers that are not mirror images of each
other.
 Diastereomers for the molecular...
Monosaccharides: Diastereomers
 Diastereomers for the molecular formula C6H12O6:
Monosaccharides: Enantiomers
 Stereoisomers that are mirror images of each other.
 Two types: D or L
Monosaccharides: Epimers
 Two diastereomers that differ around one chiral
center.
Monosaccharides: Anomers
 Stereoisomers that differ in the configuration around the
anomeric carbon.
 Two types of anome...
Monosaccharides: Anomers
Monosaccharides: Anomers
 In hemiketals, the anomeric carbon is at position 2.
Disaccharides
 Glycosides
 Formed from two monosaccharides.
 The -OH of one monosaccharide condenses with
the intramole...
Disaccharides
Disaccharides
 Common disaccharides are:
1. Sucrose
2. Lactose
3. Maltose
4. Trehalose
Disaccharides
Sucrose
 Prevalent in sugar cane and sugar beets
Sucrose
Lactose
 Found exclusively in milk.
Lactose
Maltose
 Major degradation product of starch.
Maltose
Trehalose
 Found in bacteria, yeast, invertebrates,
mushrooms and seaweed.
 Glycosidic Linkages:
 Protects organisms fr...
Trehalose
Is used:
 As a preservative for foods and to minimize
harsh flavors and odors.
 As a moisturizer in cosmetics....
Trehalose
Is:
 Involved in the regulation of developmental
and metabolic processes in plants.
 The major transport sugar...
Trehalose
 In plants, synthesis is carried out by trehalose
phosphate synthase and trehalose
phosphatase:
Trehalose
Trehalose
 Degradation:
Trehalase
Polyssacharides
 Ten or more monosaccharides bonded together
to form long chains.
 The chains are typically contain hund...
Polyssacharides
Polyssacharides
 Are classified as:
1. Cellulose
2. Chitin
3. Glycogen
4. Starches
Cellulose & Chitin
 Are polysaccharides with 1500 glucose rings
chain together.
 Function is support and protection.
 T...
Cellulose & Chitin
 Humans and most animals do not have the
necessary enzymes needed to break the
linkages of cellulose o...
Cellulose
 Is composed of beta-glucose monomers.
 Cellulose fibers are composed of long parallel
chains of these molecul...
Cellulose
Chitin
 The cell walls of fungi and the exoskeleton of
arthropods are composed of chitin.
 The glucose monomers of chiti...
Chitin
Glycogen
 Animals and some bacteria store extra
carbohydrates as glycogen.
 In animals, glycogen is stored in the liver ...
Glycogen
Glycogen
 Homopolymer of glucose.
 Two types of glycosidic linkage:
 α–(1, 4) for straight chains
 α–(1, 6) for branch...
Glycogen
 Glycogen is a very compact structure that
results from the coiling of the polymer chains.
 This compactness al...
Starches
 Starch and glycogen are composed of 300 –
1000 alpha-glucose units join together.
 It is a polysaccharide whic...
Starches
 Foods such as potatoes, rice, corn and wheat
contain starch granules which are important energy
sources for hum...
Starches
 Amylopectin is:
1. A form of starch that is very similar to
glycogen.
2. Branched but have less branches than
g...
Starches
Starches & Glycogen
 The bond orientation between the glucose
subunits of starch and glycogen allows the
polymers to form...
Summary of Carbohydrates
 CHO
 Monosaccharides:
simple sugars
 Functional group(s):
 Carboxyl
 Hydroxyl
 Disaccharid...
Summary of Carbohydrates
Summary of Carbohydrates
Summary of Carbohydrates
Proteins
Definitions
 Peptide - a short chain of amino acids bonded
together.
 Oligopeptide- a short chain of at least 2 amino
ac...
Proteins
 Are the building materials for living cells, appearing in
the structures inside the cell and within the cell
me...
Proteins
 Functions:
 Transport oxygen (Hb)
 Build tissue (Muscle)
 Copy DNA for cell replication
 Support the body a...
Proteins
 Functions:
 Hormones
 Storage (egg whites of birds, reptiles; seeds)
 Protection (antibodies)
 Toxins (botu...
Proteins
 Proteins can be characterized as extremely long-
chain polyamides. The amides contain nitrogen,
and nitrogen co...
Proteins
 Proteins are synthesized via condensation of amino
acids under the influence of enzyme catalysts.
 The 20 amin...
Proteins
Proteins
 During translation, the protein goes through
several different structural stages:
1. Primary
2. Secondary
3. Te...
Proteins
Subunit or domain
Proteins: Primary Structure
 The sequence of amino acids in the
polypeptide chain.
 The sequence of the R groups determi...
Proteins: Primary Structure
Proteins: Secondary Structure
 Folding and coiling due to H bond formation between
carboxyl and amino groups of non-adjac...
Proteins: Secondary Structures
Alpha
Beta
Proteins: Tertiary Structure
 The overall 3-dimensional shape of the
polypeptide chain.
 Hydrophobic interactions with w...
Proteins: Tertiary Structure
 Hydrophilic (polar and ionized) amino acids form
hydrogen bonds with water molecules.
 Hyd...
Proteins: Tertiary Structure
Proteins: Tertiary Structure
 The shape of a protein is typically described as
being globular or fibrous.
 Globular prot...
Proteins: Tertiary Structure
Proteins: Quaternary Structure
 Relationship among multiple polypeptide chains
forming one protein structure.
 Contain t...
Proteins: Quaternary Structure
Proteins: Enzymes
 Some proteins are structural, but some are
control proteins called enzymes.
 These enzymes can be use...
Proteins: Enzymes
Proteins: Enzymes
 Speed up the rate of chemical reactions.
 Proteins are able to function as enzymes due
to their shape...
Proteins: Enzymes
 Have a small a pocket located on the 3-D
surface of the folded protein.
 This is the binding site, wh...
 The binding site matches the shape of the
substrate molecules.
 The enzyme is then able to hold the substrate
molecules...
Other Kinds of Proteins
 Simple proteins contain only amino acids.
 Conjugated proteins contain other kinds of
molecules...
Conjugated Proteins
Conjugated Proteins
Amino Acids
 Are organic compounds.
 Each has a carboxyl group and an amino group
attached to the same carbon atom, call...
Amino Acids
 There are 20 amino acids which make up the
proteins, distinguished by the R-group.
 The structure of the R-...
Amino Acids: Polar Uncharged
 Are hydrophilic and can form hydrogen
bonds.
1. Serine
2. Threonine
3. Glutamine
4. Asparag...
Amino Acids: Nonpolar
 Are hydrophobic and are usually found in the
center of the protein.
 Also found in proteins which...
Amino Acids: Electrically Charged
 Have electrical charges that can change
depending on the pH.
1. Aspartic Acid
2. Gluta...
Amino Acids: Chemical Properties
 The simplest amino acid is glycine. It fits in
tight spaces in the 3-D structure of pro...
Amino Acids
 Amino acids are the structural elements from which
proteins are built.
 When amino acids bond to each other...
Amino Acids
 Amino acids can have either left-handed or
right-handed molecular symmetry.
 The most common are left-hande...
Amino Acids
 The human body can synthesize all of the
amino acids necessary to build proteins, except
for the ten called ...
Amino Acids: Non-essential
 The 10 amino acids that we can produce are:
alanine, asparagine, aspartic acid, cysteine,
glu...
Amino Acids: Essential
 The essential amino acids are: arginine (required
for growing children), histidine, isoleucine, l...
Amino Acids
 The failure to obtain enough of any of the 10
essential amino acids has serious health
implications and can ...
Amino Acids
Summary of Proteins & Amino Acids
 Monomer: amino acids
 20 total, 9 or 10 essential
 Functional group(s):
 Carboxyl
...
Summary of Amino Acids
Nucleic Acids
 Control the processes of heredity:
 Transcription
 Translation
 Cell Replication
 The key nucleic acid...
Nucleic Acids
 Nuclei acid consist of a long chain of units
called nucleotides.
 Nucleotides are the basic structural un...
Nucleic Acids
Nucleic Acids
 The sugar ribose is characteristic of RNA.
 The sugar deoxyribose is characteristic of
DNA.
Nucleic Acids
 For RNA, the bases are adenine, guanine,
cytosine and uracil.
 For DNA, the bases may be adenine, guanine...
Nucleic Acids
Nucleic Acids
 The larger bases adenine and guanine are
purines which differ in the kinds of atoms that
are attached to t...
DNA
 Stores information regarding the sequence of
amino acids in each of the body’s proteins.
 Is the master blueprint f...
DNA Structure
 Is a double helix.
 The bases may be attached in any order.
This gives the vast number of possibilities o...
DNA Structure
DNA Structure
 Antiparallel
1. The end of a single strand that has the
phosphate group is called the 5’ end. The
other en...
DNA Structure
DNA Structure
 Complimentary base pairing
 A-T
 G-C
 Two hydrogen bonds hold adenine to thymine.
 Three hydrogen bond...
DNA Base Pairing
RNA
 Is directly involved in the synthesis of proteins
in a process called "translation".
 mRNA itself is directed synth...
RNA Structure
RNA Base Pairing
mRNA
 The anti-sense strand is used as a template to
produce a single strand of mRNA.
 The sequence of bases on a segmen...
mRNA
 The mRNA contains three-letter codes, called
a codon. It is the code for one amino acid.
 The sequence of codes in...
mRNA
 The mRNA has regions called introns and exons.
 Introns are not a part of the pattern for the protein
to be synthe...
mRNA
tRNA
 Is directly involved in the translation of the sequence
of nucleotides in mRNA with rRNA.
 The synthesis of tRNA i...
tRNA
 Is commonly called a cloverleaf form.
 Binds an amino acid at one end opposite to
the anticodon on the other end.
...
tRNA
 The many types of tRNA have roughly the
same size and shape, varying from about 73
to 93 nucleotides.
 Besides the...
tRNA
Letter Code Modified Bases
I Inocine
mI methylinosine
mG methylguanosine
m2G dimethylguanosine
Psi Pseudouridine
D Di...
tRNA
 All tRNAs have sequences of nucleotides that
are complementary to other parts of the
molecule and base-pair to form...
tRNA
rRNA
 Associates with a set of proteins to form
ribosomes.
 Physically moves an mRNA molecule and
catalyze the assembly ...
rRNA
Translation
 Translation is the whole process by which the
base sequence of an mRNA is used to bring and
join amino acids...
Translation
ATP
 Adenosine triphosphate is a nucleotide that is
used in energetic reactions for temporary energy
storage.
 Energy is...
ATP
ATP
ATP
Summary of Nucleic Acids
 Monomer: nucleotide
 A, T (or U), C, G
 Functional group(s):
 Phosphate
 Amino
 Hydroxyl
...
Summary of Nucleic Acids
Lipids
 Fats, oils, waxes, and sterols are collectively
known as lipids.
 Fats contain only carbon, hydrogen, and
oxygen.
Lipids
 Are insoluble in water but soluble in nonpolar
solvents.
 Are also an important component of cell
membranes.
 U...
Lipids
 Important classes of lipids:
1. Phospholipids
2. Steroids
3. Glycerides
4. Waxes
Phospholipids
 Contain:
 Phosphate group on third -OH group of
glycerol.
 Two fatty acids.
 Have a polar head, which i...
Phospholipids
 Arrange themselves into double-layered
membranes with the water-soluble phosphate
ends on the outside and ...
Phospholipids
 They also form spheroid structures called
micelles.
Steroids
 Have no fatty acid component.
 Contains a backbone of 4 carbon rings in 6-
6/6-5 arrangement.
 Examples:
 Ho...
Steroids
Steroids: Cholesterol
 Cholesterol is a vital component of the cell
membranes and used by cells to synthesize
other stero...
Steroids: Cholesterol
Steroids: Cholesterol
 Cholesterol bound to high-density lipoproteins
tends to be metabolized or excreted and is
often re...
Glycerides
 Fats and oils are composed of fatty acids and
glycerol.
 Fatty acids have a long hydrocarbon chain with
a ca...
Glycerides
 Fats are generally classified as esters of fatty
acids and glycerol.
 There can be one to three ester linkag...
Glycerides: Nomenclature
Fatty Acids
 Structure:
 Two classes:
1. Saturated
2. Unsaturated
Saturated Fatty Acids
 Have no double bonds between the carbons in
its fatty acid chains.
 Animal fats are more highly s...
Unsaturated Fatty Acids
 Also called “polyunsaturated fat”.
 Contain at least one to several double bonds
between the ca...
Unsaturated Fatty Acids
 Usually these fatty acid are oils.
 Most oils are of vegetable origin.
 Triglycerides composed...
Unsaturated Fatty Acids
 Trans fat is the common name for a type of
unsaturated fat with trans-isomer fatty acids.
 Most...
Unsaturated Fatty Acids
 These saturated fats have a higher melting point,
which makes them attractive for baking and ext...
Saturated & Unsaturated Fatty Acids
Triglycerides
 Are made up of a glycerol molecule with three
fatty acid molecules attached to it.
 Glycerol contains 3 c...
Triglycerides
Waxes
 Are composed of a long-chain fatty acid
bonded to a long-chain alcohol
 They form protective coverings for plants...
Summary of Lipids
 Monomer: Fatty acid
 Functional group(s):
 Carboxyl
 Cholesterol Fused Rings
 Ester
 Polymers: ma...
Summary of Lipids
Summary of Biochemistry
Basic General, Organic and Biochemistry
Basic General, Organic and Biochemistry
Basic General, Organic and Biochemistry
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Basic General, Organic and Biochemistry

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Basic General, Organic and Biochemistry

  1. 1. General Chemistry Review Part I
  2. 2. General Chemistry: Carbon Atom 1. Atomic Theory 2. Covalent Bonding 3. Chemical Formulas
  3. 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. 4. General Chemistry of Carbon  Carbon atomic number =  6 Protons 6 Electrons 6 Neutrons  Group IV Four valence electrons
  5. 5. Atomic Theory of Carbon Ground state electronic configuration of carbon is: 1s22s22p2 [He] 2s22p2 1S2 2S2 2P2 Nucleus
  6. 6. Electronic Configuration 1 2 3 4 5 6 7 C
  7. 7. Atomic Theory of Carbon  Carbon atom ground state configuration: 1s2 2s2 2Px 1 2Py 1 2Pz 0
  8. 8. Covalent Bonding Carbon can covalently bond with other elements:  Hydrogen  Oxygen  Nitrogen  Sulfur  Halogens
  9. 9. Covalent Bonding  Carbon only forms single, double or triple bonds with other carbon atoms
  10. 10. Covalent Bonding  Carbon only forms single bonds with hydrogen and/or halogens atoms
  11. 11. Covalent Bonding  Carbon may form single bonds with nitrogen, oxygen and sulfur
  12. 12. Covalent Bonding  Carbon may also form double bonds with nitrogen, oxygen and sulfur
  13. 13. Covalent Bonding  Carbon may also form triple bonds with nitrogen, sulfur and oxygen
  14. 14. Chemical Formulas  Three classes are: 1. Molecular 2. Structural 3. Condensed
  15. 15. Molecular Formulas Show:  The types of atoms present  The numbers of each atom present in a molecule
  16. 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. 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
  18. 18. Structural Formulas: Examples
  19. 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
  20. 20. Condensed Formulas: Examples
  21. 21. Condensed Formulas: Examples
  22. 22. Organic Chemistry Review Part II
  23. 23. Organic Chemistry: Carbon Atom 1. Structural Classifications 2. Atomic Theory 3. Dipoles & Resonance 4. Isomers 5. Functional Groups 6. Organic Reactions
  24. 24. Organic Chemistry  The chemistry of compounds which contain carbon.  Carbon forms more compounds than any other element, except hydrogen.
  25. 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. 26. Structural Classification of Carbon Atoms Three main classifications are: 1. Primary Carbons 2. Secondary Carbons 3. Tertiary Carbons 4. Quaternary Carbons
  27. 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
  28. 28. Secondary Carbons  Denoted as 2° carbons.  Covalently bonded to two other carbon atoms. CH3 – CH2 – CH3
  29. 29. Tertiary Carbons  Denoted as 3° carbons.  Covalently bonded to three other carbon atoms. CH3 – CH – CH3 | CH3
  30. 30. Quaternary Carbons  Denoted as 4° carbons.  Covalently bonded to four other carbon atoms. CH3 | CH3 – C – CH3 | CH3
  31. 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:
  32. 32. Definitions  Types of valence bond theory overlap:
  33. 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.
  34. 34. Definitions Hybridization:  Atomic orbitals modify themselves to meet VESPR geometry and valence bond theory.  Three types of hybridization for carbon:
  35. 35. Hybridization: Valence Bond Theory
  36. 36. Hybridization: VSEPR Geometry
  37. 37. Hybridizations
  38. 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. 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.
  40. 40. Hybridizations sp3 hybridization of methane:
  41. 41. Hybridizations sp3 hybridization of ethane:
  42. 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.
  43. 43. Hybridizations sp2 hybridization of ethene:
  44. 44. Hybridizations sp2 hybridization and bond rotation:
  45. 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.
  46. 46. Hybridizations  sp hybridization of ethyne: No free rotation
  47. 47. Charges in Organic Molecules
  48. 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. 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. 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. 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.
  52. 52. Carbon Atom Dipoles  Carbon- Halogen Bonds
  53. 53. Carbon Atom Dipoles  C-O, C-S and C-N Covalent Bonds: δ+ δ+ δ- δ-
  54. 54. Dipolar Resonance
  55. 55. Dipolar Resonance
  56. 56. Dipolar Resonance
  57. 57. Dipolar Resonance
  58. 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. 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.
  60. 60. Hyperconjugation
  61. 61. Hyperconjugation: Examples
  62. 62. Hyperconjugation: Examples
  63. 63. Hyperconjugation: Examples
  64. 64. Isomers Compounds that have:  The same molecular formula.  Similar or different types of structural formulas.  Different arrangement of atoms.
  65. 65. Isomers: Two main classes are: 1. Structural or constitutional 2. Stereoisomers
  66. 66. Structural Isomers  Also known as constitutional isomers
  67. 67. Stereoisomers a. Configurational  Geometric or Diastereomers  Optical or Enantiomers b. Conformational or Rotamers
  68. 68. Diastereomers
  69. 69. Geometric Isomers: Examples
  70. 70. Geometric Isomers: Examples
  71. 71. Optical Isomers
  72. 72. 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).
  73. 73. 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.
  74. 74. 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).
  75. 75. 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.
  76. 76. 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.
  77. 77. 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.
  78. 78. Determining L (S, -) or D (R, +) configuration
  79. 79. L (S, -) Configuration  A common optical isomer for amino acids in Biochemistry
  80. 80. Optical Isomers: Examples
  81. 81. Summary of Isomers
  82. 82. Summary of Isomers
  83. 83. Conformational Isomers  Also known as Rotamers  Stereoisomers that can be interconverted by the rotation of atoms about a σ-bond.
  84. 84. Conformational Isomers
  85. 85. Rotamers: Examples
  86. 86. Functional Groups 1. Hydrocarbons 2. Derivatives of Hydrocarbons
  87. 87. 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.
  88. 88. Functional Groups  Organic chemists use the letter "R" to indicate an organic molecule.  The "R" can be any organic molecule.
  89. 89. 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.
  90. 90. Hydrocarbons  Two classifications: 1. Aliphatics 2. Aromatics  Aliphatic - hydrocarbons which do not contain an aromatic ring.
  91. 91. 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
  92. 92. Aliphatics 1. Alkanes 2. Cycloalkanes 3. Alkenes 4. Alkynes
  93. 93. Alkanes IUPAC ending is …ane
  94. 94. 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.
  95. 95. Alkanes  Contain single covalent bonds.  Have the same structural formula: Cn H2n+2  All carbons have single bonds therefore the molecular geometry is tetrahedral.
  96. 96. Alkanes  The names of alkanes start with the name of the alkane but end with the suffix –ane.
  97. 97. 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.
  98. 98. 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-
  99. 99. Alkanes
  100. 100. 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
  101. 101. Alkanes  Any carbon can be substituted by:  Carboxylic Acids  Esters  Amides  Thioesters  Addition of other atoms:  Ethers  Thioethers  Disulfides
  102. 102. Cycloalkanes the prefix cyclo- and the ending …ane
  103. 103. 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.
  104. 104. 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.
  105. 105. Cycloalkanes  Can have more than one alkyl group to make straight chains.  For multiple alkyl groups of the same type, use prefixes.
  106. 106. 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:
  107. 107. Cycloalkanes  The names follow those of the alkanes with the prefix cyclo- .
  108. 108. Cycloalkanes
  109. 109. Cycloalkanes
  110. 110. Cycloalkanes
  111. 111. Alkenes IUPAC ending is …ene
  112. 112. 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.
  113. 113. Alkenes  Are hydrocarbons which contain one or more double bonds.  Double bonds are:  Have the same structural formula: CnH2n
  114. 114. 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.
  115. 115. Alkenes All the alkenes with 4 or more carbon atoms in them show structural isomerism.
  116. 116. 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.
  117. 117. 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.
  118. 118. Alkenes  Can have more than one alkyl group to form branches.  For more than one alkyl group, use prefixes.
  119. 119. 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:
  120. 120. Alkenes  For multiple double bonds, use the following prefixes:  di-  tri-  tetra-  penta-  hexa-
  121. 121. Alkenes  A diene is a hydrocarbon chain that has two double bonds that may or may not be adjacent to each other.
  122. 122. Alkenes: Examples
  123. 123. Alkenes: Examples
  124. 124. Alkynes IUPAC ending is …yne
  125. 125. 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.
  126. 126. Alkynes  Are hydrocarbons which contain one or more triple bonds.  Triple bonds are:  Have the same structural formula: CnH2n-2
  127. 127. 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.
  128. 128. Alkynes All the alkynes with 4 or more carbon atoms in them show structural isomerism.
  129. 129. 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.
  130. 130. Alkynes  Many functional groups can be used as substituents.  Only one substituent is allowed.  Any hydrogen or carbon atom can be substituted by:
  131. 131. Alkynes  For multiple double bonds, use the following prefixes:  di-  tri-  tetra-  penta-  hexa-
  132. 132. Alkynes: Examples
  133. 133. Aromatics Structures that meet Huckel’s Rule
  134. 134. 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.
  135. 135. 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.
  136. 136. Aromatics  The most common examples of aromatic hydrocarbons are organic compounds, which contain one or more benzene rings. Benzene
  137. 137. Aromatics  Benzene follows Huckel’s Rule:
  138. 138. 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.
  139. 139. Aromatics  Any hydrogen or carbon atom can be substituted by:
  140. 140. 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-
  141. 141. Aromatics
  142. 142. Aromatics: Examples o-dihydroxybenzene, m-dihydroxybenzene, p-dihydroxybenzene
  143. 143. Aromatics: Examples
  144. 144. Aromatics: Examples
  145. 145. Aromatics: Examples
  146. 146. Aromatics: Examples
  147. 147. Summary of Hydrocarbon
  148. 148. Summary of Hydrocarbon
  149. 149. Summary of Hydrocarbon
  150. 150. Derivatives of Hydrocarbons Are formed when there is a substitution of a functional group at one or more carbon atoms.
  151. 151. Derivatives of Hydrocarbons 1. Prefixes 2. Haloalkanes 3. Alcohols 4. Ethers 5. Amines 6. Nitriles 7. Thiols 8. Thioethers 9. Disulfides 10. Aldehydes 11. Ketones 12. Carboxylic Acids 13. Esters 14. Amides 15. Thioesters
  152. 152. Prefixes For multiple substituents of the same type, use the following prefixes:  di-  tri-  tetra-  penta-  hexa-
  153. 153. 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
  154. 154. Haloalkanes  Classify according to the number of carbons bonded directly to the alkyl halide.
  155. 155. Haloalkanes  There can be multiple substitutions of halogens for hydrogens, and also variations where alkenes, alkynes or aromatics are involved.
  156. 156. C – O Bonds Organic Compounds 1. Alcohols 2. Ethers
  157. 157. Alcohols IUPAC ending is …ol
  158. 158. 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.
  159. 159. 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.
  160. 160. Alcohols  Are classified according to the number of carbon atoms attached directly to the carbon containing the hydroxyl group.
  161. 161. Ethers … “oxy”….IUPAC ending ….ane
  162. 162. 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.
  163. 163. Ethers: Examples
  164. 164. Ethers: Examples
  165. 165. Summary of Alcohols & Ethers
  166. 166. C - S Bonds Organic Compounds 1. Thiols 2. Thioethers 3. Disulfides
  167. 167. Thiols IUPAC ending…thiols
  168. 168. 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.
  169. 169. 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°.
  170. 170. 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.
  171. 171. 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.
  172. 172. Thiols: Examples
  173. 173. Thioethers IUPAC ending….sulfide
  174. 174. 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.
  175. 175. 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
  176. 176. Thioethers: Examples
  177. 177. Thioethers: Examples
  178. 178. Disulfides IUPAC ending…..disulfide
  179. 179. Disulfides  Another class of sulfur containing molecules that have important biological implications.  Have the generic formula:  Are products from the oxidation of two thiols.
  180. 180. 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.
  181. 181. Disulfides  Are named by naming the R groups attached to the sulfur atoms followed by the suffix - disulfide. Dimethyldisulfide
  182. 182. Disulfides: Examples
  183. 183. Disulfides: Examples
  184. 184. Disulfides: Examples
  185. 185. Carbon and Nitrogen Organic Compounds 1. Amines 2. Nitriles
  186. 186. Amines 1. IUPAC ending ….amine 2. Prefix is …amino
  187. 187. 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.
  188. 188. 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.
  189. 189. 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.
  190. 190. Amines  Are classified according to the number of carbon atoms bonded directly to the nitrogen atom.
  191. 191. Amines: Examples
  192. 192. Amines: Examples
  193. 193. Nitriles 1. IUPAC ending is …..nitrile 2. Prefix is …..cyano
  194. 194. 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.
  195. 195. 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.
  196. 196. Nitriles: Examples
  197. 197. Carbonyl Organic Compounds 1. Aldehydes 2. Ketones
  198. 198. Aldehydes (CHO) IUPAC ending is …al
  199. 199. 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.
  200. 200. 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.
  201. 201. Aldehydes  IUPAC name includes the prefix from the alkyl groups and the suffix –al.
  202. 202. Aldehydes  IUPAC name for cyclic aldehydes includes the prefix cyclo and the suffix carbaldehyde.
  203. 203. Aldehydes: Examples
  204. 204. Ketones IUPAC ending is …one
  205. 205. 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.
  206. 206. 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.
  207. 207. Ketones  IUPAC name includes the prefix from the alkyl group and the suffix -one.  For more than one ketone group, use a prefix.
  208. 208. Ketones: Examples
  209. 209. Summary of Aldehydes & Ketones
  210. 210. Carboxyl Derivatives 1. Carboxylic Acids 2. Esters 3. Amides 4. Thioesters
  211. 211. 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.
  212. 212. 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
  213. 213. Carboxylic Acids IUPAC ending is …oic acid
  214. 214. 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.
  215. 215. 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.
  216. 216. 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.
  217. 217. Carboxylic Acids  Cyclic carboxylic acids that are saturated are called cycloalkane carboxylic acids.  Dicarboxylic acids are known as alkanedioic acids.
  218. 218. Carboxylic Acids
  219. 219. Carboxylic Acids: Examples
  220. 220. Carboxylic Acids: Examples
  221. 221. Esters IUPAC ending …oate
  222. 222. 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.
  223. 223. 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.
  224. 224. 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.
  225. 225. Esters: Examples
  226. 226. Esters: Examples
  227. 227. Esters: Examples
  228. 228. Amides IUPAC ending is …amide
  229. 229. Amides  Also known as an acid amide.  Are formed when carboxylic acids react with amines.  Are nitrogen-containing organic compounds with the general formula
  230. 230. 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:
  231. 231. 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.
  232. 232. Amides  The molecular geometry centered on the nitrogen is bent and also flat as an extension of the trigonal planar geometry.
  233. 233. Amides In the IUPAC system:  For primary amides, the –e is removed from the alkane name and the suffix -amide is added.
  234. 234. 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.
  235. 235. Amides
  236. 236. Amides
  237. 237. Amides: Example
  238. 238. Amides: Example
  239. 239. Amides: Example
  240. 240. Amides: Example
  241. 241. Thioesters 1. IUPAC ending….-thioate or - carbothioate 2. Prefix….thio & ending….-ate or - carboxylate
  242. 242. 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.
  243. 243. 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.
  244. 244. Thioesters  The molecular geometry centered on the sulfur is bent and also flat as an extension of the trigonal planar geometry.
  245. 245. 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)
  246. 246. 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
  247. 247. Thioesters: Examples
  248. 248. Thioesters: Examples
  249. 249. Summary of Carboxyl Derivatives
  250. 250. Summary of Functional Groups
  251. 251. Organic Reactions 1. Chemical Bonds 2. Non-polar Reactions 3. Polar Reactions 4. Classifications
  252. 252. Chemical Bonds in Reactions 1. Bond Breaking 2. Bond Forming
  253. 253. Chemical Bond Breaking  Polar reactions involve heterolytic bond cleavage  Radical reactions involve homolytic bond cleavage
  254. 254. Chemical Bond Making
  255. 255. Non-polar Reactions Free Radicals Formation
  256. 256. Free Radicals  Are neutral and electron-deficient.  They do not meet the octet rule.  Examples:
  257. 257. Free Radicals  Stability of free radicals:
  258. 258. Free Radicals  React to complete its valence shell. General Form:
  259. 259. Non-polar Reactions
  260. 260. Non-polar Reactions  Termination step:
  261. 261. Polar Reactions 1. Nucleophiles 2. Electrophiles
  262. 262.  Lewis acid-base definition: transfer of electron pair from a base to an acid Definitions
  263. 263. 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.
  264. 264. 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.
  265. 265. Nucleophiles: Examples
  266. 266. Nucleophiles: Examples
  267. 267. 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.
  268. 268. Electrophiles  H+  NO+  HCl  Alkyl halides  Acyl halides  Cl2  Br2  Organic peracids  Carbenes  Radicals  BH3  Carbonyl compounds  Diisobutylaluminium hydride (DIBAL)  The most common in organic syntheses are:
  269. 269. Polar Reactions  Nucleophiles – transfers electrons to an electrophilic atom  Electrophiles - accept electrons from a nucleophilic atom
  270. 270. Polar Reactions General Form:  Products never exceed the octet rule.
  271. 271. Polar Reactions  The nucleophilic site can be neutral or negatively charged.
  272. 272. Polar Reactions  The electrophilic site can be neutral or positively charged.
  273. 273. Organic Reactions 1. Addition 2. Elimination 3. Substitution 4. Rearrangement 5. Condensation 6. Esterification 7. Hydrolysis 8. Oxidation & Reductions 9. Combustion
  274. 274. 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
  275. 275. Addition Reactions  Symmetrical alkenes produce one product.  Unsymmetrical alkenes produce racemic mixtures.
  276. 276. 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.
  277. 277. Addition Reactions
  278. 278. Addition Reactions  With symmetrical alkenes, addition of hydroxyl group produces one type of alcohol.
  279. 279. Addition Reactions  With unsymmetrical alkenes, addition of hydroxyl group produces different types of alcohols depending on the location of the double bond +
  280. 280. Addition Reactions Formation of hemiketals & hemiacetals:  Reactions between an acohol and either a ketone or aldehyde.
  281. 281. 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.
  282. 282. 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
  283. 283. 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).
  284. 284. Elimination Reactions General form: A → B + C
  285. 285. Elimination Reactions  1⁰ Alcohols
  286. 286. Elimination Reactions  2⁰ Alcohols
  287. 287. 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.
  288. 288. 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.
  289. 289. Elimination Reactions  Hydride shift:
  290. 290. Elimination Reactions  Alkyl shift:
  291. 291. 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 .
  292. 292. Substitution Reactions General form: A + B → C + D  Non-polar reactions:
  293. 293. Substitution Reactions  Polar reactions:
  294. 294. 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
  295. 295. Rearrangement Reactions
  296. 296. 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.
  297. 297. 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).
  298. 298. 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.
  299. 299. Condensation Reactions
  300. 300. 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).
  301. 301. Esterification Reactions  A carboxylic acid and an alcohol react together under acidic conditions to form an ester and lose water.
  302. 302. 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.
  303. 303. Esterification Reactions Pericyclic esters
  304. 304. 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.
  305. 305. 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.
  306. 306. 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.
  307. 307. 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.
  308. 308. Hydrolysis of Amides & Nitriles:  Amide acid catalyzed - HCl  Nitrile acid catalyzed – HCl or H2SO4
  309. 309. Hydrolysis of Halogenalkanes:
  310. 310. Hydrolysis of Aromatics
  311. 311. 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
  312. 312. 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-
  313. 313. Reduction & Oxidation (REDOX) Reactions 1. Oxidation States 2. Oxidations 3. Reductions
  314. 314. 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.
  315. 315. 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)
  316. 316. 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.
  317. 317. 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.
  318. 318. Oxidation States
  319. 319. Oxidation States  In nitrogen-containing compounds, the number of carbon–nitrogen bonds changes with the oxidation state of carbon.
  320. 320. Oxidation States
  321. 321. Assign oxidation states to all atoms in the following structure: C HO C H C C O H H H H H H
  322. 322. 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
  323. 323. 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
  324. 324. Problem No, both Br and I are more electronegative than C -2 + H2 Yes, the carbon atoms are reduced, the H2 molecule is oxidized
  325. 325. Problem
  326. 326. Summary of Oxidation States
  327. 327. 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.
  328. 328. 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
  329. 329. 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).
  330. 330. 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.
  331. 331. 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.
  332. 332. Summary of Oxidation of Alcohols
  333. 333. 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.
  334. 334. 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.
  335. 335. Reduction of Alcohols  The tosylate reduces to cyclohexane very easily with lithium aluminum hydride.
  336. 336. Reduction of Carboxylic Acids  Carboxylic acids are reduced to 1⁰ alcohols.
  337. 337. Reduction of Esters  Esters are reduced to 1⁰ alcohols.
  338. 338. Reduction of Amides  Amides are reduced to 1⁰, 2⁰, or 3⁰ amines.
  339. 339. Reduction of Aldehydes  Aldehydes and ketones are reduced to 1⁰ and 2⁰ alcohols respectively.
  340. 340. Summary REDOX Reactions
  341. 341. Combustion Reactions  The reaction of an organic molecule with oxygen to form carbon dioxide, heat/energy and water.
  342. 342. Combustion Reactions  Alkanes:  Alkenes:  Alcohols
  343. 343. Introduction to Biochemistry Part III – Foundations of Organic Chemistry in Biochemistry
  344. 344. Biochemistry 1. Macromolecules 2. Functional Groups 3. Organic Reactions 4. Carbohydrates
  345. 345. 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.
  346. 346. Definitions  Hydrogen bonds – ionic and hydrophilic interactions between a polar or ionic molecules and water.
  347. 347. Definitions  Hydrophobic interactions - tendency of nonpolar substances to aggregate in aqueous solution and exclude water molecules.
  348. 348. 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.
  349. 349. 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.
  350. 350. 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.
  351. 351. Macromolecules  Nonpolar molecules are hydrophobic.  Polar and ionic molecules are hydrophilic.
  352. 352. 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.
  353. 353. Functional Groups in Biochemistry 1. Hydrocarbons 2. Aromatics 3. Common Functional Groups
  354. 354. 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+).
  355. 355. 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.
  356. 356. Hydrocarbons
  357. 357. Cycloalkanes
  358. 358. Cycloalkanes
  359. 359. Cycloalkanes
  360. 360. Aromatic Compounds
  361. 361. Aromatic Compounds
  362. 362. Aromatic Compounds
  363. 363. Aromatic Compounds
  364. 364. Common Functional Groups
  365. 365. Common Functional Groups
  366. 366. Summary of Functional Groups
  367. 367. Summary of Functional Groups  Important bond linkages in Biochemistry:
  368. 368. Organic Reactions Classes: 1. Group Transfer 2. REDOX 3. Eliminations, Isomerizations, Rearrangements 4. C-C Bond Making & Breaking 5. Hydrolysis
  369. 369. Group Transfer Reactions  Nucleophilic Substitution  Transfer an electrophile from one nucleophile to another.  Commonly transferred groups: 1. Acyl 2. Phosphoryl 3. Glycosyl 4. Amino
  370. 370. Group Transfer Reactions: Acyl Group Acylation Reactions
  371. 371. Group Transfer Reactions: Phosphoryl Group Phsophorylation Reaction
  372. 372. Group Transfer Reactions: Glycosyl Group Glycosylation Reactions
  373. 373. Group Transfer Reactions: Amino Group Transamination Reactions
  374. 374. 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
  375. 375. 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.
  376. 376. REDOX Reactions
  377. 377. REDOX Reactions
  378. 378. REDOX Reactions
  379. 379. REDOX Reactions
  380. 380. Elimination Reactions  Formation of alkenes  Products are:  Trans (anti) – Major  Cis (syn)  Elimination of:  Water  Ammonia  1⁰ Amines  Alcohols
  381. 381. Elimination Reactions  Types of Mechanisms: 1. Concerted 2. Carbocation Formation: C-O bond breakage 3. Carbanion Formation: C-H bond breakage  Two Types of Reactions: 1. Dehydrations 2. Deaminations
  382. 382. Elimination Reactions: Concerted & Carbocation
  383. 383. Elimination Reactions: Carbanion
  384. 384. Elimination Reactions: Dehydration  Enzyme catalyzed reactions.  Two Types of Enzyme-Catalysis: 1. Acid: Protonation of OH group 2. Base: Abstraction of a proton
  385. 385. Elimination Reactions: Dehydradation
  386. 386. 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
  387. 387. Condensation of Amino Acids
  388. 388. Condensation of Saccharides
  389. 389. Condensation of Fatty Acids
  390. 390. Elimination Reactions: Deaminations
  391. 391. Elimination Reactions: Deaminations
  392. 392. Isomerization Reactions  Relocation of a = bond.  Intramolecular shift of a proton.  Most common are base catalyzed reactions.
  393. 393. Isomerization Reactions
  394. 394. 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.
  395. 395. Rearrangement Reactions
  396. 396. 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
  397. 397. C-C bond Breaking & Making Reactions 1. Condensation  Aldol  Claisen Ester  Other Condensations Reactions: o Amino Acids o Saccharides o Fatty Acids 2. Decarboxylations
  398. 398. Condensation Reactions: Aldol
  399. 399. Condensation Reactions: Claisen Esters
  400. 400. Decarboxylation Reactions  Removes a carboxyl group  Releases carbon dioxide.
  401. 401. Decarboxylation Reactions
  402. 402. Decarboxylation Reactions: Citric Cycle
  403. 403. Decarboxylation Reactions: Precursors of the Citric Cycle
  404. 404. 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.
  405. 405. Hydrolysis of Proteins
  406. 406. Hydrolysis of Polysaccharides
  407. 407. Hydrolysis of Fats
  408. 408. Synthesis of Common Functional Groups
  409. 409. Synthesis of Common Functional Groups
  410. 410. Biochemistry: The Chemistry of the Human Body Part IV - Macromolecules
  411. 411. Macromolecules  Many of the common macromolecules are synthesized from monomers.
  412. 412. Carbohydrates 1. Monosaccharides 2. Disaccharides 3. Polysaccharides
  413. 413. 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.
  414. 414. 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.
  415. 415. Carbohydrates  Three key classification schemes for sugars are: 1. Monosaccharides 2. Disaccharides 3. Polysaccharides
  416. 416. 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.
  417. 417. Monosaccharides
  418. 418. 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
  419. 419. Monosaccharides: Isomers
  420. 420. Monosaccharides: Diastereomers  Stereoisomers that are not mirror images of each other.  Diastereomers for the molecular formula C5H10O5:
  421. 421. Monosaccharides: Diastereomers  Diastereomers for the molecular formula C6H12O6:
  422. 422. Monosaccharides: Enantiomers  Stereoisomers that are mirror images of each other.  Two types: D or L
  423. 423. Monosaccharides: Epimers  Two diastereomers that differ around one chiral center.
  424. 424. 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.
  425. 425. Monosaccharides: Anomers
  426. 426. Monosaccharides: Anomers  In hemiketals, the anomeric carbon is at position 2.
  427. 427. 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.
  428. 428. Disaccharides
  429. 429. Disaccharides  Common disaccharides are: 1. Sucrose 2. Lactose 3. Maltose 4. Trehalose
  430. 430. Disaccharides
  431. 431. Sucrose  Prevalent in sugar cane and sugar beets
  432. 432. Sucrose
  433. 433. Lactose  Found exclusively in milk.
  434. 434. Lactose
  435. 435. Maltose  Major degradation product of starch.
  436. 436. Maltose
  437. 437. Trehalose  Found in bacteria, yeast, invertebrates, mushrooms and seaweed.  Glycosidic Linkages:  Protects organisms from extreme temperatures and drying out.
  438. 438. 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.
  439. 439. 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.
  440. 440. Trehalose  In plants, synthesis is carried out by trehalose phosphate synthase and trehalose phosphatase:
  441. 441. Trehalose
  442. 442. Trehalose  Degradation: Trehalase
  443. 443. 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
  444. 444. Polyssacharides
  445. 445. Polyssacharides  Are classified as: 1. Cellulose 2. Chitin 3. Glycogen 4. Starches
  446. 446. 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.
  447. 447. 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.
  448. 448. 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.
  449. 449. Cellulose
  450. 450. 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.
  451. 451. Chitin
  452. 452. 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.
  453. 453. Glycogen
  454. 454. 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.
  455. 455. 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.
  456. 456. 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.
  457. 457. 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.
  458. 458. 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.
  459. 459. Starches
  460. 460. Starches & Glycogen  The bond orientation between the glucose subunits of starch and glycogen allows the polymers to form compact spirals.
  461. 461. Summary of Carbohydrates  CHO  Monosaccharides: simple sugars  Functional group(s):  Carboxyl  Hydroxyl  Disaccharides  Polysaccharides
  462. 462. Summary of Carbohydrates
  463. 463. Summary of Carbohydrates
  464. 464. Summary of Carbohydrates
  465. 465. Proteins
  466. 466. 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.
  467. 467. 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.
  468. 468. 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
  469. 469. 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.
  470. 470. 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.
  471. 471. 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.
  472. 472. Proteins
  473. 473. 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.
  474. 474. Proteins Subunit or domain
  475. 475. 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.
  476. 476. Proteins: Primary Structure
  477. 477. 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.
  478. 478. Proteins: Secondary Structures Alpha Beta
  479. 479. 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.
  480. 480. 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.
  481. 481. Proteins: Tertiary Structure
  482. 482. 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.
  483. 483. Proteins: Tertiary Structure
  484. 484. 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
  485. 485. Proteins: Quaternary Structure
  486. 486. 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.
  487. 487. Proteins: Enzymes
  488. 488. 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.
  489. 489. 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 .
  490. 490.  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
  491. 491. 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)
  492. 492. Conjugated Proteins
  493. 493. Conjugated Proteins
  494. 494. 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:
  495. 495. 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
  496. 496. Amino Acids: Polar Uncharged  Are hydrophilic and can form hydrogen bonds. 1. Serine 2. Threonine 3. Glutamine 4. Asparagine 5. Tyrosine 6. Cysteine
  497. 497. 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
  498. 498. 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
  499. 499. 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.
  500. 500. 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.
  501. 501. 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.
  502. 502. 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.
  503. 503. 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.
  504. 504. 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.
  505. 505. 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.
  506. 506. Amino Acids
  507. 507. Summary of Proteins & Amino Acids  Monomer: amino acids  20 total, 9 or 10 essential  Functional group(s):  Carboxyl  Amino  Polymer  Polypeptide  Protein
  508. 508. Summary of Amino Acids
  509. 509. Nucleic Acids  Control the processes of heredity:  Transcription  Translation  Cell Replication  The key nucleic acids are:  DNA (deoxyribonucleic acid)  RNA (ribonucleic acid)
  510. 510. 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.
  511. 511. Nucleic Acids
  512. 512. Nucleic Acids  The sugar ribose is characteristic of RNA.  The sugar deoxyribose is characteristic of DNA.
  513. 513. Nucleic Acids  For RNA, the bases are adenine, guanine, cytosine and uracil.  For DNA, the bases may be adenine, guanine, cytosine or thymine.
  514. 514. Nucleic Acids
  515. 515. 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.
  516. 516. 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.
  517. 517. 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.
  518. 518. DNA Structure
  519. 519. 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.
  520. 520. DNA Structure
  521. 521. DNA Structure  Complimentary base pairing  A-T  G-C  Two hydrogen bonds hold adenine to thymine.  Three hydrogen bonds hold cytosine to guanine.
  522. 522. DNA Base Pairing
  523. 523. 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).
  524. 524. RNA Structure
  525. 525. RNA Base Pairing
  526. 526. 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.
  527. 527. 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.
  528. 528. 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.
  529. 529. mRNA
  530. 530. 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.
  531. 531. 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.
  532. 532. 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.
  533. 533. tRNA Letter Code Modified Bases I Inocine mI methylinosine mG methylguanosine m2G dimethylguanosine Psi Pseudouridine D Dihydrouridine
  534. 534. 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.
  535. 535. tRNA
  536. 536. 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.
  537. 537. rRNA
  538. 538. 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.
  539. 539. Translation
  540. 540. 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.
  541. 541. ATP
  542. 542. ATP
  543. 543. ATP
  544. 544. Summary of Nucleic Acids  Monomer: nucleotide  A, T (or U), C, G  Functional group(s):  Phosphate  Amino  Hydroxyl  Polymer:  DNA and RNA Basic Nucleotide Structure
  545. 545. Summary of Nucleic Acids
  546. 546. Lipids  Fats, oils, waxes, and sterols are collectively known as lipids.  Fats contain only carbon, hydrogen, and oxygen.
  547. 547. 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.
  548. 548. Lipids  Important classes of lipids: 1. Phospholipids 2. Steroids 3. Glycerides 4. Waxes
  549. 549. Phospholipids  Contain:  Phosphate group on third -OH group of glycerol.  Two fatty acids.  Have a polar head, which increases hydrophilicity.
  550. 550. 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.
  551. 551. Phospholipids  They also form spheroid structures called micelles.
  552. 552. Steroids  Have no fatty acid component.  Contains a backbone of 4 carbon rings in 6- 6/6-5 arrangement.  Examples:  Hormones  Cholesterol  Cell membrane components
  553. 553. Steroids
  554. 554. 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.
  555. 555. Steroids: Cholesterol
  556. 556. Steroids: Cholesterol  Cholesterol bound to high-density lipoproteins tends to be metabolized or excreted and is often referred to as "good cholesterol".
  557. 557. 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.
  558. 558. 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
  559. 559. Glycerides: Nomenclature
  560. 560. Fatty Acids  Structure:  Two classes: 1. Saturated 2. Unsaturated
  561. 561. 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.
  562. 562. 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.
  563. 563. 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.
  564. 564. 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.
  565. 565. 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.
  566. 566. Saturated & Unsaturated Fatty Acids
  567. 567. 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.
  568. 568. Triglycerides
  569. 569. 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).
  570. 570. 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
  571. 571. Summary of Lipids
  572. 572. Summary of Biochemistry

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