Introduction to Biochemistry I

1
Introduction to Biochemistry

• Part III Foundations of Organic Chemistry in
  Biochemistry

2
Biochemistry

1. Macromolecules
2. Functional Groups
3. Organic Reactions
4. Carbohydrates

3
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.

4
Definitions

• Hydrogen bonds ionic and hydrophilic
  interactions between a polar or ionic molecules
  and water.

5
Definitions

• Hydrophobic interactions - tendency of nonpolar
  substances to aggregate in aqueous solution and
  exclude water molecules.

6
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.

7
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.

8
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.

9
Macromolecules

• Nonpolar molecules are hydrophobic.
• Polar and ionic molecules are hydrophilic.

10
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.

11
Functional Groups in Biochemistry

1. Hydrocarbons
2. Aromatics
3. Common Functional Groups

12
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).

13
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-CO, and -NH2.

14
Hydrocarbons
15
Cycloalkanes
16
Cycloalkanes
17
Cycloalkanes
18
Aromatic Compounds
19
Aromatic Compounds
20
Aromatic Compounds
21
Aromatic Compounds
22
Common Functional Groups
23
Common Functional Groups
24
Summary of Functional Groups
25
Summary of Functional Groups

• Important bond linkages in Biochemistry

26
Organic Reactions Classes

1. Group Transfer
2. REDOX
3. Eliminations, Isomerizations, Rearrangements
4. C-C Bond Making Breaking
5. Hydrolysis

27
Group Transfer Reactions

• Nucleophilic Substitution
• Transfer an electrophile from one nucleophile to
  another.
• Commonly transferred groups
• Acyl
• Phosphoryl
• Glycosyl
• Amino

28
Group Transfer Reactions Acyl Group
Acylation Reactions
29
Group Transfer Reactions Phosphoryl Group
Phsophorylation Reaction
30
Group Transfer Reactions Glycosyl Group
Glycosylation Reactions
31
Group Transfer Reactions Amino Group
Transamination Reactions
32
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

33
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.

34
REDOX Reactions
35
REDOX Reactions
36
REDOX Reactions
37
REDOX Reactions
38
Elimination Reactions

• Formation of alkenes
• Products are
• Trans (anti) Major
• Cis (syn)
• Elimination of
• Water
• Ammonia
• 1 Amines
• Alcohols

39
Elimination Reactions

• Types of Mechanisms
• Concerted
• Carbocation Formation C-O bond breakage
• Carbanion Formation C-H bond breakage
• Two Types of Reactions
• Dehydrations
• Deaminations

40
Elimination Reactions Concerted Carbocation
41
Elimination Reactions Carbanion
42
Elimination Reactions Dehydration

• Enzyme catalyzed reactions.
• Two Types of Enzyme-Catalysis
• Acid Protonation of OH group
• Base Abstraction of a proton

43
Elimination Reactions Dehydradation
44
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

45
Condensation of Amino Acids
46
Condensation of Saccharides
47
Condensation of Fatty Acids
48
Elimination Reactions Deaminations
49
Elimination Reactions Deaminations
50
Isomerization Reactions

• Relocation of a bond.
• Intramolecular shift of a proton.
• Most common are base catalyzed reactions.

51
Isomerization Reactions
52
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.

53
Rearrangement Reactions
54
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
• Aldehydes
• Ketones
• Esters
• Carbon Dioxide

55
C-C bond Breaking Making Reactions

• Condensation
• Aldol
• Claisen Ester
• Other Condensations Reactions
• Amino Acids
• Saccharides
• Fatty Acids
• Decarboxylations

56
Condensation Reactions Aldol
57
Condensation Reactions Claisen Esters
58
Decarboxylation Reactions

• Removes a carboxyl group
• Releases carbon dioxide.

59
Decarboxylation Reactions
60
Decarboxylation Reactions Citric Cycle
61
Decarboxylation Reactions Precursors of the
Citric Cycle
62
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.

63
Hydrolysis of Proteins
64
Hydrolysis of Polysaccharides
65
Hydrolysis of Fats
66
Synthesis of Common Functional Groups
67
Synthesis of Common Functional Groups