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Raffi Hovasapian

Raffi Hovasapian

Amino Acids

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Table of Contents

Section 1: Preliminaries on Aqueous Chemistry
Aqueous Solutions & Concentration

39m 57s

Intro
0:00
Aqueous Solutions and Concentration
0:46
Definition of Solution
1:28
Example: Sugar Dissolved in Water
2:19
Example: Salt Dissolved in Water
3:04
A Solute Does Not Have to Be a Solid
3:37
A Solvent Does Not Have to Be a Liquid
5:02
Covalent Compounds
6:55
Ionic Compounds
7:39
Example: Table Sugar
9:12
Example: MgCl₂
10:40
Expressing Concentration: Molarity
13:42
Example 1
14:47
Example 1: Question
14:50
Example 1: Solution
15:40
Another Way to Express Concentration
22:01
Example 2
24:00
Example 2: Question
24:01
Example 2: Solution
24:49
Some Other Ways of Expressing Concentration
27:52
Example 3
29:30
Example 3: Question
29:31
Example 3: Solution
31:02
Dilution & Osmotic Pressure

38m 53s

Intro
0:00
Dilution
0:45
Definition of Dilution
0:46
Example 1: Question
2:08
Example 1: Basic Dilution Equation
4:20
Example 1: Solution
5:31
Example 2: Alternative Approach
12:05
Osmotic Pressure
14:34
Colligative Properties
15:02
Recall: Covalent Compounds and Soluble Ionic Compounds
17:24
Properties of Pure Water
19:42
Addition of a Solute
21:56
Osmotic Pressure: Conceptual Example
24:00
Equation for Osmotic Pressure
29:30
Example of 'i'
31:38
Example 3
32:50
More on Osmosis

29m 1s

Intro
0:00
More on Osmosis
1:25
Osmotic Pressure
1:26
Example 1: Molar Mass of Protein
5:25
Definition, Equation, and Unit of Osmolarity
13:13
Example 2: Osmolarity
15:19
Isotonic, Hypertonic, and Hypotonic
20:20
Example 3
22:20
More on Isotonic, Hypertonic, and Hypotonic
26:14
Osmosis vs. Osmotic Pressure
27:56
Acids & Bases

39m 11s

Intro
0:00
Acids and Bases
1:16
Let's Begin With H₂O
1:17
P-Scale
4:22
Example 1
6:39
pH
9:43
Strong Acids
11:10
Strong Bases
13:52
Weak Acids & Bases Overview
14:32
Weak Acids
15:49
Example 2: Phosphoric Acid
19:30
Weak Bases
24:50
Weak Base Produces Hydroxide Indirectly
25:41
Example 3: Pyridine
29:07
Acid Form and Base Form
32:02
Acid Reaction
35:50
Base Reaction
36:27
Ka, Kb, and Kw
37:14
Titrations and Buffers

41m 33s

Intro
0:00
Titrations
0:27
Weak Acid
0:28
Rearranging the Ka Equation
1:45
Henderson-Hasselbalch Equation
3:52
Fundamental Reaction of Acids and Bases
5:36
The Idea Behind a Titration
6:27
Let's Look at an Acetic Acid Solution
8:44
Titration Curve
17:00
Acetate
23:57
Buffers
26:57
Introduction to Buffers
26:58
What is a Buffer?
29:40
Titration Curve & Buffer Region
31:44
How a Buffer Works: Adding OH⁻
34:44
How a Buffer Works: Adding H⁺
35:58
Phosphate Buffer System
38:02
Example Problems with Acids, Bases & Buffers

44m 19s

Intro
0:00
Example 1
1:21
Example 1: Properties of Glycine
1:22
Example 1: Part A
3:40
Example 1: Part B
4:40
Example 2
9:02
Example 2: Question
9:03
Example 2: Total Phosphate Concentration
12:23
Example 2: Final Solution
17:10
Example 3
19:34
Example 3: Question
19:35
Example 3: pH Before
22:18
Example 3: pH After
24:24
Example 3: New pH
27:54
Example 4
30:00
Example 4: Question
30:01
Example 4: Equilibria
32:52
Example 4: 1st Reaction
38:04
Example 4: 2nd Reaction
39:53
Example 4: Final Solution
41:33
Hydrolysis & Condensation Reactions

18m 45s

Intro
0:00
Hydrolysis and Condensation Reactions
0:50
Hydrolysis
0:51
Condensation
2:42
Example 1: Hydrolysis of Ethyl Acetate
4:52
Example 2: Condensation of Acetic Acid with Ethanol
8:42
Example 3
11:18
Example 4: Formation & Hydrolysis of a Peptide Bond Between the Amino Acids Alanine & Serine
14:56
Section 2: Amino Acids & Proteins: Primary Structure
Amino Acids

38m 19s

Intro
0:00
Amino Acids
0:17
Proteins & Amino Acids
0:18
Difference Between Amino Acids
4:20
α-Carbon
7:08
Configuration in Biochemistry
10:43
L-Glyceraldehyde & Fischer Projection
12:32
D-Glyceraldehyde & Fischer Projection
15:31
Amino Acids in Biological Proteins are the L Enantiomer
16:50
L-Amino Acid
18:04
L-Amino Acids Correspond to S-Enantiomers in the RS System
20:10
Classification of Amino Acids
22:53
Amino Acids With Non-Polar R Groups
26:45
Glycine
27:00
Alanine
27:48
Valine
28:15
Leucine
28:58
Proline
31:08
Isoleucine
32:42
Methionine
33:43
Amino Acids With Aromatic R Groups
34:33
Phenylalanine
35:26
Tyrosine
36:02
Tryptophan
36:32
Amino Acids, Continued

27m 14s

Intro
0:00
Amino Acids With Positively Charged R Groups
0:16
Lysine
0:52
Arginine
1:55
Histidine
3:15
Amino Acids With Negatively Charged R Groups
6:28
Aspartate
6:58
Glutamate
8:11
Amino Acids With Uncharged, but Polar R Groups
8:50
Serine
8:51
Threonine
10:21
Cysteine
11:06
Asparagine
11:35
Glutamine
12:44
More on Amino Acids
14:18
Cysteine Dimerizes to Form Cystine
14:53
Tryptophan, Tyrosine, and Phenylalanine
19:07
Other Amino Acids
20:53
Other Amino Acids: Hydroxy Lysine
22:34
Other Amino Acids: r-Carboxy Glutamate
25:37
Acid/Base Behavior of Amino Acids

48m 28s

Intro
0:00
Acid/Base Behavior of Amino Acids
0:27
Acid/Base Behavior of Amino Acids
0:28
Let's Look at Alanine
1:57
Titration of Acidic Solution of Alanine with a Strong Base
2:51
Amphoteric Amino Acids
13:24
Zwitterion & Isoelectric Point
16:42
Some Amino Acids Have 3 Ionizable Groups
20:35
Example: Aspartate
24:44
Example: Tyrosine
28:50
Rule of Thumb
33:04
Basis for the Rule
35:59
Example: Describe the Degree of Protonation for Each Ionizable Group
38:46
Histidine is Special
44:58
Peptides & Proteins

45m 18s

Intro
0:00
Peptides and Proteins
0:15
Introduction to Peptides and Proteins
0:16
Formation of a Peptide Bond: The Bond Between 2 Amino Acids
1:44
Equilibrium
7:53
Example 1: Build the Following Tripeptide Ala-Tyr-Ile
9:48
Example 1: Shape Structure
15:43
Example 1: Line Structure
17:11
Peptides Bonds
20:08
Terms We'll Be Using Interchangeably
23:14
Biological Activity & Size of a Peptide
24:58
Multi-Subunit Proteins
30:08
Proteins and Prosthetic Groups
32:13
Carbonic Anhydrase
37:35
Primary, Secondary, Tertiary, and Quaternary Structure of Proteins
40:26
Amino Acid Sequencing of a Peptide Chain

42m 47s

Intro
0:00
Amino Acid Sequencing of a Peptide Chain
0:30
Amino Acid Sequence and Its Structure
0:31
Edman Degradation: Overview
2:57
Edman Degradation: Reaction - Part 1
4:58
Edman Degradation: Reaction - Part 2
10:28
Edman Degradation: Reaction - Part 3
13:51
Mechanism Step 1: PTC (Phenylthiocarbamyl) Formation
19:01
Mechanism Step 2: Ring Formation & Peptide Bond Cleavage
23:03
Example: Write Out the Edman Degradation for the Tripeptide Ala-Tyr-Ser
30:29
Step 1
30:30
Step 2
34:21
Step 3
36:56
Step 4
38:28
Step 5
39:24
Step 6
40:44
Sequencing Larger Peptides & Proteins

1h 2m 33s

Intro
0:00
Sequencing Larger Peptides and Proteins
0:28
Identifying the N-Terminal Amino Acids With the Reagent Fluorodinitrobenzene (FDNB)
0:29
Sequencing Longer Peptides & Proteins Overview
5:54
Breaking Peptide Bond: Proteases and Chemicals
8:16
Some Enzymes/Chemicals Used for Fragmentation: Trypsin
11:14
Some Enzymes/Chemicals Used for Fragmentation: Chymotrypsin
13:02
Some Enzymes/Chemicals Used for Fragmentation: Cyanogen Bromide
13:28
Some Enzymes/Chemicals Used for Fragmentation: Pepsin
13:44
Cleavage Location
14:04
Example: Chymotrypsin
16:44
Example: Pepsin
18:17
More on Sequencing Larger Peptides and Proteins
19:29
Breaking Disulfide Bonds: Performic Acid
26:08
Breaking Disulfide Bonds: Dithiothreitol Followed by Iodoacetate
31:04
Example: Sequencing Larger Peptides and Proteins
37:03
Part 1 - Breaking Disulfide Bonds, Hydrolysis and Separation
37:04
Part 2 - N-Terminal Identification
44:16
Part 3 - Sequencing Using Pepsin
46:43
Part 4 - Sequencing Using Cyanogen Bromide
52:02
Part 5 - Final Sequence
56:48
Peptide Synthesis (Merrifield Process)

49m 12s

Intro
0:00
Peptide Synthesis (Merrifield Process)
0:31
Introduction to Synthesizing Peptides
0:32
Merrifield Peptide Synthesis: General Scheme
3:03
So What Do We Do?
6:07
Synthesis of Protein in the Body Vs. The Merrifield Process
7:40
Example: Synthesis of Ala-Gly-Ser
9:21
Synthesis of Ala-Gly-Ser: Reactions Overview
11:41
Synthesis of Ala-Gly-Ser: Reaction 1
19:34
Synthesis of Ala-Gly-Ser: Reaction 2
24:34
Synthesis of Ala-Gly-Ser: Reaction 3
27:34
Synthesis of Ala-Gly-Ser: Reaction 4 & 4a
28:48
Synthesis of Ala-Gly-Ser: Reaction 5
33:38
Synthesis of Ala-Gly-Ser: Reaction 6
36:45
Synthesis of Ala-Gly-Ser: Reaction 7 & 7a
37:44
Synthesis of Ala-Gly-Ser: Reaction 8
39:47
Synthesis of Ala-Gly-Ser: Reaction 9 & 10
43:23
Chromatography: Eluent, Stationary Phase, and Eluate
45:55
More Examples with Amino Acids & Peptides

54m 31s

Intro
0:00
Example 1
0:22
Data
0:23
Part A: What is the pI of Serine & Draw the Correct Structure
2:11
Part B: How Many mL of NaOH Solution Have Been Added at This Point (pI)?
5:27
Part C: At What pH is the Average Charge on Serine
10:50
Part D: Draw the Titration Curve for This Situation
14:50
Part E: The 10 mL of NaOH Added to the Solution at the pI is How Many Equivalents?
17:35
Part F: Serine Buffer Solution
20:22
Example 2
23:04
Data
23:05
Part A: Calculate the Minimum Molar Mass of the Protein
25:12
Part B: How Many Tyr Residues in this Protein?
28:34
Example 3
30:08
Question
30:09
Solution
34:30
Example 4
48:46
Question
48:47
Solution
49:50
Section 3: Proteins: Secondary, Tertiary, and Quaternary Structure
Alpha Helix & Beta Conformation

50m 52s

Intro
0:00
Alpha Helix and Beta Conformation
0:28
Protein Structure Overview
0:29
Weak interactions Among the Amino Acid in the Peptide Chain
2:11
Two Principals of Folding Patterns
4:56
Peptide Bond
7:00
Peptide Bond: Resonance
9:46
Peptide Bond: φ Bond & ψ Bond
11:22
Secondary Structure
15:08
α-Helix Folding Pattern
17:28
Illustration 1: α-Helix Folding Pattern
19:22
Illustration 2: α-Helix Folding Pattern
21:39
β-Sheet
25:16
β-Conformation
26:04
Parallel & Anti-parallel
28:44
Parallel β-Conformation Arrangement of the Peptide Chain
30:12
Putting Together a Parallel Peptide Chain
35:16
Anti-Parallel β-Conformation Arrangement
37:42
Tertiary Structure
45:03
Quaternary Structure
45:52
Illustration 3: Myoglobin Tertiary Structure & Hemoglobin Quaternary Structure
47:13
Final Words on Alpha Helix and Beta Conformation
48:34
Section 4: Proteins: Function
Protein Function I: Ligand Binding & Myoglobin

51m 36s

Intro
0:00
Protein Function I: Ligand Binding & Myoglobin
0:30
Ligand
1:02
Binding Site
2:06
Proteins are Not Static or Fixed
3:36
Multi-Subunit Proteins
5:46
O₂ as a Ligand
7:21
Myoglobin, Protoporphyrin IX, Fe ²⁺, and O₂
12:54
Protoporphyrin Illustration
14:25
Myoglobin With a Heme Group Illustration
17:02
Fe²⁺ has 6 Coordination Sites & Binds O₂
18:10
Heme
19:44
Myoglobin Overview
22:40
Myoglobin and O₂ Interaction
23:34
Keq or Ka & The Measure of Protein's Affinity for Its Ligand
26:46
Defining α: Fraction of Binding Sites Occupied
32:52
Graph: α vs. [L]
37:33
For The Special Case of α = 0.5
39:01
Association Constant & Dissociation Constant
43:54
α & Kd
45:15
Myoglobin's Binding of O₂
48:20
Protein Function II: Hemoglobin

1h 3m 36s

Intro
0:00
Protein Function II: Hemoglobin
0:14
Hemoglobin Overview
0:15
Hemoglobin & Its 4 Subunits
1:22
α and β Interactions
5:18
Two Major Conformations of Hb: T State (Tense) & R State (Relaxed)
8:06
Transition From The T State to R State
12:03
Binding of Hemoglobins & O₂
14:02
Binding Curve
18:32
Hemoglobin in the Lung
27:28
Signoid Curve
30:13
Cooperative Binding
32:25
Hemoglobin is an Allosteric Protein
34:26
Homotropic Allostery
36:18
Describing Cooperative Binding Quantitatively
38:06
Deriving The Hill Equation
41:52
Graphing the Hill Equation
44:43
The Slope and Degree of Cooperation
46:25
The Hill Coefficient
49:48
Hill Coefficient = 1
51:08
Hill Coefficient < 1
55:55
Where the Graph Hits the x-axis
56:11
Graph for Hemoglobin
58:02
Protein Function III: More on Hemoglobin

1h 7m 16s

Intro
0:00
Protein Function III: More on Hemoglobin
0:11
Two Models for Cooperative Binding: MWC & Sequential Model
0:12
MWC Model
1:31
Hemoglobin Subunits
3:32
Sequential Model
8:00
Hemoglobin Transports H⁺ & CO₂
17:23
Binding Sites of H⁺ and CO₂
19:36
CO₂ is Converted to Bicarbonate
23:28
Production of H⁺ & CO₂ in Tissues
27:28
H⁺ & CO₂ Binding are Inversely Related to O₂ Binding
28:31
The H⁺ Bohr Effect: His¹⁴⁶ Residue on the β Subunits
33:31
Heterotropic Allosteric Regulation of O₂ Binding by 2,3-Biphosphoglycerate (2,3 BPG)
39:53
Binding Curve for 2,3 BPG
56:21
Section 5: Enzymes
Enzymes I

41m 38s

Intro
0:00
Enzymes I
0:38
Enzymes Overview
0:39
Cofactor
4:38
Holoenzyme
5:52
Apoenzyme
6:40
Riboflavin, FAD, Pyridoxine, Pyridoxal Phosphate Structures
7:28
Carbonic Anhydrase
8:45
Classification of Enzymes
9:55
Example: EC 1.1.1.1
13:04
Reaction of Oxidoreductases
16:23
Enzymes: Catalysts, Active Site, and Substrate
18:28
Illustration of Enzymes, Substrate, and Active Site
27:22
Catalysts & Activation Energies
29:57
Intermediates
36:00
Enzymes II

44m 2s

Intro
0:00
Enzymes II: Transitions State, Binding Energy, & Induced Fit
0:18
Enzymes 'Fitting' Well With The Transition State
0:20
Example Reaction: Breaking of a Stick
3:40
Another Energy Diagram
8:20
Binding Energy
9:48
Enzymes Specificity
11:03
Key Point: Optimal Interactions Between Substrate & Enzymes
15:15
Induced Fit
16:25
Illustrations: Induced Fit
20:58
Enzymes II: Catalytic Mechanisms
22:17
General Acid/Base Catalysis
23:56
Acid Form & Base Form of Amino Acid: Glu &Asp
25:26
Acid Form & Base Form of Amino Acid: Lys & Arg
26:30
Acid Form & Base Form of Amino Acid: Cys
26:51
Acid Form & Base Form of Amino Acid: His
27:30
Acid Form & Base Form of Amino Acid: Ser
28:16
Acid Form & Base Form of Amino Acid: Tyr
28:30
Example: Phosphohexose Isomerase
29:20
Covalent Catalysis
34:19
Example: Glyceraldehyde 3-Phosphate Dehydrogenase
35:34
Metal Ion Catalysis: Isocitrate Dehydrogenase
38:45
Function of Mn²⁺
42:15
Enzymes III: Kinetics

56m 40s

Intro
0:00
Enzymes III: Kinetics
1:40
Rate of an Enzyme-Catalyzed Reaction & Substrate Concentration
1:41
Graph: Substrate Concentration vs. Reaction Rate
10:43
Rate At Low and High Substrate Concentration
14:26
Michaelis & Menten Kinetics
20:16
More On Rate & Concentration of Substrate
22:46
Steady-State Assumption
26:02
Rate is Determined by How Fast ES Breaks Down to Product
31:36
Total Enzyme Concentration: [Et] = [E] + [ES]
35:35
Rate of ES Formation
36:44
Rate of ES Breakdown
38:40
Measuring Concentration of Enzyme-Substrate Complex
41:19
Measuring Initial & Maximum Velocity
43:43
Michaelis & Menten Equation
46:44
What Happens When V₀ = (1/2) Vmax?
49:12
When [S] << Km
53:32
When [S] >> Km
54:44
Enzymes IV: Lineweaver-Burk Plots

20m 37s

Intro
0:00
Enzymes IV: Lineweaver-Burk Plots
0:45
Deriving The Lineweaver-Burk Equation
0:46
Lineweaver-Burk Plots
3:55
Example 1: Carboxypeptidase A
8:00
More on Km, Vmax, and Enzyme-catalyzed Reaction
15:54
Enzymes V: Enzyme Inhibition

51m 37s

Intro
0:00
Enzymes V: Enzyme Inhibition Overview
0:42
Enzyme Inhibitors Overview
0:43
Classes of Inhibitors
2:32
Competitive Inhibition
3:08
Competitive Inhibition
3:09
Michaelis & Menten Equation in the Presence of a Competitive Inhibitor
7:40
Double-Reciprocal Version of the Michaelis & Menten Equation
14:48
Competitive Inhibition Graph
16:37
Uncompetitive Inhibition
19:23
Uncompetitive Inhibitor
19:24
Michaelis & Menten Equation for Uncompetitive Inhibition
22:10
The Lineweaver-Burk Equation for Uncompetitive Inhibition
26:04
Uncompetitive Inhibition Graph
27:42
Mixed Inhibition
30:30
Mixed Inhibitor
30:31
Double-Reciprocal Version of the Equation
33:34
The Lineweaver-Burk Plots for Mixed Inhibition
35:02
Summary of Reversible Inhibitor Behavior
38:00
Summary of Reversible Inhibitor Behavior
38:01
Note: Non-Competitive Inhibition
42:22
Irreversible Inhibition
45:15
Irreversible Inhibition
45:16
Penicillin & Transpeptidase Enzyme
46:50
Enzymes VI: Regulatory Enzymes

51m 23s

Intro
0:00
Enzymes VI: Regulatory Enzymes
0:45
Regulatory Enzymes Overview
0:46
Example: Glycolysis
2:27
Allosteric Regulatory Enzyme
9:19
Covalent Modification
13:08
Two Other Regulatory Processes
16:28
Allosteric Regulation
20:58
Feedback Inhibition
25:12
Feedback Inhibition Example: L-Threonine → L-Isoleucine
26:03
Covalent Modification
27:26
Covalent Modulators: -PO₃²⁻
29:30
Protein Kinases
31:59
Protein Phosphatases
32:47
Addition/Removal of -PO₃²⁻ and the Effect on Regulatory Enzyme
33:36
Phosphorylation Sites of a Regulatory Enzyme
38:38
Proteolytic Cleavage
41:48
Zymogens: Chymotrypsin & Trypsin
43:58
Enzymes That Use More Than One Regulatory Process: Bacterial Glutamine Synthetase
48:59
Why The Complexity?
50:27
Enzymes VII: Km & Kcat

54m 49s

Intro
0:00
Km
1:48
Recall the Michaelis–Menten Equation
1:49
Km & Enzyme's Affinity
6:18
Rate Forward, Rate Backward, and Equilibrium Constant
11:08
When an Enzyme's Affinity for Its Substrate is High
14:17
More on Km & Enzyme Affinity
17:29
The Measure of Km Under Michaelis–Menten kinetic
23:19
Kcat (First-order Rate Constant or Catalytic Rate Constant)
24:10
Kcat: Definition
24:11
Kcat & The Michaelis–Menten Postulate
25:18
Finding Vmax and [Et}
27:27
Units for Vmax and Kcat
28:26
Kcat: Turnover Number
28:55
Michaelis–Menten Equation
32:12
Km & Kcat
36:37
Second Order Rate Equation
36:38
(Kcat)/(Km): Overview
39:22
High (Kcat)/(Km)
40:20
Low (Kcat)/(Km)
43:16
Practical Big Picture
46:28
Upper Limit to (Kcat)/(Km)
48:56
More On Kcat and Km
49:26
Section 6: Carbohydrates
Monosaccharides

1h 17m 46s

Intro
0:00
Monosaccharides
1:49
Carbohydrates Overview
1:50
Three Major Classes of Carbohydrates
4:48
Definition of Monosaccharides
5:46
Examples of Monosaccharides: Aldoses
7:06
D-Glyceraldehyde
7:39
D-Erythrose
9:00
D-Ribose
10:10
D-Glucose
11:20
Observation: Aldehyde Group
11:54
Observation: Carbonyl 'C'
12:30
Observation: D & L Naming System
12:54
Examples of Monosaccharides: Ketose
16:54
Dihydroxy Acetone
17:28
D-Erythrulose
18:30
D-Ribulose
19:49
D-Fructose
21:10
D-Glucose Comparison
23:18
More information of Ketoses
24:50
Let's Look Closer at D-Glucoses
25:50
Let's Look At All the D-Hexose Stereoisomers
31:22
D-Allose
32:20
D-Altrose
33:01
D-Glucose
33:39
D-Gulose
35:00
D-Mannose
35:40
D-Idose
36:42
D-Galactose
37:14
D-Talose
37:42
Epimer
40:05
Definition of Epimer
40:06
Example of Epimer: D-Glucose, D-Mannose, and D-Galactose
40:57
Hemiacetal or Hemiketal
44:36
Hemiacetal/Hemiketal Overview
45:00
Ring Formation of the α and β Configurations of D-Glucose
50:52
Ring Formation of the α and β Configurations of Fructose
1:01:39
Haworth Projection
1:07:34
Pyranose & Furanose Overview
1:07:38
Haworth Projection: Pyranoses
1:09:30
Haworth Projection: Furanose
1:14:56
Hexose Derivatives & Reducing Sugars

37m 6s

Intro
0:00
Hexose Derivatives
0:15
Point of Clarification: Forming a Cyclic Sugar From a Linear Sugar
0:16
Let's Recall the α and β Anomers of Glucose
8:42
α-Glucose
10:54
Hexose Derivatives that Play Key Roles in Physiology Progression
17:38
β-Glucose
18:24
β-Glucosamine
18:48
N-Acetyl-β-Glucosamine
20:14
β-Glucose-6-Phosphate
22:22
D-Gluconate
24:10
Glucono-δ-Lactone
26:33
Reducing Sugars
29:50
Reducing Sugars Overview
29:51
Reducing Sugars Example: β-Galactose
32:36
Disaccharides

43m 32s

Intro
0:00
Disaccharides
0:15
Disaccharides Overview
0:19
Examples of Disaccharides & How to Name Them
2:49
Disaccharides Trehalose Overview
15:46
Disaccharides Trehalose: Flip
20:52
Disaccharides Trehalose: Spin
28:36
Example: Draw the Structure
33:12
Polysaccharides

39m 25s

Intro
0:00
Recap Example: Draw the Structure of Gal(α1↔β1)Man
0:38
Polysaccharides
9:46
Polysaccharides Overview
9:50
Homopolysaccharide
13:12
Heteropolysaccharide
13:47
Homopolysaccharide as Fuel Storage
16:23
Starch Has Two Types of Glucose Polymer: Amylose
17:10
Starch Has Two Types of Glucose Polymer: Amylopectin
18:04
Polysaccharides: Reducing End & Non-Reducing End
19:30
Glycogen
20:06
Examples: Structures of Polysaccharides
21:42
Let's Draw an (α1→4) & (α1→6) of Amylopectin by Hand.
28:14
More on Glycogen
31:17
Glycogen, Concentration, & The Concept of Osmolarity
35:16
Polysaccharides, Part 2

44m 15s

Intro
0:00
Polysaccharides
0:17
Example: Cellulose
0:34
Glycoside Bond
7:25
Example Illustrations
12:30
Glycosaminoglycans Part 1
15:55
Glycosaminoglycans Part 2
18:34
Glycosaminoglycans & Sulfate Attachments
22:42
β-D-N-Acetylglucosamine
24:49
β-D-N-AcetylGalactosamine
25:42
β-D-Glucuronate
26:44
β-L-Iduronate
27:54
More on Sulfate Attachments
29:49
Hylarunic Acid
32:00
Hyaluronates
39:32
Other Glycosaminoglycans
40:46
Glycoconjugates

44m 23s

Intro
0:00
Glycoconjugates
0:24
Overview
0:25
Proteoglycan
2:53
Glycoprotein
5:20
Glycolipid
7:25
Proteoglycan vs. Glycoprotein
8:15
Cell Surface Diagram
11:17
Proteoglycan Common Structure
14:24
Example: Chondroitin-4-Sulfate
15:06
Glycoproteins
19:50
The Monomers that Commonly Show Up in The Oligo Portions of Glycoproteins
28:02
N-Acetylneuraminic Acid
31:17
L-Furose
32:37
Example of an N-Linked Oligosaccharide
33:21
Cell Membrane Structure
36:35
Glycolipids & Lipopolysaccharide
37:22
Structure Example
41:28
More Example Problems with Carbohydrates

40m 22s

Intro
0:00
Example 1
1:09
Example 2
2:34
Example 3
5:12
Example 4
16:19
Question
16:20
Solution
17:25
Example 5
24:18
Question
24:19
Structure of 2,3-Di-O-Methylglucose
26:47
Part A
28:11
Part B
33:46
Section 7: Lipids
Fatty Acids & Triacylglycerols

54m 55s

Intro
0:00
Fatty Acids
0:32
Lipids Overview
0:34
Introduction to Fatty Acid
3:18
Saturated Fatty Acid
6:13
Unsaturated or Polyunsaturated Fatty Acid
7:07
Saturated Fatty Acid Example
7:46
Unsaturated Fatty Acid Example
9:06
Notation Example: Chain Length, Degree of Unsaturation, & Double Bonds Location of Fatty Acid
11:56
Example 1: Draw the Structure
16:18
Example 2: Give the Shorthand for cis,cis-5,8-Hexadecadienoic Acid
20:12
Example 3
23:12
Solubility of Fatty Acids
25:45
Melting Points of Fatty Acids
29:40
Triacylglycerols
34:13
Definition of Triacylglycerols
34:14
Structure of Triacylglycerols
35:08
Example: Triacylglycerols
40:23
Recall Ester Formation
43:57
The Body's Primary Fuel-Reserves
47:22
Two Primary Advantages to Storing Energy as Triacylglycerols Instead of Glycogen: Number 1
49:24
Two Primary Advantages to Storing Energy as Triacylglycerols Instead of Glycogen: Number 2
51:54
Membrane Lipids

38m 51s

Intro
0:00
Membrane Lipids
0:26
Definition of Membrane Lipids
0:27
Five Major Classes of Membrane Lipids
2:38
Glycerophospholipids
5:04
Glycerophospholipids Overview
5:05
The X Group
8:05
Example: Phosphatidyl Ethanolamine
10:51
Example: Phosphatidyl Choline
13:34
Phosphatidyl Serine
15:16
Head Groups
16:50
Ether Linkages Instead of Ester Linkages
20:05
Galactolipids
23:39
Galactolipids Overview
23:40
Monogalactosyldiacylglycerol: MGDG
25:17
Digalactosyldiacylglycerol: DGDG
28:13
Structure Examples 1: Lipid Bilayer
31:35
Structure Examples 2: Cross Section of a Cell
34:56
Structure Examples 3: MGDG & DGDG
36:28
Membrane Lipids, Part 2

38m 20s

Intro
0:00
Sphingolipids
0:11
Sphingolipid Overview
0:12
Sphingosine Structure
1:42
Ceramide
3:56
Subclasses of Sphingolipids Overview
6:00
Subclasses of Sphingolipids: Sphingomyelins
7:53
Sphingomyelins
7:54
Subclasses of Sphingolipids: Glycosphingolipid
12:47
Glycosphingolipid Overview
12:48
Cerebrosides & Globosides Overview
14:33
Example: Cerebrosides
15:43
Example: Globosides
17:14
Subclasses of Sphingolipids: Gangliosides
19:07
Gangliosides
19:08
Medical Application: Tay-Sachs Disease
23:34
Sterols
30:45
Sterols: Basic Structure
30:46
Important Example: Cholesterol
32:01
Structures Example
34:13
The Biologically Active Lipids

48m 36s

Intro
0:00
The Biologically Active Lipids
0:44
Phosphatidyl Inositol Structure
0:45
Phosphatidyl Inositol Reaction
3:24
Image Example
12:49
Eicosanoids
14:12
Arachidonic Acid & Membrane Lipid Containing Arachidonic Acid
18:41
Three Classes of Eicosanoids
20:42
Overall Structures
21:38
Prostagladins
22:56
Thromboxane
27:19
Leukotrienes
30:19
More On The Biologically Active Lipids
33:34
Steroid Hormones
33:35
Fat Soluble Vitamins
38:25
Vitamin D₃
40:40
Vitamin A
43:17
Vitamin E
45:12
Vitamin K
47:17
Section 8: Energy & Biological Systems (Bioenergetics)
Thermodynamics, Free Energy & Equilibrium

45m 51s

Intro
0:00
Thermodynamics, Free Energy and Equilibrium
1:03
Reaction: Glucose + Pi → Glucose 6-Phosphate
1:50
Thermodynamics & Spontaneous Processes
3:31
In Going From Reactants → Product, a Reaction Wants to Release Heat
6:30
A Reaction Wants to Become More Disordered
9:10
∆H < 0
10:30
∆H > 0
10:57
∆S > 0
11:23
∆S <0
11:56
∆G = ∆H - T∆S at Constant Pressure
12:15
Gibbs Free Energy
15:00
∆G < 0
16:49
∆G > 0
17:07
Reference Frame For Thermodynamics Measurements
17:57
More On BioChemistry Standard
22:36
Spontaneity
25:36
Keq
31:45
Example: Glucose + Pi → Glucose 6-Phosphate
34:14
Example Problem 1
40:25
Question
40:26
Solution
41:12
More on Thermodynamics & Free Energy

37m 6s

Intro
0:00
More on Thermodynamics & Free Energy
0:16
Calculating ∆G Under Standard Conditions
0:17
Calculating ∆G Under Physiological Conditions
2:05
∆G < 0
5:39
∆G = 0
7:03
Reaction Moving Forward Spontaneously
8:00
∆G & The Maximum Theoretical Amount of Free Energy Available
10:36
Example Problem 1
13:11
Reactions That Have Species in Common
17:48
Example Problem 2: Part 1
20:10
Example Problem 2: Part 2- Enzyme Hexokinase & Coupling
25:08
Example Problem 2: Part 3
30:34
Recap
34:45
ATP & Other High-Energy Compounds

44m 32s

Intro
0:00
ATP & Other High-Energy Compounds
0:10
Endergonic Reaction Coupled With Exergonic Reaction
0:11
Major Theme In Metabolism
6:56
Why the ∆G°' for ATP Hydrolysis is Large & Negative
12:24
∆G°' for ATP Hydrolysis
12:25
Reason 1: Electrostatic Repulsion
14:24
Reason 2: Pi & Resonance Forms
15:33
Reason 3: Concentrations of ADP & Pi
17:32
ATP & Other High-Energy Compounds Cont'd
18:48
More On ∆G°' & Hydrolysis
18:49
Other Compounds That Have Large Negative ∆G°' of Hydrolysis: Phosphoenol Pyruvate (PEP)
25:14
Enzyme Pyruvate Kinase
30:36
Another High Energy Molecule: 1,3 Biphosphoglycerate
36:17
Another High Energy Molecule: Phophocreatine
39:41
Phosphoryl Group Transfers

30m 8s

Intro
0:00
Phosphoryl Group Transfer
0:27
Phosphoryl Group Transfer Overview
0:28
Example: Glutamate → Glutamine Part 1
7:11
Example: Glutamate → Glutamine Part 2
13:29
ATP Not Only Transfers Phosphoryl, But Also Pyrophosphoryl & Adenylyl Groups
17:03
Attack At The γ Phosphorous Transfers a Phosphoryl
19:02
Attack At The β Phosphorous Gives Pyrophosphoryl
22:44
Oxidation-Reduction Reactions

49m 46s

Intro
0:00
Oxidation-Reduction Reactions
1:32
Redox Reactions
1:33
Example 1: Mg + Al³⁺ → Mg²⁺ + Al
3:49
Reduction Potential Definition
10:47
Reduction Potential Example
13:38
Organic Example
22:23
Review: How To Find The Oxidation States For Carbon
24:15
Examples: Oxidation States For Carbon
27:45
Example 1: Oxidation States For Carbon
27:46
Example 2: Oxidation States For Carbon
28:36
Example 3: Oxidation States For Carbon
29:18
Example 4: Oxidation States For Carbon
29:44
Example 5: Oxidation States For Carbon
30:10
Example 6: Oxidation States For Carbon
30:40
Example 7: Oxidation States For Carbon
31:20
Example 8: Oxidation States For Carbon
32:10
Example 9: Oxidation States For Carbon
32:52
Oxidation-Reduction Reactions, cont'd
35:22
More On Reduction Potential
35:28
Lets' Start With ∆G = ∆G°' + RTlnQ
38:29
Example: Oxidation Reduction Reactions
41:42
More On Oxidation-Reduction Reactions

56m 34s

Intro
0:00
More On Oxidation-Reduction Reactions
0:10
Example 1: What If the Concentrations Are Not Standard?
0:11
Alternate Procedure That Uses The 1/2 Reactions Individually
8:57
Universal Electron Carriers in Aqueous Medium: NAD+ & NADH
15:12
The Others Are…
19:22
NAD+ & NADP Coenzymes
20:56
FMN & FAD
22:03
Nicotinamide Adenine Dinucleotide (Phosphate)
23:03
Reduction 1/2 Reactions
36:10
Ratio of NAD+ : NADH
36:52
Ratio of NADPH : NADP+
38:02
Specialized Roles of NAD+ & NADPH
38:48
Oxidoreductase Enzyme Overview
40:26
Examples of Oxidoreductase
43:32
The Flavin Nucleotides
46:46
Example Problems For Bioenergetics

42m 12s

Intro
0:00
Example 1: Calculate the ∆G°' For The Following Reaction
1:04
Example 1: Question
1:05
Example 1: Solution
2:20
Example 2: Calculate the Keq For the Following
4:20
Example 2: Question
4:21
Example 2: Solution
5:54
Example 3: Calculate the ∆G°' For The Hydrolysis of ATP At 25°C
8:52
Example 3: Question
8:53
Example 3: Solution
10:30
Example 3: Alternate Procedure
13:48
Example 4: Problems For Bioenergetics
16:46
Example 4: Questions
16:47
Example 4: Part A Solution
21:19
Example 4: Part B Solution
23:26
Example 4: Part C Solution
26:12
Example 5: Problems For Bioenergetics
29:27
Example 5: Questions
29:35
Example 5: Solution - Part 1
32:16
Example 5: Solution - Part 2
34:39
Section 9: Glycolysis and Gluconeogenesis
Overview of Glycolysis I

43m 32s

Intro
0:00
Overview of Glycolysis
0:48
Three Primary Paths For Glucose
1:04
Preparatory Phase of Glycolysis
4:40
Payoff Phase of Glycolysis
6:40
Glycolysis Reactions Diagram
7:58
Enzymes of Glycolysis
12:41
Glycolysis Reactions
16:02
Step 1
16:03
Step 2
18:03
Step 3
18:52
Step 4
20:08
Step 5
21:42
Step 6
22:44
Step 7
24:22
Step 8
25:11
Step 9
26:00
Step 10
26:51
Overview of Glycolysis Cont.
27:28
The Overall Reaction for Glycolysis
27:29
Recall The High-Energy Phosphorylated Compounds Discusses In The Bioenergetics Unit
33:10
What Happens To The Pyruvate That Is Formed?
37:58
Glycolysis II

1h 1m 47s

Intro
0:00
Glycolysis Step 1: The Phosphorylation of Glucose
0:27
Glycolysis Step 1: Reaction
0:28
Hexokinase
2:28
Glycolysis Step 1: Mechanism-Simple Nucleophilic Substitution
6:34
Glycolysis Step 2: Conversion of Glucose 6-Phosphate → Fructose 6-Phosphate
11:33
Glycolysis Step 2: Reaction
11:34
Glycolysis Step 2: Mechanism, Part 1
14:40
Glycolysis Step 2: Mechanism, Part 2
18:16
Glycolysis Step 2: Mechanism, Part 3
19:56
Glycolysis Step 2: Mechanism, Part 4 (Ring Closing & Dissociation)
21:54
Glycolysis Step 3: Conversion of Fructose 6-Phosphate to Fructose 1,6-Biphosphate
24:16
Glycolysis Step 3: Reaction
24:17
Glycolysis Step 3: Mechanism
26:40
Glycolysis Step 4: Cleavage of Fructose 1,6-Biphosphate
31:10
Glycolysis Step 4: Reaction
31:11
Glycolysis Step 4: Mechanism, Part 1 (Binding & Ring Opening)
35:26
Glycolysis Step 4: Mechanism, Part 2
37:40
Glycolysis Step 4: Mechanism, Part 3
39:30
Glycolysis Step 4: Mechanism, Part 4
44:00
Glycolysis Step 4: Mechanism, Part 5
46:34
Glycolysis Step 4: Mechanism, Part 6
49:00
Glycolysis Step 4: Mechanism, Part 7
50:12
Hydrolysis of The Imine
52:33
Glycolysis Step 5: Conversion of Dihydroxyaceton Phosphate to Glyceraldehyde 3-Phosphate
55:38
Glycolysis Step 5: Reaction
55:39
Breakdown and Numbering of Sugar
57:40
Glycolysis III

59m 17s

Intro
0:00
Glycolysis Step 5: Conversion of Dihydroxyaceton Phosphate to Glyceraldehyde 3-Phosphate
0:44
Glycolysis Step 5: Mechanism, Part 1
0:45
Glycolysis Step 5: Mechanism, Part 2
3:53
Glycolysis Step 6: Oxidation of Glyceraldehyde 3-Phosphate to 1,3-Biphosphoglycerate
5:14
Glycolysis Step 6: Reaction
5:15
Glycolysis Step 6: Mechanism, Part 1
8:52
Glycolysis Step 6: Mechanism, Part 2
12:58
Glycolysis Step 6: Mechanism, Part 3
14:26
Glycolysis Step 6: Mechanism, Part 4
16:23
Glycolysis Step 7: Phosphoryl Transfer From 1,3-Biphosphoglycerate to ADP to Form ATP
19:08
Glycolysis Step 7: Reaction
19:09
Substrate-Level Phosphorylation
23:18
Glycolysis Step 7: Mechanism (Nucleophilic Substitution)
26:57
Glycolysis Step 8: Conversion of 3-Phosphoglycerate to 2-Phosphoglycerate
28:44
Glycolysis Step 8: Reaction
28:45
Glycolysis Step 8: Mechanism, Part 1
30:08
Glycolysis Step 8: Mechanism, Part 2
32:24
Glycolysis Step 8: Mechanism, Part 3
34:02
Catalytic Cycle
35:42
Glycolysis Step 9: Dehydration of 2-Phosphoglycerate to Phosphoenol Pyruvate
37:20
Glycolysis Step 9: Reaction
37:21
Glycolysis Step 9: Mechanism, Part 1
40:12
Glycolysis Step 9: Mechanism, Part 2
42:01
Glycolysis Step 9: Mechanism, Part 3
43:58
Glycolysis Step 10: Transfer of a Phosphoryl Group From Phosphoenol Pyruvate To ADP To Form ATP
45:16
Glycolysis Step 10: Reaction
45:17
Substrate-Level Phosphorylation
48:32
Energy Coupling Reaction
51:24
Glycolysis Balance Sheet
54:15
Glycolysis Balance Sheet
54:16
What Happens to The 6 Carbons of Glucose?
56:22
What Happens to 2 ADP & 2 Pi?
57:04
What Happens to The 4e⁻ ?
57:15
Glycolysis IV

39m 47s

Intro
0:00
Feeder Pathways
0:42
Feeder Pathways Overview
0:43
Starch, Glycogen
2:25
Lactose
4:38
Galactose
4:58
Manose
5:22
Trehalose
5:45
Sucrose
5:56
Fructose
6:07
Fates of Pyruvate: Aerobic & Anaerobic Conditions
7:39
Aerobic Conditions & Pyruvate
7:40
Anaerobic Fates of Pyruvate
11:18
Fates of Pyruvate: Lactate Acid Fermentation
14:10
Lactate Acid Fermentation
14:11
Fates of Pyruvate: Ethanol Fermentation
19:01
Ethanol Fermentation Reaction
19:02
TPP: Thiamine Pyrophosphate (Functions and Structure)
23:10
Ethanol Fermentation Mechanism, Part 1
27:53
Ethanol Fermentation Mechanism, Part 2
29:06
Ethanol Fermentation Mechanism, Part 3
31:15
Ethanol Fermentation Mechanism, Part 4
32:44
Ethanol Fermentation Mechanism, Part 5
34:33
Ethanol Fermentation Mechanism, Part 6
35:48
Gluconeogenesis I

41m 34s

Intro
0:00
Gluconeogenesis, Part 1
1:02
Gluconeogenesis Overview
1:03
3 Glycolytic Reactions That Are Irreversible Under Physiological Conditions
2:29
Gluconeogenesis Reactions Overview
6:17
Reaction: Pyruvate to Oxaloacetate
11:07
Reaction: Oxaloacetate to Phosphoenolpyruvate (PEP)
13:29
First Pathway That Pyruvate Can Take to Become Phosphoenolpyruvate
15:24
Second Pathway That Pyruvate Can Take to Become Phosphoenolpyruvate
21:00
Transportation of Pyruvate From The Cytosol to The Mitochondria
24:15
Transportation Mechanism, Part 1
26:41
Transportation Mechanism, Part 2
30:43
Transportation Mechanism, Part 3
34:04
Transportation Mechanism, Part 4
38:14
Gluconeogenesis II

34m 18s

Intro
0:00
Oxaloacetate → Phosphoenolpyruvate (PEP)
0:35
Mitochondrial Membrane Does Not Have a Transporter for Oxaloactate
0:36
Reaction: Oxaloacetate to Phosphoenolpyruvate (PEP)
3:36
Mechanism: Oxaloacetate to Phosphoenolpyruvate (PEP)
4:48
Overall Reaction: Pyruvate to Phosphoenolpyruvate
7:01
Recall The Two Pathways That Pyruvate Can Take to Become Phosphoenolpyruvate
10:16
NADH in Gluconeogenesis
12:29
Second Pathway: Lactate → Pyruvate
18:22
Cytosolic PEP Carboxykinase, Mitochondrial PEP Carboxykinase, & Isozymes
18:23
2nd Bypass Reaction
23:04
3rd Bypass Reaction
24:01
Overall Process
25:17
Other Feeder Pathways For Gluconeogenesis
26:35
Carbon Intermediates of The Citric Acid Cycle
26:36
Amino Acids & The Gluconeogenic Pathway
29:45
Glycolysis & Gluconeogenesis Are Reciprocally Regulated
32:00
The Pentose Phosphate Pathway

42m 52s

Intro
0:00
The Pentose Phosphate Pathway Overview
0:17
The Major Fate of Glucose-6-Phosphate
0:18
The Pentose Phosphate Pathway (PPP) Overview
1:00
Oxidative Phase of The Pentose Phosphate Pathway
4:33
Oxidative Phase of The Pentose Phosphate Pathway: Reaction Overview
4:34
Ribose-5-Phosphate: Glutathione & Reductive Biosynthesis
9:02
Glucose-6-Phosphate to 6-Phosphogluconate
12:48
6-Phosphogluconate to Ribulose-5-Phosphate
15:39
Ribulose-5-Phosphate to Ribose-5-Phosphate
17:05
Non-Oxidative Phase of The Pentose Phosphate Pathway
19:55
Non-Oxidative Phase of The Pentose Phosphate Pathway: Overview
19:56
General Transketolase Reaction
29:03
Transaldolase Reaction
35:10
Final Transketolase Reaction
39:10
Section 10: The Citric Acid Cycle (Krebs Cycle)
Citric Acid Cycle I

36m 10s

Intro
0:00
Stages of Cellular Respiration
0:23
Stages of Cellular Respiration
0:24
From Pyruvate to Acetyl-CoA
6:56
From Pyruvate to Acetyl-CoA: Pyruvate Dehydrogenase Complex
6:57
Overall Reaction
8:42
Oxidative Decarboxylation
11:54
Pyruvate Dehydrogenase (PDH) & Enzymes
15:30
Pyruvate Dehydrogenase (PDH) Requires 5 Coenzymes
17:15
Molecule of CoEnzyme A
18:52
Thioesters
20:56
Lipoic Acid
22:31
Lipoate Is Attached To a Lysine Residue On E₂
24:42
Pyruvate Dehydrogenase Complex: Reactions
26:36
E1: Reaction 1 & 2
30:38
E2: Reaction 3
31:58
E3: Reaction 4 & 5
32:44
Substrate Channeling
34:17
Citric Acid Cycle II

49m 20s

Intro
0:00
Citric Acid Cycle Reactions Overview
0:26
Citric Acid Cycle Reactions Overview: Part 1
0:27
Citric Acid Cycle Reactions Overview: Part 2
7:03
Things to Note
10:58
Citric Acid Cycle Reactions & Mechanism
13:57
Reaction 1: Formation of Citrate
13:58
Reaction 1: Mechanism
19:01
Reaction 2: Citrate to Cis Aconistate to Isocitrate
28:50
Reaction 3: Isocitrate to α-Ketoglutarate
32:35
Reaction 3: Two Isocitrate Dehydrogenase Enzymes
36:24
Reaction 3: Mechanism
37:33
Reaction 4: Oxidation of α-Ketoglutarate to Succinyl-CoA
41:38
Reaction 4: Notes
46:34
Citric Acid Cycle III

44m 11s

Intro
0:00
Citric Acid Cycle Reactions & Mechanism
0:21
Reaction 5: Succinyl-CoA to Succinate
0:24
Reaction 5: Reaction Sequence
2:35
Reaction 6: Oxidation of Succinate to Fumarate
8:28
Reaction 7: Fumarate to Malate
10:17
Reaction 8: Oxidation of L-Malate to Oxaloacetate
14:15
More On The Citric Acid Cycle
17:17
Energy from Oxidation
17:18
How Can We Transfer This NADH Into the Mitochondria
27:10
Citric Cycle is Amphibolic - Works In Both Anabolic & Catabolic Pathways
32:06
Biosynthetic Processes
34:29
Anaplerotic Reactions Overview
37:26
Anaplerotic: Reaction 1
41:42
Section 11: Catabolism of Fatty Acids
Fatty Acid Catabolism I

48m 11s

Intro
0:00
Introduction to Fatty Acid Catabolism
0:21
Introduction to Fatty Acid Catabolism
0:22
Vertebrate Cells Obtain Fatty Acids for Catabolism From 3 Sources
2:16
Diet: Part 1
4:00
Diet: Part 2
5:35
Diet: Part 3
6:20
Diet: Part 4
6:47
Diet: Part 5
10:18
Diet: Part 6
10:54
Diet: Part 7
12:04
Diet: Part 8
12:26
Fats Stored in Adipocytes Overview
13:54
Fats Stored in Adipocytes (Fat Cells): Part 1
16:13
Fats Stored in Adipocytes (Fat Cells): Part 2
17:16
Fats Stored in Adipocytes (Fat Cells): Part 3
19:42
Fats Stored in Adipocytes (Fat Cells): Part 4
20:52
Fats Stored in Adipocytes (Fat Cells): Part 5
22:56
Mobilization of TAGs Stored in Fat Cells
24:35
Fatty Acid Oxidation
28:29
Fatty Acid Oxidation
28:48
3 Reactions of the Carnitine Shuttle
30:42
Carnitine Shuttle & The Mitochondrial Matrix
36:25
CAT I
43:58
Carnitine Shuttle is the Rate-Limiting Steps
46:24
Fatty Acid Catabolism II

45m 58s

Intro
0:00
Fatty Acid Catabolism
0:15
Fatty Acid Oxidation Takes Place in 3 Stages
0:16
β-Oxidation
2:05
β-Oxidation Overview
2:06
Reaction 1
4:20
Reaction 2
7:35
Reaction 3
8:52
Reaction 4
10:16
β-Oxidation Reactions Discussion
11:34
Notes On β-Oxidation
15:14
Double Bond After The First Reaction
15:15
Reaction 1 is Catalyzed by 3 Isozymes of Acyl-CoA Dehydrogenase
16:04
Reaction 2 & The Addition of H₂O
18:38
After Reaction 4
19:24
Production of ATP
20:04
β-Oxidation of Unsaturated Fatty Acid
21:25
β-Oxidation of Unsaturated Fatty Acid
22:36
β-Oxidation of Mono-Unsaturates
24:49
β-Oxidation of Mono-Unsaturates: Reaction 1
24:50
β-Oxidation of Mono-Unsaturates: Reaction 2
28:43
β-Oxidation of Mono-Unsaturates: Reaction 3
30:50
β-Oxidation of Mono-Unsaturates: Reaction 4
31:06
β-Oxidation of Polyunsaturates
32:29
β-Oxidation of Polyunsaturates: Part 1
32:30
β-Oxidation of Polyunsaturates: Part 2
37:08
β-Oxidation of Polyunsaturates: Part 3
40:25
Fatty Acid Catabolism III

33m 18s

Intro
0:00
Fatty Acid Catabolism
0:43
Oxidation of Fatty Acids With an Odd Number of Carbons
0:44
β-oxidation in the Mitochondrion & Two Other Pathways
9:08
ω-oxidation
10:37
α-oxidation
17:22
Ketone Bodies
19:08
Two Fates of Acetyl-CoA Formed by β-Oxidation Overview
19:09
Ketone Bodies: Acetone
20:42
Ketone Bodies: Acetoacetate
20:57
Ketone Bodies: D-β-hydroxybutyrate
21:25
Two Fates of Acetyl-CoA Formed by β-Oxidation: Part 1
22:05
Two Fates of Acetyl-CoA Formed by β-Oxidation: Part 2
26:59
Two Fates of Acetyl-CoA Formed by β-Oxidation: Part 3
30:52
Section 12: Catabolism of Amino Acids and the Urea Cycle
Overview & The Aminotransferase Reaction

40m 59s

Intro
0:00
Overview of The Aminotransferase Reaction
0:25
Overview of The Aminotransferase Reaction
0:26
The Aminotransferase Reaction: Process 1
3:06
The Aminotransferase Reaction: Process 2
6:46
Alanine From Muscle Tissue
10:54
Bigger Picture of the Aminotransferase Reaction
14:52
Looking Closely at Process 1
19:04
Pyridoxal Phosphate (PLP)
24:32
Pyridoxamine Phosphate
25:29
Pyridoxine (B6)
26:38
The Function of PLP
27:12
Mechanism Examples
28:46
Reverse Reaction: Glutamate to α-Ketoglutarate
35:34
Glutamine & Alanine: The Urea Cycle I

39m 18s

Intro
0:00
Glutamine & Alanine: The Urea Cycle I
0:45
Excess Ammonia, Glutamate, and Glutamine
0:46
Glucose-Alanine Cycle
9:54
Introduction to the Urea Cycle
20:56
The Urea Cycle: Production of the Carbamoyl Phosphate
22:59
The Urea Cycle: Reaction & Mechanism Involving the Carbamoyl Phosphate Synthetase
33:36
Glutamine & Alanine: The Urea Cycle II

36m 21s

Intro
0:00
Glutamine & Alanine: The Urea Cycle II
0:14
The Urea Cycle Overview
0:34
Reaction 1: Ornithine → Citrulline
7:30
Reaction 2: Citrulline → Citrullyl-AMP
11:15
Reaction 2': Citrullyl-AMP → Argininosuccinate
15:25
Reaction 3: Argininosuccinate → Arginine
20:42
Reaction 4: Arginine → Orthinine
24:00
Links Between the Citric Acid Cycle & the Urea Cycle
27:47
Aspartate-argininosuccinate Shunt
32:36
Amino Acid Catabolism

47m 58s

Intro
0:00
Amino Acid Catabolism
0:10
Common Amino Acids and 6 Major Products
0:11
Ketogenic Amino Acid
1:52
Glucogenic Amino Acid
2:51
Amino Acid Catabolism Diagram
4:18
Cofactors That Play a Role in Amino Acid Catabolism
7:00
Biotin
8:42
Tetrahydrofolate
10:44
S-Adenosylmethionine (AdoMet)
12:46
Tetrahydrobiopterin
13:53
S-Adenosylmethionine & Tetrahydrobiopterin Molecules
14:41
Catabolism of Phenylalanine
18:30
Reaction 1: Phenylalanine to Tyrosine
18:31
Reaction 2: Tyrosine to p-Hydroxyphenylpyruvate
21:36
Reaction 3: p-Hydroxyphenylpyruvate to Homogentisate
23:50
Reaction 4: Homogentisate to Maleylacetoacetate
25:42
Reaction 5: Maleylacetoacetate to Fumarylacetoacetate
28:20
Reaction 6: Fumarylacetoacetate to Fumarate & Succinyl-CoA
29:51
Reaction 7: Fate of Fumarate & Succinyl-CoA
31:14
Phenylalanine Hydroxylase
33:33
The Phenylalanine Hydroxylase Reaction
33:34
Mixed-Function Oxidases
40:26
When Phenylalanine Hydoxylase is Defective: Phenylketonuria (PKU)
44:13
Section 13: Oxidative Phosphorylation and ATP Synthesis
Oxidative Phosphorylation I

41m 11s

Intro
0:00
Oxidative Phosphorylation
0:54
Oxidative Phosphorylation Overview
0:55
Mitochondrial Electron Transport Chain Diagram
7:15
Enzyme Complex I of the Electron Transport Chain
12:27
Enzyme Complex II of the Electron Transport Chain
14:02
Enzyme Complex III of the Electron Transport Chain
14:34
Enzyme Complex IV of the Electron Transport Chain
15:30
Complexes Diagram
16:25
Complex I
18:25
Complex I Overview
18:26
What is Ubiquinone or Coenzyme Q?
20:02
Coenzyme Q Transformation
22:37
Complex I Diagram
24:47
Fe-S Proteins
26:42
Transfer of H⁺
29:42
Complex II
31:06
Succinate Dehydrogenase
31:07
Complex II Diagram & Process
32:54
Other Substrates Pass Their e⁻ to Q: Glycerol 3-Phosphate
37:31
Other Substrates Pass Their e⁻ to Q: Fatty Acyl-CoA
39:02
Oxidative Phosphorylation II

36m 27s

Intro
0:00
Complex III
0:19
Complex III Overview
0:20
Complex III: Step 1
1:56
Complex III: Step 2
6:14
Complex IV
8:42
Complex IV: Cytochrome Oxidase
8:43
Oxidative Phosphorylation, cont'd
17:18
Oxidative Phosphorylation: Summary
17:19
Equation 1
19:13
How Exergonic is the Reaction?
21:03
Potential Energy Represented by Transported H⁺
27:24
Free Energy Change for the Production of an Electrochemical Gradient Via an Ion Pump
28:48
Free Energy Change in Active Mitochondria
32:02
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Lecture Comments (16)

1 answer

Last reply by: Professor Hovasapian
Fri Dec 27, 2019 7:40 AM

Post by William Dawson on December 22, 2019

Why are BCAA's (Leucine, Isoleucine, Valine) functionally associated ?

1 answer

Last reply by: Professor Hovasapian
Thu Aug 23, 2018 8:16 AM

Post by Anthony Villarama on August 21, 2018

This professor is so good. He is organize an explains very well. But what I like about his teaching most is he doesn't go around the bush.

0 answers

Post by Mohamed E Sowaileh on June 12, 2016

Hello Dr. Hovasapian,

Thank you for the immediate response. I am very grateful to you for the invaluable guidance you gave me. May God bless you.

sorry for my very late response, I forgot that I asked you a question!

3 answers

Last reply by: Professor Hovasapian
Wed May 11, 2016 2:30 AM

Post by Mohamed E Sowaileh on May 8, 2016

Dr. Raffi Hovasapian ,

I hope you are doing very well,

Someone has never taken a deep and comprehensive general chemistry course, do you recommend him to take G. chemistry course first, because I guess biochemistry then would be a lot more easier and more understandable than if I didn't take G. chemistry. am I correct? or do you think that the quick review you made is quite sufficient? I appreciate your help.

 Thank you.  

1 answer

Last reply by: Professor Hovasapian
Fri Sep 12, 2014 5:17 PM

Post by Jenika Javier on September 12, 2014

Why are all amino acids in the L-Configuration and what will the consequences of this be?

2 answers

Last reply by: tashi thukhotsong
Thu Oct 10, 2013 1:42 PM

Post by tashi thukhotsong on October 7, 2013

shouldn't hydrogen be perpendicular to  R-group alpha-Amino acids drawn at 3:52. Not sure if the orientation is correct??

1 answer

Last reply by: Shannen Brown
Tue Jun 25, 2013 2:39 AM

Post by Mahir Ahmed on May 5, 2013

Hi Sir
Iam adamant that there something unusual with this site,if you want to watch the lectures they are ok,but if you want to download them using internet download manager(IDM)you get two separate FLV files ,one for the explanation and one for Dr Hovasapian.Please help.
Thanks

Amino Acids

Lecture Slides are screen-captured images of important points in the lecture. Students can download and print out these lecture slide images to do practice problems as well as take notes while watching the lecture.

  • Intro 0:00
  • Amino Acids 0:17
    • Proteins & Amino Acids
    • Difference Between Amino Acids
    • α-Carbon
    • Configuration in Biochemistry
    • L-Glyceraldehyde & Fischer Projection
    • D-Glyceraldehyde & Fischer Projection
    • Amino Acids in Biological Proteins are the L Enantiomer
    • L-Amino Acid
    • L-Amino Acids Correspond to S-Enantiomers in the RS System
    • Classification of Amino Acids
  • Amino Acids With Non-Polar R Groups 26:45
    • Glycine
    • Alanine
    • Valine
    • Leucine
    • Proline
    • Isoleucine
    • Methionine
  • Amino Acids With Aromatic R Groups 34:33
    • Phenylalanine
    • Tyrosine
    • Tryptophan

Transcription: Amino Acids

Hello and welcome back to Educator.com, and welcome back to Biochemistry.0000

Today, we're going to start our discussion of biochemistry proper with the first of the biological macromolecules- the proteins, and proteins are made of amino acids.0004

Let's just jump right on in.0015

OK.0018

Of the biological macromolecules, proteins are the most abundant.0020

You have lipids which are your fats; you have the nucleic acids.0025

You have the carbohydrates, the sugars; and you have proteins.0028

Proteins are the most abundant.0032

Proteins are the ones that actually do everything.0034

They're the work horses of physiological systems.0037

Let's go ahead and write that down; let's do a blue ink today.0042

OK.0047

Of the biological macromolecules, proteins are the most abundant and the most diverse.0050

OK.0075

Proteins are made up of amino acids strung together like pearls on a string, like beads on a string.0076

Proteins are made up of amino acids strung together- that's it.0084

That's all a protein is.0098

It could be 2 or 3 amino acids strung together, or it could be a thousand amino acids strung together- that's it.0100

OK.0110

There are 20 common amino acids that make up the majority of proteins.0111

Well, they make up all the proteins, but I'll go ahead and just write the majority because that's the way I have it written.0128

OK.0139

All 20 are actually called alpha-amino acids and have the following structure.0143

OK.0166

Let me see where should I put this; that's fine, I'll go ahead and put it in the center.0168

We have C, COO, O-; OK, we have an H, we have NH3+ - did I put a plus, yes I did - and we have R.0173

OK, so this right here, this is called the alpha-carbon, and it is the alpha-carbon because it is the C that is attached to the carbonyl group; and the carbonyl group - you remember from organic chemistry - is this thing right here.0190

In this particular case, it is carboxylic acid because you have C, double bonded O, single bonded O, minus, the H has been taken off; it's usually COOH, and we'll talk about why I wrote the minus and the plus here a little bit later, but that's it.0223

It's called the alpha-carbon.0237

The alpha-carbon is not the first carbon in the chain.0238

The first carbon is the carbon of the carbonyl 1, 2, and as there are others; but the alpha-carbon is the one that's actually attached to the carbonyl carbon.0241

It's very, very important to distinguish that, and we'll talk a little bit more about that when we get into larger molecules and things like that, when we talk about alpha, beta, gamma, delta- things like that.0251

OK.0260

Now, the only thing that is different from one amino acid to the next is the R-group.0267

It's this thing right here.0294

That's the only thing that's different; everything else is actually still the same.0295

There is an alpha-carbon; there is an H attached to it.0299

There is an amino group, that's why we call it an alpha-amino acid.0301

This is the acidic group, the COOH or COO-, it's the carboxylate, it has lost its hydrogen ion; so carboxylic acid, carbon alpha-amino acid- this is the only thing that changes for the 20 different amino acids.0306

OK.0324

Different R-groups give different properties, and this is what makes proteins so amazing.0327

The body coated in your DNA is, of course, the instructions for how to make the protein, and the protein is just based on a series of amino acids strung together - this one, this one, this one, this one - depending on how we string them together and how many we get different properties for the different proteins because different proteins have to serve different functions.0350

This is what's so amazing.0372

You have this incredible, incredible diversity of things that proteins do, I mean all kinds of things- things that you would never think are connected, and yet all of that is based on the properties of these 20 amino acids, 20, that's it.0374

I mean it's just as extraordinary as having those 4 bases that make up the DNA.0389

I mean it really is kind of extraordinary that you can actually have this level of diversity of function just from so few pieces.0393

OK.0406

Now, let's go ahead, let me redraw this structure here, just so we have it on the same page.0409

A C, O-, there is an H, there is an R-group, and there is an amino group, and I'll put 3, and I'll put a positive charge on the nitrogen.0417

OK.0429

Notice that 4 different groups are attached to the same carbon.0430

The 4 different groups are attached to the alpha-carbon.0443

Let's go back to blue.0453

1, 2, 3, 4, you have the H, you have the carboxylic acid group, the carboxylate, you have the amino group, and you have the R-group- 4 different groups attached to a central carbon.0454

OK.0465

The alpha-carbon, the alpha C is a chiral center; and I hope that you remember what a chiral center is from organic chemistry.0470

Anytime you have 4 different groups attached to a single carbon, that carbon is a chiral center; and what that means is that, the arrangement of these 4 groups in space is such that you actually get two different versions of this particular molecule.0482

You get something called a left handed version, and you get something called a right handed version.0497

Let's write this out, each amino acid, except for glycine, and we'll see why later, because glycine, this R-group happens to be an H, so there are 2 hydrogens attached to the alpha-carbon, so it doesn’t come in an enantiomeric pair.0511

It doesn’t have a left handed, right handed version- it's just glycine.0534

Each amino acid exists as an enantiomeric pair, what we would call left handed and right handed- that's the best way to think about it.0550

In other words, what happens if I have a solution of, let's say alanine, some amino acid, if I have a solution of alanine and if I have separated that solution out into its left handed alanine, right handed alanine, if I pass some plain polarized light through that solution, one of them is going to rotate it to the left, one of them is going to rotate it to the right.0575

It has to do with how these 4 groups are arranged in space; and enantiomers, as you remember, are mirror images that are not super impulsible.0603

My left hand and right hand are mirror images of each other.0612

There is a mirror right here, but I can’t take my right hand, put it on top of my left hand, and have it match equally- it won't happen.0615

That's all that means, and you hopefully you remember that from organic chemistry; if not, I would definitely urge you to either go back and take a look through your books in the discussion about chirality, or take a look at the videos here at Educator.com for organic chemistry discussing chirality.0624

OK.0640

Let me go back to red here.0643

Configuration in biochemistry, in other words, configuration is just the arrangement of atoms or groups in space around the central atom; so, configuration in biochemistry is based on the D/L system and the reference molecule against which configurations for other molecules is decided.0645

OK, so let me see.0706

Configuration in biochemistry is based on the D/L system, and the reference molecule against which configurations for other molecules is decided is glyceraldehyde.0707

That’s just the convention that we have chosen- glyceraldehyde.0717

Now, let's go ahead and talk a little bit about glyceraldehyde.0725

When we decide on what this configuration of our protein is going to be, we're going to base it on what the configuration of glyceraldehyde is; and then we're going to decide whether it’s going to be a D-amino acid or an L-amino acid, and this is what we're going to discuss right now.0726

Let me go ahead and I wonder if I should draw it here.0741

No, let me go ahead and draw it on the next page.0745

Yes, let me go ahead and do it on the next page here so we have it on one.0748

Let me draw glyceraldehyde here.0752

This is C, this is going to be COH, this is going to be H, this is going to be CH2OH and OH.0755

I strongly urge you to draw out these structures.0768

It's one thing to see them on a page, and it's one thing to see them as figures in your book; and you might be able to go through them, and after a couple of days of just sort of looking over them, looking over them, you might think that you actually have memorized them or understand them- I promise you, you don't.0772

There is a very big difference between being able to write out a structure- passive learning versus active learning .0787

You have to be able to actively draw out a particular structure.0794

That's the only way that your mind will ever really truly know that it understands something, if you could actually produce it, not actually say it's this, it's this, it's this.0797

OK.0809

This is something called L-glyceraldehyde.0810

OK.0819

This thing is actually something called a Fischer projection.0820

Yes, that's fine.0828

This is called a Fischer projection and it is equivalent to this.0830

C...you remember dashes and wedges from organic chemistry?0841

This is H, this is OH, and this is C - oops, sorry - this is C.0850

I'll go ahead and put that there and like that.0861

OK.0863

These wedges, that means that this group and this group, so this carbon right here this alpha-carbon, this is the alpha-carbon, because again, it is attached to the carbonyl group.0864

This carbon is in the plain of the page, but I hold a molecule at space - you remember, carbon is tetravalent, it has 4 groups on it, but those 4 groups are arranged in a tetrahedral arrangement, they're not just one on top of each other like a square, it isn't planar molecule, it is a 3-dimentional molecule.0877

When I hold that carbon like that, this H and this OH actually come out toward me.0894

They come out form the plain of the page toward me.0899

The dashes mean that it’s going away from me.0902

A Fischer projection is just a line version representing this.0905

Anything on the vertical axis, so this and this, it means they're pointing away from you; this and this, the H and the OH, they're coming out at you.0909

A Fischer projection allows us to just use lines without necessarily have to use this dashes and wedges.0920

That's all this means, so L-glyceraldehyde is this particular arrangement.0926

Now, let's go ahead and do D-glyceraldehyde right underneath.0932

I have C, I have COO, I have the H here, I'm going to leave the CH2OH like that, but 'm going to put the hydroxy on the right, and I'm going to put the hydrogen on the left.0940

Notice, the only thing that i have changed is 2 substituents.0952

Anytime you switch the position of 2 substituents, you reverse the orientation, you change L to D, you change D to L.0954

If I switch the other 2 also, I switch it back to the original.0963

That's what it is; you have to switch 2 constituent and it changes the orientation in space.0967

Now, this equivalent would be, just draw it out, and again you want to definitely draw as many of these as possible - oops sorry 1, 2, 3, 4, 1, 2 ,3, 4 - let's go ahead and do some wedges there and this time the hydroxy is on the right, the hydrogen is on the left and we have CH2OH.0972

OK, this is D-glyceraldehyde.0997

There you go.1005

OK.1007

Now, let's go back to blue.1009

OK.1011

All amino acids and biological proteins - well, all proteins are going to be biological, biological proteins, sorry, that's a little redundant but OK - are the L-enantiomer or enantiomer.1014

The pronunciation is irrelevant; it's the chemistry that's important.1040

Their configurations, for all of the amino acids, match L-glyceraldehyde.1046

When we say amino acid, we're talking about an alpha-amino acid, we're talking about an L-alpha-amino acid - that's it - but we're not always going to say L-alpha-amino acid; we just want to know what it means and what are these that we are dealing with if the question of stereochemistry actually does come up.1063

Sometimes it does; sometimes it doesn't.1081

OK.1084

Now, let’s go ahead and draw out the structures.1086

Let me redraw L-glyceraldehyde here on top.1088

This is C, this is a COH - and please, please, please confirm my structures, sometimes we get so carried away with drawing out these carbons, and hydrogens, and oxygens, and sulfurs, and nitrogens, that we're going to make mistakes, so by all means, please confirm these structures, we're all human.1093

OK.1115

Our H is on the left for glyceraldehyde, our hydroxy is on the right, and we have the CH2OH, so this is L-glyceraldehyde.1116

Now, our proteins look like this.1124

Let me do the amino acids; I'll do these in red.1129

This is C, this is COO-, this is H, this is NH3+, and this is the R-group.1133

Notice, this is the alpha-carbon of L-glyceraldehyde, this is the alpha-carbon of the amino acid, the carbonyl group is on top, hydroxy on left, amino group on the left, hydrogen on the right, hydrogen on the right, this group CH2OH, R-group.1144

This is why glyceraldehyde is the reference molecule.1164

The configuration of an amino acid is based on L-glyceraldehyde.1167

This is what all amino acid in your body look like.1172

This is an L-amino acid, and let me go ahead and draw the equivalence one last time.1176

OK.1187

And again, when you see these lines you are looking at a Fischer projection- anything on the vertical axis is pointing away from you; anything on the horizontal axis is coming out towards you.1188

You have H, you have NH3+, you have the carboxylate, and of course, you have the R-group, whatever that happens to be.1199

OK.1211

Now, just so you know - let me go ahead and do this one in blue - just so you know, when you guys took biochemistry, and you guys were studying stereochemistry, you didn't learn the D/L system; what you learned was something called the R/S system.1212

In other words, you took those 4 groups on there and you assigned each one of a priority based on the molecular weight of the atom that's attached to the carbon.1229

For example here, the hydrogen would be the lowest priority, the nitrogen would be - oh actually, let's go - nitrogen would be first priority, and then this carbon would be second priority, the R-group would probably be third priority, and hydrogen would be the last priority.1239

You take that molecule and you arrange it in such a way that the hydrogen is pointing away from you, out of the page, and then when you look at the other 3 groups, you count 1, 2, 3 or 1, 2, 3.1257

If it goes clockwise, we call it S-configuration, if it goes counter clockwise, we say S-configuration.1270

If when you're looking at it, it goes clockwise, it's called the R-configuration.1279

So, just so you know, L-amino acids, they correspond - it doesn't matter- they correspond to S-enantiomers in the R/S system, so just so you know that this R/S system exist, we didn't just throw it out; it's just in biochemistry, they tend to use the D/L based on glyceraldehyde.1283

OK.1312

I wonder if I should...no that's fine.1318

Well, you know what, let me go ahead and draw it out.1323

OK.1325

If I had a carbon and if I had hydrogen pointing straight back behind me so that I can't see it, it’s actually blocked by this carbon, this is going to come out NH3+; what you would be looking at is something like this.1326

OK.1346

This is first priority, this second priority, this is not an H, this is the R-group.1347

Sorry, see, I told you.1354

That’s the R-group; R-group is going to be third priority.1357

We are moving in a counter clockwise direction when we count 1, 2, 3- S-configuration.1359

Again, not a big deal.1366

It's L-glyceraldehyde that is the standard, but thought you should know this just in case.1368

OK.1373

Now, let's go ahead and talk about the classification of amino acids.1374

Now, we classify amino acids - well, let me just go ahead and write this out first and talk about it...classification of amino acids - we classify amino acids for any number of reasons; a part of it is to help you memorize them, so it's much easier as you know to memorize things in groups.1380

If I have 20 things that I have to memorize and you will certainly have to memorize the structures and the names for these amino acids, it's easier to memorize it in groups, so there is a utilitarian reason.1402

There is also another reason: we can classify them based on their chemical properties, so there are some that are going to be polar, some that are going to be aromatic R-groups, some that have charged R-groups, some that have uncharged R-groups.1413

The truth is there is a bunch of ways to actually classify depending on what it is that you're trying to do.1430

Again, there are 20 amino acids, and they, for the most part, behave the same way; but there are reasons why, later on you'll see, certain proteins have certain amino acids in certain specific places when we talk about enzymes.1435

Again, classification of amino acids is just something that we do.1450

Our classification is going to be based on the following: we will classify according to properties of the R-group, and we are going to basically break this up into 5 different groups.1456

Our first group is going to be the nonpolar R-group.1466

Our second is going to be the aromatic R-group, and then we’re going to have polar R-group, and then we're going to have positively charged R-group, so there is a group of amino acids that have a positively charged R-group under normal pH conditions, under normal physiological pH, which is in the range of about 7-7.4 - and again, we will talk about that in a minute - and negatively charged R-group.1475

OK.1542

What I'm going to do is, I'm going to draw out these structures by hand, of the 20 amino acids; and I'm going to designate the group.1543

I’m going to give you the 3 letter short hand designation, the single letter designation for each of these amino acids.1550

I’m going to be drawing these at the way that these amino acids are found under normal pH conditions for the body, which is again, in the range of about 7-7.4 or about 7.3.1556

We're going to talk about pH and acid base behavior of amino acids a little bit later, so don't let the these charges or why it is that certain things are charged and why there are not.1570

Don't let that throw you; it will make sense after the fact.1583

Right now, I just want to talk about the classification of these amino acids.1585

OK, so let's go ahead and start out with the amino acids with nonpolar R-groups.1589

I wonder if I should start here or that's fine; let's go ahead and go red.1596

I guess I can start here: amino acids with nonpolar R-groups.1604

Alright, so, the first one we want to look at, this is C, this is COO-, and I'm not going to draw up a double bond, I'm just going to write this group, the carboxylate group, the COO- - hopefully you know now that it's a carboxylate group - COO-, pH is here, NH3+, and H.1620

This is glycine; its three letter designation is Gly, and its single letter designation is a G.1648

The particular group is an H; this one does not come in an enantiomeric pair.1660

It’s the only one that doesn't because the H and the H are the same.1664

OK.1668

The next one, let's go ahead and do...if the R-group is a CH3+, so now, our R-group is right there; this is called alanine, and it is Ala, and its single letter designation is A.1670

OK.1696

Let's go ahead and do the third one- H.1697

Notice, this part is all the same, the only thing that’s changing here is the R-group.1706

We have the CH, we have CH3, and we have CH3.1711

Our R-group is right there.1720

This is called valine or some people pronounce it as valine.1723

Again, pronunciation is irrelevant; what's relevant is the chemistry.1728

So, that's 3 of them: glycine, alanine, valine- I say valine, anyway.1734

OK.1739

And, let's do, there is a fourth and a fifth so should I do leucine?1740

Yes, it's fine, I'll go ahead and do leucine next.1748

C, it's a C, COO-, H, NH3+, and I hope you'll forgive me for repeating myself; I'm going to repeat myself several times because by repeating myself, when you hear it enough, it will start to sink in- you have to draw this by hand.1751

You're probably wondering why don't I just put up a nice figure of this and just run through them - glycine, valine, proline, leucine, isoleucine - because that's nice.1773

A couple of reasons: 1, I'd like to encourage you to actually refer to your book.1785

Biochemistry books are beautifully written, all of them are beautifully written and beautifully illustrated, so I encourage you to use these videos along with your book, and take a look at the figures in that book; that way you'll have 2 sources that solidify the information.1790

Another reason I don't do that is, again, because of passive learning.1807

We can convince ourselves that we can look at something and we can understand what's going on.1810

We don't understand it unless we are able to produced it with our hand.1813

There is a connection between what the hand does actively, and what the mind actually understands and knows.1816

You need to draw these out.1820

Is it tedious?1822

Yes, maybe; but it's absolutely worth it.1823

There is nothing, nothing, nothing like knowing that you can actually produce any molecule under any circumstance that is full command of your biochemical knowledge.1826

OK.1836

No more lecturing- not for a while.1837

OK.1840

We have CH2, and we have CH, CH3, CH3, so you notice this one actually just like valine except that extra carbon group there.1841

This is leucine, and it is Leu, and it's single letter designation is L, and this is your R-group right here; and last but certainly not least, a very unusual amino acid.1856

So, we will go ahead and put an NH2+ - notice, this one is not an NH3, and I'll tell you why in just a minute - this is going to be C.1877

Let's go, I'm going to draw a C here and a C there, and that's there, so this is going to be CH2, this is going to be H2, and this is going to be H2.1888

The reason I have 2 hydrogens on this one, it's still a plus charge, is because again, nitrogen, this time, it's actually connected; this amino group is actually connected to the R-group.1900

The R-group is right here, but it happens to be connected, so, tetravalent nitrogen has a positive charge here, 3 hydrogens, and one of them is bonded to carbon, here nitrogen is bonded to 2 carbons that's why it only has 2 hydrogens here.1911

This one is called proline, and it is Pro, and its single letter designation is a P.1924

OK.1934

These things - the glycine, alanine, valine, leucine and proline - they represent the first group of nonpolar R-groups.1935

There is no polarity here; there is no electronegative element to create a dipole, so that's it.1944

OK.1952

Let's go ahead and do our...actually you know what, we have a couple of more.1953

I'm sorry.1962

We have 2 more, yes, all right.1965

Let's do C, COO-, we have H, and we have NH3- getting ahead of ourselves, sorry about that.1967

Now, we have a C, CH3, H, CH2, CH3- this one is called isoleucine.1979

There is no capital in there.1997

This is isoleucine, and it is Ile; and its single designation is I, and this group is right there.1999

There you go.2011

Leucine, isoleucine, iso just means we've rearrange that, so 1, 2, 3, there are 4 carbons, 1, 2, 3, 4, just one of those carbons is arranged differently- that's all.2012

And, let's do methionine.2023

OK, so we've got C, COO-, H, NH3+; we have CH2, CH2, sulfur, and CH3.2026

This is called methionine, and still nonpolar, Met; and its single letter designation is an M.2048

Let me draw out the group; there we go.2062

This is the first group of amino acids, the ones that are have nonpolar R-groups.2066

OK.2072

Let's go ahead now, and move on to the second group: the amino acids that have aromatic R-groups.2073

OK, aromatic R-groups.2079

OK.2089

Let's do C, COO-, H, N, H.2090

You know what, I'm going to do this in blue.2099

I think blue is my favorite color.2105

I know it doesn’t matter, but for some odd reason, I just think that it looks better in blue, I don't know why- personal taste, I guess.2110

We have blue, so aromatic R-groups: C, COO-, H, we have our NH3+, and we have CH2, and then we have this benzene ring; and this is phenylalanine, and it is Phe, and its single letter designation is F.2118

OK.2155

I wonder if I should do...that's fine, I guess I can do it over here.2157

OK.2163

C, COO-, our H, our NH3+, and now, we'll do CH2, we have our benzene ring again, and we also have a hydroxy attached to that benzene ring.2164

This is going to be tyrosine, three letter designation is Tyr, single letter designation is a Y.2181

OK.2192

Now, let's do C, COO-, H, NH3, again, a very unusual amino acid because you have an indole group actually attached to this.2194

Let's go, C, let me draw it out this way, like that, I will put a nitrogen, yes, that's fine I'll put a nitrogen there, and then I'll go that way, that way, that way.2213

I'll go ahead and do my aromatic ring like that, and H; and this is called tryptophan.2233

Tryptophan, three letter designation is Trp, and curiously enough the single letter designation is W.2245

Let's make sure we have this right: double bond, this is aromatic, there is a hydrogen on there, 2, 3, so this a carbon, it has an H attached to it.2253

These are all carbons, of course; this is a benzene ring.2264

So, this whole thing right here is an indole.2268

Our R-group here is that one; our R-group here is that one, and our R-group here is this one.2270

We have 3 amino acids that have aromatic R-groups.2279

OK.2283

I'm going to go ahead and stop at this lesson here for today, and the next lesson, we're going to continue with our classification of amino acids; and we'll get into more properties of those amino acids.2284

Thank you for joining us here at Educator.com and Biochemistry.2295

We'll see you next time, bye-bye.2298

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