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Raffi Hovasapian

Raffi Hovasapian

Glycolysis IV

Slide Duration:

Table of Contents

I. 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
II. 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
III. 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
IV. 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
V. 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
VI. 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
VII. 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
VIII. 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
IX. 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
X. 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
XI. 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
XII. 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
XIII. 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 (8)

1 answer

Last reply by: Professor Hovasapian
Thu Apr 7, 2016 1:22 AM

Post by Jinhai Zhang on April 6, 2016

Prof:
Since in general biology, we learned that some bacteria which dislikes O2 can use S2- as electron acceptor. And they are still called anaerobic?  

1 answer

Last reply by: Professor Hovasapian
Tue Aug 27, 2013 11:26 PM

Post by Eduardo Cesar Melo Barbosa on August 27, 2013

Professor Hovasapian, on your first slide for this lecture, you wrote that DHAP is converted into Glyceraldehyde-3- Phosphate and the enzyme used is triose phosphate kinase, but isn't triose phosphate isomerase? Or are both names used?

3 answers

Last reply by: Professor Hovasapian
Mon Jun 3, 2013 2:36 AM

Post by Gaston Dominguez on March 12, 2013

Professor Hovasapian, These are fantastic lectures. I have no doubt i'm going to get an A in my biochem exam because you've helped clear the concepts so well. Thank you!

Glycolysis IV

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
  • Feeder Pathways 0:42
    • Feeder Pathways Overview
    • Starch, Glycogen
    • Lactose
    • Galactose
    • Manose
    • Trehalose
    • Sucrose
    • Fructose
  • Fates of Pyruvate: Aerobic & Anaerobic Conditions 7:39
    • Aerobic Conditions & Pyruvate
    • Anaerobic Fates of Pyruvate
  • Fates of Pyruvate: Lactate Acid Fermentation 14:10
    • Lactate Acid Fermentation
  • Fates of Pyruvate: Ethanol Fermentation 19:01
    • Ethanol Fermentation Reaction
    • TPP: Thiamine Pyrophosphate (Functions and Structure)
    • Ethanol Fermentation Mechanism, Part 1
    • Ethanol Fermentation Mechanism, Part 2
    • Ethanol Fermentation Mechanism, Part 3
    • Ethanol Fermentation Mechanism, Part 4
    • Ethanol Fermentation Mechanism, Part 5
    • Ethanol Fermentation Mechanism, Part 6

Transcription: Glycolysis IV

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

In the last lesson, we finished off our discussion of the glycolytic pathway.0004

I am going to continue, and talk a little bit more about glycolysis; but what I am going to talk about in this lesson is the feeder pathways to glycolysis- basically all of the carbohydrates in the body, how do they enter the glycolytic pathway.0009

And then, after that, I am going to talk a little bit about the fates of pyruvate.0024

You remember pyruvate was the final molecule; the 2 molecules of pyruvate that glucose was converted into, I am going to talk a little bit about what it is that happens to them- lactic acid fermentation and ethanol fermentation.0027

Let's go ahead and get started.0040

OK, as you can see, this first page here, there is a lot going on.0044

What I have here are the feeder pathways, the pathways that other carbohydrates in the body take in order to get to glycolysis.0051

For example, when you eat a regular table sugar, sucrose, what does the body do to that?0060

How does it take that sucrose, and how does it metabolize it?0067

Does it go through the glycolytic pathway?0070

Does it take another pathway?0072

What is it that happens?0074

Your starch that you eat, glycogen, what happens to these things?0077

And that is what is going on here; I am just going to run through each individual pathway.0081

We are not going to go and get into a lot of detail, but I do want you to see where each thing goes, where it comes from.0085

I think it is really, really important; what I have here are - in boxes - the major sugars that we are concerned with.0092

I have the starch and the glycogen, fructose, sucrose.0099

Here is glucose, of course, the central position; well, it is not central here, but it is glycolysis, glucose, trehalose, lactose, galactose and mannose.0104

These are the primary carbohydrates for the body, and we want to see what happens to them.0113

Now, in red, you are going to see the enzymes that actually catalyze these particular transformations.0119

And, of course this, in blue, 1, 2, 3, I will talk about them in a little bit.0125

It is going to talk about the dietary pathway for a particular carbohydrate or the cellular, the tissue pathway for a particular carbohydrate; and, of course, there is the liver pathway.0130

That is going to be 1, 2, 3, and I will get to those when I actually talk about those individually.0141

I guess the best place to start is right in the middle; I am going to start with starch, and I am going to start with glycogen.0146

Look over here; we have the starch.0154

Let’s say you happen to eat some starchy food.0156

Well, the dietary pathway, what happens is the enzyme alpha-amylase starts to break down the starches.0160

You have alpha-amylase in your saliva that actually does the first phase of breakdown.0173

And then, of course, once it goes into your stomach, that enzyme is actually neutralized; and another alpha-amylase takes over in your intestine.0178

Eventually, what happens is it is all converted into glucose, and once it is glucose, then, it can start the glycolytic pathway.0189

Hexokinase + ATP goes to glucose 6-phosphate, and, of course, it will just continue on and get to the end of the glycolytic pathway.0197

Starch passes through glucose and into the regular glycolytic pathway.0207

Now, as far as glycogen is concerned, you remember when we talked about the carbohydrate glycogen?0213

Your body stores glucose units as this polymer called glycogen, and if for any reason, if your blood sugar drops too low, the body mobilizes this glycogen.0218

Remember, it is highly, highly branched; it goes and it breaks off all those glucose units, and it sends them into the glycolytic pathway.0229

What happens, as far as this cellular tissue pathway for glucose to enter the glycolytic pathway, a glycogen, an inorganic phosphate comes in; and this enzyme called phosphorylase actually breaks off individual monomers from the ends of the glycogen molecule.0237

It is converted to glucose 1-phosphate; well, glucose 1-phosphate is then converted to glucose 6-phosphate by the enzyme phosphoglucomutase, and now that it is glucose 6-phosphate, it can just continue on into the glycolytic cycle.0257

You see how that happens, dietary and then cellular tissue pathway.0271

OK, let’s talk about galactose; actually, let’s talk about lactose.0277

Lactose is that disaccharide, which is glucose and galactose.0283

What happens is lactase ends up breaking up that disaccharide, and the molecule of glucose goes on normally into the glycolytic pathway.0289

The galactose monomer, it goes through a couple of conversions.0299

It is turned into uridine diphosphate galactose, uridine diphosphate glucose, and then that is converted to glucose 1-phosphate; and then the glucose 1-phosphate, as we see here in the center, is converted to glucose 6-phosphate, and then it can go on and continue in the glycolytic pathway.0303

OK, now, let me see; we have taken care of lactose.0322

We have the glucose; we have starch and glycogen.0325

In the case of mannose, mannose is converted into mannose 6-phosphate, and then it is converted to fructose 6-phosphate.0328

It is a little further down the glycolytic pathway, but that is how it enters glycolysis, which is right here, this central pathway right here.0337

Trehalose, the enzyme trehalase breaks it up into glucose monomers, and glucose enters the glycolytic pathway, as usual.0346

The sucrose, the table sugar that you eat, it is a disaccharide of glucose and fructose.0357

Well, the sucrase breaks it up; the glucose enters the cycle normally.0362

Fructose, it has 2 possible fates; one possible fate is when fructose, by the action of the hexokinase + adenosine triphosphate, is converted to glucose 6-phosphate.0368

It can enter the glycolytic pathway that way at fructose 6-phosphate or in the liver.0380

What the liver does is this fructokinase converts fructose to fructose 1-phosphate, and then, fructose 1-phosphate aldolase takes the fructose and breaks it up into 2 molecules- glyceraldehyde and dihydroxyacetone phosphate.0387

Now, the glyceraldehyde is converted by triose kinase to glyceraldehyde-3-phospahate, and now, it can enter the second phase of glycolysis.0401

It comes in down halfway through the glycolytic pathway, and the dihydroxyacetone phosphate, as we know, is converted by the triosephosphate kinase, again, into glyceraldehyde-3-phospahte; and it enters the glycolytic pathway that way- that is it.0410

I am not sure about the extent to which your particular teacher is necessarily going to have you memorize this entire thing.0428

Perhaps he or she will want you to know, at the very least, maybe the dietary pathway for starch and the cellular tissue pathway for glycogen, but I did want you to see it.0434

All of the carbohydrates that you eat, somehow or other, they all end up in the glycolytic pathway- that is it, that is what is going on here.0445

OK, great, now, let’s talk about the fates of the pyruvate that is formed during glycolysis.0457

We take this glucose molecule; we break it up.0465

We subject it to 10 steps, and we end up with these 2 molecules of pyruvate.0469

Well, what happens to pyruvate?0474

Well, we know what happens to pyruvate aerobically; well, I am going to tell you right now.0477

Let me see; let me go do this in blue, I think.0484

When there is plenty of oxygen to go around, under aerobic conditions, the pyruvate that is formed, pyruvate continues on and is oxidized to a molecule called acetyl coenzyme A; and it enters the citric acid cycle - the Krebs cycle - eventually becoming CO2 and H2O once it enters the electron transport chain.0496

Now, the NADH from glycolysis, remember we actually formed 2 molecules of NADH- those 4 electrons?0549

It passes its electrons to the electron transport chain becoming NAD+ again; this is important.0565

Under aerobic conditions, when there is enough oxygen available in the body, when the cells have enough oxygen to work with, the NADH that is formed in glycolysis can actually pass its electrons to that oxygen because that is what the electron transport chain is.0581

It takes those high energy electrons from these coenzymes, and it passes them along a chain and ultimately its oxygen that ends up taking those electrons.0595

It ends up being reduced; that is what oxygen does.0604

Oxygen oxidizes things; it, itself, gets reduced.0606

When there is plenty of oxygen, the NADH can actually turn back into NAD+ when it gives up its hydride, when it gives up its electrons.0610

That is very important because we need to regenerate the NAD+ so that glycolysis can continue with step 5.0618

We need that NAD+ to make the…I am sorry; it is step 6.0626

We need that NAD+ because we need to oxidize that glyceraldehyde-3-phosphate.0631

If we ran out of NAD, if NADH cannot give up its electrons, glycolysis comes to a halt because there is not going to be enough NAD+ to keep glycolysis going.0637

That is what is going on; under aerobic conditions, when there is plenty of oxygen, everything is fine.0648

NADH goes to NAD+ and glycolysis can continue; now, what happens under anaerobic conditions?0653

Well, under anaerobic conditions or hypoxic conditions - low oxygen or no oxygen - what is the NADH going to do?0660

It has to give up its electrons somehow because it has to turn back into NAD+, so that it can go back and actually continue doing its work on glycolysis.0667

Well, the body has figured out a way to do that, now, the anaerobic fates of pyruvate.0675

Alright, under hypoxic conditions - well, I am going to say hypoxic anaerobic, so either low oxygen or no oxygen, anaerobic conditions - NADH cannot pass its electrons to oxygen because there is no oxygen.0692

It cannot pass its electrons to O2 to become NAD+ again, and a depletion of NAD+ stops glycolysis.0728

We do not want that to happen; when glycolysis stops, very, very bad things happen.0755

Now, NAD+ must be regenerated somehow.0762

OK, now, cells do this by transferring their electrons - the NADH - to pyruvate, directly to pyruvate, to form lactate and or ethanol.0779

In other words, we are reducing pyruvate; we are passing electrons to pyruvate in the form of hydride, in the form of hydrogen, so transferring electrons to pyruvate.0819

Alright, we are reducing pyruvate.0831

OK, the first of these methods is lactic acid fermentation.0838

Let me go ahead and actually start this on the next page; I think I am just going to do this in red for a change of pace.0845

The first fate of pyruvate is lactic acid fermentation.0852

This is what your body does- lactic acid fermentation.0858

When you are heavily exercising, heavily exercising, heavily exercising, your body starts to crave oxygen.0862

You start to run out of oxygen; when there is not enough oxygen for the body for regular aerobic cellular respiration to continue, the cell has to be able to regenerate that NAD+ to keep glycolysis going.0868

In order to do that, it takes the pyruvate that is formed in glycolysis; and it converts it to lactate.0882

That is the sore that you feel when your muscles start to give up, when your muscles start to fail.0889

That soreness that you feel, that is the lactic acid, the lactate building up in your muscles.0895

OK, lactic acid fermentation, here is the chemistry.0900

This is CH3; we have our pyruvate molecule, and it is going to go like this.0908

NADH + H+ in and NAD+ out.0921

NADH gives its electrons to pyruvate and converts it to lactate.0927

C, C, C, this stays; H3, this becomes OH, and H, O-.0933

This is pyruvate; this is lactate.0945

This is actually L-lactate; I am going to draw it this way.0953

I am going to put the OH over here; it is L-lactate.0959

OK, we have taken this carbonyl, this double bond, and we have added 2 hydrogens across the double bond.0963

OK, the carbonyl is here; we have added a hydrogen to the oxygen, a hydrogen to the carbon.0972

We have reduced the pyruvate; in the process of reducing it, we have actually recovered NAD+.0977

Now, glycolysis can continue; now, the body can do something else with the lactate.0983

That is what is going on; now, the ΔG for this reaction - I will go ahead and put that there - it is pretty high actually.0988

ΔG is -25.1kJ/mol, or I should say low, depending on the number is high, but it is negative.0997

So, this is a highly exergonic reaction; OK, that is it.1005

Glucose is converted into pyruvate via glycolysis.1016

Now, pyruvate is converted into - let me make this arrow a little bit longer – lactate, and we have NAD+ in NADH.1022

That is the cycle; glucose - step 6, NAD+ in, NADH out - goes to pyruvate.1045

This is glycolysis, what we just did.1053

Under anaerobic conditions, NADH gives its electrons, gives its hydrogens to pyruvate, reducing it to lactate; and then, the process recovering NAD+, so that the glycolytic cycle can continue, otherwise, the glycolytic cycle will stop and bad things happen.1057

OK, now, I probably should have done that…that is OK.1076

All right, some cells like erythrocytes, they do not have mitochondria.1082

They have no mitochondria, so they cannot metabolize under aerobic conditions because that is where oxidative phosphorylation takes place- in the mitochondria.1096

They have no mitochondria, so they do this lactate acid fermentation even under aerobic conditions.1109

That is how they regenerate the NAD+.1121

They do this even under aerobic conditions all the time.1125

OK, that is lactic acid fermentation; now, we will talk about the other fate of pyruvate- ethanol fermentation.1138

I think I will go back to black for this one just for a change of pace.1145

Ethanol fermentation, OK, yeast ferments glucose to ethanol.1150

The pyruvate, that glycolysis, so yeast takes glucose, goes through glycolysis, converts it to pyruvate; but now, instead of the lactic acid, instead of lactate, it actually produces ethanol.1171

That is how we get our ethanol; that is how we get our drinking alcohol.1184

OK, what we have here is C, C and C.1188

We have that; we have that, and we have this.1194

This is a 2 step process actually.1199

I will go ahead and do this.1202

CO2 is released, and the enzyme is pyruvate decarboxylase; and it also requires a coenzyme called TPP.1207

TPP is a thiamine pyrophosphate.1224

It is the coenzyme that is derived from vitamin B1, which is thiamine, and it also requires magnesium ion.1228

This is the enzyme; it requires this, and it requires that.1237

Let me go ahead and write what TPP is, and I will talk about it in a minute.1241

I will do this mechanism; it is very, very important.1246

TPP, profoundly important coenzyme, as you know, vitamin deficiency, bad things start to happen.1248

TPP is thiamine pyrophosphate, and do not worry.1256

We will be drawing all of this out in just a minute; the first thing that it does is it converts it into C, CH3.1265

It converts it into acetaldehyde; it takes the pyruvate, and it actually knocks off this carboxyl group.1275

It goes away a CO2; this COO-, this carboxyl group goes away a CO2 leaving just the acetaldehyde, and then, the second step.1282

This is where the NADH comes in.1298

It gives its electrons over; it regenerates NAD+, and it produces our famous ethanol.1302

There is H there; there is H there, and there is OH here.1313

Here we go, and this is alcohol dehydrogenase.1319

OK, there you go.1329

Alright, now, let's see what else do we want to say.1335

The ethanol fermentation pyruvate first step is catalyzed by pyruvate decarboxylase to form acetaldehyde, and acetaldehyde is converted into ethanol.1340

Let me go ahead and write those out; this is ethanol.1350

This is acetaldehyde, and this is pyruvate.1355

OK, let me go, now, thiamine pyrophosphate.1367

OK, let's go ahead and talk about the thiamine pyrophosphate, and let's talk about this first reaction- the pyruvate decarboxylase reaction.1373

OK, let me do this in blue.1383

I wonder if I can draw the structure; well, that is OK.1388

TPP, as we said, it is a coenzyme that is derived from thiamine, which is vitamin B1.1392

You ingest the thiamine - the vitamin B1 - and the body converts it into its active form, which is a thiamine pyrophosphate.1411

It adds a pyrophosphate onto this structure that I am going to draw in a second, and then, it goes ahead and does what it does with this enzyme pyruvate decarboxylase.1418

OK, let's go ahead and work on some structures here.1428

Let me go ahead and do this in blue; I think I will do this structure in black actually.1432

I have got a little 6-membered ring here.1438

I have got a nitrogen up here; I have got a nitrogen up here.1443

This is aromatic; I have NH2.1447

I have got CH3; I have got a CH2 group here.1452

I have got a C; I have got a...aha, here is where we get really, really interesting.1459

There, this is carbon; this is sulfur, and I will go ahead and put that there.1468

I will go ahead and do that; Do not worry.1475

I do not think you are going to have to memorize the structure for thiamine pyrophosphate.1479

It is the mechanism that is important.1484

This is going to be a plus charge on there because we have 4 things attached.1487

We have, of course, a hydrogen there, the sulfur; and let me see what else do we have.1492

Aha, we have CH2; we have CH2.1496

Now, we have our pyrophosphate; we have O, P, O, P, O- there we go.1501

Let me go ahead and make sure all the oxygen and charges are there.1509

So, this is TPP; this is thiamine pyrophosphate.1512

What is important is this thing right here, this ring.1515

OK, this is called a thiazolium ring.1521

This is this thiazolium ring; all of the chemistry takes place at that carbon.1526

OK, and you are accustomed to this already; just like when we did NAD+, all of the chemistry takes place at one place.1532

The rest of the molecule is just used for...basically, the enzyme uses it to hold it, to bind it, to make sure everything...it is a handle.1539

All of the chemistry usually takes place in one location over and over again; it is not multiple locations.1550

OK, now, the H, this H right here, the H on the...let me number these by the way.1556

This is no. 1, no. 2, no. 3, no. 4 and no. 5 on this thiazolium ring.1566

The H on the no. 2 carbon of the ring - well, there are 2 rings, so the thiazolium ring - of the thiazolium ring is acidic, and when it is lost, when it is deprotonated, it creates a nucleophilic carbanion.1574

It creates a nucleophile, a nucleophilic carbanion, a carbon that is actually carrying a little bit of a…well, a negative charge.1610

As you will see in a minute, that negative charge is stabilized, but it is carrying a negative charge, so it is highly nucleophilic, OK, carbanion that adds to carbonyls, OK, that attacks that carbonyl carbon.1622

OK, now, let's go ahead and see if we can make sense of what is going on.1640

Let's go ahead and do this mechanism; I am going to try and do the mechanism on one page.1645

Hopefully, I will be able to do it; if not, well, that is OK.1650

We will go to 2 pages; let me see if I should go here first, and then here.1655

No, that is OK; I want to have it all on 1 page.1664

Let me go ahead and do this in black, and then, I will probably do the electron moving in red.1668

Alright, we are going to concentrate just on that ring.1673

Let me go ahead and draw this first; I have got N.1679

I have got C, S here.1686

I have got R1, R2, and I have got a double bond, double bond there.1690

This is a positive charge; I have this H, and I have CH3.1696

OK, everything starts when…we said this proton here, on this no. 2 carbon of the thiazolium ring, is acidic.1701

I will do it this way; when it is lost, what you end up with is this carbanion.1714

We have got R1; I have got N.1719

I am going to draw this a little bit better: N, S here.1725

So, there is now, an electron there, and it is negatively charged; so this is plus.1734

This is CH3; this is R2.1741

Have I forgotten anything else?1743

No, I think everything is good, and now, we have our pyruvate.1745

Let me go ahead and draw my pyruvate molecule.1750

I will go ahead and draw the pyruvate in blue; this is C, C and C.1755

I have got O-; there is that carbonyl, right?1760

Pyruvate, and this is CH3; what it is going to do is it is going to attack the carbonyl like we said.1766

So, I will do this in blue; it attacks the carbonyl, and this goes and actually grabs a hydrogen ion, and it becomes the following.1771

Let me go just here because I am going to need some room.1783

Let me see; I have got...well, you know what, it is OK.1790

Let me go back to black; I have got R1, boom.1796

This is N; this is C, S there, there, there.1800

Now, I have got myself a C; I have got a COO-.1808

Here, I have...no, sorry; I decided to do this in blue.1816

I think it is probably best if I do this in blue, so let me go ahead and just make sure that everything else is on here.1820

I have go a double bond, a positive charge; let me go ahead and write my R2 here, my CH3 here.1827

Now, let me go to blue, and let me do...and I am also going to move my arrow.1834

I am going to put my arrow over here, so I have got some room.1844

Now, I am in blue, and now, I have got C; I have got C.1848

I have got C; this is H3.1853

This is now OH, and this is O and O-.1855

OK, so far so good; this carbanion, right?1863

Nucleophile, it attacks the carbonyl; the carbonyl, this goes ahead and grabs an H from the surrounding medium to become an alcohol group right here.1867

Now, what happens is the following.1876

Oops, let me do this electron movement in red.1879

That bounces down there; this bond breaks.1885

This bond breaks; this goes off as CO2.1891

This bond breaks and forms a double bond here, and it forces these electrons onto the nitrogen, which is carrying a positive charge.1894

So, it actually clenches the positive charge on that.1901

What we end up with is the following; let me go back to black.1907

CO2 is gone, and now, we have...let me see, boom, boom.1915

I will do N; I will do S, that.1927

No, that is not there anymore because these electrons moved.1932

OK, this is R, and now, we have this double bond, which I will do in blue in just a minute.1936

This is there; let me see.1945

This is R2; this is CH3.1948

Now, I will go back to blue; now, we have a double bond.1950

We have a C, and we have an OH, right?1954

And we have a CH3, so that is what is there.1959

Now, this actually undergoes a little bit of a resonance.1964

These electrons were pushed onto nitrogen.1970

Now, what happens is these electrons are going to go like that, and they are going to go back up to the carbon here, so, we have this resonance structure.1975

Let me draw this in black; we have got...let me see: nitrogen, sulfur, that, that, that.1987

Now, we have a single bond; we have a C.1998

No, I said I was going to do that in blue; I keep forgetting I do not want to do that in black.2003

This is R2; this is R1.2007

This is CH3; now, let me go to blue.2010

Now, I have this carbon with 2 electrons on it and that.2014

It has a hydroxy group; it has a CH3 group, and this, right here, is your resonance stabilization, right here.2018

This double arrow, single double arrow- resonance.2026

Once we form this, these electrons can bounce back up here and actually stabilize.2030

This negative charge on the carbon is actually stabilized because it can redistribute itself and actually come, and the nitrogen is actually sharing that negative charge.2036

That is why this works; OK, now, what we have is the following.2045

Once we have this; let me see.2053

Where are we?2057

Let me make sure hydroxy, FOTEP.2059

I wonder if I should go ahead and do it that way; OK, that is fine.2070

I will go ahead and go here; I know there is a lot going on.2074

Do not worry; we will make sense of everything here.2082

This is N, and this is S.2084

We have that; OK, and then we have - let's see - our R1.2095

We have R2; we have that.2106

We have our CH3; OK, and now, I have got the C, and I have got the O, and I will write the OH that way.2108

I have got the CH3; OK, and let's see.2120

I am going to draw a little bit of an H+ here.2125

Because this carbanion, basically, what I am going to do, it takes a hydrogen ion from the medium to become that.2129

OK, it forms this; there is resonance stabilization here.2138

A hydrogen ion attaches to here; now, you have this thing attached.2145

OK, now, here is what happens.2150

These electrons move here.2154

These electrons go and grab a hydrogen ion.2159

OK, and what you are left with is...here is where I definitely should have gone the other page.2165

Now, what happens is, what ends up leaving is our acetaldehyde.2173

I will do this in blue; once this grabs this H, this bond over here to the thiazolium ring, actually breaks; and what you end up with is the following molecule.2183

You end up with C, C, O, H, CH3.2196

That is this thing; this COO, that is this.2203

This H is this H, and this CH3 is that CH3.2207

This is our acetaldehyde; that is what the enzyme ends up actually releasing, and then once this happens, you are back to the form that you were before.2211

OK, this goes and grabs this H+ that becomes this H.2224

This comes here; this H is this H.2232

This O is this O; this carbon is this carbon, and this CH3 is this CH3.2235

OK, this H that this bond grabs, it recovers the thiazolium that is protonated, and then, it can begin the cycle again.2240

Let's run through this one more time; we have the thiazolium ring on the TPP.2249

We lose a proton, and we form this nucleophilic carbanion.2254

This nucleophilic carbanion attacks the pyruvate, the alpha-keto on the pyruvate - OK - and when it does that, it is now, attached to it covalently.2257

Now, of course, it is primed because now, there is a place for electrons to actually go.2269

This is called an electron sync; this positive charge on the nitrogen allows...it pulls electrons toward it, and when it does that, it makes it very, very easy for this negative charge on the oxygen to actually form a second double bond with a carbon to form CO2.2276

CO2 is a very stable molecule; this happens a lot in biochemistry.2291

Decarboxylation forming CO2 happens very, very easily.2295

It forms the CO2; this CO2, this bond, breaks, so CO2 is lost in this reaction, and what you end up with is this structure right here.2301

Well, these electrons push back up; they form the carbanion again.2311

This is a resonance structure; this negative charge is actually shared between the carbon and the nitrogen.2316

If you want, you can think of this actually grabbing another hydrogen from here to become this thing.2324

OK, a hydrogen comes in and becomes this, and now, these electrons go over here to form a double bond.2330

These electrons are pushed, and they grab a hydrogen ion to recover the thiazolium, which is protonated, and, of course, the acetaldehyde goes away.2342

Yes, this is the pyruvate decarboxylase reaction; this is the first part of the ethanol fermentation process.2357

We will not go ahead and talk about the second part that is just a dehydrogenase reaction.2363

We may talk about it later, we may not, but I definitely wanted you to see this.2368

This is our first introduction to a major coenzyme- the thiamine pyrophosphate.2372

OK, we are going to go ahead and close off our discussion of this phase of glycolysis for today.2377

Thank you so much for joining us at Educator.com; we will see you next time, bye-bye.2383

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