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Raffi Hovasapian

Raffi Hovasapian

Glycolysis II

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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 (5)

2 answers

Last reply by: Zachary McCoy
Tue Sep 16, 2014 8:07 AM

Post by Zachary McCoy on September 11, 2014

23:34
Just in case anyone is confused, Professor Hovasapian accidentally circled the wrong hydrogen at 23:34. He meant to circle the hydrogen that's a part of the C1 hydroxyl group (non-ring form).

Professor, you're the best!!! And I'm not just saying it.

1 answer

Last reply by: Professor Hovasapian
Wed Sep 11, 2013 8:38 PM

Post by Vinit Shanbhag on September 11, 2013

why do we need phosphatases in cell if we have bifunctional enzymes?

Glycolysis II

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
  • Glycolysis Step 1: The Phosphorylation of Glucose 0:27
    • Glycolysis Step 1: Reaction
    • Hexokinase
    • Glycolysis Step 1: Mechanism-Simple Nucleophilic Substitution
  • Glycolysis Step 2: Conversion of Glucose 6-Phosphate → Fructose 6-Phosphate 11:33
    • Glycolysis Step 2: Reaction
    • Glycolysis Step 2: Mechanism, Part 1
    • Glycolysis Step 2: Mechanism, Part 2
    • Glycolysis Step 2: Mechanism, Part 3
    • Glycolysis Step 2: Mechanism, Part 4 (Ring Closing & Dissociation)
  • Glycolysis Step 3: Conversion of Fructose 6-Phosphate to Fructose 1,6-Biphosphate 24:16
    • Glycolysis Step 3: Reaction
    • Glycolysis Step 3: Mechanism
  • Glycolysis Step 4: Cleavage of Fructose 1,6-Biphosphate 31:10
    • Glycolysis Step 4: Reaction
    • Glycolysis Step 4: Mechanism, Part 1 (Binding & Ring Opening)
    • Glycolysis Step 4: Mechanism, Part 2
    • Glycolysis Step 4: Mechanism, Part 3
    • Glycolysis Step 4: Mechanism, Part 4
    • Glycolysis Step 4: Mechanism, Part 5
    • Glycolysis Step 4: Mechanism, Part 6
    • Glycolysis Step 4: Mechanism, Part 7
    • Hydrolysis of The Imine
  • Glycolysis Step 5: Conversion of Dihydroxyaceton Phosphate to Glyceraldehyde 3-Phosphate 55:38
    • Glycolysis Step 5: Reaction
  • Breakdown and Numbering of Sugar 57:40

Transcription: Glycolysis II

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

In the previous lesson, we did an overview of glycolysis.0004

Now, we are going to actually get into the details of glycolysis, and we are going to discuss each step of it in a reasonable amount of detail, concentrating on mechanism – that is what is going to be important - and a little bit about the enzymes; but mostly, it is about mechanism- how do these transformations take place.0008

Let’s just jump in and get started; OK, let me see.0025

I guess I will stick with black, so step 1 of glycolysis, it is going to be the phosphorylation of glucose.0032

It is going to be the conversion of glucose to glucose-6-phosphate.0041

It is the phosphorylation of glucose0046

In terms of an actual...in structures and reaction, you have something like this.0056

Let me do these, actually, in blue; it is a good idea.0063

We have our glucose molecule, and we have the C and the OH; and the reaction that takes place is the following.0069

And, of course, we have these biochemical symbols; ATP comes in.0087

ADP goes out; magnesium ion is required for this, and we usually go ahead and put the enzyme down below, and we said that the enzyme for this transformation is the hexokinase - OK - and we are left with the following.0094

We are left with C, O and a PO32-, the phosphoryl group on the no. 6 carbon of the glucose, so OH, OH and OH.0114

There you go; that is the transformation that takes place.0135

From this to this, this is what we have put on.0138

OK, now recall, oops, let me go back to black here.0142

Recall that a kinase - OK- is an enzyme that facilitates, catalyzes, the transfer of the terminal phosphoryl group, which I will go ahead and draw the picture here, P, O, O.0154

This is a phosphoryl group right here, right- PO32-, not PO43-.0198

It is phosphate that facilitates the transfer of the terminal phosphoryl from ATP to the substrate, and the substrate is the nucleophile.0205

This is actually a nucleophilic substitution reaction, and we will also say N.B. that hexokinase - now, we are getting into all the little details - the enzyme actually requires magnesium ion.0223

Actually, that is right there; it requires the magnesium Mg2+, and the ATP that is bound to the active site of the enzyme is actually Mg ATP 2-, not ATP 4-.0251

It is not just free ATP, not ATP 4-, so it looks like this.0283

We have O, P; actually, I am going to draw the structures in blue.0290

I will try to be as consistent as possible, although, no guarantees.0295

O, P, O, P, O, P, O, ribose and adenine, I think that is right.0300

I have 1; I have 2, and I have 3.0312

That is 1-; that is 2-.0316

That is 3-, and that is the 4-.0319

The Mg, the 2, actually coordinates here.0321

OK, what you are left with, 2+, 2-, you are actually just left with Mg ATP 2-.0326

That is what is in the active site; the magnesium is required by this enzyme to facilitate this process.0332

If you want, you can consider the magnesium as a coenzyme, if you want, but that is perfectly fine.0340

It needs it in order to do what it does.0345

OK, now, let's go ahead and take a look at the mechanism; again, it should reasonably familiar to you from organic chemistry- basic nucleophilic substitution reaction.0349

One last thing I would like to say; so hexokinase, like all of the enzymes for glycolysis, like all of the glycolytic enzymes, is soluble and cytosolic, so this takes place in the cytosol.0359

OK, now let’s take a look at the mechanism here.0394

A mechanism is how this transformation is affected; all the little details, the electron pushing- that is what we are going to be doing.0399

It is a simple nucleophilic substitution, pretty much.0405

You have a nucleophile; you have an electrophile.0418

It comes in, replaces, kicks something off- that is it.0420

Let’s go ahead and draw our glucose here; let me do this in blue.0424

We have our glucose molecule, and we have this C, and we have this OH up here on the…I will go ahead and put the hydrogens in this time.0430

That is that; this is going to be H and OH, and, of course, we have our ATP.0442

This is O, P, O, P, O, P, O, ribose and adenine.0451

We have our double bond to the phosphorus, double bond to the phosphorus.0461

We have that minus; we have that minus.0466

I am going to go ahead and leave the Mg off just for the sake that I do not want to make things too busy- alpha-phosphorus, beta-phosphorus, gamma-phosphorus, the terminal phosphor.0468

This is the phosphoryl group right here, this, this, this, this.0478

This comes in that way, kicks these electrons on to there.0482

What you end up with is your glucose 6-phosphate.0489

That is fine; I will go ahead and redraw it.0496

So, what you end up with is that, C, O; and you have the PO32-.0499

That is going to be attached to that; let me go ahead and finish this glucose off here, and we have this.0507

And, of course, now, we have adenosine diphosphate.0516

We have O, P, O, P, O ribose, adenine, double bond, double bond, there and there and there- that is it.0519

Just comes in, nucleophile kicks that off- very, very simple, very straight forward.0536

Well, we have glucose 6-phosphate.0545

This thing right here, what is actually formed is the glucose 6-phosphate.0551

I am going to actually do this a little bit better.0556

I am going to write Glc, and I am going to actually write that no. 6 carbon, Glc, O, P - so that we actually see the structure altogether, it is always nice to see structures - plus ADP.0560

This is 3- + H+, and this H+, you are wondering where it come s from.0578

You know what, I am sorry; let me do this a little bit differently.0594

Well, actually you know what, that was fine.0613

This right here, let’s try this again, so CH2, O, P.0617

Let’s do this, and this right here is our ADP.0626

This is ADP, and it is 3-; and we have the H+.0632

Now, this H+, this comes from the C6, OH deprotonating- losing a proton.0640

Again, we are just, sort of, keeping track of everything, that every little thing- that is what is going on.0658

When this OH attacks and goes over here, now, what you have is an oxygen that is attached to the carbon.0662

It is attached to the phosphorus, and it is attached to the hydrogen, so it is carrying a positive charge.0669

It releases that hydrogen to become just this because oxygen is divalent.0672

It prefers to have 2 things attached to it; I just wanted to show you where this thing actually comes from.0680

You are going to form glucose 6-phosphate; you are going to form ADP, and you are going to release a proton in the solution- that is it.0685

That is the mechanism; that is step 1 of glycolysis.0691

OK, let’s take a look at step 2; let’s go back to black here.0696

Step 2, this is the conversion of glucose-6-phosphate to fructose 6-phosphate.0703

In terms of structures, I think I will just going to go ahead and keep it black.0723

Let’s see; we have got this C, O and P.0728

I am just going to go ahead and write it as a P; we have this, that, that and that.0736

This is our glucose 6-phosphate, and this is going to be...0744

OK, and again, we are going to require magnesium for this, and the enzyme that catalyzes this is the isomerase, the hexose isomerase or let’s call it phosphohexose isomerase or isomerase; and the transformation we are affecting is this one: CH2, OH, OH, OH, OH.0751

And, of course, this C over here still has its phosphate group- that is it, glucose-6-phosphate to fructose 6-phosphate.0787

Let me number the carbons in red; this is 1, 2, 3, 4, 5, 6.0799

And now, we have 1, 2, 3, 4, 5, 6.0808

It is still a 6-membered sugar; it is just attached differently- that is all.0814

That is the numbering; this is our glucose 6-phosphate, and this is our fructpse-6-phosphate.0821

Now, the ΔG for this reaction is 1.7kJ/mol.0830

You notice, it is actually pretty small; it is essentially reversible that is why we wrote it this way instead of just in 1 direction like the previous reaction.0837

I apologize; I actually forgot to write the ΔG for that.0846

Let me tell you the ΔG for that reaction was -16.7kJ/mol, so it is highly exergonic.0851

In this particular case, 1.7, just slightly endergonic, but enough to make it reversible- not a problem.0860

OK, now, let’s talk about the mechanism for this reaction.0868

This is going to be our first real, reasonably complicated mechanism; it is not complicated.0872

It is just a little bit involved; let’s see what we can do.0877

I am going to go back to black here, so our mechanism.0882

Now, what is happening ultimately is that the oxygen C1 bond, this bond, is breaking and OC2 bond is forming.0890

OK, so let’s go ahead and start with…yes, I think I have enough room to do it in here.0916

Let’s go ahead and start off with our glucose molecule.0922

We have the C and the O and the P; this is our glucose 6-phosphate.0930

This is OH, OH, OH.0936

Alright, the first thing that is going to happen is going to be binding.0941

It is going to bind to the enzyme, and the ring is going to open- binding and ring opening.0946

We are going to end up with a straight chain version of this carbon; let me go ahead and draw that and I will draw the enzyme around it.0955

I have got 1, 2, 3, 4, 5 and 6.0963

I have got my aldehyde here; I have an OH group and an H group.0972

This is glucose, still; that is there.0979

This OH is there, and this OH is there; and this is going to be O, and this is our phosphate, right?0983

Let’s just make sure that we have everything straight, and if I make a mistake, please watch very, very carefully.0989

Now, this has bound to the enzyme; let me write the word “binding” a little bit better.0995

I get really, really, quick in my writing and I blow over the words.1002

It binds to the enzyme; the ring opens, and now, this is actually in the enzyme, in the active site of the enzyme.1008

I am going to draw the enzyme like this; OK, that is, sort of, the pocket of the enzyme.1016

Now, I am going to put a little B here with a couple of electrons, and this is just some amino acid residue that acts as a general base.1027

In other words, and we know what bases do: bases take protons.1037

Sometimes we are going to be writing it with an A, which is some acidic residue, some amino acid residue in the protein that happens to act as a general acid catalyst.1041

We know what acids do: they actually give protons- that is all.1054

When you see the A and the B- that is what is happening; sometimes, we will specifically list the particular residue.1058

We will actually say that it is a lysine or it is an arginine or whatever it is; but in this case, we are just taking about generic amino acid that acts as a base.1065

So, here is what happens; let’s go ahead and pull off this hydrogen here.1077

This base will pull off this hydrogen here; let me do this in blue actually since we want to see this, or maybe it is a better idea to do this one in red.1084

This will pull off this hydrogen; these electrons will go here, and they will pull an H from solution and attach it to the O.1097

I will go ahead and do that, and then what you end up with is the following.1115

OK, you end up with…let me see.1125

That is OK; I will go ahead and put it over here.1130

Oops, let me go back to black.1135

We have 1, 2, 3, 4, 5 and 6.1140

Now, what we have is an OH and an H.1146

We have a double bond there; we have another OH here, and then, of course, we have the rest of it.1153

We have the H; no, wait a minute.1163

We just pulled that H off; OK, we have our OH here, and then we have our OH here and our OH here.1166

And then we have our O and our P like that, and we have our enzyme, right?1176

This is our enzyme; now, we have this base that has a hydrogen attached to it.1183

So, we will put a little positive charge on there; this base is what took it.1189

Now, what happens is the following; let me go back to red.1194

Now, these electrons over here, they go down this way.1199

This goes here; the electrons hop back on to there.1207

OK, and when that happens, this hydrogen right here, once this binds, this ends up with a positive charge.1212

This is going to give up its hydrogen; this is going to turn into…let me see.1223

Let’s go ahead and do it this way; let me come down here.1233

Actually you know what, I think I am going to go over to this side.1240

I am going to go over here; I am going to write it as C, C, C, C, 1, 2, 3, 4, 5 and 6.1245

So, what I am left with is an OH here, an H there, a double bond there.1254

I have my OH here, my OH here, my OH here, my O and my phosphate group there- good.1264

OK, I have my enzyme, and now, my base is back to where it was because I took its proton, and these electrons ended up on it- not a problem there.1276

I will go ahead and an H leaves.1288

This H is this H, so I will put another 3 lines underneath it.1292

Once this actually forms the double bond, again, then now, it is carrying a positive charge because there are 3 bonds to the oxygen, so it is going to release that as a proton.1297

This is what you end up having; we basically changed.1304

A double bond has moved from the no. 1 carbon to the no. 2 carbon.1309

OK, so now, what happens is the following: 1, 2, 3, 4, 5.1313

Now, you have got the electrons on the hydroxy on the no. 5 carbon, will attack there; and this one will go ahead and pull another some hydrogen ion from the environment.1320

What you end up with is - 1, 2, 3, 4, 5 - a 5-membered ring.1340

The double bond has moved from the no. 1 carbon to the no. 2 carbon, and then the hydroxy closes the ring again.1350

The hydroxyl in the no. 5 carbon re-closes the ring to form the fructose instead of the glucose.1356

Now, what you have is ring closing, and - I do not know what it is, I cannot seem to write very clearly today, sorry about that- dissociation from the actual enzyme.1363

The enzyme will now release the substrate, and what you are left with is our final product, which is boom, boom, boom, boom, boom.1385

What you have is C, OH.1396

Yes, this H is this H, and then you have OH.1407

You have OH; you have OH, and, of course, we still have our C, which is our 6 attached to the phosphate.1414

There you go- from glucose 6-phosphate to fructose 6-phosphate.1422

That is the mechanism; OK, and hopefully, it does not look like I have missed anything here.1428

We have got some general base catalysis; a base takes a hydrogen1433

A base gives the hydrogen back, and now, it is back to where it started.1437

That is what an enzyme does; it always goes back to where it began.1441

OK, so let’s see what we have got here.1446

OK, now, we are on step 3, so step 3.1454

We have the conversion of fructose 6-phosphate to fructose 1,6-biphosphate.1461

OK, that is going to look like this.1479

C, OH, OH, OH, OH, C, O and P, and this is going to go that way.1486

And again, we are going to have this ATP come in.1500

ADP is going to leave; Mg2+ is going to be required, and this is phosphofructokinase-1, better known as PPK-1.1505

And what you are going to end up with is the same molecule, except now, you have a C, an O and a P.1525

You know what, let me make this a little bit smaller so that we have a little bit more room.1533

OK, let me make sure this is properly erased.1544

We have got zero there, there - not zero, O, sorry.1548

We have C, O and our phosphate.1553

We have our C, O and our phosphate there; we have our OH here.1556

We have our OH here, and we have our OH here.1561

This is our fructose 6-phosphate.1565

This is our fructose 1,6-biphosphate.1572

Woo, all these structures, all these names, they will make you crazy.1577

OK, now, let’s go back to black; now, the ΔG for this reaction is equal to -14.2, and this is kJ/mol.1587

OK, now, the mechanism is exactly like it was before.1600

It is just the basic nucleophilic substitution reaction.1605

It is nucleophilic.1610

This, right here, is what accessed the nucleophile, and that is it.1616

It attacks the terminal phosphoryl, the ATP and it is transferred over nucleophilic substitution - OK - at the oxygen of C1; and this is the C1 now.1621

Red, that is the C1; that is all that is happening.1648

OK, let’s go back here; now, let me do this one in red.1654

OK, this step is irreversible - as you can see from the highly -ΔG - under cellular conditions.1662

There are certain reactions in the glycolytic pathway that have high -ΔGs but under standard conditions, under cellular conditions, they can actually be quite reversible.1680

In fact, we will see one in just a minute, but this one, under cellular conditions, is irreversible - OK - and is the step that actually commits to glycolysis.1694

OK, the glucose 6-phosphate and the fructose 6-phosphate, they can go down other paths, but the fructose 1,6-biphosphate, it means glycolysis- that is it.1722

It is committed to glycolysis.1752

Let’s make this a little clear just in case.1758

OK, now this PPK-1, it is a regulatory enzyme and is the primary regulation point.1777

This step is the primary regulation point for glycolysis.1797

OK, say just a couple of more things about this particular enzyme here.1816

Low ATP levels, it actually activates this enzyme.1821

Low ATP levels activate the PPK-1, and sufficient ATP levels inhibit shutdown PPK-1.1836

This is a primary control point to tell the body "OK, engage in glycolysis or slow down glycolysis or stop glycolysis".1860

OK, now, let's go ahead and talk about step 4.1871

Step 4 involves the cleavage of the fructose 1,6-biphosphate- very, very important reaction here.1877

This is where we are going to actually break it down; OK, let's go ahead and draw out what this looks like.1895

That is OK; I will go ahead and leave this in black.1904

We have zero - O, sorry, I keep saying zero, I keep thinking about mathematics - C, O and P; and we have OH, and we have OH.1908

We have OH, and we have CO; and we have P.1928

We have our fructose 1,6-biphosphate.1934

I am going to number these, actually, in just a minute.1942

This is going to be the enzyme aldolase or aldolase, and we are going to end up forming...I will go ahead and put them here.1947

C, C, C, that is there, H; and this is going to be O, and this is going to be P.1961

This is going to be glyceraldehyde-3-phosphate + the dihydroxyacetone phosphate.1973

I will go ahead and put the carbonyl over here.1983

I will put the O and the P, and I will go ahead and put the OH here, and I will go ahead and put the H2 over here.1987

Well, this right here is our fructose 1,6-biphosphate.1996

This is our glyceraldehyde-3-phosphate, and this is our dihydroxyacetone phosphate.2004

And now, let's go ahead and number some of the carbons; this is 1, 2, 3, 4, 5, 6.2015

Our glyceraldehyde is going to come from carbon 4.2024

That is 5; that is 6, and again, we will do this a little bit later.2029

It is not a problem, 4, 5, 6; and this is going to be 1, 2, 3, 1 on the phosphate, right?2033

That is correct, 1, 2 and 3.2040

I think I have got that right; now, the ΔG for this particular reaction is equal to 23.8kJ/mol.2046

Now, notice, this is highly endergonic; however, this is standard conditions.2057

Now, under cellular conditions, the ΔG is quite small; and the reaction is quite reversible, which is why we wrote it that way.2062

Again, just because we have a standard ΔG, the standard is what we use to...in general, it is our standard.2094

It is our point of reference; however, under cellular conditions are different- different concentrations.2105

Under cellular conditions, this is actually a reversible reaction, not an endergonic reaction.2111

OK, it is quite reversible; so now, let's get into the mechanism of this thing.2117

This is going to be a little bit long, but it is reasonably straightforward.2122

Let us start; I will go ahead and go back to black.2127

Our mechanism, alright, let's go ahead and start with our fructose molecule.2132

This is CO, and then this is P.2145

We have OH, OH, OH; and we have CO there.2152

We have our fructose 1,6-biphosphate.2158

The first thing that is going to happen is binding to the enzyme and ring opening.2162

And now, I am going to draw out the molecule in its open form and the surrounding enzyme.2175

We have a 6 carbon; we have C, C, C, C, C, and we have C.2183

Now, we have that.2190

Remember, we have our carbonyl on our no. 2 carbon now?2196

This OH group is here; this OH group is here.2201

This OH group is here; and, of course, we have another phosphate group there.2204

Now, let me draw my enzyme around it; this is, now, in the active site of the enzyme, a little pocket.2209

And now, I have got an actual lysine residue; and this one, I will say specifically, this is a lysine residue that is going to be responsible for a lot of the chemistry here.2218

We have another general base catalyst; we have another general base catalyst, and we have an acid catalyst, which acid means, it is actually attached to some H.2229

It has an H to give up, so just some general catalyst.2244

This is our enzyme.2249

There we go; OK, here is what happens first.2259

Let me go ahead and do this in red; these electrons on the nitrogen, they come here.2264

The double bond goes after that, and the electrons are shifted over that way.2270

What happens next?2278

OK, now, what you have is the following.2281

Well, let's go back to black.2289

We have C, C, C, C, C, C.2295

Now, we have O and P.2300

Now, we have an OH on that no. 2.2305

And this is, of course, now, attached covalently to the nitrogen of the lysine.2311

Let me go ahead and put my OH there, my OH here, my OH here.2319

Let me make sure I have everything drawn out.2325

N, and we have an H there; we have an H there.2329

And this is, of course, attached to lysine; so let me redraw my enzyme.2334

That is like that, and we said we had a base over here.2341

We have a base over here; now, we have an acid, which is carrying a...the electrons are, now, on the acid, so it is like that.2346

What happens next is the following.2356

Let me go ahead and just draw the...this is the enzyme, our pocket.2359

Let me go back to red and talk about what happens next.2369

OK, these electrons on the general base catalyst, they end up taking the...I am going to put this H here.2373

This H is part of that; it actually takes the H on the nitrogen.2386

Let me go back to red; these electrons move over there.2394

And let me go ahead and show my black.2403

Actually, you know what, I am going to keep this as red; I am going to do this, and I am going to go, say, H+, H2O.2408

OK, that way, OK.2423

These electrons on this base go ahead and pull a hydrogen off of the nitrogen.2427

The electrons on the nitrogen go here to form a double bond with the carbon.2432

OK, and then, it is going to push these electrons; these electrons are going to go and take a hydrogen from the environment, and this is where the water comes from.2437

This OH and this H+, water is released from this; and what you end up with is the following.2448

You end with C, C, C, C, C, C.2457

You end up with this amine, this shift base; you have got that.2465

You have got the O, and you have got the P.2469

You have an OH here, an OH here; let me go ahead and make sure all of these are taken cared of before I deal with anything else.2473

Actually, you know what, I am going to have to make this a little bit further to this side because I need more room on the right.2480

My apologies; let me make sure these get erased properly.2487

OK, and make this a little bit closer here, so C, C, C, C, C, C.2493

We have this thing attached to the nitrogen; we have our hydroxy there.2501

We have our hydroxy there, our hydroxy there.2507

We have the oxygen; we have the phosphate.2511

And over here, we still have our O and our phosphate there.2514

Now, let's go ahead and draw in our enzyme.2520

OK, this is, of course, connected to a lysine residue.2525

We have our base that now, has an attached hydrogen, right?2532

We still have our general acid, which is containing its electrons, so it is there; and this base is right there.2537

Now, we still have this hydrogen attached, so this nitrogen is carrying a positive charge.2547

OK, there we go.2555

And now, let me say a couple of things about it; we put this in blue.2560

This nitrogen, double bonded to a carbon, OK, this thing, this linkage, OK, if you do not remember from organic chemistry, it is called an imine or an imine.2567

I say imine; some people say imine.2587

I do not know, or you probably hear it more often referred to as a shift base.2588

It is carbonyl, not carbonyl; it is a carbon double bonded to a nitrogen, and this happens to be a protonated shift base.2595

Protonated just means that the nitrogen is carrying a hydrogen, so it is carrying a positive formal charge- that is all that is going on there.2601

OK, now, the next step is going to be the following, and this is really, really interesting.2608

Let me see if we can actually follow this along.2613

OK, let's go to red; now, these electrons, OK, let's see what we can do.2622

Let me write this H a little bit differently here.2630

Let me actually put the bond there.2635

Let me go back to red; we are going to take this proton.2640

These electrons are going to come here to form a carbonyl.2645

These electrons is going to push these electrons up here - OK - to form a double bond.2650

It is going to push these electrons back on to the nitrogen to take care of that positive charge, and let me see if we have missed anything here.2659

This is the bond that we are breaking right here, right?2670

1, 2, 3, 1, 2, 3, we are going to break it up into 2, 3, carbon fragments- that is what is happening here.2674

Now, let's go ahead and come down here.2682

This is all so reversible, so let's rewrite what it is that we have got.2688

Let me actually draw the individual fragments.2696

We have C, C and C; and we have C, C and C.2700

We have our O, and we have our phosphate.2708

We have, now, a single bond to the nitrogen, H; and this is attached to the lysine.2712

We actually have a double bond there, right?2720

We actually formed a double bond right there, and we still have our OH group there.2722

Here, we have our H; this double bond that we formed, this is an H.2729

We have our hydroxy, and then we have our O and our phosphate.2737

Hopefully, I have not missed anything here; now, let me go ahead and draw my enzyme- there we go.2744

OK, now, our base actually has an attached hydrogen, so that is going to be that.2757

Our acid is still there; our base still has its hydrogen attached.2765

Let's go ahead and put that, and now, the lysine is, of course, attached that way; so it looks like we have got everything.2772

Notice, now, we have a 3-carbon fragment that is still attached to the enzyme through this nitrogen bond, and we have this 3-carbon fragment, which is the glyceraldehyde-3-phosphate, which is entirely free.2778

At this point, the enzyme releases the glyceraldehyde-3-phosphate.2790

I will go ahead and write that; this molecule, right here - let me do this in blue - is released by the enzyme.2796

This is going to be our C, C, C; and this is going to be our glyceraldehyde-3-phosphate.2806

OK, now, what we are left with is just this species that is covalently attached to the enzyme, still, through this nitrogen bond; and let's see what we can do with that one.2817

Oh, I guess I should probably say, you see this linkage right here, this double bond N?2832

Just so you know, this linkage is called an enamine.2843

OK, that right there, you have and en, an alkene, and an amine' so this is called an enamine.2849

Let me see if there is anything else that we want to say about this; we have released our glyceraldehyde-3-phosphate.2857

This is glyceraldehyde-3-phosphate, and now, let's take care of the next species.2862

Let's go ahead and draw - let's go back to that - out our 3-carbon fragment.2870

This is actually a double bond; this is an N.2882

This is lysine.2888

We still have our enzyme here.2893

We have our base there with the plus charge.2897

We have our base here with this plus charge.2904

We have our A, the minus charge, electron because now, it is carrying the electron.2909

I will go ahead and do that; this is O, and this is a phosphate.2917

This is H, and this is OH, correct?2923

So far, so good; OK, here is what happens.2927

Oops, I forgot that, and, of course, I have the electrons here; now, let me go to red.2931

Let me see; this is going to go and grab...alright.2936

Now, these electrons on the nitrogen are going to move over here.2941

It is going to push these electrons to come and grab that, and it is going to push this back on to that.2946

What you end up with is the following arrangement; you are going to end up back with your imine, your shift base linkage.2953

Let me go back to black here; we have C, C and C.2963

Let's go ahead and do that, H.2969

Let's go ahead and put a positive charge there; it is connected to our lysine.2973

This is O, and this is P; and we have an H here, and we have our hydroxy there.2978

Our enzyme is, now, this way.2985

Now, we have recovered that base there.2990

We have recovered the base here, and we still have our A with that.2996

Now, let's see what happens.3003

Wait, let me make sure I have got everything written out, plus charge, carbon.3008

We have our imine; OK, we have our enzyme.3013

It looks like everything is there; it does not look like I have forgotten anything.3018

OK, now, what we are left with is the following.3021

Now, what happens...OK, from organic chemistry, hopefully, you remember; if not, it is not a problem.3026

I will actually go ahead and do the mechanism in just a minute, but I am going to draw it a little bit differently here.3033

What happens is the following.3040

Water comes in to actually break this bond, to hydrolyze this bond.3045

When water hydrolyzes this bond, it releases this dihydroxyacetone phosphate, so this is what goes away.3052

What ends up going away is this molecule, and that is going to be the C, C, C, O, phosphate, hydroxy.3062

I will draw it exactly as is; water is going to come in.3075

It is going to break this imine bond, and it is going to release this second substrate; and it is going to leave the enzyme as lysine, NH2, B, B, and H, A.3078

The enzyme goes back to what it goes to, and now, what I am going to do is in the next page, I am going to actually draw out the mechanism for this cleavage just so you know.3107

You can see it in any organic chemistry textbook; I do not think this particular mechanism is in your biochemistry textbook, but you can find it in your OCAM textbook, but I will go ahead and go through it.3117

Let me just write out what happens with this one.3127

H2O, it hydrolyzes the NC imine bond.3131

It breaks that bond right there, and it releases everything.3149

OK, let's go ahead and take a look at how that happens.3153

Again, it is nice to have as much detail as possible; let me go ahead and do this one in black.3157

Hydrolysis of the imine goes like this.3164

OK, we have our lysine; we have our N.3181

We have our double bonded to the C, C, C; I am not going to draw everything out because we are just concerned with this linkage, right?3185

OK, H2O, couple of electrons, comes in, attacks right there; that pushes that double bond.3196

It grabs a hydrogen ion from the environment, and it turns into the following.3207

It turns into lysine, N, H, C, H + C, C, O, H.3213

This is H2O; H2O comes in.3238

Well, now, when H2O is attached to this carbon, it is going to be like this.3242

It is going to release one of those into solution, that is why I have it this way.3246

So, if you want, I can put a little -H+ there to let you know that the water is actually going to release one of its hydrogen ions.3250

Well, this actually grabs a hydrogen ion; it is not the same hydrogen ion.3258

This one released; it is not the one that is attached.3260

This happens to be hydrogen ion that is available in the particular medium that is taking place.3263

What you are left with is this; now, what happens is it continues on.3269

You have an electron on the oxygen, which comes here, and it actually kicks this off to quench this positive charge.3274

Now, you end up releasing; now, you have your lysine, and you have your NH2 that is recovered.3281

And then, of course, you have your C, C, C.3290

And again, we are going to lose a hydrogen ion; once these electrons come here, now, you are going to have an oxygen that has 3 bonds.3295

It is going to release this hydrogen into solution leaving just the carbonyl.3302

And now, you have your O and your P; and, of course, you have your OH and your H, and that is the dihydroxyacetone phosphate.3308

This is the mechanism for imine hydrolysis, for shift base hydrolysis.3317

OK, now, one last thing and I think we should be OK.3324

I wonder if I should do this on the next page.3332

No, you know what, I can do it on this page; that is not a problem.3336

That was step 4; now, we will do step 5 to close off the preparatory phase of glycolysis.3340

Step 5 is conversion of the dihydroxyacetone phosphate to the glyceraldehyde-3-phosphate.3346

OK, we have a 3-carbon fragment; we have C, C and C.3377

This is there; this is O.3384

Excuse me; I will go ahead and put the hydroxy on this side for now.3387

And this is going to be a reversible reaction, and we are going to form C, C, C.3393

And we are going to form the aldehyde down here, OH, and we have O; and we have our P.3403

This is our dihydroxyacetone phosphate; this is our glyceraldehyde-3-phosphate.3415

1, 2, 3 and the ΔG for the O; let's go ahead and write down the...this is triosephosphate isomerase or isomerase, and the ΔG for this reaction equals 7.5kJ/mol.3422

OK, let's see; let's go ahead and leave that there.3456

Alright; OK, now, the final thing that I am going to talk about is just the actual breakdown of the sugar and the numbering of the carbons just so we see what it is that we are actually looking at.3460

Let me go ahead and do this in red just for a little change of pace.3472

We have got 1, 2, 3, 4, 5, 6, 1, 2, 3, 4, 5, 6.3477

OK, we have this, and we have our phosphate.3484

We have our carbonyl there; we have a hydroxy there.3489

We have a hydroxy there; we have a hydroxy there, and we have that one.3494

Now, let's go ahead number the carbons; I am going to number them 1, 2, 3, 4, 5 and 6 in blue.3502

We have taken this fructose 1,6-biphosphate and we split it right after the no. 3 carbon.3520

OK, now, this part, that became the following: C, C, C, O, P, right?3526

That is the carbonyl; that is the hydroxy.3544

This became the dihydroxyacetone phosphate.3548

the 1, 2, 3 carbon, that became the dihydroxyacetone phosphate.3552

The 4, 5, 6 carbon, it turned into C, O, H.3558

This O becomes oxidized to the carbonyl; this C retains its hydroxy, and this C retains its phosphate group.3571

This is 4.3582

Let's go to black; this is 1.3589

This is 2; this is 3.3591

This is 4; this is 5, and this is 6.3594

Now, this right here turns into C, C, C.3598

It is the no. 3 carbon that ends up getting oxidized to the carbonyl.3611

This hydroxy stays the same, and this stays the same.3615

Now, we have the 1, the 2 and the 3.3619

Now, if I were to flip this - OK, let me flip this over - I have got C, C, C.3626

I have 3; let me do the numbers afterwards- 3, 2, 1.3640

In our final products of the glyceraldehyde-3-phosphate, there is 1 molecule of it.3660

There is another molecule of it; one of those molecules comes from the 1, 2, 3 carbon.3669

It is the 3 that ends up with the aldehyde group; another one comes from the 4, 5, 6.3674

It is the no. 4 carbon that is carrying the aldehyde group.3679

So, this is an accounting of what carbons turn into what, and what functional groups are attached to what carbon.3683

There you go; this is a detailed discussion of the preparatory of glycolysis- the first 5 steps.3692

In the next lesson, we will, of course, discuss the last 5 steps- the conversion to pyruvate.3698

Thank you so much for joining us here at Educator.com3703

We will see you next time, bye-bye.3707

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