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Raffi Hovasapian

Raffi Hovasapian

Gluconeogenesis I

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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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Gluconeogenesis I

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
  • Gluconeogenesis, Part 1 1:02
    • Gluconeogenesis Overview
    • 3 Glycolytic Reactions That Are Irreversible Under Physiological Conditions
    • Gluconeogenesis Reactions Overview
    • Reaction: Pyruvate to Oxaloacetate
    • Reaction: Oxaloacetate to Phosphoenolpyruvate (PEP)
    • First Pathway That Pyruvate Can Take to Become Phosphoenolpyruvate
    • Second Pathway That Pyruvate Can Take to Become Phosphoenolpyruvate
    • Transportation of Pyruvate From The Cytosol to The Mitochondria
    • Transportation Mechanism, Part 1
    • Transportation Mechanism, Part 2
    • Transportation Mechanism, Part 3
    • Transportation Mechanism, Part 4

Transcription: Gluconeogenesis I

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

In the last several lessons, we discussed glycolysis, and we finished discussing glycolysis.0004

Today, we are going to start talking about gluconeogenesis, which is instead of the breakdown of glucose, this is how the body actually makes glucose when it needs to do so.0011

Now, you are going to see in a minute that a lot of the reactions of gluconeogenesis are the same.0020

They are just run in reverse, however, it is not just glycolysis run in reverse.0026

If you remember in the glycolysis reactions, there are 3 reactions in particular that were highly exergonic, very, very high negative free energy.0030

They are virtually irreversible under physiological conditions.0038

Well, because they are irreversible; there is no way for the enzymes to actually go backward, just reverse glycolysis.0042

Those particular reactions, gluconeogenesis actually bypasses and uses its own set of enzymes for its metabolic pathway.0049

Let’s go ahead and write all these down formally and see what is going on.0057

OK, so let’s see; we will stick with black today.0063

Often times, the body needs to synthesize glucose instead of breaking it down.0071

OK, so we will concentrate on the gluconeogenesis that takes place in the mammalian liver.0099

We will concentrate on how the mammalian liver does this.0110

OK, so gluconeo - I will just call it that for short - gluconeogenesis is not the reverse of glycolysis, not just the reverse of glycolysis.0125

OK, now, we can start; recall, there are 3 glycolytic reactions that are irreversible under physio conditions.0151

OK, let’s go ahead and list what they are.0182

The first one, we have glucose going to glucose 6-phosphate.0187

We had a ΔG, and in parentheses, I will just write physio ΔG; and notice, there is no standard, no degree sign noted.0193

These are actually under physiological conditions, not biochemical standard conditions, so negative, somewhere in the range of -33kJ/mol; and then, the second reaction is going to be the fructose 6-phosphate to the fructose 1,6-biphosphate.0201

That one carries a ΔG of about -22kJ/mol, and the last is the phosphoenolpyruvate to pyruvate.0230

That is the final reaction in the glycolytic sequence, and this one carries a ΔG of, under physio conditions of about -16, -17kJ/mol- all of them irreversible.0245

Gluconeogenesis has to bypass these reactions.0257

It cannot just use these reactions; excuse me.0261

Gluconeogenesis bypasses these steps with its own set of enzymes, and these reactions are, themselves, sufficiently exergonic to make sure that gluconeogenesis is irreversible.0267

Well, are sufficiently exergonic to make sure that gluconeogenesis - well, let me go ahead - to make sure that they are irreversible in themselves.0329

They are irreversible; it is the reactions that are irreversible.0340

Essentially, it is going to commit to gluconeogenesis; it is not going to back down somewhere in the middle.0343

These particular reactions, themselves, are highly exergonic to push gluconeogenesis forward.0350

Sure that they are irreversible, themselves- let’s just go ahead and say it that way.0356

OK, so let’s go ahead and take a…we are going to look back at a schematic - well, I am going to draw it out - of glycolysis, and I will show you where the bypass reactions take place.0362

Let’s go ahead and do this one in…let me go ahead…well, you know what, I will just stick with black for the time being.0371

Here are the steps of glycolysis; I am hoping I can get this all in one page.0378

Let me see; I have got glucose to glucose 6-phosphate.0383

I am going to use just some short-hand notation here, glucose 6-phosphate to fructose 6-phosphate, and then, to fructose 1,6-biphosphate; and at that point, we go to glyceraldehyde-3-phosphate.0390

I will write glyceraldehyde-3-phosphate, and we also produced a - I will do it over here, that is OK, I will do it over here -dihydroxyacetone phosphate, which, itself, is converted to the glyceraldehyde-3-phosphate.0405

We produced 2 molecules - right - out of the glyceraldehyde-3-phosphate from the 1 molecule of glucose, and then, we start the second phase.0420

We go to 1,3-biphosphoglycerate, and then, we go to 3-phosphoglycerate, then we go to 2-phosphoglycerate, then we go to phosphoenolpyruvate; and, of course, our final step is 2 molecules of pyruvate.0427

OK, these are going to be the bypass steps; let me go and do these in red.0448

The glycolysis is this way; gluconeogenesis, we are going to run this way, and here is what happens.0452

The conversion from pyruvate to phosphoenolpyruvate, as we go back, it takes place in a 2-step process.0457

The first step is actually going to form oxaloacetate, and then from oxaloacetate, that one is going to go to phosphoenolpyruvate.0463

Now, let me go ahead and I will write the enzymes in blue.0479

The conversion of pyruvate to oxaloacetate takes place under the guidance of an enzyme called pyruvate carboxylase, and the conversion from oxaloacetate to phosphoenolpyruvate takes place under an enzyme called PEP carboxykinase or carboxykinase.0483

Again, it depends on how you want to pronounce it; it does not really matter.0505

OK, now, let’s go back to red.0511

Now, the second bypass step is going to be from the fructose 1,6-biphosphate to the fructose 6-pospahate.0515

This one goes like that, and its enzyme is fructose 1,6-biphosphatase.0520

It takes away a phosphoryl group, and the last bypass step is the one from glucose 6-phosphate to glucose; and that one - exactly what you think - it is glucose 6-phosphatase- there you go.0540

Glycolysis runs this way; gluconeogenesis runs this way.0563

All of the enzymes, all of these other reactions, are the reverse of glycolysis because these reactions under physiological conditions, the ΔG is very, very close to 0.0567

If it is not 0 itself, it is very close to 0; it is irreversible.0577

Remember we had double arrows for most of them, but for this one, this one and this one- irreversible.0581

It needs another set of enzymes to make sure they run this way.0586

And again, these reactions running in this direction up towards glucose, each of these is efficiently exergonic to make sure that gluconeogenesis pushes forward.0590

It is fantastic that it actually does this; OK, now, let’s go ahead and take a look at the individual reactions.0599

We are going to go ahead and start with this bottom one- the pyruvate carboxylase and the PEP carboxykinase.0605

Let’s write out the reactions, and then, we will talk about the mechanism.0612

I am not sure about the extent to which your teachers are going to actually have you learn mechanisms.0617

I think there are going to be certain set of reactions; you are limited in time, whether you are taking a quarter system class or whether you are taking a semester system class.0622

So, I am guessing only a handful of mechanisms are the ones that you are going to be needing.0630

In this particular course in biochemistry here at Educator, I am going to tend to place a lot of the mechanisms.0635

I am going to show them simply for the sake of…I think it is really, really important that you understand and become comfortable with mechanistic biochemistry, with the mechanism of organic chemistry.0642

Those of you that go on particularly into research and or pharmacy school or things like that, mechanisms are going to be a big part of what you do, at least academically.0653

It is important to become comfortable with those things; I want you to see as many of them as possible.0663

OK, having said that, let’s go ahead and write the reactions down.0667

Let me go ahead and write the reactions in blue here.0673

The first one is going to be…so again, a 2-step from pyruvate to phosphoenolpyruvate.0677

The first one is going to be like this.0689

That is fine; OK, we will go C, C, C.0699

This is there; I will go ahead and put the double bond up here, the CH3 there.0706

OK, this is going to be plus; it is going to be H, O, C, O, O-.0712

This is going to be bicarbonate; well, let me go ahead and write the reaction first and then I will…OK, ATP is going to come in.0719

ADP and PI are going to leave; the coenzyme biotin is going to be very, very necessary in this particular reaction, and then, of course, the enzyme itself is, as we said, pyruvate carboxylase.0732

OK, now, it is going to form the oxaloacetate, which is going to be C, C, C, C.0751

We have this; we have that, and we have, of course, this carboxy group that we put on there, and let me…well, that is fine.0761

I will go ahead and put the Hs on also; it is not all together that big a deal.0774

In red, let me write, this is oxaloacetate.0779

This is bicarbonate - bicarbonate or bicarbonate - and this is our pyruvate.0785

OK, and again, this enzyme biotin, this is going to be the next to the coenzymes of vitamins that we are going to be discussing in just a little bit - very, very important - and the enzyme for this is pyruvic carboxylase.0793

OK, let me go ahead and write the second reaction, and then, we will jump into the mechanism.0809

The second reaction is, now, we are going to take this oxaloacetate, so C, C, C, C.0813

I am going to leave off the hydrogens in this one; I hope you guys do not mind.0820

Again, anytime you see a carbon that has nothing attached to it or seems to be missing some things, just attach a hydrogen to it.0824

This is there, and this is there.0830

This is our oxaloacetate, and we are going to add to this not adenosine triphosphate but a guanosine triphosphate.0834

Interestingly enough, this goes that way.0841

GDP - guanosine diphosphate - actually ends up leaving; in this particular step, CO2 is lost.0847

The CO2 that we added is now, lost, and the enzyme for this is PEP carboxykinase; and our final molecule is the phosphoenolpyruvate.0853

We have our C; we have our C.0868

We have our C; this is, of course, a double bond there.0872

We have our group there; we have our oxygen, and we have our phosphate.0875

I will just go ahead and put PO32-.0881

This is our oxaloacetate.0885

This is our GDP; I will just go ahead and leave that there, and this is our phosphoenolpyruvate- our PEP.0889

Pyruvate to oxaloacetate, oxaloacetate to phosphoenolpyruvate- 2 bypass steps, OK?0895

Alright, let me go ahead and just circle this.0902

Notice that CO2 comes in in the form of bicarbonate.0906

CO2 leaves in the form of CO2; now, let’s talk about the mechanism.0910

Actually, you know what, before I talk about the mechanism, I am going to…well, here, I will just go ahead and talk about it.0916

OK, so let’s do this one in red.0924

Now, there are 2 pathways for pyruvate, 2 pathways that pyruvate can take to become phosphoenolpyruvate in the gluconeogenesis.0928

OK, there are 2 paths that it can actually take.0960

A pyruvate is not the only precursor to gluconeogenesis.0964

Pyruvate is the first molecule that enters the cycle, but there are several other molecules that can actually act as precursors to pyruvate depending on, if it is directly pyruvate that goes into gluconeogenesis, it is going to take a particular pathway.0968

If it is not pyruvate in this thing that I am going to draw, if it happens to be lactate that is converted to pyruvate, it actually takes a different pathway.0985

It is almost similar; it takes place in the same place physically, but it is a different pathway.0992

Let me go ahead and talk about those, and I will discuss both.1000

Let me see if I can…OK, I will try to make it as big as possible.1005

This is going to be our mitochondrion, and this is where it actually is going to take place.1011

Now, actually, you know what, I am going to need a little bit more room here.1019

OK, let me go ahead and go a little bit lower here.1034

I hope I can squeeze it all in; I am sure I can.1040

Alright, let me just take a couple of minutes to draw this here; we have pyruvate over here.1045

This is going to be one pathway, and I will go ahead and put a pyruvate over here too.1049

This is going to be another pathway; this one, what is going to happen here is, I will go ahead and write pyruvate again.1053

I will go ahead and write oxaloacetate there, and then, I will bring it back down here.1065

I will write malate, and I will do this.1078

I will do malate; I will do oxaloacetate, and then, I will go to our phosphoenolpyruvate.1084

And over here, I am going to come from lactate, and again, I will come to pyruvate.1095

OK, and I will go to this one; I will go to oxaloacetate.1105

And from oxaloacetate, I will go to phosphoenolpyruvate and phosphoenolpyruvate to there.1118

OK, the first one, I am going to discuss when I discuss the mechanism is going to be this one right here.1125

It is going to be the one on the left when pyruvate is directly the precursor to gluconeogenesis.1129

Now, let me go ahead and finish some of these by actually drawing in some things that come in and some things that leave.1135

CO2 comes in; this is going to be step 1.1145

And then, over here, we have NADH + H+ comes in, and NAD+ leaves.1151

And then, from malate to oxaloacetate, we have NAD+ coming in and NADH + H+ goes there.1167

And over here, this is where the CO2 - OK - leaves.1180

Now, let me go ahead and write some enzymes here.1186

In step 1, we have the pyruvate oxaloacetate.1190

That is going to be our pyruvate carboxylase, and over here, this is going to be mitochondrial malate dehydrogenase.1194

OK, over here, this is going to be cytosolic.1223

I will write malate - D-E-H - dehydrogenase.1230

This is the same reaction, except one of the enzymes actually does it in the mitochondria.1234

The other one does it in the cytosol, so these are different.1238

OK, and, of course, the last enzyme, this was the cytosolic phosphoenolpyruvate carboxykinase.1243

That is the second step of our particular reaction.1255

OK, now, over here, this is what is, kind of, important.1260

Let me go ahead and go back to red.1264

NAD+ comes in, and NADH + H+ leaves.1268

This is step 1; this is step 2.1278

Here, this is lactate dehydrogenase.1284

And again, I will be talking about all of this in just a little bit, but I want you to have...I am just going to go through a quick rundown of what it is that is going on, and then, we will discuss it in detail.1289

Here, it is going to be the same; it is going to be the pyruvate carboxylase.1300

Here, it is going to be...this enzyme right over here that catalyzes that step, this is called mitochondrial PEP carboxykinase.1304

OK, let's stop and take a look at what is going on here.1325

Basically, in the pathway that we are going to follow, the pyruvate is actually transported into the mitochondrion.1329

The pyruvate is converted into oxaloacetate, the normal reaction, but because the mitochondrion does not have an active transporter, it does not have a way of actually bringing in or taking out the oxaloacetate molecule.1336

What it has to do is it actually converts it into malate, and then, it sends the malate out of the mitochondrion; and then, it reconverts it back to oxaloacetate.1350

Once it gets to oxaloacetate, then, it is back in the cytosol.1362

Now, the cytosolic PEP carboxykinase converts it to PEP.1365

However, if lactate is the actual precursor molecule, and lactate is, first of all, converted to pyruvate and the same thing, pyruvate is brought into the mitochondrion, now, in this case, pyruvate is converted to oxaloacetate via the pyruvate carboxylase reaction.1370

While it is in the mitochondrion - OK - it actually just goes ahead and directly converts it to the phosphoenolpyruvate.1388

This time, this reaction is mitochondrial PEP carboxykinase versus this one that actually takes place in the cytosol.1395

In this pathway, the second part of that bypass reaction from pyruvate to phosphoenolpyruvate, the first step takes place in the mitochondrion.1404

The second step takes place in the cytosol; in this other pathway, both steps takes place in the mitochondrion, and then, of course, it just sends out the PEP into the cytosol to continue on with the gluconeogenesis.1412

The first one we are going to talk about is this one; the mechanisms are essentially the same.1425

I mean, these are just isozymes; they are the same enzyme.1430

They are not the same enzyme; they are the enzymes that actually catalyze the same reaction, but they are encoded by different genes of the DNA.1435

That is all that is going on here; I just wanted you to see that there are 2 different pathways depending on the precursor molecule- pyruvate directly or something that is not pyruvate directly if the pyruvate happens to come from lactate.1441

OK, now, let's go ahead and talk about the mechanism.1456

OK, let me go back to black here.1461

Again, let's see.1465

Pyruvate is transported from the cytosol to the mitochondrion.1470

OK, let me write the reaction one more time; what we have is - oops, that is OK, I will go ahead and leave it in blue - C, C, C.1495

We have this; we have that.1508

We have our pyruvate molecule, and we are going to add to this H, O, C.1511

Bicarbonate is going to be the other reactant in this, and we are going to end up with our C, C, C, C.1519

That is there; that is there, and let me see.1528

What am I missing?1532

I have my...that, and, of course, I will go ahead and just leave off the hydrogens.1536

That is going to be our oxaloacetate, and what is going to come in is ATP.1540

What is going to leave is ADP + PI.1545

When you see ATP come in and ADP and PI leaves, that means the phosphoryl group does not stay on the molecule.1549

That means that the energy on ATP is being used to drive this reaction- that is what is going on here.1557

ATP comes in, both products of ATP, which is ADP and PI, both of them end up leaving.1564

What is really coming into this reaction is the energy of ATP.1571

And again, we have biotin, is the coenzyme that is necessary; and we have the pyruvate carboxylase.1575

OK, now, let's go ahead and run through the mechanism.1586

There is going to be little bit of, well, a fair amount of drawing here; the mechanism is not necessarily complicated, but it is a little involved.1589

Let me go ahead and do the mechanism in...you know what, I will just keep it in blue- not a problem.1596

I will try to do the electron movements in red, if I remember.1604

OK, let's go ahead and start drawing what we have got here.1609

Let's go ahead and do…we have: a D-ribose phosphate, phosphate.1613

And this last one, I will actually draw in because it is necessary to draw it in.1624

And over here, I am going to draw out my bicarbonate.1631

OK, now, I will draw this.1640

OK, this is going to be catalytic site 1.1648

There are 2 catalytic sites on this particular enzyme, the pyruvate carboxylase.1652

Part of the reaction takes place in one part, and then, the other part takes place in the second site.1657

This is catalytic site 2, and you will see how this biotin does this extraordinary, extraordinary thing.1662

It is absolutely fantastic.1671

OK, let me go ahead and I am probably going to need a little bit more room here, but that is OK.1675

I will do lysine, and then, we have our N, COO, then 1, 2, 3, 4, 5...let's see.1680

We are going to have a 1, 2, 3, 4, 5, 1, 2, 3, 4, there is a sulfur.1695

There is a nitrogen; there is a nitrogen.1705

There is a carbonyl; we have an H.1707

We have an H, and OK.1711

This is how it begins; you have the enzyme, which is this thing right here.1715

OK, and attached to a lysine residue is this biotin molecule, this biotin coenzyme.1722

So, it is going to be involved, and what it is actually going to end up doing is, whatever ends up happening over here, it is going to take this molecule.1730

See this long arm?1737

It actually acts as a tether; it actually moves things from one place to another place on the enzyme.1740

It is going to end up swinging and bringing whatever is formed over here over to this side, so that a particular reaction can take place over there.1744

This is absolutely fantastic, and this is not the only time we will see this.1752

We will see this another time later on with a different coenzyme.1756

Before we begin, this is how it starts; now, let's go ahead and do some electron movements here.1761

Let me do these in red; this is going to be just a standard SN 2.1766

This comes over here and does that and does that, and in the process, what it ends up doing is...I am going to go ahead and write it this way.1771

ADP actually leaves in this reaction, and what you end up getting is, you get H, O, C, O, and then, P, O, O, O.1788

This is what we have; this phosphate, right here, this phosphoryl group, is now attached here.1804

That is this one, right here, OK?1810

That happens there; now, I will go ahead and do - since I have written this in red - the electron movements in black.1814

There are electrons on here; what happens is these electrons and oxygen, CO2 is a molecule that very, very, very badly wants to be formed.1823

It goes like that, and it kicks away the actual full phosphate molecule; and then, this hydrogen breaks off.1832

It just leaves, and what you are left with is CO2; what you are left with, at this point, is the following.1841

Now, let's go ahead and draw our site again.1852

Yes, that is fine; I guess I have got enough room here.1857

We have that; we have our lysine.1861

We have our nitrogen, 1, 2, 3, 4, 5.1865

We have our carbonyl; we have that, that, that, that, that.1871

There is an S there; we have another 5-membered ring.1875

There is a nitrogen; there is a nitrogen.1878

There is an H; there is an H, and there is our carbonyl.1880

And now, what we have is this carbon dioxide molecule, right?1885

We ended up forming a carbon dioxide molecule over here in site 1.1890

That is that; now, what is going to happen is these electrons - oops, let me do this in red - on nitrogen - they are nucleophilic - they are going to actually attack the electrophilic carbonyl - happens all the time - and you are going to end up with that.1895

Let me actually go back to black; this is the enzyme just to make sure we know what is happening, and this is site 2.1912

OK, now, what happens is it attacks here; now, this COO is attached to the nitrogen.1921

This H ends up leaving.1928

OK, it releases an H+; now, what you have is the following.1932

Now, what you have is...let me draw it down here, so we have some room.1938

This is site 1; this is site 2.1942

We have our lysine.1947

We have our nitrogen, and we have 1, 2, 3, 4, 1, 2, 3, 4, 5.1953

That is going to be there; we have this.1964

We have a sulfur; we have N.1970

We have N; we have a carbonyl, and now, what we have is this COO- that is covalently attached to the biotin molecule, and all of this is happening over here at site 1.1974

Now, what happens is this long arm tether, it takes it from site 1.1986

It moves it over to site 2; it flips around, so we can now, expose this CO2 to what is happening over here in site 2.1994

I will draw it like this; this swings over to site 2.2001

It is absolutely fantastic, this biological tether.2011

Just a simple carbon chain- that is all it is, and it can do this; and it is amazing.2015

It is a huge distance that can actually cover these biological tethers.2021

OK, now, when it swings over to this side, now, it is going to turn over and expose this carbon dioxide that is attached here over to site 2.2025

Now, let's see what it looks like; let me go back to black.2036

This is our enzyme just to make sure we remember.2039

OK, now, we are looking like this.2045

Let me draw it down here; now, reactions are taking place in site 2.2055

We have our lysine; we have our N, 1, 2, 3, 4, 5.2062

Now, notice, the carbonyl is on this side, and I have got my 5-membered rings here, my carbonyl.2070

I have my nitrogen; I have my nitrogen.2080

I have my COO- attached there; I have my sulfur.2082

Hopefully, I have not forgotten anything; again, like I said, there are so many atoms floating around that it is very, very possible that I forgot, and I hope that you are actually confirming many of these structures for me.2086

Now, at this point, what happens is the following.2098

This actually breaks off from the biotin.2102

This goes like that, and what we end up getting is...now, what happens, when that happens, now, CO2 is free over here at site 2.2107

It is free to react, and this is where pyruvate comes in.2120

C, C, C, O-, O, and I am going to actually draw out all of the Hs here this time.2126

So, that comes in, and now, what happens is the following.2137

When that comes in, then we get...let me go back to black.2151

OK, we have lysine, N, 1, 2, 3, 4, 5.2159

That is there, and we have 1, boom, boom, boom, boom, boom, boom.2169

That is there; this is a nitrogen.2176

This is a nitrogen; this is a sulfur.2179

Oops, sorry; what did I do?2183

Oh, sorry about that; I need to actually form…I am in black, right?2189

Yes, I am in black; this is a carbonyl here.2195

What happens is it does not actually go on to the nitrogen; well, it can.2199

It does not really matter how you do this; I mean, you can put the electrons on the nitrogen, or it is more conventional to put them in terms of a double bond; so you end up with something like that.2204

Now, what you actually end up here is this thing.2215

The electrons are on the oxygen, negative charge.2220

The electrons here- double bond, and then, of course, you have your CO2 molecule, which broke off; and then, of course, you have your pyruvate molecule, which is now, in the catalytic site 2.2223

OK, and this is site 1; now, what ends up happening is the following.2245

These electrons move back down to form the carbonyl; these electrons over here grab one of the Hs on the pyruvate.2250

They push this bond over to here, and they push these up to here.2258

Again, boom, boom, takes a hydrogen, sorry, I should attach a hydrogen here.2265

There we go; this takes that hydrogen because it wants it, pushes the electrons this way to form the enol.2274

This goes up that way; that is what is happening here.2282

OK, now, once this happens, what you end up with is the following.2286

Let me go back to black; now, let me go to my next page.2293

OK, let me go to my next page, alright.2299

Alright, now, I have my lysine.2306

I have this 1, 2, 3, 4, 5.2312

Let me just go ahead and draw this in, boom, boom, boom, nitrogen, nitrogen.2317

Carbonyl is reformed; this is sulfur.2324

There is my carbonyl; now, I have my CO2.2327

I lost my - change of color, so forgive me - COO there, and now, I have a C.2332

I have H2; there is a double bond here.2344

There is a negative charge there; there is a C there.2347

This is my pyruvate; OK, now, what happens is the following.2352

Again, this is site 2; this comes back down here.2357

This will attack that one; this will push something there like that, and then, of course, what you end up with is the release by the enzyme at this point.2363

And now, notice what you have got; now, this comes down, pushes these electrons from the double bond to attack the carbon of the carbon dioxide, which is electrophilic.2379

It pushes these over here, so now, the negative charge ends up over here; and what you end up with is C, C, C, C.2390

You end up with that.2400

Oops, and I will go ahead and put the Hs here.2405

You end up with your oxaloacetate.2411

There you go; this CO2 right here, that is what was brought in as bicarbonate.2417

The bicarbonate reacted with the ATP, and got itself a phosphate group to activate it; and then, it went ahead and lost its phosphate group.2427

Now, it is free in site 1; it reacted with the biotin.2440

The biotin moved it over to site 2; it released the CO2.2445

It roamed around freely in site 2; it took in the pyruvate molecule.2450

Well, a pyruvate gave up one of its hydrogens to the biotin, to recover the biotin, and then, at that point, it has been activated in this form to actually react with the CO2 to add this carboxyl group to the other end of the pyruvate to form oxaloacetate- an absolutely extraordinary mechanism.2460

There you have it; this is the first half of the bypass reaction for the first step of gluconeogenesis.2479

I am going to stop this lesson here; in the next lesson, we will continue on with the rest of it.2485

Thank you so much for joining us here at Educator.com; we will see you next time, bye-bye.2491

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