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Raffi Hovasapian

Raffi Hovasapian

Glycolysis III

Slide Duration:

Table of Contents

I. Preliminaries on Aqueous Chemistry
Aqueous Solutions & Concentration

39m 57s

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

38m 53s

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

29m 1s

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

39m 11s

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

41m 33s

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

44m 19s

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

18m 45s

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

38m 19s

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

27m 14s

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

48m 28s

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

45m 18s

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

42m 47s

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

1h 2m 33s

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

49m 12s

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

54m 31s

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

50m 52s

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

51m 36s

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

1h 3m 36s

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

1h 7m 16s

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

41m 38s

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

44m 2s

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

56m 40s

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

20m 37s

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

51m 37s

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

51m 23s

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

54m 49s

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

1h 17m 46s

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

37m 6s

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

43m 32s

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

39m 25s

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

44m 15s

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

44m 23s

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

40m 22s

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

54m 55s

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

38m 51s

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

38m 20s

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

48m 36s

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

45m 51s

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

37m 6s

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

44m 32s

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

30m 8s

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

49m 46s

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

56m 34s

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

42m 12s

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

43m 32s

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

1h 1m 47s

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

59m 17s

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

39m 47s

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

41m 34s

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

34m 18s

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

42m 52s

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

36m 10s

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

49m 20s

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

44m 11s

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

48m 11s

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

45m 58s

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

33m 18s

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

40m 59s

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

39m 18s

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

36m 21s

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

47m 58s

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

41m 11s

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

36m 27s

Intro
0:00
Complex III
0:19
Complex III Overview
0:20
Complex III: Step 1
1:56
Complex III: Step 2
6:14
Complex IV
8:42
Complex IV: Cytochrome Oxidase
8:43
Oxidative Phosphorylation, cont'd
17:18
Oxidative Phosphorylation: Summary
17:19
Equation 1
19:13
How Exergonic is the Reaction?
21:03
Potential Energy Represented by Transported H⁺
27:24
Free Energy Change for the Production of an Electrochemical Gradient Via an Ion Pump
28:48
Free Energy Change in Active Mitochondria
32:02
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Lecture Comments (4)

1 answer

Last reply by: Professor Hovasapian
Tue Jul 31, 2018 12:30 AM

Post by Swati Sharma on July 27 at 01:36:20 PM

Dear Professor,

I carefully studied all the mechanisms as you were writing I was writing too . I was wondering if these mechanisms would be asked in the MCAT Biochemistry section or what kind of questions should I be prepared from on the mechanisms?. I would be grateful if you could just let me know any kind of random questions on mechanisms.

I am preparing for MCAT on my own I just hope I am doing fine. I am preparing from your detailed lectures so that I can deal with any Biochemistry passages.

Regards
Swati

1 answer

Last reply by: Professor Hovasapian
Fri Mar 28, 2014 5:32 PM

Post by Alan Delez on March 26, 2014

Hi Dr. Hovasapian,

On step 10 I was wondering why the carboxylate does not protonate

Glycolysis III

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 5: Conversion of Dihydroxyaceton Phosphate to Glyceraldehyde 3-Phosphate 0:44
    • Glycolysis Step 5: Mechanism, Part 1
    • Glycolysis Step 5: Mechanism, Part 2
  • Glycolysis Step 6: Oxidation of Glyceraldehyde 3-Phosphate to 1,3-Biphosphoglycerate 5:14
    • Glycolysis Step 6: Reaction
    • Glycolysis Step 6: Mechanism, Part 1
    • Glycolysis Step 6: Mechanism, Part 2
    • Glycolysis Step 6: Mechanism, Part 3
    • Glycolysis Step 6: Mechanism, Part 4
  • Glycolysis Step 7: Phosphoryl Transfer From 1,3-Biphosphoglycerate to ADP to Form ATP 19:08
    • Glycolysis Step 7: Reaction
    • Substrate-Level Phosphorylation
    • Glycolysis Step 7: Mechanism (Nucleophilic Substitution)
  • Glycolysis Step 8: Conversion of 3-Phosphoglycerate to 2-Phosphoglycerate 28:44
    • Glycolysis Step 8: Reaction
    • Glycolysis Step 8: Mechanism, Part 1
    • Glycolysis Step 8: Mechanism, Part 2
    • Glycolysis Step 8: Mechanism, Part 3
    • Catalytic Cycle
  • Glycolysis Step 9: Dehydration of 2-Phosphoglycerate to Phosphoenol Pyruvate 37:20
    • Glycolysis Step 9: Reaction
    • Glycolysis Step 9: Mechanism, Part 1
    • Glycolysis Step 9: Mechanism, Part 2
    • Glycolysis Step 9: Mechanism, Part 3
  • Glycolysis Step 10: Transfer of a Phosphoryl Group From Phosphoenol Pyruvate To ADP To Form ATP 45:16
    • Glycolysis Step 10: Reaction
    • Substrate-Level Phosphorylation
    • Energy Coupling Reaction
  • Glycolysis Balance Sheet 54:15
    • Glycolysis Balance Sheet
    • What Happens to The 6 Carbons of Glucose?
    • What Happens to 2 ADP & 2 Pi?
    • What Happens to The 4e⁻ ?

Transcription: Glycolysis III

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

In the last lesson, we talked about the first phase of glycolysis often called the preparatory phase.0004

And today, we are just going to continue on until the end of glycolysis, what they often call the pay-off phase.0010

Again, there is no real reason to break this up into this place or that place.0017

I mean, glycolysis is this pathway with 10 reactions, but sometimes, I think it helps to categorize it in a certain way; but it is not absolutely necessary.0021

Do not feel that you have to know pay-off phase or preparatory phase or things like that.0034

It is the reactions that are important, the mechanisms and the enzymes; that is what we want you to concentrate on.0038

OK, so let’s get started; I am going to do just a little bit of quick recap from the last steps.0044

In the last lesson, I actually left off the mechanism before step 5, which was the conversion of the dihydroxyacetone phosphate to the glyceraldehyde-3-phosphate.0051

I am going to go ahead and do that really quickly, and then we will jump into step 6 through 10.0061

Let’s see here.0068

In the last lesson, I left off the mechanism for step 5, which was the dihydroxyacetone phosphate to the glyceraldehyde 3-phosphate.0073

Here we go; let’s go ahead and draw our molecule here.0101

Yes, let me see; let me go ahead and do this in blue, I think.0107

OK, we have got C, C, C, and we have got OH.0111

I will put an H there; I will put an H there.0116

We have our carbonyl; let me make that double bond a little bit more clear here.0120

We have our carbonyl there, and we have our C, our O and our P.0125

This is the phosphoryl group, and let me go ahead and draw my enzyme.0130

Actually, you know what, yes, that is fine; I will go ahead and draw my enzyme, something like that, and we have just some B, some general basic group that is going to involve some of this general base catalysis.0136

It is going to abstract the proton, and then, of course, general acid catalysis is the donation of a proton.0154

This is our enzyme, and here is the dihydroxyacetone phosphate inside the pocket of the enzyme.0161

This is going to abstract this proton, and these electrons are going to move over here; and these electrons are going to go ahead and grab a hydrogen ion from the environment, and what you end up getting is this now.0170

We have - let me draw the molecule first - C, a double bond C, single bond C; and then we have our O - let’s see, O - and let me go ahead and put this H here.0185

Let me put this H here; I have an OH here, and I have an O, and I have the phosphate.0201

Let me see if I have forgotten anything; and again, I am not going to put down all of the hydrogens.0211

The ones that are unnecessary I will just leave off just to save a little bit of space.0217

Let me go ahead and mark off the enzyme again, so this is our enzyme.0221

And, of course, now, our base is attached here, so let’s put a little positive charge on there.0226

Now, what is going to happen is these electrons are going to pop down here.0233

These are going to abstract this hydrogen; these electrons are going to move back to the base to recover the base, and what you end up with once you lose this hydrogen ion...0243

When these electrons come down here to form the carbonyl - this oxygen, now, is carrying a positive charge - it is going to release this hydrogen, so that it is left only with the carbonyl.0260

What you end up with - and let’s go ahead and write released by enzyme - and then, what you get is - of course, I will put the carbonyl there, I will put the hydrogen there, I will put the OH group there, put that there, and I will put that like that, I will go ahead and put the H2 here - what you have is the glyceraldehyde-3- phosphate.0270

This is the mechanism for step 5; OK, let me write this down: glyceraldehyde-3-phosphate.0297

That is the mechanism for step 5; now, we can go ahead and jump into the rest of glycolysis.0306

OK, let me go back to black here.0311

Step 6 is going to be the oxidation of glyceraldehyde-3-phosphate to 1,3-bisphosphoglycerate- very, very important step.0320

This is where it actually starts the real process- oxidation of the glyceraldehyde-3-phosphate to 1,3-bisphosphoglycerate.0328

Woo, these names are long; OK, here is the over-all reaction.0351

Let’s see; we have got our...let me put the carbonyl up there, H.0357

We have OH, and we have O; and we have P.0366

I will do that; we have H here.0371

We have H2; this is going to be plus our inorganic phosphate.0374

Let me go there; inorganic phosphate is going to be actually one of the reactants here.0382

I will go ahead and do a double arrow this way, and I will go ahead and do…0387

NAD+ comes in, and NADH and H+ leave.0395

This is an oxidation; this is oxidized.0403

The NAD+ is reduced to NADH, and the enzyme that facilitates this, catalyzes this - let me see - glyceraldehyde-3-phosphate dehydrogenase; and we know what dehydrogenases do.0407

They take away hydrogens; that is what they do, and they use NAD+ to do it.0432

OK, now, the final products of this is going to be the 1,3-bisphosphoglycerate.0438

That is going to look like this: C, C and C, and let’s go ahead and leave that carbonyl there.0444

We have gone ahead and attached - let me draw the full structure out, and then, of course, I will do a shorthand notation a little bit later - OH and H there; and we have the O, and we have the PO32-.0452

This PO32- and this PO32-, they are the same thing.0467

It is just here, I have drawn out the structure; here, I have just used the shorthand.0472

And again, I will just go ahead and put 2 hydrogens there; OK, there you go.0475

This is the conversion: glyceraldehyde-3-phosohate to 1,3-bisphosphoglycerate.0479

It is an oxidation; it involves the phosphorylation and oxidation.0484

Notice, it is not just the P; it is the actual O and the P.0490

Everything is attached, so the ΔG for this is 6.3kJ/mol.0494

OK, now, let’s go ahead and run through the mechanism for this.0505

A little bit of an involved mechanism, nothing really strange happening, just, it seems like a lot is going on.0509

Let’s go through this very, very carefully; it is a very important mechanism.0516

Let’s go ahead and do this one in…I think I will go ahead and do this one in blue.0521

Well, you know what, yes, that is fine; I will go ahead and do it in blue.0528

OK, so let me go ahead and write "mechanism" here.0532

It is going to take me a little bit to draw everything out; I think that is going to be the slowest part here.0538

I apologize for that.0543

Again, illustrations are really, really nice, but when doing mechanisms, well, when doing everything, I really, really prefer to write everything out because again, the act of writing things out manually really, sort of, solidifies them in your mind.0548

You have to be able to draw the structures; you have to be able to move electrons from one place to another.0560

It is one thing to understand what is happening just by looking at it passively; it is another to actually do it actively- completely different.0566

OK, let’s go ahead and draw the little enzyme here.0573

OK, we have got NAD+ in this little fold, and let’s go ahead and put our glyceraldehyde 3-phosphate molecule in here.0578

But, first of all, let’s go ahead and put some…actually yes, let me go ahead and do that now.0587

I have got C - I wonder if…yes it is fine, I am not going to keep going back and forth - C, C, C.0593

And notice, I have actually put the aldehyde down at the bottom; here, I put it up at the top, but I put it down at the bottom to show how the mechanism is actually working.0601

I am going to go ahead and put this H here.0609

I will put this OH here, and I will put O; and I will put the PO32- up here.0613

And again, I am going to leave off some of the hydrogens that are…well, maybe not.0618

I will go ahead and put it there; I will go ahead and put that here.0622

OK, we have got a cysteine residue, and there is an S and an H.0627

Remember cysteine, it has that sulfur.0634

And then, of course, over here, there is a histidine residue, and this is going to be very, very important, this histidine.0638

We have got boom, boom.0645

It has this 5-membered ring with some nitrogens in there and some double bonds.0650

And, of course, this nitrogen has an electron pair on it, so it is going to act as a base.0659

It is going to do some abstraction; here is the first thing that happens.0668

These electrons take this hydrogen.0674

These electrons are pushed, and they attack the carbonyl; and these electrons jump onto the oxygen.0679

OK, so what you end up with is the following.0688

Let me go ahead and redraw, like that.0693

We have our NAD+, and now, we have this glyceraldehyde-3-phosphate actually covalently linked to the sulfur, to the enzyme itself- very, very important.0701

That does not always happen.0712

OK, we have got our C, our C and our C; and we have an O- over here.0716

This is going to be OH; this is going to be O, and this is going to be PO32-.0724

I have H2; I have H, and this is linked to sulfur, and this is the cysteine.0732

And now, let’s go ahead and have our histidine.0743

Again, we will go ahead and draw our 5-membered ring with a couple of nitrogens in it, that now, has a hydrogen that it abstracted.0746

There is a hydrogen here.0756

There is that, and there is that; and now, because of this hydrogen, there is a positive charge on nitrogen - right - formal charge, positive.0760

OK, and this is going to be coordinated hydrogen bonding, something like that.0771

Now, we have this; now, here is what is going on.0777

Actually, I think I will do this in red; these electrons move down here.0781

OK and there is also - oops, sorry - a hydrogen here that I forgot about.0786

This is actually a very, very important one; now, let me go back to red.0793

These electrons on the oxygen moved down to reform the carbonyl, and they actually pushed this hydride to NAD+.0797

Now, what happens, let’s move on to the next page; let’s see what we have got.0807

OK, now, let’s redraw in blue.0815

We have got something like that.0822

Now, the NAD+ has been reduced to NADH, and we have our C, C, C.0828

This is there; this is linked to S, which is the cysteine.0836

Let me put the OH there and an H and an H2 and an O, PO32-; and we still have our histidine - OK - little 5-membered ring, nitrogen, nitrogen.0841

There is an H there, double bond there; there is an H there, and we have a positive charge.0861

OK, from here, here is what happens.0866

Alright, now, NAD+ comes in to replace the NADH, just a turnover of the NAD+ and NADH.0872

We are trying to recover the enzyme because we are almost finished with the mechanism.0884

Inorganic phosphate comes in- P.0892

That comes in; NADH leaves.0900

OK, let me write that down, red.0906

The NADH leaves, and another NAD+ takes its place.0913

Let me go back to blue; OK, this is our inorganic phosphate, remember abbreviated Pi.0929

Here is what happens; when everything comes in...let me redraw this.0937

That is fine; I will go ahead and...that is there.0946

Now, we have an NAD+ there.0950

We have our C, our C, our C.0954

We have our carbonyl; it is attached to that.0958

We have our cysteine, OH, H, O, PO32-.0962

This is H2; we have our histidine.0969

Let me go ahead and draw that out; OK, we have that, that.0974

We have an H; we have an H.0980

We have a positive charge; OK, now, here is what happens.0984

Now, let me go ahead and put my phosphate; I am going to do my inorganic phosphate in red.0988

My phosphate, this is this thing; it comes in, H, O- minus.0992

OK, this attacks the carbonyl.0999

The carbonyl electrons, I am just going to do it in a circle; they jump up to the oxygen.1005

They jump back down to form the carbonyl; I am going to represent it like this in a single step, and then, this goes and grabs that, and these electrons jump back on to the nitrogen, and what you end up with, after release of the product…1009

Again, inorganic phosphate comes in, nucleophilic attack on the carbon; it attacks the carbonyl.1033

OK, the standard mechanism of a carbonyl reaction jump up to the oxygen, drop back down to form the carbonyl.1039

We often represent it as a circle like this; it pushes these electrons that were bonded to the sulfur of the cysteine residue.1044

They grab another hydrogen breaking that bond to the enzyme, to the sulfur.1050

Once that is done, you can go ahead and release this; now, the phosphate is actually attached here through the O, and what you end up getting - I will go ahead and do that on the next page - is the following.1057

I will do this in blue; what you get is C, C, C.1072

Excuse me; you have your carbonyl, and now, you have your O and PO32-.1077

This stays there; this is O.1084

You raise that; we have PO32-.1089

This is H2; this is H- there you go.1094

Now, that, and let me go ahead and draw what the enzyme looks like now, after it has released.1102

Again, you have recovered your initial state of the enzyme; you have NAD+ in that fold.1107

You have your cysteine residue with the sulfur that is, now, protonated again.1114

And then, of course, you have your histidine residue with that really, really interesting thing, and you have this.1119

And, of course, there is some coordination here- the electrons on the nitrogen and the proton on the cysteine residue.1131

And now, it is ready for another catalytic cycle- that is it.1138

There you go; that is the mechanism for step 6.1143

OK, now, let’s move on to step 7.1148

Step 7 is the phosphoryl transfer - excuse me - from what we just made, which is the 1,3-bisphosphoglycerate.1155

I am just going to call it BPG to ADP to form ATP.1159

This is one of the reactions where we are actually using the…this is a coupling reaction.1161

A 1,3-bisphophoglycerate - if you remember - was one of the molecules that has a very, very high free negative free energy of hydrolysis, much higher than the free energy of a hydrolysis of ATP.1169

So, we can actually reverse the ATP reaction, couple it with this reaction and still have enough energy left over for it to actually move forward and still be negative.1201

We are using this to form ATP to recover some of the ATP that we invested in the preparatory phase.1210

OK, let’s go ahead and draw out the general reaction here.1217

We have C, C, C, and I will go ahead and flip it back up, so it looks like this: CO3, PO32-.1221

We have OH; we have H.1229

We have O, and we have our PO32-.1233

This time, the other molecule here is going to be adenosine diphosphate.1237

We will go O, P, O, P, O, and we have our ribose; and we have our adenine, and let’s go ahead and put our double bonds on our phosphorus, make sure that we have everything here.1244

OK, that looks good; now, this is going to be - go ahead and draw that and that - slightly reversible.1256

We are going to need magnesium ion, and the enzyme that catalyzes this reaction is phosphoglycerate kinase or kinase, depending what you want.1265

Now, notice, kinase, as we know in general, are enzymes that catalyze the transfer of the terminal phosphoryl group from adenosine triphosphate to some substrate.1283

Here, it is going in reverse; it is actually taking some phosphoryl group that is on a substrate, and it is giving it back to ADP to actually form ADP, and that is absolutely fine because we know enzymes catalyze not only the forward reaction but the reverse reaction.1296

All enzymes do that; OK, the products of this reaction are going to be…let’s see, phosphoglycerate.1310

Let’s see; this is going to be C, C, C.1324

I will put the carbonyl up here, there and OH and H, and we have H2.1328

We have O and PO32- + adenosine triphosphate.1337

This is going to be O, P, O, P, O, P, O with ribose and with adenosine, and there we go.1345

Let's make sure we have everything; there we go.1359

What I transferred was this right here- that, OK - not the whole thing.1362

Notice this O- that stayed behind; a phosphoryl and a phosphate are not the same thing.1367

Phosphate is PO43-; a phosphoryl is PO32-.1373

This is what I transferred back to the ADP to form the ATP; it came off from here.1379

OK, the overall ΔG for this reaction is -18.5kJ/mol- plenty of energy left over.1385

Now, here is - let me go ahead and do this in red now - the formation of ATP - excuse me - by transfer of a phosphoryl group from a molecule, a substrate from a molecule - whatever molecule is involved - to ADP to form ATP is called substrate level phosphorylation.1398

It is called substrate level; you will hear this a lot.1447

Now, we distinguish this from something called respiration linked phosphorylation - OK - which is the mechanism by which ATP is formed during - woo, getting a little fast here - the final phase of oxidative phosphorylation, when we oxidized glucose under aerobic conditions all the way to carbon dioxide and water by which ATP is formed during the final phase of oxidative phosphorylation; and we will be taking about this later on on the course- phosphorylation along the electron transport chain.1458

The NADH that was formed in the reaction that we just did, in the conversion of the 3-phosphoglycerate to the 1,3-bisphosphoglycerate to the 3-phosphoglycerate, those electrons in a mitochondria are given over to the electron transport chain, and ultimately, they reach oxygen.1560

It is oxygen that ends up being reduced, and the final phase about the oxidative phosphorylation ends up creating a whole bunch of adenosine triphosphate.1581

We have that respiration linked formation, respiration linked phosphorylation, which forms adenosine triphosphate in that mechanism; and we have this, which is substrate level phosphorylation, where a molecule actually gives up its phosphoryl group to ADP to form ATP- that is all that is going on here.1591

OK, now, let’s go ahead and do a quick mechanism for this; it is a simple nucleophilic substitution, so nothing complicated here.1610

Let’s see; let’s go ahead and do that in blue.1618

Mechanism is nucleophilic substitution.1627

OK, let’s draw our C, C, C, and a P.1637

I will go ahead and actually draw everything out: OH, and H, H2O, PO32-.1651

And then, of course, we have our ADP; we also have the O, P, O, P, O, ribose, adenine.1667

I know I could probably use shorthand for this; sorry about that.1681

OK, we have that, and we have that- that is it.1686

That is all that is going on, and that will give you your product- that is it.1691

The phosphoryl group, the PO32- is just transferred over to the ADP, but it is the ADP that actually does the attacking.1694

To me, it has always been a little weird; when they are talking about transferring a group from something to something, but it is that something that is actually doing the attacking, that never really made sense to me, but that is what is happening.1704

The ADP is acting as the nucleophile, and it is literary taking the group.1714

It is not really being transferred to the group; it is taking the group.1718

OK, now, let’s go and do step 8.1723

Let’s see; we are almost there.1728

Step 8 is the conversion of 3-phosphoglycerate to 2-phosphoglycerate.1732

We are just going to move this phosphoryl group up to the no. 2 carbon up there, so conversion of 3…I will just say 3-PG to 2-PG.1737

OK, the reaction is the following; we have C, C, C.1752

Excuse me; this is OH, H, O and PO32-.1757

I will go ahead and put that there, and let’s see.1766

This is going to be there; magnesium is required.1769

The enzyme is phosphoglycerate mutase, and it looks like this: C, C, C.1774

That carboxyl group stays the same; now, the phosphoryl group is on here and CH2, and the hydroxy, the alcohol group, is now, moved to the no. 3 carbon, so 3-phosphoglycerate to 2-phosphoglycerate.1791

OK, alright; let’s go ahead and do the mechanism for this.1808

It is essentially 2 nucleophilic substitution reactions.1814

Let me go ahead and just write that, and then, I will start the mechanism on the next page.1818

Mechanism- it is essentially 2 nucleophilic substitution reactions.1826

OK, let’s start this on the next page.1845

That is fine; I am just going to list these as steps.1853

I wonder if I should do it vertically; yes, that is fine.1857

I will do it vertically; alright, so we have got C, C and C.1860

We have that; we have OH, and we have our PO32-, and we have our H2, and we have…let me go ahead and do it this way: 1, 2, 3, 4, 5.1864

I will go ahead and do histidine, is connected, of course, to the enzyme; and we have got that.1885

I will go ahead and put N there, and I will go ahead and put my nitrogen there; and I have got P.1895

I will go ahead and draw this out; there we go, and we have a positive, and we have an H here.1909

OK, on the enzyme, there is a histidine residue, and that histidine residue happens to be phosphorylated.1920

What is going to happen is this phosphoryl group is going to end up here, and then this phosphoryl group is going to end up going back there.1929

It is going to be 2 steps, so let’s go ahead and do that.1938

What you are going to end up with is, once this thing ends up over here…and again, it is going to be nucleophilic attack, this thing on the phosphorus kicking the electrons over there.1945

Let me go ahead and write C.1960

You know what, I am going to need a little bit more room; I am going to make this a little bit smaller.1965

I want to do this on one page; let me just go here and go C, C, C.1968

OK, this is going to be O, and this is going to be PO32-.1976

This is going to be O, and this is going to be PO32-.1981

I am going to ignore the hydrogens for now; excuse me.1985

We have got that, N, N; now, there is an H on there.1991

I have got that, that, and I have got histidine; and it is attached to the enzyme.1999

There is an H here and a positive charge; OK, now, actually, you know what, I am going to do this a little bit differently.2007

Let me redraw this; I want to show the distribution.2016

I have got 1, 2, 3, 4, 5.2023

That is N; that is N.2028

There is that hydrogen, and now, there is this hydrogen; and, of course, the positive charge is shared between those 2 nitrogens now.2031

OK, this is 3-phosphoglycerate.2041

This is 2,3-bisphosphoglycerate.2047

And, of course, our final step, when this is going to be transferred over to here, we are going to end up with C, C, C.2051

This goes there; this is going to be PO32-.2062

This is going to be OH; that is fine.2068

I will go ahead and put the hydrogens in, and it is going to be back to where we were before, so N, N.2073

I will just put PO32-; it is going to be like that.2084

There is going to be H, histidine, enzyme, positive charge- there we go.2090

These are the steps; nucleophilic attack here to take this phosphoryl group to become 2,3-bisphosphoglycerate.2100

It becomes 2,3-BPG.2109

OK, this is 3-PG, 3-phosphoglycerate to 2,3bisphosphoglycerate.2113

And then, of course, you have got attack here; go ahead and take this one, transfer of some protons, and what you end up with is the 2-phosphoglycerate and recovery of this, recovery of the enzyme and the histidine residue with the phosphorylated imidazole ring on the, well, on the ring.2117

OK, now, let’s talk a little bit about this.2143

Now, the catalytic cycle, this particular catalytic cycle - excuse me - begins when 2,3-BPG, which is already present in the cell in very trace amounts - OK - phosphorylates the imidazole or imidazole ring of histidine.2147

There is 2,3-bisphosphoglycerate already in the cell in very trace amounts.2212

It goes ahead and phosphorylates the ring on histidine, and that begins the cycle, the step 1 of what we just did- that is it.2216

That is how it keeps it going; that is how the ring actually ends up being phosphorylated to begin with because of 2,3-PG that is there already in tiny amounts.2227

OK, now, let’s go to step 9.2239

This is going to be the dehydration of 2-phosphoglycerate to phosphoenolpyruvate- very, very, very important.2245

Phosphoenolpyruvate- this is PEP, so the dehydration of 2-PG to phosphoenolpyruvate2262

Dehydration means you are removing the element of water; you are taking away water.2276

OK, let’s go ahead and write out the structures here.2281

There is that; there is O, and there is PO32-.2289

There is C, and there is OH; I am actually going to draw this OH on the other side just so you can see what it is that is actually being taken away.2294

OK, well, there is another H here too, so I guess, I will put that there.2309

What is being taken away is this: dehydration, the H and the OH- that is what is going away.2313

Let’s go ahead and draw that, and, of course, the elements of water.2325

Water is leaving, and the enzyme that catalyzes this is called enolase, and a magnesium ion is required for this.2330

As you can see, magnesium ion is required for almost all of these reactions.2339

Definitely make sure you have enough magnesium in your body.2345

Our final product, is going to be C, C, C.2349

We have that, and we have this; and we have our O and our PO32-, and let’s go ahead and put an H2 right there.2355

OK, the ΔG for this reaction is 7.5kJ/mol, and do not worry about that endothermic because as you will see in a minute, the next reaction is highly exergonic.2369

No, not endothermic- endergonic.2382

The next reaction is highly exergonic, so it will pull that forward- not a problem.2386

The dehydration is 2-PG to phosphoenolpyruvate.2390

Dehydration- removing the elements of water, catalyzing; this is our PEP- very, very, very important molecule.2394

OK, let’s go ahead and run through the mechanism here.2401

Let’s see.2405

Yes, let me go ahead and start on the next page; I will do the mechanism in blue.2409

OK, let me go ahead and draw this out; I am going to draw it out this way.2419

I have got C, C; I do not know how big I…no, that is OK.2428

Let me see; Should I do it here, there?2436

That is OK; I will do it vertically- not a problem.2439

OK, C, C, C, we have that, and we have that; and we have our O and our PO32-, and we have our H, and we have our H, our H and our OH there.2442

Now, let me go ahead and draw my enzyme around it.2466

OK, and now, I have got coordination to 2 magnesiums.2473

There is coordination on that oxygen, and there is coordination on that oxygen; and there is coordination on that oxygen.2481

And then, of course, I have a lysine residue, which is lysine 3,45.2489

Excuse me, and we have the nitrogen there; and we have our Glc-2,11, C, carbonyl and an O and an H to get started.2496

OK, this is what is going to happen; let me do this in red: abstraction of that hydrogen, movement there, movement there.2518

OK, now, let’s go ahead and see what this looks like now.2533

I am going to go back to blue; now, I have got my C, my C, my C.2541

I have got O-; I have got O- there.2547

This is now, a double bond here.2553

OK, let me go ahead and draw everything in.2557

I have got my O and my PO32-.2561

I have got my OH here; I have my…no, I just - wait a minute - took that hydrogen away.2565

OK, let me make sure I have got everything, my H.2573

OK, I have my magnesium ion, and I have my other magnesium ion.2577

I am still coordinated, like that- very, very important.2585

And now, let me redraw my enzyme.2589

OK, and I have my lysine 3,45-nitrogen.2595

Now, I have a hydrogen; I have a hydrogen, and I have a hydrogen.2604

The nitrogen is actually carrying a positive charge, and I have my Glc-2,11.2608

OK, I have got C; I have got that.2616

I have got that, and I have got that; OK, here is what happens.2619

This is a negative charge; this is a negative charge.2624

Let me go back to red; OK, this drops down to reform the carbonyl.2629

This moves over there, and it pushes this over here to grab this; and it pushes these electrons on to here.2637

Then what you have is released by the enzyme, and, of course, H2O, this; and that is that.2652

That is the dehydration; OK, and what you end up with, your final product is - I will draw this in blue - you end up with C, C, C, double bond.2670

Let me go ahead and put that double bond there, leave that a minus charge.2687

I will go ahead and put the PO32- there.2692

We have H, and we have H; this is phosphoenolpyruvate.2697

This is our PEP molecule- there you go.2702

I hope that made sense, OK, now, step 10, the final step.2708

OK, step 10 is going to be the transfer of a phosphoryl group from the phosphoenolpyruvate to ADP to form ATP.2718

Again, another substrate level phosphorylation, the creation of ATP.2746

The reaction looks like this; I will draw this vertically: C, H2, O, PO32-.2752

That is that, so it is going to be + O, P, O, P, O, ribose and adenosine.2765

This goes there; this goes there.2781

This goes there, so this, that is the group that is going to end up over here.2783

OK, this is our PEP; this is our ADP.2793

I wonder if I should draw it on this page or…yes it is fine.2801

I can draw it on this page- not a problem.2807

OK, this requires magnesium; it requires potassium, and it is catalyzed by pyruvate kinase, and you end up with the final product of C, C, C.2814

We have a carboxyl there; we have a ketone there, and we have H3+.2834

Then, what you have is O, P, O, P, O, P, O, ribose, adenine, double bond, double bond, double bond.2844

That is O-; that is O-.2860

That is O-; that is O-.2863

This PO3 is that PO3 right there.2865

It is moved from here to here, and this is the final product.2869

Notice now, we have carboxyl group, and we have a carbonyl that is alpha.2874

This is an alpha-keto acid because you have a ketone group that is alpha to the main carbonyl, which is the carboxylic acid group- very, very important.2880

OK, the ΔG for this reaction, -31.4kJ/mol- highly, highly, highly exergonic, virtually irreversible under cellular conditions.2889

This is it; once it gets to this point, it just pulls it forward.2904

OK, now, let’s go ahead; let’s see.2909

A couple of things we want to say about this; this is, again, a substrate level phosphorylation.2913

Let me do this in red; this, again, is a substrate level phosphorylation to form ATP, to form adenosine triphosphate.2919

OK, now, the initial product is not the pyruvate.2947

It is - well, I will show you in a second - the initial product after the nucleophilic substitution because again, we are just transferring the phosphoryl group, so this is a basic nucleophilic substitution reaction.2954

Nucleophilic substitution- the attack of the ADP on the PEP.2980

The initial product after the nucleophilic substitution is this.2987

It is actually going to be - let me do this in blue - C, C, C.2992

This is going to be here; this is going to be O-.3002

This is actually going to be an OH; OK, it is actually going to be OH, and this is the double bond that is actually going to be there because you remember, that is where it is, so we have H2.3004

Now, what happens is tautomerization.3015

When you have something like this, when you have an enol, which is an alkene and an alcohol attached, it actually prefers to be the carbonyl instead of the alkene.3021

The double bond prefers to be carbon oxygen instead of carbon-carbon3031

In fact, that is what actually pulls the reaction forward.3035

It really, really, really wants to be a carbonyl; that is what actually gives it the high negative free energy for this reaction.3039

It tautomerizes, and that is when it becomes C, C, C, the alpha-keto acid that we know of; and this is going to be C.3048

This is CH3 now; this is the enol form, and this is the keto form.3061

You will see this a lot in biochemistry; anytime you have something like this, where you have an alkene and an alcohol attached, generally under cellular conditions of pH7, somewhere around there, the keto form is going to be the one that is most stable.3068

OK, now, this is another energy coupling reaction.3083

We have actually seen it before when we are talking about bioenergetics.3097

OK, the hydrolysis of the phosphoenolpyruvate, which has a very high free energy of hydrolysis, is coupled to the synthesis of ATP because there is more than enough energy to actually accomplish this synthesis, the synthesis of ATP.3103

And the best part is, there is still more than enough free energy left over to make this step irreversible, and you saw that already - very, very high ΔG, high negative, irreversible.3138

I hope I spelled that correctly; OK, let’s just go ahead and write out what we have got here.3171

We have PEP + H2O - just reminding you of how we put this together - goes to pyruvate plus that.3179

The ΔG for this is -61.9kJ/mol.3193

The hydrolysis of PEP releases 61.9kJ of free energy.3199

Well, the synthesis of ATP from ADP and inorganic phosphate, ATP + H2O - woo crazy, all these symbols, all these names, how do we keep it all straight - it is +30.5.3204

When we add these together, H2O, H2O, PI, PI, we have our reaction that we just ran.3226

The phosphoenolpyruvate + ADP goes to pyruvate + adenosine triphosphate.3233

Substrate level phosphorylation, ΔG for the overall reaction is -31.4kJ/mol- incredible, absolutely incredible.3244

OK, now, let’s go back to black, and let’s do a glycolysis balance sheet.3254

What happened to the carbons?3266

What happened to the phosphoryl groups?3268

What happened to the electrons?3269

OK, let me see; yes, that is fine.3271

We have another page; we have got glucose + 2 ATP.3277

This is all the things that were invested in glycolysis, and you are going to see all the thing that came out of glycolysis; and then we are going to go ahead and cancel and see what the net reaction is.3284

We invested 2 ATP; we invested 2 NAD+.3292

We invested 4 ADPs, and we invested 2 inorganic phosphates.3298

What we got out was 2 pyruvate, 2 ADP, 2NADH, 2 hydrogen ion, 4 ATP and 2 molecules of water.3305

Now, when we go ahead and we cancel common terms on the left right side of the arrow, we are left with the following.3329

let me see, cancelling common terms.3336

We are left with glucose + 2 NAD+ + 2 ADPs + inorganic phosphates, gives us 2 molecules of pyruvate, 2 molecules of NADH, 2 hydrogen ion, a net gain of 2 adenosine triphosphate - very, very important - and 2 molecules of water.3344

This is what is important; this is what happened.3377

This is what glycolysis did, right there; OK, now, 1. the 6 carbons of glucose.3381

I am going to write that out; I am just going to write C.3392

The 6 carbons of glucose became the 2 x 3 carbons of pyruvate.3400

Let’s go ahead and go to the next page here.3415

OK, no. 2, the 2 ADP and the 2 inorganic phosphates, they became the 2 molecules of adenosine triphosphate.3420

And last, but certainly not least, the 4 electrons has 2 hydrides taken from the glyceraldehyde-3-phosphate.3437

Remember that reaction, NAD+ to NADH?3459

We pulled away hydrogens from there, so the 4 electrons, which left as 2 hydrides, 1, 2, and then, 3, 4.3462

There is 4 electrons, those electrons are energetic.3470

Those are what are going to end up in the electron transport chain for respiration linked phosphorylation.3474

So, the 4 electrons - as the 2 hydrogens taken from the glyceraldehyde-3-phosphate - are transferred to NAD+, to the 2 NAD+; and they become the 2 NADH, ultimately being transferred.3478

NADH goes on to give up its hydrides, to give up these 4 electrons to the electron transport chain.3518

Ultimately, they end up with oxygen being transferred from, they are ultimately being transferred from the 2 NADH to the electron transport chain.3526

We have accounted for the carbons; we have accounted for the phosphoryls, and we have accounted for the electrons.3545

This is glycolysis; OK, thank you so much for joining us here at Educator.com.3550

We will see you next time, bye-bye.3555

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