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Raffi Hovasapian

Raffi Hovasapian

Enzymes III: Kinetics

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 (11)

2 answers

Last reply by: Swati Sharma
Tue Mar 27, 2018 7:00 AM

Post by Swati Sharma on March 26 at 10:31:52 AM

Dear Dr Raffi,

I wanted to ask you that I am going to prepare for my MCAT exams and I was planning to use your general chemistry videos, but I am very confused of what section should I use, as there is one AP general chemistry and one simple general chemistry and the same applies to  Biology, and so therefore I am really lost of which general chemistry videos should I use for my MCAT prep, according to college level. If you could please let know it could save me time from watching all the videos. And also if you tell me that if these videos are good source for MCAT prep

2 answers

Last reply by: Gabriel Au
Fri Oct 10, 2014 7:59 PM

Post by Gabriel Au on October 9, 2014

Hey professor Hovasapian,
I have been watching many of your videos for many classes and I think you do a great job! I was wondering If you will ever do a series of videos specifically for complex variables?

1 answer

Last reply by: Professor Hovasapian
Wed Dec 4, 2013 3:40 AM

Post by Assaf Tolkowsky on December 4, 2013

Just a pointer - you have a mistake with the algebra at 42:46 - Km is (k-1+k2)/k1 and not (k1+k2)/k-1 like you wrote down

0 answers

Post by tiffany yang on November 13, 2013

Dear professor,
Can you please explain why when [E]total increases, why Km stays the same?

and what does Kcat depends on?

is catalystic efficiency independent from enzyme concentration? what does it depend on?

Thank you so much. I truly truly appreciate it.

1 answer

Last reply by: Professor Hovasapian
Sat May 4, 2013 3:37 AM

Post by Brian Phung on May 1, 2013

Hi I was wondering how do I determine the inhibition mechanism meaning if its competitive or noncompetitive inhibition by the shapes of plots of (kcat)ATP versus [I] and (kcat/Km)ATP versus [I] were used to determine the inhibition mechanism?

Enzymes III: Kinetics

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
  • Enzymes III: Kinetics 1:40
    • Rate of an Enzyme-Catalyzed Reaction & Substrate Concentration
    • Graph: Substrate Concentration vs. Reaction Rate
    • Rate At Low and High Substrate Concentration
    • Michaelis & Menten Kinetics
    • More On Rate & Concentration of Substrate
    • Steady-State Assumption
    • Rate is Determined by How Fast ES Breaks Down to Product
    • Total Enzyme Concentration: [Et] = [E] + [ES]
    • Rate of ES Formation
    • Rate of ES Breakdown
    • Measuring Concentration of Enzyme-Substrate Complex
    • Measuring Initial & Maximum Velocity
    • Michaelis & Menten Equation
    • What Happens When V₀ = (1/2) Vmax?
    • When [S] << Km
    • When [S] >> Km

Transcription: Enzymes III: Kinetics

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

Today, we are going to start talking about enzyme kinetics.0004

Kinetics is just a fancy word for rate of a reaction, how fast does this reaction go.0009

Kinetics is, sort of, the beginning of our understanding of mechanism.0016

With biochemistry, with all of chemistry, our ultimate goal is to understand the mechanism, how something goes from one thing to another, in the case of an enzyme, how an enzyme takes a particular substrate and how it converts it to product.0022

Each individual little step, every single electron, where it goes, every single atom, every single hydrogen ion that is transferred from here to there- that is our ultimate goal because if we understand the mechanism, then we know how to control it.0038

We know how to fiddle with it, how to do whatever we want to it because we understand how it works.0050

Kinetics is, sort of, the first step of understanding that mechanism.0057

It is the oldest approach to understanding mechanism, and it is still very, very, very important.0062

Let's jump in and see what we can do; now, we are going to deal with the quantitative aspects of kinetics, and I am going to go through a derivation of the Michaelis-Menten equation.0069

Hopefully, it will not be too bad; ultimately, we are not going to be concerned with the derivation.0082

Your teacher will let you know about the extent to which you need to know the derivation or not the derivation, but we will go through it.0086

It is the final form of the equation and how the enzyme behaves; that is what is important.0093

It is more of a global understanding; let's see what we can do.0098

OK, now, as we said, the fundamental approach - let's see here - to studying a mechanism is to determine the rate of an enzyme-catalyzed reaction/rxn and more importantly and how this rate actually changes with changes in substrate concentration.0102

In other words, if I start with a certain amount of enzyme that will hold constant and if I add a certain amount of substrate to this enzyme solution and if I measure how fast these substrate molecules are being turned over into product, that gives me a rate.0175

It will often be expressed in terms of, let's say, millimoles or micromoles per minute or perhaps in molarity, millimolar or micromolar per minute or per second.0195

A rate is some change in some value per unit time.0205

That is what a rate is, how fast something is happening; well, if I start with a different initial concentration, does that change the rate?0209

As it turns out, the answer is yes.0216

Ultimately, substrate concentration controls how fast or how slow an enzyme-catalyzed reaction is going to go.0220

Now, it is never always this simple.0227

With normal chemical reaction, it is not even that simple; you can just imagine how complex it can become in the case of an enzyme-catalyzed reaction where you have, maybe, more than 1 substrate, where you have multiple steps in a mechanism, not just 1 or 2 but perhaps 7 or 8 before the enzyme releases the product.0231

Again, we are going to be making some simplifying assumptions to make it tractable, so that we can actually deal with it, but ultimately, it is about how the substrate concentration affects how fast an enzyme-catalyzed reaction can go.0250

OK, let's see what we have.0266

Now, since the substrate concentration will denote it like that, S with a bracket.0270

Concentration - you remember from chemistry - always has brackets, and those brackets are normally in moles per liter.0277

In the case of biochemistry, it will usually be millimolarity, occasionally micromolarity because you are talking about pretty small amount, at least as far as the enzyme is concerned, and often the substrate is well.0283

Since S changes, as the reaction proceeds, we simplify matters by measuring initial rates.0296

And you remember or you should remember, at least, or I hope you remember initial rates from general chemistry when you were doing the kinetics portion, although I do understand that the kinetics portion of general chemistry is generally that portion of chemistry that one would like to forget.0326

That is the one that seems to leave the mind the quickest because it was so very odd compared to the other concepts because it was heavily mathematical.0339

In any case, as you know, you put a substrate in with an enzyme, the substrate concentration actually changes.0347

So, as an experimenter, how can one...and since the substrate concentration is changing, how can I actually try different substrate concentrations to get some, sort of, a relationship between substrate concentration and speed of the reaction?0355

Well, if we measure how fast the reaction is going in the beginning, right when we put the substrate and the enzyme together, let's say, within the first 30 seconds or, at most, the first minute, we never want to let it go past that.0370

Well, during that timeframe, because the substrate concentration in general is usually going to be so much more than the enzyme concentration - right - enzyme, well, is not used up in a reaction, so the enzyme concentration is very small.0383

One enzyme molecule can handle millions of substrate molecules.0398

Because that is the case, in the first part of a reaction, the first 30 seconds, the first minute, maybe the first minute and a half, the substrate concentration does not really change all that much, especially since the substrate concentration is so much bigger than the enzyme concentration.0401

So, for all practical purposes, the substrate concentration that I start the experiment with, it is going to be held constant.0417

If I start with 10 millimoles or 20 millimoles or 30 millimoles, even though substrate is being used up, compared to the 20 millimoles, 30 millimoles, 40 millimoles, that I start off with, it is going to be completely negligible.0425

Now, we can actually do that; even though substrate concentration changes with an enzyme-catalyzed reaction because of the difference, because there is so much substrate, I can pretend that it does not really change.0440

Now, I can actually run my experiment; I can actually collect some data.0450

Since S changes to the reaction when we simplify matters by measuring initial rates of reaction, how fast the reaction is going at the beginning before other complications start to slow the reaction down.0456

Now, as we said, since the concentration of S is so much greater than the concentration of enzyme during the first minute or 2, the substrate concentration is essentially constant.0470

OK, now, what this does is this allows us to choose various initial concentrations - like I said, 10, 20, 40, 80, 160, however - then, plot the rate of reaction that we measure as a function of these different initial concentrations.0510

In other words, what we are saying is that the rate - I will call it initial velocity, so we will use the symbolism that is pretty common, well, actually, you know what, let me go ahead and just write it as rate first, and I will go ahead and use the symbolism - is going to be some function of S.0568

In other words, you are going to have S on the X axis.0590

OK, that is going to be your independent variable, and the rate is going to be your dependent variable.0594

That is going to be your Y axis.0598

Rate or speed of the reaction, we will often symbolize with v0, initial velocity.0602

Sort of, this is 0 making reference to that fact that we are dealing with an initial rate.0608

v0 is equal to some function of the substrate concentration.0613

Different substrate concentrations, different values, and you end up getting this curve.0620

Well, when we do this, when we actually run the experiment, we get the following.0625

We take some enzyme; we start with different substrate concentrations.0631

Let's say we run 10 different initial concentrations, we get 10 data points.0636

We measure the speed at the beginning of the reaction.0640

We get the following graph.0645

We get something that looks like this, so let's take a look at this- very, very, very important graphical representation.0650

This is a plot of substrate concentration on the X axis and reaction rate on the Y axis.0657

Do not worry about what the Vmax, half Vmax and Km mean right now.0664

We will get to that in a minute when we talk about this Michaelis-Menten equation that we want to deal with.0668

OK, if I start with an initial concentration of a substrate concentration of 0, well, nothing is going to happen.0673

As I increase my initial substrate concentration, I am going to measure a rate.0682

I try another initial concentration, I am going to measure an initial rate.0688

Another experiment, another concentration, I measure another rate; I do this several times.0693

In this case, it looks like 1, 2, 3, 4, 5, 6, 7, 8, 9, 9 experiments.0698

You can do as many as you like; obviously, the more that you do, the better data you get.0703

When I connect all of those dots, I get this thing.0707

This is a very, very, very characteristic enzyme behavior- reaction rate versus substrate concentration.0712

Let's just talk a little bit about what is happening here just qualitatively; let's get a sense of what is happening.0722

You notice in the beginning almost this...well, that is OK.0728

At low concentrations of substrate, what happens is you have basically almost a straight line here - right - of 2 about right here?0735

For very, very low concentrations, what you have is, sort of, a linear behavior, in other words, just something that is like the rate equals some constant times the concentration of S.0745

That is just some line - that is it - a linear relationship, but as the substrate concentration increases, notice that the speed actually starts to slow down.0760

You might ask yourself, well why is that, why does it slow down?0772

Well, think about it; it actually makes sense.0775

You only have so much enzyme; you keep adding substrate.0778

You keep adding substrate; you keep adding substrate.0781

At some point, you have added so much substrate; around this point, you have added so much substrate that, now, the enzyme is completely tied up with substrate.0784

In other words, it is bound to the substrate; it is converting it to product.0795

The minute it releases that product, yes, it is a free enzyme again, but immediately, another substrate binds to it.0798

So, for all practical purposes, at some point, you have tied up all of the enzymes that can turn molecules over, that can turn substrates over.0804

It does not matter how much more substrate you add; you can keep adding substrate.0813

You are not going to make the reaction go any faster because there is only so much enzyme there that can react, that can actually do the job.0816

That is why you see this tapering off behavior, and you know intuitively that at some point, you are just going to keep adding so much substrate- that is it.0824

There is only so fast that the enzyme is going to turn these substrates over.0835

That is what this is here; this is an upper limit on the speed of the enzyme.0840

Enzymes achieve this, what we call, maximum velocity, maximum speed.0844

There is some maximum speed faster than which the enzyme...it is not just going to go.0850

No matter how much more substrate or no matter what else you do to it, it is just not going to go any faster than it can go, than it can turn over the molecules.0855

Let's write all this out.0864

At low substrate concentrations, the rate increases.0870

So, there is an increase; as you increase concentration, the rate, it is faster.0878

The rate increase linearly, or I will just say "almost linearly", which seems to make sense.0882

I mean it is reasonably intuitive; now, as the substrate concentration increases, the rate slows down with each increasing concentration, and notice, you are having a big increase in the initial concentration; but you are getting a very, very little increase in rate.0890

It is definitely slowing down here; the rate increase slows until a point is reached where increasing the substrate concentration has no effect on the rate.0912

OK, this Vmax is exactly what you think it is, this maximum velocity, Vmax, the fastest this enzyme can go.0950

OK, it is here that the enzyme is saturated.0976

In other words, it is completely tied up with substrate; it is completely saturated, and no matter how much more S is added, it will only go as fast as it can turn substrate over or convert substrate to product.0989

Again, what we would like here is to have some, sort of, quality, be able to explain this behavior.1031

We explain this behavior by saying that at some point, your initial substrate concentration, the minute you put it into this enzyme solution, it just binds up all of the enzyme.1037

Now, there is no free enzyme floating around; here, there was free enzyme.1048

The more substrate you added, the more free enzyme actually started to operate.1052

So, you have got a faster turnover overall, but at some point, your substrate is going to completely saturate the enzyme.1059

Now, all of the free enzyme is bound up, and since there is no more enzyme that is free, you can add as much substrate as you want.1066

It is not going to make it go any faster than it is already going; that is its maximum velocity.1074

Now, when you do these experiments, when you do reaction rate and substrate concentration experiments, you are probably wondering where does this Vmax come from.1079

OK, if your data is reaction rate versus substrate concentration, this maximum velocity is something that you are going to have to estimate.1087

You are going to have to take a look at your data, and you are going to have to extrapolate some maximum velocity.1095

Usually, it is not a problem; you just go a couple of units above something like that, and you draw a line.1100

Now, in the next lesson, we will talk about a way to actually get an analytical method for coming up with the Vmax, the maximum velocity, which is a really, really fantastic method.1106

Do not worry about that; we will be talking about that, but when you have just reaction rate and concentration data, this is something that is just extrapolated.1116

It is estimated; you look at your graph, and you just draw a line based on experience or whatever other information you have at your disposal.1122

OK, now, what we have here is empirical behavior.1132

You took some enzymes; you took some initial concentrations, measure the rates; this is how an enzyme behaves.1138

What Michaelis and Menten did is they postulated a few things based on what is happening, and they decided to derive an equation to see if they can come up with some equation that explains this behavior- OK, that is it.1143

They wanted to have some mathematical formula that matches this.1156

That is usually how it works in science; you come up with some data.1162

You graph it, and then, you try your best to go back and theoretically see if you can find an equation which fits the data.1166

That is usually how it works; we, sort of, learn it in reverse especially when we are learning things like math and physics.1174

We learn the formulas, and then, simultaneously we will talk about the data, but this is how it really happens.1178

You have the data first, the graph first, and then, you try to fit the equation to the graph by making some assumptions and fiddling around with a bunch of equations until something works.1186

Alright, now, this is empirical behavior.1198

OK, Michaelis and Menten postulated the following; let me actually move here.1210

Again, any theoretical discussion begins with a series of postulates, and then, you, sort of, take it from there; and you see where your math leads you, or you see where your chemistry leads you theoretically, and then, you compare it with the data.1227

That is how it works; Michaelis and Menten postulated the following.1240

They postulated that the enzyme and the substrate, there is some k1 - rate constant - and k-1, and they form something called an enzyme substrate complex.1247

Enzyme substrate bind, you have this enzyme substrate complex.1262

They assumed that this was the fast step, that this happens very quickly, and then, of course, the enzyme substrate complex, that is the one that actually breaks down into enzyme and product.1267

So, there is another equilibrium here.1279

They call this k2, and they call this -2 into enzyme and product.1283

Their postulate was that this was the slow step, and if you remember from general chemistry, the slow step in a mechanism, in a series of steps, that is the step that controls the rate of the reaction.1288

As it turns out, now, because step 2 is slower, the overall reaction rate depends on this concentration of enzyme substrate rather than just substrate- that is it.1301

That is what they postulated, that this was the slow step, and this behavior actually depends on the concentration of enzyme substrate, not necessarily just the concentration of substrate.1341

They decided to take it from there.1357

Let's see; let's go ahead and take a look at this one more time.1364

Again, under low concentrations of sub...well, let's write all this out.1374

When the concentration of substrate is low, it is still going to be mostly free enzyme.1382

In other words, the enzyme substrate complex has not formed.1399

It is not saturated; the enzyme is not saturated with substrate.1403

It is still mostly free enzyme.1406

The rate still depends just on substrate concentration.1411

Remember what we had?1417

Let me draw it over here; we said E + S goes to ES, and then, from here, goes to enzyme + product.1420

At low concentrations of substrate, we are still mostly free substrate and free enzyme.1430

The speed of the reaction is still just contingent on the substrate concentration.1436

The rate is still just a direct function of substrate concentration/S- the substrate concentration.1442

That is what explains the linearity; when it is just depending on one thing, you are generally going to get some, sort of, a linear behavior.1460

OK, now, but as the concentration of substrate/S rises, the enzyme, now, is mostly in its bound state, right?1468

The enzyme becomes saturated; the enzyme becomes bound up with the substrate.1498

Now, it is no longer here; now, it is mostly this, thus, the second step of this Michaelis-Menten postulate takes over, and that is where we experience deviation from linear behavior.1502

We have deviation from a linear behavior, and this deviation comes from the fact that it is no longer contingent just on substrate concentration; but it depends on enzyme substrate concentration.1535

Clearly, from here to here, things get rather complicated because now, it is the enzyme substrate that is controlling how fast the reaction is going.1552

OK, now, a second assumption here or postulate, if you will, I will say in these proceedings, is the steady state postulate, steady state assumption.1562

OK, I will just call it assumption.1590

The steady state assumption...again, we have to, sort of, make things as easy as possible for us that we can deal with the mathematics in reasonably decent way.1602

The steady state says this; the formation of the enzyme substrate complex is quick - right, a fast step, this is the fast step - and once it is formed, the concentration of this enzyme substrate complex remains constant.1611

That does not fluctuate; it achieves a steady state.1644

It does not mean things stop; it just means it has achieved a steady state.1648

This concentration is not going wildly up and down.1654

If that were the case, there is no way we can handle this mathematically, at least not in any simple fashion.1658

A second assumption of proceedings is the steady state assumption; this is a very important assumption.1664

The formation of the enzyme substrate complex is quick, but once it is formed, the concentration of enzyme substrate, it stays reasonably constant.1669

OK, in other words, that is the rate of enzyme substrate breakdown is the same as the rate of enzyme substrate formation- that is it.1691

In other words, you saturated your enzyme; now, you have enzyme substrate complex.1720

As quickly as the enzyme turns over the substrate and kicks out a product, another substrate actually binds.1724

You are never going to end up with some enzyme substrate concentration that goes from 10 to 50 to 3 to 5 to 47 to 8.1731

Once it gets there, that is it; it usually just stay there.1740

That is the steady state assumption; it allows us - in a minute, as you will see - to set rates equal to each other so that we can make the mathematics a little bit more tractable.1743

OK, now, let's go ahead and rewrite what we have here.1753

We have our enzyme plus our substrate.1758

It is going to form our enzyme substrate complex, and that is going to break down into enzyme plus product.1762

This is the Michaelis-Menten 2-step mechanism; now, we say mechanism here.1768

Mechanism means individual steps in a reaction- what atoms move, which electrons move.1773

We talk about mechanism a little bit more broadly in terms of steps.1782

I will call it a mechanism; this is not a mechanism formally.1786

This is more just reaction steps because lots of things might happen between here and here.1789

Even though this is one step at the molecular level, at the atomic level, several things might be going on.1795

Again, there is a rate constant in this direction; there is a rate constant in this direction- the breakdown of the enzyme substrate complex.1800

Well, the breakdown of the enzyme substrate complex to product has its own rate constant, K, and the formation of enzyme product.1811

Well, enzyme and product might come back together to form enzyme substrate, right?1822

This is always in equilibrium; things go back and forth.1825

This we will call it k-2; now, in this case, the k-2, this step, it can be ignored.1828

It can be ignored because in the beginning of a reaction, which is really all we are concerned with, the concentration of product is negligible.1842

The first minute or 2 of a reaction, the concentration of product does not matter.1858

Because the concentration of product does not matter, the reformation of enzyme substrate complex from product and enzyme, we can pretend that it does not really happen.1862

We can just, sort of, knock this out of consideration, so when we do our mathematics, we are only going to be concerned with this step forward, this step backward and this step forward.1872

Enzyme substrate forming enzyme substrate complex, enzyme substrate complex breaking down into enzyme substrate free or breaking down into enzyme product- that is it.1884

That is all we are going to be concerned with when we deal with mathematics.1894

Rate is determined by how fast this enzyme substrate complex breaks down- that is it.1901

That is how fast it is; it is controlled by that thing.1917

It breaks down to product; we know that the rate, which we are calling v0, initial velocity.1923

Now, because the Michaelis-Menten postulate was that this second step is the slow step, that is the rate-determining step.1934

That means that the rate law for this, the rate equation that equates concentration of this to how fast a reaction is going, is going to be this: the rate constant of this step times the concentration of the reactant.1942

That is how we do it if you remember from chemistry and kinetics.1959

The rate of a reaction is equal to some rate constant times the concentration of the particular reactant in that reaction.1963

In this particular case, this is the fast step; that does not control the rate.1971

The slow step, this step, from ES to E + P, that is what controls the rate.1976

Therefore, this is the reaction we are concerned with- this way, right?1980

We said we can ignore this; we are concerned this way; the rate of our ultimate overall reaction is going to be the rate at which this breaks down.1987

That rate is given mathematically by k2 x S; k2 is the rate constant.1994

ES is the concentration of the enzyme substrate complex- basic, first order kinetics.1999

This exponent here is 1; we are not going to get into what the order of the reaction is right now.2005

We are just going to stay nice and simple, so let me go back to black.2010

OK, now, we have this; this is our starting point right here.2015

Now, the thing is, the concentration of enzyme substrate complex, this is not easily measured experimentally.2024

We have to find different expressions for ES so that we can substitute into this expression.2047

In other words, we need to express ES in terms of things that are easily measured, and we can do that.2055

Let's find some alternatives for substituting - I hope I spelled that correct - into this ES thing.2062

OK, excuse me.2086

Now, we are going to get into the mathematical derivation, and again, please do not worry if you do not necessarily follow this derivation.2090

The only reason I am actually doing the derivation is so you have some sense of what is actually happening, that these things do not just fall out of the sky.2097

Again, it is good to see a derivation; it is good to listen, to think about what is happening just to, sort of, see it even if it is only passively.2107

At least your mind is starting to wrap itself around what is happening.2116

The ultimate form of the Michaelis-Menten equation is what we are going to be concerned with, but I think the derivation is just important to see.2120

We are going to introduce some thing; actually, let me go ahead and do this derivation in blue.2129

Let's introduce some notation here, introduce this thing called ET.2135

This is the total enzyme concentration; OK, well, the total concentration of enzyme comes from 2 sources.2145

You are going to have free enzyme, and you are going to have the enzyme that is actually bound up as the enzyme substrate complex, right?2157

That is it; those are your sources that comes up to the total enzyme concentration.2164

Our total enzyme concentration is equal - oops, let me make this a little bit better - to free enzyme concentration plus the enzyme that is tied up as enzyme substrate.2172

These things we can measure; this we can measure.2189

That is easy; we know how much enzyme we are actually using.2193

This is very, very easy; notice, we have already started to express ES in terms of things that we can measure.2198

OK, now, rate formation, now the rate of ES formation...OK, actually let me do these a little bit separately.2205

Now, we are going to write 2 rate equations.2229

And again, a rate equation is some rate constant times the concentration of the reactants.2233

Now, the rate of enzyme substrate formation is equal to enzyme substrate formation comes from here.2239

It is this step right here, this step.2254

It is equal to k1 times the concentration of free enzyme times the concentration of S- that is it.2258

Again, the rate of a given reaction is the rate constant in the direction of that reaction times the concentration of the reactants.2267

In this case, you have that reactant and that reactant, so it is this, this.2276

Well, it is equal to k1.2281

Let us rearrange E; E is equal to the total enzyme concentration minus the enzyme that is tied up as substrate.2288

It is equal to E total - ES, and that times S- that is it.2296

I just substituted; I have just moved this over here.2309

That is E; I have substituted to here, and I end up with this.2312

That is my rate of formation of enzyme substrate complex.2316

Now, my rate of enzyme substrate breakdown because that is what is happening here.2321

Enzyme substrate is forming; enzyme substrate is breaking down.2331

Breakdown of the enzyme substrate complex can happen in 2 directions.2336

It can happen in this direction to form enzyme and product; it can happen in this direction to form enzyme and substrate.2340

We account for both; in this direction, it is equal to k-1 because it is now this direction, so we use that rate constant, and the reactant is if our reaction is going in this direction, that is the reactant.2345

It is k2 times the enzyme substrate complex.2364

Now, the reaction in this direction, again, ES is the reaction, but k2 - that is it, they are additive - k2 times enzyme substrate concentration.2368

I hope this makes sense; again, anytime you have some reaction, AA + BB going to, let's say, CC, and if there is some equilibrium, if the reaction that we are looking at in that direction, well, it is going to be the rate constant - k1 - times the concentration of this and times the concentration of that because we always deal in terms of the concentration of reactants.2385

If we are looking at the reaction in this direction, well, the rate constant, we call it k-1 - that is the symbol - but now, in this direction, this is the reactant.2413

Because that is the reactant, it is going to be k-1 times the concentration of that because now, the reaction is going in this direction.2422

We are just not writing it left to right; the forward reaction formation, that is this one.2430

The breakdown happens in 2 ways; it can break down in that direction.2438

It can break down in that direction; each of those is represented here.2442

OK, now is when we are going to apply the steady state assumption.2447

The steady state assumption says that the rate of breakdown of ES is the same as the rate of formation of ES.2452

I am going to set this equation equal to that equation.2458

That is the steady state assumption; here is where the math comes in.2465

We need to simplify the math; if I do not have the steady state assumption, I cannot do anything here.2470

Let's go ahead and do that one.2475

OK, now, I have got k1 times the total enzyme concentration minus enzyme substrate concentration times substrate concentration is equal to k-1 enzyme substrate concentration plus k2 enzyme substrate concentration.2479

Now, after some algebra, I will just write algebra…, and you can check the algebra for yourself if you want.2515

You are going to get something that looks like this; you are going to get the enzyme substrate.2523

We are going to solve for this ES thing; it is equal to the total enzyme concentration times the substrate concentration all divided by k2 + k1 / k-1 + S.2527

I will go ahead and put this, something like that.2552

Now, this thing, this is defined - it is a definition right now, we will give a better definition in a minute - as the Km.2556

We call it a capital Km; this is the Michaelis-Menten constant.2570

OK, now, I am going to rewrite this.2588

Because we call it Km, I am going to put Km in there, so I have, now, ES is equal to the total enzyme concentration times the concentration of S over Km + S.2592

Now, I have an expression for this ES; that is what I wanted.2607

Well, all of these things are actually pretty easily measured.2612

That is hard to measure, but ET is easy to measure; that is easy to measure, and this one we will see in just a minute.2616

Now, we said - let me go back to blue here - the initial velocity is equal to k2 x enzyme substrate concentration.2624

Well, now, I am going to take this, which is this, this expression, and I am going to substitute into here.2638

Therefore, I have v0 is equal to k2 times total enzyme concentration times substrate concentration over this thing called Km + S.2644

Notice, this Km constant, it is just a combination of the 3 constants that are involved in the reaction.2656

You have reaction 1, reaction 2, reaction 3- that is it.2663

That is all you are doing; we are just calling it 1 constant because we do not want a bunch of Ks floating around.2667

Alright, now, let's take a look.2674

Now, Vmax, the maximum velocity occurs when the enzyme is saturated, right?2679

When the enzyme is fully saturated, we have that curve, that line up at the top when the enzyme is saturated.2694

That is when the total enzyme concentration happens to equal the enzyme substrate concentration.2710

In other words, when the enzyme is saturated, that means it is all enzyme substrate complex.2720

Well, that means that is the same as all of the enzyme concentration that I started with.2727

So, ES happens to equal ET; the total enzyme concentration, all of the enzyme is now enzyme substrate, so I can set those equal to each other.2734

The maximum velocity equals k2 ET, right?2751

We said that v0 is equal to k2 ES.2762

Well, ES is ET, so Vmax, now, because at maximum velocity, the enzyme substrate concentration equals ET, so v0, which happens to be the maximum velocity now - not just some initial rate - is equal to k2 ET, right?2766

That just comes from this; this, at maximum velocity, ES is equal to ET.2785

I put ET in here, and instead of calling it initial velocity because the velocity is now maximum when these 2 are equal, I just call it Vmax.2791

Now, I can write it.2801

Now, v0 is equal to Vmax x S/Km + S.2807

This is what we wanted; OK, we had k2 ET up at the top.2823

We call that the Vmax, maximum velocity; this is the Michaelis-Menten equation.2832

This is what we were hoping for.2837

This equation is the equation for that thing, that line that we say, which we are actually going to see in a second again.2843

This equation expresses that; now, each of these - this is what is nice - quantities, in other words, the initial rate that we measure the velocity, the maximum velocity, the substrate concentration and this Michaelis-Menten, this thing, are all easily experimentally determined and/or measurable.2853

We took that expression that involved the enzyme substrate complex.2897

We fiddled with it because we did not want to deal with the concentration of enzyme substrate complex, and we expressed it in terms of something that we can measure.2903

We know the substrate concentration; that is what we are controlling.2912

These other things are all easily measurable- that is it.2916

This is the Michaelis-Menten equation; this equation represents, under the postulates, the steady state postulate and the Michaelis-Menten postulate of the second step being the rate-limiting step, this describes that curve that we saw.2922

This says that the initial rate is contingent on...it depends on a maximum velocity.2937

It depends on substrate concentration, and it also depends on something called the Michaelis-Menten constant, which we will talk about a little bit more in just a second.2945

Now, let's see what happens when the v0 is equal to 1/2 of Vmax.2954

Again, special cases, we like to just, sort of, see what happens mathematically.2970

Well, when you set v0 to 1/2 Vmax, you end up with Vmax/2 - you just plug it into that equation - equals Vmax x the concentration of S over Km plus the concentration of S.2974

The Vmaxs go away; you can cross multiply.2996

You end up with Km plus the concentration of S equals 2 times the concentration of S.3000

Go ahead and subtract, and you get Km equals the concentration of S.3008

This is beautiful; this says that when we measure an initial rate, which is half as fast as the enzyme is ever going to get half the maximum velocity.3014

It is at that, when that is the case, the Km is actually equal to the substrate concentration at that point.3028

Whatever substrate concentration I happen to pick, that is my Michaelis-Menten constant.3040

That is this thing; this is the definition we want.3044

That is beautiful; this Km is equal to the substrate concentration, which gives us a velocity equal to 1/2 Vmax.3048

Again, let's go ahead and take a look at our...alright.3080

Yes, alright, now, we can talk about Vmax, 1/2 Vmax, Km.3095

We go ahead and we run our reaction data with different initial concentrations.3101

We end up getting this thing; we go ahead and we take a guess, an estimate, of this maximum velocity.3105

For this particular enzyme, whatever it happens to be, I go ahead and once I actually estimate a maximum velocity, I take half of that maximum velocity.3111

I come down; I draw a horizontal line.3120

I see where it touches the graph, and then, I go down, then, whatever this is, it is that substrate concentration, which will allow me to be at half my maximum velocity for this enzyme- that is it.3123

That is the definition of Km; that is the best definition of Km.3139

It is a nice experimental definition of Km; again, Km is the substrate concentration - moles per liter, millimoles per liter, micromoles per liter - at which the enzyme is at half maximum velocity.3142

OK, you run the experiment; you can find the maximum velocity from that, then, from maximum velocity, you can take half of it, and then you can find the Km.3157

Now, you have got yourself a perfectly valid equation: v0 = Vmax x the concentration of S/Km + S concentration.3167

Now, you can use whatever you want.3180

Let's say you want to slow it down a little bit for your experiment, whatever you are doing, or let's say you want to speed it up faster than half the velocity max, let's say you want the velocity to be up here, you can control the substrate concentration; and you have this equation.3185

In other words, you found Km, and you found Vmax- that is it.3200

You have an equation for that particular enzyme; that is what we want.3205

We want some sort of a quantitative description; now, let's take a look at this equation.3209

When the substrate concentration is a lot less than Km on the denominator, we can ignore the S.3215

OK, because it does not make that big of a contribution to the denominator, we can ignore S in the denominator.3230

The equation becomes v0 = Vmax/Km x the S concentration.3250

As we said before, this is a linear equation, thus, the almost linearity for small concentrations of S.3266

In other words, under small concentrations of S, the Michaelis-Menten equation reduces to a linear equation.3276

It supports the data; now, when the concentration of S is a lot greater than Km, now, Km can be ignored.3282

We ignore Km in the denominator, and the equation becomes v0 = Vmax x S/S.3298

These cancel implying that v0 = Vmax, which is exactly what this graph says.3320

As your concentration rises really, really high, so much higher than what the Km is, the Km becomes negligible.3326

In this equation, the velocity becomes Vmax- asymptotic behavior.3332

As you go in this direction, you actually approach your maximum velocity.3340

This equation confirms low-end behavior, high-end behavior, and it also matches everything else in between.3346

Now, the question is this: “Do enzymes actually behave this way?".3355

The answer is yes; enzymes actually behave this way even for situations that are not necessarily postulated by Michaelis and Menten, where you have not this simple 2-step process, where the 2nd step - the breakdown of the enzyme substrate complex - is the slow step.3359

It is very, very interesting; this is characteristic enzyme behavior- steady state kinetics.3377

It is called Michaelis-Menten kinetics; the names in and of themselves do not really matter all that much.3385

What matters is the actual behavior.3390

Thank you for joining us here at Educator.com; we will see you next time for a further discussion of enzyme kinetics, bye-bye.3394

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