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Raffi Hovasapian

Raffi Hovasapian

Enzymes II

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 (2)

1 answer

Last reply by: Professor Hovasapian
Sun May 26, 2013 4:20 PM

Post by marsha prytz on May 26, 2013

in the example of phosphohexose isomerase, when the enzyme is acting as an acid you are moving the H+ on carbon #2 instead of carbon #1 where the proton was actually put in the base reaction. Does that mean the double bond moves to the c/o bond of carbon #2 or was that a mistake and the H+ from carbon #1 is actually the one supposed to be moving?......I hope this makes sense

Enzymes II

Lecture Slides are screen-captured images of important points in the lecture. Students can download and print out these lecture slide images to do practice problems as well as take notes while watching the lecture.

  • Intro 0:00
  • Enzymes II: Transitions State, Binding Energy, & Induced Fit 0:18
    • Enzymes 'Fitting' Well With The Transition State
    • Example Reaction: Breaking of a Stick
    • Another Energy Diagram
    • Binding Energy
    • Enzymes Specificity
    • Key Point: Optimal Interactions Between Substrate & Enzymes
    • Induced Fit
    • Illustrations: Induced Fit
  • Enzymes II: Catalytic Mechanisms 22:17
    • General Acid/Base Catalysis
    • Acid Form & Base Form of Amino Acid: Glu &Asp
    • Acid Form & Base Form of Amino Acid: Lys & Arg
    • Acid Form & Base Form of Amino Acid: Cys
    • Acid Form & Base Form of Amino Acid: His
    • Acid Form & Base Form of Amino Acid: Ser
    • Acid Form & Base Form of Amino Acid: Tyr
    • Example: Phosphohexose Isomerase
    • Covalent Catalysis
    • Example: Glyceraldehyde 3-Phosphate Dehydrogenase
    • Metal Ion Catalysis: Isocitrate Dehydrogenase
    • Function of Mn²⁺

Transcription: Enzymes II

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

Today, we are going to continue our discussion of enzymes, and we are going to start off by talking a little bit more about the enzyme substrate complex and how it actually facilitates, how it does what it does, how it contributes to an enzyme doing what it does.0004

Let's just go ahead and get started; we mentioned that you have an enzyme that comes in contact with its particular substrate, and it forms something called the enzyme substrate complex.0018

OK, this enzyme substrate complex is absolutely key to understanding why an enzyme does what it does and how it does what it does.0032

Now, catalysts, we know, they bring about their effects by binding well...catalysts, let's not use the word catalyst.0042

Let's go ahead and just call them enzymes.0066

OK, enzymes bring about their effects - let's start again, shall we, alright - by binding well not to the substrate as is but fitting well or binding well with the transition state.0072

In other words, let me talk about this a little bit.0116

When an enzyme...yes, I mean an enzyme is going to recognize its particular substrate.0120

That is part of the specificity of an enzyme; an enzyme is not just random.0125

It has a particular substrate that it works with and only that substrate, maybe another one, but it is very, very specific for the molecule that it wants to bind.0129

When it binds that molecule, it is not just going to bind the substrate as is.0138

It recognizes the substrate, and then, what happens is, it plays around.0145

It moves a little bit; it twists the substrate around a little bit.0152

The best binding interactions, the optimal binding that takes place between a substrate and an enzyme, in other words, when it is at its most optimal enzyme substrate complex state, it is when the enzyme has actually bound well to the transition state of the substrate.0158

In other words, the substrate, in order for it to actually go through and go from substrate to product, it has to pass through some transition state.0178

Well, the enzyme does what it does not by binding well to the substrate, but the best binding happens because it binds well to the transition state; and we will show what happens energetically in just a minute.0186

Enzymes bring about their effects by binding well not to the substrate as is, but by fitting well, binding well, with the transition state.0199

That is what is important; now, this is actually best explained diagrammatically.0207

I am going to put up an image in just a moment, and then, we will go through that.0215

Let's say that the particular reaction we want to talk about, let's say that our particular reaction is the breaking of a stick.0221

OK, I have this stick, no catalyst, no anything.0247

In order for me to break it, I have to take that stick, and I have to invest a little bit of energy and actually bend that stick.0253

I have to take it to this point, right?0259

I have to take it to a point where it is just about to break and at that point, a little extra push, and you end up getting 2 pieces, right?0261

It breaks right there; now, what a catalyst does is the following.0270

I have to invest a certain amount of energy before boom.0276

That is this; here is the stick.0280

Here is the broken stick; this point right here, the transition state, that is this point right here.0285

I have to put in a bunch of energy in order to get it to that point, and then, after that, boom.0290

I go over, and I end up with my 2 pieces.0296

Now, let's take a look at a diagram what a catalyst actually does.0300

What a catalyst does is it recognizes that stick, and then, what it does is it fiddles with that stick.0306

It twists it; it changes it.0312

What the catalyst does, it actually bends it; the catalyst, the interactions that the stick has with the amino acid residues in the active site of the enzyme, every time it does that, it actually takes it to the transition state for me.0315

That is what a catalyst does.0330

Here is the substrate energy; here is the product energy.0334

Without a catalyst, I have to go up to here, but because the catalyst, what it does, the enzyme, it takes it to the transition state for me.0337

It takes it to the bent position; it is in this position that all of the interactions are really, really tight and strong between the enzyme and the substrate.0348

At that point, it has already raised the energy level up to here, here, here, here, here.0358

Now, the only thing that the reaction has to do is just go over that hump.0365

Now, it has less energy that the actual reaction has to invest in order to go over that hump.0369

That is how an enzyme, a catalyst lowers the activation energy.0375

It is not so much of lowering of the activation energy; that is true.0381

I mean the transition state is a transition state; in order for the stick to go from single stick to a broken stick to pieces, it has to pass through this transition state.0384

Instead of us putting in the energy to actually bend it, the interactions between the amino acids, the weak interactions, the hydrogen bonding, the hydrophobic interactions, the ionic dipole interactions, all of those things, they end up stabilizing the transition state enzyme complex.0395

And now, it is already at its transition state.0416

Now, because it is here, all it has to do is - poop - go over and form product.0420

That is what is happening; the energy that comes from all of the small interactions of binding, those actually lower the activation energy.0425

Really, what you are doing is you are taking this, and you are bringing it closer to this and that.0435

A substrate energy level is not going to change; a substrate is at a certain energy level.0443

The products are at a certain energy level; that does not change.0447

What does change is the amount of energy that we have to invest to make it go over that transition state.0450

The enzyme is there to do most of the work for us; that is why reaction rates proceed faster.0458

In the process of forming this enzyme substrate complex, which is really an enzyme transition state complex because the optimal binding between the 2 happens when the substrate is in its transition from here.0464

It is just ready to go over; now, all the molecules have more than enough energy to go over.0478

All of them will; 100% of them will, not just 3% or 5% or 10%.0483

That is where this comes from; OK, this difference in energy...let me see.0487

Actually, let's do another diagram here; I am going to do another energy diagram.0499

We have something like this; we have our substrate and our product.0508

This is the uncatalyzed reaction- something like that.0514

Here, this is the enzyme substrate complex.0518

This is substrate; this is enzyme substrate.0524

This other one does not matter; because it is in this form, because the substrate is already in its transition state when it is bound to the enzyme, now, this transition state is here.0527

Now, instead of all of this energy, all I have to do is go - poop - a little bit that way, just a little bit of energy in order to get from here all that way to product.0539

That is what is happening; the transition state is easier to reach.0549

The energy for that instead of us putting it in to make it go over this hump, the enzyme with its weak interactions - hydrogen bonding, hydrophobic interactions, ionic interactions - that it has with the substrate, bending it and twisting it and already taking it into the transition state, now, we do not have to work as hard to get over that transition state.0554

All it does is it brings the transition state within reach of us.0581

That is all that is doing; that is how enzyme works.0585

This difference in energy, in other words, the difference in energy from here, now, here, this difference comes from weak interactions between substrate and functional groups on the amino acid residues of the active site.0592

This is called binding energy.0651

OK, now, these weak interactions, I can do a little bit better than that.0662

Actually, it is hydrogen bonding, bonding hydrophobic interactions, ionic interactions, account for an enzyme's specificity.0687

When an enzyme binds to its substrate, every time some weak interaction takes place, it actually acts as a support for the substrate.0734

Every time there is some hydrogen bonding interaction, every time there is some ionic interaction, some hydrophobic interaction, that energy is released as free energy, and what that does is that brings the transition state, the amount of energy that we need to invest.0745

In order to get to the transitions state, it makes it a lot smaller.0759

That is what it is doing.0763

The best way to think about it is let's say you are standing on a stair step or something.0767

You know that if you lean over too far, you are just going to fall over.0773

Gravity is going to pull you; it is just going to pull you down.0777

Well, if you were to lean over a little bit, let's say one of your friends grabs your hand, now, you can, sort of, release yourself.0781

Your friend is supporting you; he has you.0786

Let's say you lean over a little further; now, another friend comes and basically, let's say, grabs your other hand and maybe another friend is holding you from the back.0788

At this point, you can, sort of, let your entire weight fall on your friends.0796

Those friends are the weak interactions; they are supporting the substrate.0801

You are the substrate; they are supporting you.0805

You do not have to expend any energy in order not to fall over; now, they are the ones that are actually taking the energy and supporting you.0809

That is what an enzyme does; an enzyme supports a substrate so that the substrate does not have to support itself, and it takes it to the transitions state.0816

Now, it is very, very simple; now, your friends can just, sort of, take you, lean you down and put you down on the ground, if that is the reaction that needs to take place, and it happens in a very controlled manner as opposed to just - boom - falling over.0825

That is what an enzyme does; well, these interactions, they not only account for the lowering of the transitions state energy, the activation energy.0839

They also account for the specificity of an enzyme.0847

In other words, an enzyme is going to reach out for the substrate that has the most affinity for its particular active site, and the more tightly the substrate binds, the more weak interactions, the more tightly it binds, now, it is more specific.0851

It is not just any random molecule that can wander into the active site of an enzyme, but they do.0870

I mean, molecules wander into active site of enzymes all the time, but the enzyme is not going to interact with them because there is no way that the enzyme is going to twist and turn to make that particular substrate, whatever it happens to be, bound tightly; but there is usually 1 substrate, the substrate for that enzyme that binds beautifully, that binds tightly.0876

It is the substrate that the enzyme is designed for, that it evolved for.0896

That is what makes enzymes so amazing.0900

The evolved for specific substrates; it is absolutely fantastic.0904

These weak interactions, they also account for an enzyme's specificity.0909

OK, the key point, the point that we actually want to makes is the following.0914

I will do this in red- the key point.0923

Optimal interactions between substrate and enzyme happen when the substrate is in its transition state.0929

The closer the substrate gets to its normal transition state, it is at that point that it binds very, very, very tightly with the enzyme, and it is at that point that the reaction actually takes place because it is already at the transition state.0969

There is no actual energy; it says "boom"- that is it.0983

It happens; OK, now, let's go back to black.0985

An enzyme is much, much larger than its substrate.0997

OK, now, although substrate molecules tend to be flexible, although substrates can be flexible because of the sheer size of enzymes and the fact that they are made up of amino acids, enzymes enjoy greater flexibility.1010

This is very convenient.1045

Now, since optimal enzyme substrate interactions occur not between enzyme and substrate as is, but between enzyme and transition state for the substrate, the enzyme will often - always actually - undergo changes in conformation to accommodate this.1050

An enzyme is very flexible; it has a certain active site.1137

It recognizes the substrate, starts to bind with it.1142

As the binding in interactions get stronger, it binds more with it, twists and turns it this way.1146

The enzyme will twist; the enzyme will turn.1152

The enzyme will open; the enzyme will close.1155

It will conform to something, so if I want to grab this thing, this is the enzyme, this is my substrate, I do not just...yes, I mean, it fits, but I have to...notice, I am changing my fingers.1158

I am conforming to actually fit the substrate.1175

Now, the binding is really tight; now, the substrate is held really, really well.1180

This is the enzyme that is very, very flexible; there is an induced fit.1184

If this were something else, holding it this way as a pen, it is inducing me to do this.1188

If I wanted to hold it a different way, it would induce me to hold it like this.1197

This and this are 2 different things.1201

This is one enzyme; this is another enzyme.1205

We call it induced fit; that is the whole idea.1208

This changes in conformation that enzymes undergo.1211

It is called induced fit because the fit is induced by the particular substrate.1214

Let me write that in red- very, very important.1227

That is all that it is; it is actually pretty intuitive.1231

There is nothing about this particular nomenclature induced fit that is strange.1234

It is when an enzyme conforms to a substrate when it changes, closes, twists, turns - very, very important, very deep important functionality of an enzyme - and then, later, when we talk about regulatory enzymes, it is going to play an even bigger role.1242

Let's go ahead and let's look at a couple of images of induced fit.1259

They are not the best, but I think it just, sort of, gives you the idea; it is nice to see a couple of pictures at the very least so something like this.1265

Here is your substrate; you have this active site here.1271

It fits in there; when it actually fits, the enzyme closes in on it.1275

It is an induced fit, not just that is it; substrate comes it- that is it.1281

The enzyme just stays there; that is not what happens.1285

This one right here, here we have 2 substrates; we have 1.1288

We have 2; you have an enzyme which is actually open.1291

These need to come in contact with each other in order to react.1297

They come; they enter the space, closes, closes, closes.1302

In this particular case, it actually brings the molecules in close contact, so that the molecule can react again, another way of lowering the activation energy.1307

It goes ahead, the product is formed, and then, the enzyme opens up again- that is it.1317

It is induced fit; it can actually release its particular product and other substrate or whatever it is that it happens to do.1322

OK, now, let's look at...actually, let me go to blue here.1333

Let's look at some catalytic mechanisms.1350

Now, that we have talked a little bit about enzymes generally, let's talk about some catalytic mechanisms.1354

How do enzymes mechanistically, specifically do what they do?1361

OK, now, in this particular case, I am going to be introducing some mechanisms and using some examples of some enzymes that do what it is that they do.1367

You do not have to know these enzyme names; at this stage, it is only general.1378

We want you to have a general idea of acid-base catalysis, metal ion catalysis, covalent catalysis.1382

Later, when we start talking about the metabolic pathways, that is when we are going to get into the specifics, and these enzymes that we talk about here, you are going to see them again; so do not worry about it.1389

Here, we are concerned about just general notions.1398

Later, we will get into actual specific mechanisms.1402

The basic catalytic mechanisms that we are going to be concerned with most are going to be general acid-base catalysis, covalent catalysis and metal ion catalysis.1407

OK, let's talk first about general acid-base catalysis.1435

Well, acid-base catalysis is exactly what you think it is.1452

An acid is something that donates protons, and a base is something that takes protons.1459

I do not like to call it "accepts a proton"'; I like the idea of "taking" better because it just seems to be more appropriate, but that is fine.1463

You can look at it however you want to look at it, and that is it.1469

General acid-base catalysis is when specific functional groups on the amino acid residues that are lining the active site when they act as proton donors or proton acceptors, proton takers.1474

Catalysis, when specific functional groups on amino acid side chains donate or - that is fine, we will just go ahead and say "accept" because that is the accepted standard nomenclature - accept hydrogen ions.1491

OK, now, there are...I am going to go through a little bit of a list here of amino acids- their acid form and their base form.1522

Particular amino acids, let's just go ahead, amino acid, let's see.1538

Its acid form, in which form it actually has hydrogen ion to give away, and its base form, it is the form of the functional group where it is not going to give a proton.1546

It is going to actually take a hydrogen ion from a substrate of another amino acid.1560

Let me see; we have glutamate, and we have aspartate.1567

This is the acid form; this H is available for donation.1576

Its base form, this site, the O-, is available of protonation.1580

It can take an H; I will see this one again in just a minute.1587

Lysine, arginine RNH3+.1593

This has a proton that it can donate.1601

RNH2, this has a site that can actually accept a proton or take a proton.1605

Let's see; let's have cysteine, RSH, RS-- proton to give, proton to accept.1612

Actually, let me go to the next page here; we have histidine.1626

Histidine will show up all over the place.1631

Let me go ahead and write the top again, acid form, base form.1636

OK, we have histidine; we have R, C, C, N, C, N.1651

Let's see; it is there.1660

This is there; this is H.1665

This is H; let me see.1668

This is H, and that is a plus; yes, I do not think I have missed anything.1670

Let's go ahead and put that H there; that is the acid form.1674

It has an H that it can give up, and the base form is...it has a site that it can accept a proton; and let me see.1677

Let's go ahead and have...another possibility is serine.1698

We have ROH, RO-; it has an H to give up.1703

It has an H that it can accept, and let's just go ahead and do one more, maybe a tyrosine, where we have R.1707

Let's make this a little bit nicer, shall we.1722

Yes, there we go, ROH.1727

And again, we have this not unlike this one, O-.1731

It has an H to give up; it has an O- that can accept an H.1736

OK, now, let's go ahead and do an example of an acid-base catalysis mechanism just to show you how this thing actually works.1741

Let me go ahead and do this in blue; now, let me...I wonder if I should do it here.1753

Yes, that is fine; I guess I can do it here.1758

Our example, we are going to be using...this enzyme that we are going to be talking about as an example of general acid-base catalysis is phosphohexose isomerase.1762

It is going to be involved in the glycolytic pathway, which we will talk about in the second half of the course.1785

Let me go ahead and draw a little something here.1791

I will go ahead and draw this, and let me go ahead and...that is OK.1795

I will go ahead and do it here, so 1, 2, 3, 4, 5, 6.1800

I will go ahead and put my aldehyde group here.1809

Let me see my OH, my H, OH, H, OH, OH, O, PO3, yes PO32-.1814

OK, now, I have got a glut C, O-.1826

Alright, again, general acid-base catalysis, all that it means is that this is the enzyme, and here, we have this glutamate residue; and we said that glutamate, when it acts as a base, it has the COO-.1840

It is in a position to accept a proton, which might make something easier for the particular substrate.1856

In this case, we have this aldehyde here.1862

General acid-base catalysis is just that.1867

These functional groups along the...this is the enzyme, and this happens to be an amino acid residue in the active site of the enzyme.1871

They can accept protons or donate protons, whatever is needed in order to make the reaction go- that is it.1882

In this particular case, here is what happens; it actually takes this proton.1891

These electrons move here; let me do this in red actually.1896

Let me show the movements of electrons in red; my apologies.1899

It is probably better that way; it takes or it accepts that proton.1902

These electrons move here; these electrons go there and pull some other hydrogen from solution.1907

What you end up with is the following.1914

Again, we have this glutamate, which is, now, glutamic acid, OH.1918

Now, we have C, C, C, C, C, C.1928

Now, this is H, and this has become OH.1939

This is now a double bond; this is also OH.1943

This is OH; this is OH.1948

This is OH, and this is O, PO4, PO3 - sorry about that - PO32-, right.1951

In this particular case, it acted as a base; it took this proton so that electrons can move to form something else.1962

Now, something else happens; now, it is going to act...I am sorry.1970

Yes, it acted as a base; now, the next step of this particular mechanism, and again, we will revisit it in the future, it is going to act as an acid.1973

It is going to give back a proton, so here is how that works.1981

Let me go ahead and write this as this way.1986

These electrons move here; these electrons grab this, and they push the bond back to there.1992

Now, it is acting as an acid; now, it is going to give this hydrogen back to this, but this time, instead of attaching to this carbon, it is going to attach to the carbon right above it.2000

All we have done is we have actually shifted something.2012

Well, we are not going to worry about what is actually happening here.2016

We are changing the carbonyl; we are moving it to this carbon and putting it on the second carbon, but all we have done is this amino acid has acted as a base by taking a proton facilitating this reaction, and then, now, it is going to act as an acid by giving up its proton back to this particular molecule.2020

This is an example of general acid-base catalysis; that is all it is.2035

It is the movement of protons; that is all.2038

That is all; that is all.2041

This new name, general acid-base catalysis, it sounds really complicated- it is not.2044

It is just some amino acid residue, some functional group on there that is giving up a proton, taking a proton, giving up a proton, taking a proton- that is it.2048

It is interacting with the substrate.2056

OK, let's take a look at, now, a covalent catalysis.2060

Let's do this in blue; let's try again, blue.2067

Now, covalent catalysis is where the enzyme or the coenzyme - sometimes both - forms a transient covalent bond with the substrate.2078

Remember we said that the interactions that exist between enzyme and substrate are weak interactions- hydrogen bonding, hydrophobic, ionic dipole and ion.2110

There is no covalent interaction, but in the actual catalytic mechanism, in order for the reaction to move forward, it might have to bind with the substrate; or the coenzyme might have to bind with the substrate temporarily in order for it to do what it needs to do.2119

Let's see an example of that.2135

An example of this, we are going to use the glyceraldehyde-3-phosphate dehydrogenase.2141

An again, you are going to see all of these again; this is also another glycolytic enzyme, one of the enzymes involved in glycolysis.2158

OK, let's see if we can draw this out here.2166

Let's see; I am going to go ahead and do it this way, and I will go ahead and put a cysteine residue here, and it has an S, and it has an H, and over here, I am going to go ahead and put a histidine residue, boom, boom, boom, boom, boom.2170

I will just go ahead and put my nitrogens there and there, double bond, double bond.2186

This is there; this is H.2193

OK, now, we have our substrate; let me go ahead and do the substrate in red.2195

I have got C, C and C.2200

This is O, PO32-.2205

This is here; this is H, and this is just H2.2209

OK, here is the following.2214

Now, what happens is this; this is actually a combination of acid-base catalysis and covalent catalysis.2218

I will do this electron movement in black; this goes ahead and takes that.2224

It pushes these electrons up to here to attack the carbon, and it actually ends up going that way; and what you end up getting is the following.2230

You end up getting cysteine, S, connected to a C, O-, H, C, C, O, PO32-.2247

Now, the enzyme, itself, this is the enzyme here.2260

This is the enzyme; this is actually covalently attached to the glyceraldehyde-3-phosphate, and it is going to go on and do whatever it does.2265

And now, the histidine residue...where are my double bonds?2274

There they are; now, this is protonated.2282

This is a nitrogen, plus charge; this is protonated.2286

Now, that is it; there is a base catalysis happening here.2290

This acts as a base, takes this proton; it pushes these electrons to form a covalent bond with the glyceraldehyde-3-phosphate.2294

This is just temporary; it is going to go on to do something else.2300

These electrons are going to come back down; this is going to go back and grab another...it is going to just do whatever it is...another phosphate is actually going to come in here.2303

That is what is going to happen; we will worry about that mechanism later, but just general covalent catalysis, it where the enzyme or the coenzyme temporarily attaches itself covalently to the substrate.2311

OK, and let's go ahead and finish this off with metal ion catalysis.2324

Metal ion catalysis and the...this is, sort of, self-evident.2332

It is where a metal ion is involved in the catalytic process- that is it.2340

I am going to use isocitrate dehydrogenase.2345

This is one of the enzymes in the citric acid cycle, which we will get to again.2355

Let's go ahead and see, 1, 2, 3, 4, 5.2360

Let's see what we have got here, 1, 2, 3, 4, 5.2365

That is that, COOO-, H, OH, O-.2372

I guess it does not really matter where we put it; here, what happens is the following.2385

Here, what we have is isocitrate.2396

The reaction that is going to take place is like this.2400

NAD+ goes to NADH + H+.2405

What we end up with is the following: 1, 2, 3, O-.2411

Yes, that is correct, and then, of course, we have our carbonyl, COO dehydrogenase; and we have CO-, O, O.2429

What happens here is the following; now, I am going to go ahead and use my Mn.2442

Let me do the metal in red.2451

This dehydrogenase, what it does, dehydrogenase does 1 thing; it actually pulls hydrogens away, and it oxidizes.2456

This hydrogen and this hydrogen, they go away; that is where that hydrogen and that hydrogen come from.2461

This oxidizes this molecule, and it turns this alcohol into a carbonyl.2468

This carbon is that carbon; now, it turns it into a carbonyl.2473

Well, this carbonyl is actually coordinated to manganese, and what ends up happening, this manganese is actually, it is a positive charge.2476

It is actually pulling electrons this way, so it is making these electrons here...it is creating, sort of, a positive charge on oxygen.2485

It is actually pulling these electrons that way; it is actually facilitating the next step of the reaction, which is this one, electrons here, electrons here, electrons here.2492

This CO2 group is about to go away; that is what is happening.2505

That is the next step; this metal ion, which tends to coordinate with negative groups strategically placed to support them, to stabilize them, to make the movement of electrons a little bit easier, whatever it is that it can do to lower the activation energy and to make this reaction move forward in the easiest, quickest, most convenient way possible- that is it.2510

Mn2+ helps by interacting with the oxygens shown as well as increasing the electron withdrawing power of that carbonyl.2538

It is, now, the carbonyl wants the electrons more; well, because the electrons wants the electrons more, it is going to pull on these electrons.2588

These electrons are going to pull on these electrons, and it is going to make it easier for this carbon dioxide to go away.2593

This bond is what we end up actually breaking carbonyl, thus, facilitating what we call a decarboxylation.2598

There you have it- general acid-base catalysis, covalent catalysis, metal ion catalysis.2621

These 3 mechanisms are going to account for the majority of the mechanisms that we see in all of the pathways that we discuss when we start discussing metabolism.2628

Thank you so much for joining us here at Educator.com.2636

We will see you next time for a further discussion of enzymes, bye-bye.2640

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