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Raffi Hovasapian

Raffi Hovasapian

Enzymes VI: Regulatory Enzymes

Slide Duration:

Table of Contents

I. Preliminaries on Aqueous Chemistry
Aqueous Solutions & Concentration

39m 57s

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

38m 53s

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

29m 1s

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

39m 11s

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

41m 33s

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

44m 19s

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

18m 45s

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

38m 19s

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

27m 14s

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

48m 28s

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

45m 18s

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

42m 47s

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

1h 2m 33s

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

49m 12s

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

54m 31s

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

50m 52s

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

51m 36s

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

1h 3m 36s

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

1h 7m 16s

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

41m 38s

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

44m 2s

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

56m 40s

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

20m 37s

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

51m 37s

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

51m 23s

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

54m 49s

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

1h 17m 46s

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

37m 6s

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

43m 32s

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

39m 25s

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

44m 15s

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

44m 23s

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

40m 22s

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

54m 55s

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

38m 51s

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

38m 20s

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

48m 36s

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

45m 51s

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

37m 6s

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

44m 32s

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

30m 8s

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

49m 46s

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

56m 34s

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

42m 12s

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

43m 32s

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

1h 1m 47s

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

59m 17s

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

39m 47s

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

41m 34s

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

34m 18s

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

42m 52s

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

36m 10s

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

49m 20s

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

44m 11s

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

48m 11s

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

45m 58s

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

33m 18s

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

40m 59s

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

39m 18s

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

36m 21s

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

47m 58s

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

41m 11s

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

36m 27s

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

1 answer

Last reply by: Professor Hovasapian
Tue Jan 31, 2017 7:04 AM

Post by Maksim Avazhanskiy on January 28, 2017

Hello,

What is a regulatory enzyme Vs unregulated enzyme?
Is unregulated enzyme any enzyme without any sited that can affect its rate?
If so then when we looked at inhibition reciprocal plots these were representing regulatory behavior and the plots without any inhibitors represented unregulated enzyme

Thank you,
Max.

1 answer

Last reply by: Professor Hovasapian
Mon Aug 5, 2013 12:16 PM

Post by brian loui on August 2, 2013

Hello Professor.  at 37:48 when you discuss the different forms of glycogen phosphorylase, "phosphorylase a" is the phosphorylated form and the more active form.  In general, is it always the case that the phosphorylated form is the more active form?

Enzymes VI: Regulatory Enzymes

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 VI: Regulatory Enzymes 0:45
    • Regulatory Enzymes Overview
    • Example: Glycolysis
    • Allosteric Regulatory Enzyme
    • Covalent Modification
    • Two Other Regulatory Processes
    • Allosteric Regulation
    • Feedback Inhibition
    • Feedback Inhibition Example: L-Threonine → L-Isoleucine
    • Covalent Modification
    • Covalent Modulators: -PO₃²⁻
    • Protein Kinases
    • Protein Phosphatases
    • Addition/Removal of -PO₃²⁻ and the Effect on Regulatory Enzyme
    • Phosphorylation Sites of a Regulatory Enzyme
    • Proteolytic Cleavage
    • Zymogens: Chymotrypsin & Trypsin
    • Enzymes That Use More Than One Regulatory Process: Bacterial Glutamine Synthetase
    • Why The Complexity?

Transcription: Enzymes VI: Regulatory Enzymes

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

Today, our topic is going to be regulatory enzymes; regulatory enzymes do exactly what the name suggest.0004

They regulate the speed of certain processes.0011

Most enzymes participate in metabolic pathways.0016

The product of one enzyme reaction becomes the substrate for the next enzyme reaction and on down the line.0020

One or more of those enzymes in a metabolic pathway is going to regulate the flow of substrates through there.0027

It controls what the body needs when it needs it - very, very important regulatory enzyme activity.0034

OK, let’s see what we have got.0040

Let’s repeat what we just said in writing here.0044

In metabolism, both catabolic and anabolic groups of enzymes, they work in sequences - excuse me - called metabolic pathways to achieve a certain goal, and that goal is some molecule that they need to either completely breakdown or completely synthesize.0048

OK, now, the product of one enzyme in the sequence - excuse me - as we said, becomes the substrate for the next enzyme in the sequence.0097

OK, a good example of this is glycolysis.0137

It is going to be one of the first metabolic pathways that we actually look at when we get to the second part of this class.0141

An example - oops - is glycolysis, and glycolysis is the breakdown of the conversion – I will go ahead and call it the breakdown because it is a catabolic pathway - the breakdown of 1 glucose molecule to 2 molecules of something called pyruvate, 2 molecules of pyruvate.0149

It is a beginning of how the body metabolizes the sugar that you intake in order to produce energy.0191

OK, the sequence goes like this.0199

We have glucose going to glucose 6-phosphate going to fructose 6-phosphate going to fructose 1,6-biphosphate going to glyceraldehyde-3-phosphate and dihydroxyacetone.0203

The dihydroxyacetone is converted to another molecule of glyceraldehyde-3-phosphate.0228

Now, we have 2 glyceraldehyde-3-phosphates.0236

This goes to 1,3-biphosphoglycerate, goes to 3-phosphoglycerate, goes to 2-phosphoglycerate, goes to phosphoenolpyruvate, and then, finally, we have our pyruvate.0242

This is a metabolic pathway; it is glycolysis.0264

These are the individual steps, and each step is catalyzed by a particular enzyme- a separate enzyme.0266

OK, we have 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 10 enzymes in this metabolic pathway.0277

One or more of these enzymes is going to be a regulatory enzyme.0284

It is going to control the flow of glucose through this pathway.0288

I mean, this is the first one; this is the last one.0294

Now, the regulatory enzyme does not have to be the first or the last.0298

It tends to be often, and it can be somewhere in the middle, too; but ultimately, what it is controlling, it is controlling the flow of the initial substrate all the way through product.0302

That is all that is going on here; OK, let’s see.0312

One or more enzymes along a given pathway, they have the capacity to affect the overall rate of the pathway.0317

I will just say the rate at which substrate flows through the pathway - it is probably a little better description - by increasing or decreasing catalytic activity.0352

As you can see, the reason the body works as well as it does is because of this regulation.0386

There are millions of things going on, millions of reactions happening simultaneously.0394

The body needs to maintain a certain steady state, some reasonable degree of equilibrium at all times, but the body is subject to all kinds of external effectors, if you will- temperature, hydrogen ion concentration, the food that we eat, all kinds of things going on, immune stress.0398

The body needs to adjust that- regulatory enzymes, regulatory proteins.0420

That is what they do - OK - in catalytic activity - alright - in response to specific signals, obviously, in response to specific signals.0425

For example, if there is too much of certain molecule in the body and the body needs to, sort of, cut that back so that excess is actually used up, a regulatory enzyme will shut down a particular pathway that is producing that molecule temporarily until that concentration of molecule diminishes, and then it will open up the flood gates again to allow more- that is it.0444

That is all that is going on here- specific signals.0464

OK, those are the regulatory enzymes.0468

Now, these - let me go back to black, I like black, actually, oh, 2, oh, nice - regulatory enzymes do exactly what they are named for.0470

They regulate the overall rate at which substrate and/or product appears or disappears- very, very intuitive notion.0517

There is nothing particularly counterintuitive about regulation; we do it all the time in our daily lives.0540

OK, now, let’s talk about some of the mechanisms of regulation, what do enzymes do to regulate, how do they go about it.0544

OK, let me go to...I have some green ink now- very nice.0551

I will go to blue; OK, the first one we are going to talk about is called allosteric regulatory, an allosteric mechanism, allosteric regulatory enzyme.0560

OK, this is one that requires the reversible - very, very important - binding of a second substrate - actually, I do not want to call it a substrate, I was going to put it in quotes, but I will not do that - the binding of a second molecule at an allosteric site.0582

An allosteric site just means, it is another site on the enzyme.0624

That is not the active site of the enzyme; that is all it means, just a fancy name for another site somewhere else on the enzyme, so it could be...if the substrate binds here, well, the allosteric site might be close by.0629

It might be over here; it might belong to a completely different subunit.0640

If you have a multi-subunit protein, which is often the case, allosteric sites are often found on other subunits of the protein.0643

A regulatory enzyme is one that requires the reversible binding of a second molecule at an allosteric site - OK - not the active site.0651

OK, now, these second molecules are called...we want fancy names for them.0668

They are called allosteric modulators, and again, modulation is just a fancy word for change.0685

They are allosteric changers, allosteric modulators or allosteric effectors.0690

You are going to see all of these words floating around in the literature.0695

Now, they can be metabolites; they can be anything.0702

They can be metabolites; they can be intermediates along the pathway, not necessarily initial product - I am sorry - not necessarily substrate or final product.0707

They could be anyone in the metabolites in between, or they can be metabolites that have molecules that have nothing to do with the actual pathway itself.0719

They can come from completely different source; it can be anything.0729

Just think of it as a random molecule; they can be metabolites.0735

They can be cofactors; you know, we have talked about cofactors.0738

They can be small molecules; they can be the actual substrate itself.0744

It can also act as an allosteric modulator, so the substrate can actually control how that enzyme does what it does; so I will just put etc.0751

OK, that is one process; we are going to be looking at this in detail in just a minute, but I just want to list the process.0765

Allosteric regulation usually involves some other site on the protein.0771

It could be a single subunit protein; it could be a multi-subunit protein.0777

It is just another site that affects how the enzyme does what it does.0781

OK, another process is something called covalent modification, so another way that modification.0787

OK, covalent modification - let me see if I am actually going to be defining it a little bit later - activity is modulated by adding or subtracting.0807

OK, covalent modification, this is the covalent.0813

I am going to talk about this a little bit later, but I might as well go ahead and write it down now.0819

It is the covalent - now, I will write it this way - adding or subtracting some molecular group covalently.0824

Let's say you have a particular enzyme that is doing something.0850

If we add some small molecule to it, let say, a phosphoryl group , a PO32- and attach it covalently somewhere on the protein, now, because that protein has that thing attached to it, it is either going to be more active or less active depending on the nature of the particular enzyme.0855

That is what we mean by covalent modification; we do something to the protein, add or subtract some molecular group.0875

It could be anything; it could be a big group.0880

It could be a small group, and it changes the nature.0881

It changes the catalytic activity of that enzyme, and it is done covalently.0885

OK, now, in either case, in the case of covalent modification or allosteric regulation, the regulatory enzymes, they tend to be multi-subunit proteins.0895

Multi-subunit because it allows for, well, a greater degree of complexity just by nature of the fact that you have multiple subunits, and we already know that proteins, they, sort of, they shift.0929

They move; they breathe, if you will.0942

A change in one part of a protein in a different subunit has a greater degree of control on the shift that takes place near the active site.0945

Regulatory proteins, because of their complex nature, they tend to be multi-subunit because it allows for a greater control, and that is really what we want.0955

The body wants really, really fine-tuned control.0964

It does not want broad strokes control; it wants very, very fine strokes control- detailed, very, very careful.0970

OK, we have allosteric regulation, and we have covalent modification.0977

I am going to list 2 other mechanisms, and we may talk about them a little bit towards the end.0982

There are 2 other regulatory processes.0991

One is addition or interaction of a regulatory protein.1002

OK, let's make sure that we have everything straight here because we already know that enzymes are proteins.1013

We are using the word protein and enzyme; let’s see if we can straighten this out.1024

You have an enzyme; it needs to be regulated in some capacity.1029

Well, one of the ways that that happens is, you have other proteins that interact with the enzyme in regulatory capacity.1033

In other words, their job is to interact with the enzyme in order to help regulate the enzyme.1042

Those are the regulatory proteins, so we definitely differentiate.1047

In this particular case, the regulatory enzyme itself, we specifically refer to it as an enzyme unless we are talking about it generically as a protein.1054

When we say regulatory protein, we are not talking about the regulatory enzyme itself.1061

We are talking about the protein that interacts with it in order to help regulate the enzyme- very, very important.1066

OK, and another process that occurs is proteolytic cleavage- very fancy name for basically just cutting off a piece of the protein, of the enzyme, to make it active as opposed to its, sort of, being inactive.1073

Proteolytic cleavage is where the enzyme activates or regulates when peptide fragments are removed from the enzyme.1096

Now, it is important to know about proteolytic cleavage, is that proteolytic cleavage is irreversible.1134

Once you cut off a piece of that enzyme to activate it or let it perform its regulatory function, it is not going to go back.1140

Now, if the body needs it, it is going to have to produce a new version of that enzyme.1149

Proteolytic cleavage is irreversible.1155

The other processes, they are reversible.1159

OK, now, very, very important, more than one process can occur for a given regulatory enzyme.1170

A regulatory enzyme does not have to choose between these 4.1180

It can have allosteric modulation; it can enjoy a covalent modulation.1184

It can participate in regulatory protein activity, and/or it can do proteolytic cleavage.1189

It can do all of them or just one of them.1197

It is not limited, and this, again, has to do with really, really fine strokes.1201

This is not a big, broad strokes kind of thing; regulation is very, very important.1208

It has to be able to control it in very, very small amounts, so it uses different mechanisms of regulatory control.1213

More than one process can occur.1221

Sorry; I am going to be a little redundant here.1232

More than one regulatory process can occur for a given enzyme.1238

OK, now, let’s talk about these things in a little bit more detail; let’s begin with allosteric regulation.1252

Let me go ahead and go to red now just for the heck of it, a little change of pace.1259

Excuse me; we said allosteric regulation is where some other molecule binds to another part of the enzyme and controls the activity, either increases the activity or decreases the activity.1269

We will call it positive allosteric modulation, negative allosteric modulation.1282

If it increases catalytic activity, it is positive effection.1287

Now, in allosteric regulation, there may be more than one allosteric regulatory site.1295

There is no law that says you have only one place on that molecule that controls it.1316

You might have 1, 2, 3; you might have 3 on 1 subunit.1320

You might have 3 on another subunit, as many as you need to control that enzyme- that is it.1324

You can have more than 1 allosteric site.1331

Now, if the modulator is the substrate itself, which we said it can be, right - it does not have to be a different molecule, it could be a substrate itself that acts in a regulatory capacity - the enzyme is called homotropic.1336

A homotropic regulatory enzyme is one where the substrate itself controls the rate at which the substrate flows through the metabolic pathway.1377

You can also refer to the modulator itself as a homotropic modulator.1391

It just means that it is the same as the substrate for that enzyme called a homotropic.1397

If the regulatory modulator, if the molecule that binds to the allosteric site, if it is different, well, we call it heterotropic enzyme.1408

If different, then, we call it heterotropic.1421

OK, now, allosteric modulators, they work by stimulating conformational changes in the protein/enzyme to increase or decrease activity- that is it.1435

It will bind to one site; it will cause the protein to shift a little.1485

The shift in one subunit may cause the other subunit to shift a little that will either make the enzyme have more affinity for its substrate or less affinity for its substrate- speed up the reaction, slow down the reaction.1489

OK, let’s see.1504

When the enzyme is inhibited - negative - by the end product of a metabolic pathway, we call it feedback inhibition.1511

OK, an example of this would be the conversion of L-threonine to L-isoleucine.1564

OK, L-threonine, one product, 2 intermediate - I am sorry - 1 intermediate, 2 intermediate, 3 intermediate, 4 intermediate and convert to L-isoleucine, so 1, 2, 3, 4, 5 steps.1582

What happens is, the isoleucine, the product of this particular metabolic pathway in the conversion of threonine to isoleucine, it acts as an allosteric modulator.1605

It will actually inhibit this enzyme, which is the first step in the metabolic pathway.1617

What it ends up doing is it actually slows it down.1622

When the end product is the allosteric modulator, we call it feedback inhibition.1636

It is a special case; OK, now, let’s talk about covalent modification.1643

Let’s go back to blue.1649

Covalent modification, this is where regulatory enzyme activity is modulated - which again, is a fancy word for "changed" - effected by adding or subtracting - or you might say attaching/de-attaching because that is what we are doing - some molecular group covalently.1653

OK, now, the group which is attached/de-attached...actually let me, I need a...OK, the group, this group, is attached or de-attached by a separate enzyme, which should not come as a surprise because every biological process in the body, virtually all of them, are somehow catalyzed.1708

There is some enzyme that does that task, so it does not just happen; some enzyme makes it happens.1755

The group is attached or de-attached by a separate enzyme.1761

OK, now, of the several molecular groups that act as covalent modulators or covalent regulators - I will say modulators - the phosphoryl, the PO32- appears to be the most common.1771

For a particular enzyme that is regulated by covalent modification, some PO3- group is attached to the enzyme to affect it some way, and it is de-attached to affect it in another way.1814

The phosphoryl group appears to be the most common, so you are going to have something like this.1831

You have the enzyme and then, ATP, ADP, and now, you have enzyme, and attached to it, you have a phosphoryl group attached to it.1836

Now, it has been covalently modified; there is this PO32- that is attached to it.1855

OK, now, serine, tyrosine, threonine and histidine are common amino acids on the regulatory enzyme to which the PO32- attaches, right?1862

It is going to attach to some oxygen or nitrogen.1900

That is what is going on here; serine, tyrosine, threonine and histidine, they tend to be 4 very, very common amino acids that you find on an enzyme to which the PO32- is attached.1905

OK, now, enzymes which actually attach the PO32- are called protein kinases or kinases- again, pronunciation, irrelevant.1920

When we talk about a kinase, we are talking about an enzyme whose purpose is to attach phosphoryl groups to some other enzyme or regulatory enzyme.1950

The protein kinase is not a regulatory enzyme; its function is to attach a phosphoryl to the regulatory enzyme.1961

Now, enzymes which dephosphorylate or de-attach, the enzymes which de-attach the PO32- - excuse me - are called phosphatases.1968

I will write protein phosphatase.1998

A kinase attaches phosphoryl group.2005

A phosphatase de-attaches, removes phosphoryl group.2010

OK, and then a final word: addition or removal of this PO32-, it can affect the regulatory enzyme in an infinite number of ways.2012

I will just write many ways; there is not only 1 way that it affects it, so lots of things can happen.2049

Let’s go ahead and do an example of this.2054

An example would be the enzyme, the regulatory enzyme glycogen phosphorylase.2058

OK, the reaction that this particular enzyme catalyzes is the following.2081

We have multiple glucose units.2087

I will just put glucosen, which is actually glycogen.2092

What it does is it adds an inorganic phosphate.2097

It breaks off one of those glucoses, and it adds a phosphate to it.2102

So, what you end up getting is a glycogen unit, which is missing 1 glucose unit, plus you get glucose 1-phosphate- that is it.2106

Glycogen is, it is just a bunch of glucose units, and what this glycogen phosphorylates does is it pulls off one of those glucose units and attaches a PI to it.2124

This enzyme catalyzes this reaction.2137

Now, what we have is the following.2142

Let's go ahead...yes, it is OK; I can draw it over here.2148

OK, we have a serine, and we have a serine.2153

This glycogen phosphorylates something like this, 2 units, and at each unit, there is a serine residue.2160

Serine has an OH group; serine has an OH group, and what happens is the following.2168

Let's write serine O, PO32-.2180

So, kinase activity, the protein kinase that acts on this particular enzyme, what it does is it attaches phosphoryl groups to both serine residues.2191

Now, you have a different form of this glycogen phosphorylase.2202

Now, the phosphatase, as we said, removes these PO3 groups.2208

This particular version of it is called glycogen phosphorylase a.2214

It is more active.2224

By phosphorylating this, we have actually, positively modulated it.2228

We have actually made the enzyme more active; we have increased the rate at which glucose units are being taken off this glycogen molecule.2234

That is phosphorylase a.2244

Without the phosphoryl groups, you have phosphorylase b.2246

This is less active.2255

It is just a question of perspective; it is not a question of "it starts here and it becomes this" or "it starts here and it becomes this".2259

There is 2 forms of it; it just depends on what you want to take as your starting point.2266

If you want to take this as your starting point, it is becoming phosphorylated.2270

If you want to take this as your starting point, it is becoming dephosphorylated.2274

A kinase phosphorylates; A phosphatase dephosphorylates.2278

One is less active; one is more active.2282

Again, this idea of less and more, these are relative terms.2286

You have to choose one as your starting point and decide which is less or more.2290

If you choose this as your starting point, this is more active; if you choose this as your starting point, this is less active.2294

That is what is important; it is not as if there is 1 degree of activity, and then, everything else is measured from there.2300

It is relative; it does not matter which one you are starting off with.2308

OK, that is an example of a covalent modification.2314

Again, you want to keep a completely open mind with respect to any of this.2336

Anything can happen; it is not just 1 side that it phosphorylates.2343

It could be 2 sites; it could be 5 sites, 10 sites, 30 sites.2347

That is what gives it the kind of control that enzymes need.2353

Perhaps, the phosphorylation of 1 or 2 sites changes it a little bit but not quite enough.2357

It actually induces the phosphorylation of, maybe, 5 other sites.2363

Now, the enzyme is exactly at the degree of control where it needs for that particular set of circumstances at that given moment in that context.2367

That is what we are talking about; phosphorylation of a regulatory enzyme can take place at 1 site, multiple sites or very, very many sites- very many.2377

OK, and often, 1 site must be phosphorylated before another site can actually be phosphorylated.2399

That "can" is the most important word.2425

If a particular enzyme requires, let say, site 5 to be phosphorylated, well, in order for site 5 to be phosphorylated, first, sites, 1, 2, 3 have to be phosphorylated.2429

Let’s just keep 4 out of it for right now.2442

The idea is, not only does it allow it for really, really, fine tuning of the type of control, but it actually controls the degree to which accidental regulation.2446

If it just randomly attaches to no. 5, and all of a sudden, it changes the activity of that enzyme, maybe that is not what is required at that particular moment.2456

This allows, sort of, a safety valve.2465

It has to go ahead and phosphorylate 1, 2 and 3 before 5 is phosphorylated, and then, when 5 is phosphorylated - boom - now, the enzyme can go ahead and regulate the activity the way it is supposed to.2469

It allows not only regulatory control.2481

It allows for the elimination of random regulatory control, things that should not happen- very, very important.2485

OK, now, let’s go ahead and talk about proteolytic cleavage, and then, we will close it off that way.2496

Let me see; I think I will go ahead and go to the next page here, and let me go ahead and do this in red proteolytic cleavage.2504

OK, now, some regulatory enzymes, they demonstrate regulation by becoming active only when 1 or more small peptide fragments are removed from the inactive enzyme.2519

OK, the inactive form of an enzyme, the inactive precursor - let’s call it that - is called zymogen, in other words, something that is going to generate an enzyme- zymogen.2580

OK, now, the proteases, protease is an enzyme that cuts proteins at specific points.2608

The proteases chymotrypsin and trypsin are 2 good examples.2621

The zymogens chymotrypsin and trypsin are active enzymes.2642

They are activated by the removal of certain pieces of the zymogens that give birth to the chymotrypsin and trypsin.2650

Well, the zymogens are chymotrypsinogen and trypsinogen- that is it.2657

We just add the GEN to the end; let’s see if we can write this out- chymotrypsinogen and trypsinogen.2664

Let’s go ahead and draw these out just to show you.2680

In the case of chymotrypsinogen - let’s go ahead and just draw this out here, something like that - we have the terminal amino end.2685

We have the terminal carboxyl end; it has 245 amino acid residues through a series of steps.2703

We end up with 3 fragments; this is 1 long peptide chain of 245 amino acids.2714

We cut some pieces out of it, so what we end up with is the following.2722

We end up with some Ps that includes 1 to 13.2726

The amino acids 14 and 15 are removed, and we end up with 16-146, and 147 and 148, those amino acids are cut out.2734

Those are removed, so we end up with 149 to 245.2749

Now, these 3 pieces, they are going to be attached by disulfide bridges, and those disulfide bridges, when they come together or when the protein actually folds, that is when you have your chymotrypsin.2759

Your chymotrypsinogen is just a single long peptide chain.2773

The enzyme itself has had 2 pieces cut out and the connections.2779

Let me go ahead and just actually put in the disulfide bridges.2783

Let's go here - OK - and then, we will go...let’s see.2793

Let’s do 1 here S, S, and then, there is another S, S; and then, we have that one right there S, S.2800

This is your active chymotrypsin from the chymotrypsinogen- that is it.2816

That is proteolytic cleavage activation of an enzyme.2824

Let’s just do one more; we might as well do trypsin and trypsinogen while we are here.2828

Let’s see, we have trypsinogen.2833

The zymogen is some single peptide chain, 1-245, and what ends up leaving is a val, 4 asps and a lys; and what you end up getting is 7-245.2840

The first 6 amino acids are just cut off, and what you end up with now, is your active trypsin.2870

This is the one that is active; this trypsinogen, it is inactive.2878

OK, now, there are - excuse me - many enzymes that use more than one of these mechanisms, more than one regulatory process.2885

That is fine; I will call it a process instead of a mechanism.2912

There are many enzymes that use more than 1 regulatory process.2916

I think we have mentioned it before; an enzyme does not have to choose between allosteric regulation, covalent modification.2920

It can be one of them; it can be all of them.2927

All of these things allow for a very, very, very fine tuning ability for regulatory control.2931

An example of this would be bacterial glutamine synthase.2940

It uses multiple allostery.2954

In other words, it has more than 1 allosteric sites.2962

It also uses covalent modification and something that we did not actually talk about in detail.2967

It has associated regulatory proteins.2980

You know what, I will write it this way; I will call it regulatory protein association.2990

And again, there are these things called regulatory proteins.3004

Their only task is to interact with the regulatory enzyme in order to help it control its catalytic activity.3008

OK, it is a separate protein whose job is to function as a regulator by interacting with it- yes, that is it.3016

OK, the big question is, why the complexity or regulatory activity?3028

The answer is very, very obvious.3036

Very careful control- that is what you want.3040

And again, it is the difference between very, very broad strokes kind of action, very, very fine strokes action.3046

The control needs to be very carefully done.3055

That is why you have this degree of complexity- absolutely fantastic, absolutely beautiful.3059

One of the most beautiful areas of biochemistry is regulatory enzyme activity and absolutely a fertile, fertile area of research for any of you that are considering what am I interested in, what would I like to do.3064

There is so much that we just do not know.3077

Thank you for joining us here at Educator.com; we will see you next time, bye-bye.3081

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