Home » Chemistry » Biochemistry » Protein Function I: Ligand Binding & Myoglobin

Raffi Hovasapian

Raffi Hovasapian

Protein Function I: Ligand Binding & Myoglobin

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Table of Contents

Section 1: Preliminaries on Aqueous Chemistry
Aqueous Solutions & Concentration

39m 57s

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

38m 53s

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

29m 1s

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

39m 11s

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

41m 33s

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

44m 19s

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

18m 45s

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

38m 19s

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

27m 14s

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

48m 28s

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

45m 18s

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

42m 47s

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

1h 2m 33s

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

49m 12s

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

54m 31s

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

50m 52s

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

51m 36s

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

1h 3m 36s

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

1h 7m 16s

Intro
0:00
Protein Function III: More on Hemoglobin
0:11
Two Models for Cooperative Binding: MWC & Sequential Model
0:12
MWC Model
1:31
Hemoglobin Subunits
3:32
Sequential Model
8:00
Hemoglobin Transports H⁺ & CO₂
17:23
Binding Sites of H⁺ and CO₂
19:36
CO₂ is Converted to Bicarbonate
23:28
Production of H⁺ & CO₂ in Tissues
27:28
H⁺ & CO₂ Binding are Inversely Related to O₂ Binding
28:31
The H⁺ Bohr Effect: His¹⁴⁶ Residue on the β Subunits
33:31
Heterotropic Allosteric Regulation of O₂ Binding by 2,3-Biphosphoglycerate (2,3 BPG)
39:53
Binding Curve for 2,3 BPG
56:21
Section 5: Enzymes
Enzymes I

41m 38s

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

44m 2s

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

56m 40s

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

20m 37s

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

51m 37s

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

51m 23s

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

54m 49s

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

1h 17m 46s

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

37m 6s

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

43m 32s

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

39m 25s

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

44m 15s

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

44m 23s

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

40m 22s

Intro
0:00
Example 1
1:09
Example 2
2:34
Example 3
5:12
Example 4
16:19
Question
16:20
Solution
17:25
Example 5
24:18
Question
24:19
Structure of 2,3-Di-O-Methylglucose
26:47
Part A
28:11
Part B
33:46
Section 7: Lipids
Fatty Acids & Triacylglycerols

54m 55s

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

38m 51s

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

38m 20s

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

48m 36s

Intro
0:00
The Biologically Active Lipids
0:44
Phosphatidyl Inositol Structure
0:45
Phosphatidyl Inositol Reaction
3:24
Image Example
12:49
Eicosanoids
14:12
Arachidonic Acid & Membrane Lipid Containing Arachidonic Acid
18:41
Three Classes of Eicosanoids
20:42
Overall Structures
21:38
Prostagladins
22:56
Thromboxane
27:19
Leukotrienes
30:19
More On The Biologically Active Lipids
33:34
Steroid Hormones
33:35
Fat Soluble Vitamins
38:25
Vitamin D₃
40:40
Vitamin A
43:17
Vitamin E
45:12
Vitamin K
47:17
Section 8: Energy & Biological Systems (Bioenergetics)
Thermodynamics, Free Energy & Equilibrium

45m 51s

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

37m 6s

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

44m 32s

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

30m 8s

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

49m 46s

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

56m 34s

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

42m 12s

Intro
0:00
Example 1: Calculate the ∆G°' For The Following Reaction
1:04
Example 1: Question
1:05
Example 1: Solution
2:20
Example 2: Calculate the Keq For the Following
4:20
Example 2: Question
4:21
Example 2: Solution
5:54
Example 3: Calculate the ∆G°' For The Hydrolysis of ATP At 25°C
8:52
Example 3: Question
8:53
Example 3: Solution
10:30
Example 3: Alternate Procedure
13:48
Example 4: Problems For Bioenergetics
16:46
Example 4: Questions
16:47
Example 4: Part A Solution
21:19
Example 4: Part B Solution
23:26
Example 4: Part C Solution
26:12
Example 5: Problems For Bioenergetics
29:27
Example 5: Questions
29:35
Example 5: Solution - Part 1
32:16
Example 5: Solution - Part 2
34:39
Section 9: Glycolysis and Gluconeogenesis
Overview of Glycolysis I

43m 32s

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

1h 1m 47s

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

59m 17s

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

39m 47s

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

41m 34s

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

34m 18s

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

42m 52s

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

36m 10s

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

49m 20s

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

44m 11s

Intro
0:00
Citric Acid Cycle Reactions & Mechanism
0:21
Reaction 5: Succinyl-CoA to Succinate
0:24
Reaction 5: Reaction Sequence
2:35
Reaction 6: Oxidation of Succinate to Fumarate
8:28
Reaction 7: Fumarate to Malate
10:17
Reaction 8: Oxidation of L-Malate to Oxaloacetate
14:15
More On The Citric Acid Cycle
17:17
Energy from Oxidation
17:18
How Can We Transfer This NADH Into the Mitochondria
27:10
Citric Cycle is Amphibolic - Works In Both Anabolic & Catabolic Pathways
32:06
Biosynthetic Processes
34:29
Anaplerotic Reactions Overview
37:26
Anaplerotic: Reaction 1
41:42
Section 11: Catabolism of Fatty Acids
Fatty Acid Catabolism I

48m 11s

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

45m 58s

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

33m 18s

Intro
0:00
Fatty Acid Catabolism
0:43
Oxidation of Fatty Acids With an Odd Number of Carbons
0:44
β-oxidation in the Mitochondrion & Two Other Pathways
9:08
ω-oxidation
10:37
α-oxidation
17:22
Ketone Bodies
19:08
Two Fates of Acetyl-CoA Formed by β-Oxidation Overview
19:09
Ketone Bodies: Acetone
20:42
Ketone Bodies: Acetoacetate
20:57
Ketone Bodies: D-β-hydroxybutyrate
21:25
Two Fates of Acetyl-CoA Formed by β-Oxidation: Part 1
22:05
Two Fates of Acetyl-CoA Formed by β-Oxidation: Part 2
26:59
Two Fates of Acetyl-CoA Formed by β-Oxidation: Part 3
30:52
Section 12: Catabolism of Amino Acids and the Urea Cycle
Overview & The Aminotransferase Reaction

40m 59s

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

39m 18s

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

36m 21s

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

47m 58s

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

41m 11s

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

36m 27s

Intro
0:00
Complex III
0:19
Complex III Overview
0:20
Complex III: Step 1
1:56
Complex III: Step 2
6:14
Complex IV
8:42
Complex IV: Cytochrome Oxidase
8:43
Oxidative Phosphorylation, cont'd
17:18
Oxidative Phosphorylation: Summary
17:19
Equation 1
19:13
How Exergonic is the Reaction?
21:03
Potential Energy Represented by Transported H⁺
27:24
Free Energy Change for the Production of an Electrochemical Gradient Via an Ion Pump
28:48
Free Energy Change in Active Mitochondria
32:02
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Lecture Comments (7)

1 answer

Last reply by: Professor Hovasapian
Mon Feb 8, 2016 12:42 AM

Post by Widad Hassan on February 7, 2016

hello sir,
i have a question concerning the oxidation ofthe heme of myoglobin:
i read somewhere that the oxidation of fe(II) is based on acid catalysis, but how does this work, since it's only possible during desoxyMb?

thank you :)

1 answer

Last reply by: Professor Hovasapian
Fri Jan 24, 2014 3:49 AM

Post by Udoka Ofoedu on January 23, 2014

Hey sir ,
  Please where are the lectures for post-translational modifications in proteins . Thank you !

2 answers

Last reply by: Shannen Brown
Tue Jun 25, 2013 6:37 PM

Post by Shannen Brown on June 25, 2013

Hi there!

I was wondering if any of the lectures had protein folding?
I had a quick look but just thought I'd double check in case I missed it.

Thanks :)

Protein Function I: Ligand Binding & Myoglobin

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
  • Protein Function I: Ligand Binding & Myoglobin 0:30
    • Ligand
    • Binding Site
    • Proteins are Not Static or Fixed
    • Multi-Subunit Proteins
    • O₂ as a Ligand
    • Myoglobin, Protoporphyrin IX, Fe ²⁺, and O₂
    • Protoporphyrin Illustration
    • Myoglobin With a Heme Group Illustration
    • Fe²⁺ has 6 Coordination Sites & Binds O₂
    • Heme
    • Myoglobin Overview
    • Myoglobin and O₂ Interaction
    • Keq or Ka & The Measure of Protein's Affinity for Its Ligand
    • Defining α: Fraction of Binding Sites Occupied
    • Graph: α vs. [L]
    • For The Special Case of α = 0.5
    • Association Constant & Dissociation Constant
    • α & Kd
    • Myoglobin's Binding of O₂

Transcription: Protein Function I: Ligand Binding & Myoglobin

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

Today, we are going to start our discussion of protein function.0004

We have already taken a look at amino acids and primary structure.0008

We have taken a look at a secondary structure, tertiary structure and quaternary structure.0013

Now, we are going to talk about protein function.0018

In particular, we are going to be talking about ligand binding, and we are going to be spending a fair amount of time talking about this protein called myoglobin.0022

OK, let’s see what we can do.0030

Proteins, they interact with other molecules.0034

That is our beginning.0038

You know what, let me...I think I want to go to a different color to start off with.0043

Proteins interact with other molecules.0054

Let’s define something called a ligand or a ligand.0066

It depends; a lot of people pronounce it ligand.0071

I prefer to pronounce it ligand; any molecule - excuse me - that binds - here is the key word - reversibly to a protein, now, this can be any molecule even another protein- that is it.0074

A ligand is any molecule that binds reversibly to a protein.0122

Now, the binding site is exactly what you think it is.0127

The binding site, it is a place on the protein where the ligands bind.0132

OK, now, a protein may bind several ligands at several sites.0152

Again, we are not putting any restrictions on this.0173

We can have 1 binding site, 2 binding sites, 37 binding sites, whatever is necessary for that protein to function and do what it does.0177

Protein may bind several ligands at several binding sites.0184

OK, and binding is specific for that ligand.0192

It is not just any molecule that comes around, and the protein will bind to it.0197

It is very, very specific; binding is specific for that ligand.0202

OK, now, proteins are not static or fixed.0216

They are very, very, very flexible.0233

They are very flexible.0240

Well, I am not going to repeat and say that they definitely move; they definitely move.0247

I mean, we know that; they are very, very flexible and very, very accommodating to different things.0251

OK, now, when a protein changes confirmation to accommodate the binding of a ligand, this is called induced fit.0257

You have often heard this term induced fit used to describe an enzyme from your other bio courses when you talked about enzymes.0298

An enzyme, it is induced fit in order for it to bind its particular substrate.0307

Well it is the same thing; I mean, an enzyme is just a protein molecule.0312

The only difference between an enzyme and a substrate, we do not call a substrate a ligand because the enzyme actually does something to the substrate and changes it.0315

It changes molecular form and spits out another different molecule all together, whereas for a protein that binds the ligand, it does not do anything to the ligand.0326

That is the difference, but essentially it is the same thing.0335

A protein is a protein that behaves a certain way; OK, let's see.0339

Now, in multi-subunit proteins, - excuse me - changes in the conformation of 1 subunit will cause changes in the conformations of 1 or more of the other subunits.0346

OK, now, as we said before, enzymes are a special class of ligand binding protein.0405

Again, not all proteins bind ligands; the proteins that do, they are called ligand binding proteins.0414

Enzymes are a special class of them; in so far as the ligand that they bind, they actually do something to it and then release it, whereas, for a normal ligand binding protein, it interacts with that ligand and then the ligand just leaves.0420

There is no molecular change that is affected on that particular ligand.0436

OK, let’s talk about molecular oxygen as a ligand.0441

Oxygen binding proteins, in our case, we are going to be concerned with myoglobin.0451

OK, that is OK; I will go ahead and mention hemoglobin because I am going to talk about this generally at first, and then, I will go ahead and stick specifically with myoglobin and talk about hemoglobin in a subsequent lesson.0472

OK, now, tissues need oxygen, but O2 is not very soluble in aqueous solution.0484

It cannot just dissolve in the blood, and then, when it gets to wherever it needs to get to in another part of the body, just do what it does.0511

We have to find a way of actually carrying it from one point of the body to the other, so not very soluble from the lungs to the other parts of the body, not very soluble in aqueous solution.0518

Now, the body had to find a way to deliver O2.0530

Now, proteins that can carry O2 make sense but no amino acid residue, no amino acid side chain is available that actually binds molecular oxygen.0548

There is no way just from a protein structure itself with all of these amino acids, there is no place on that protein where molecular oxygen will just stick to and bind to it.0575

Proteins carrying O2 make sense, but no amino acid side chain binds O2 reversibly.0587

It might bind O2, but it is not just a question of binding it.0606

I need to bind it; I need to transport it to where it needs to go, and then, I need to be able to release it.0611

That is the whole idea; there is no point in just holding on to the O2 if I cannot deliver my pay load, but no side chain binds it reversibly.0615

That is what is important; OK, now, iron - I should say iron(2+), the ferrous, the 2+ oxidation state - it binds O2 reversibly, and in higher organisms like we are, the O2 is carried by a structure called heme, which is a large ring-structured – which you will see a picture in just a minute – molecule, which is a prosthetic group incorporated into various proteins.0625

OK, now, recall what a prosthetic group is some molecular species associated with the protein and which a protein requires in order to function properly, requires for proper functioning.0713

Example, well, you guessed it.0775

Our example is going to be...OK, our protein is going to be our myoglobin.0779

Our prosthetic group, that is going to be our heme.0789

Actually, it is going to be the protoporphyrin.0802

Let me use the Roman designation - IX, and the ligand, itself, is going to be oxygen.0813

The heme is the porphyrin ring system plus the iron.0822

I am sorry, let me go ahead.0833

The prosthetic group, that is going to be our heme, which is going to be protoporphyrin IX plus our iron plus Fe2+ and our ligand - I guess I could have just left it - is O2.0834

Again, heme is the protoporphyrin ring plus the iron.0850

OK, now, let’s go ahead and yes, that is fine.0855

Let's go ahead and take a look at some pictures here.0862

The first picture we have is our ring system, this protoporphyrin IX.0866

We have this ring structure right here; this is the prosthetic group that is actually embedded inside of the protein, in this particular case, myoglobin.0871

Notice here, it does not have the iron attached to it.0880

When it is attached to it, that is when it actually becomes heme.0884

This is our protoporphyrin IX.0887

Now, these groups right here, like that and that, that metal group, that metal group, this alkene, this alkene, these, this ring structure is the basic structure.0896

OK, they have different things attached to it.0910

Different proteins have different porphyrin systems.0916

In the case of myoglobin, it is going to be the protoporphyrin IX.0920

These happen to be the functional groups that are attached to this ring system.0924

It is this ring system right here, - let me do this in red - that is going to be your basic structure and to it, these things actually change so you have different porphyrins.0929

Let's go back to black; now, this is our heme.0942

Heme is the iron and the protoporphyrin 9; As you see, you have this functional group.0946

You have the methyl here; you have this alkene here.0954

You have this alkene here; you have another methyl group, and here is your iron.0960

The iron is actually attached, is coordinated to the nitrogens in 4 places.0966

There are 2 additional sites that are going to be coordinated to the iron.0973

One of them, the oxygen is going to bind to; the other one is what actually attaches this thing to the protein, itself, via histidine residue, which you will see in just a minute.0978

I just wanted you to get an idea of what this look like.0987

This is the heme, protoporphyrin system, heme, spiral ring0990

I do not know about the extent to which your teacher actually wants specifics about the structure of this ring system- very, very important.0994

And again, different porphyrin systems have different metals; it does not have to always be iron.1002

It could be magnesium; it could be copper.1006

It could be zinc; it could be whatever.1009

We have actually created porphyrin ring systems synthetically that have different transition metals altogether.1011

It might be cobalt, who knows.1018

OK, let’s go ahead, and now, let’s take a look at myoglobin with its heme group.1021

Here is the myoglobin molecule; you see this ribbon diagram and the heme.1029

This is the heme right in there.1035

OK, I do not know if you can see it; it is attached to a little histidine.1039

In this particular case, it does not look like there is an oxygen attached anywhere.1044

It is just the heme group and the myoglobin, and then, in this particular case, this is the same thing, a slightly twisted view.1049

This time, it does not have the contour mapping on top of it, just the ribbon diagram, and here, you see the heme.1057

This is the heme group, and in this particular case, you do see the oxygen attached to it.1067

Protein is myoglobin; the heme is the prosthetic group.1075

It is associated with the protein, and the ligand that is reversibly attached, comes and goes.1078

That, in this case, is going to be the oxygen molecule; OK, now, let’s go on.1085

OK, the iron(2+), as we said a second ago, has 6 coordination sites.1095

In other words, there are going to be 6 bonds to the iron(2+) metal- 6 coordination sites.1103

When we talk about things being bonded to transition metals, we talk about them being coordinated to it.1111

It is just the language that inorganic chemistry uses when talking about metalloprotein and things like that.1118

OK, 4 of these sites are to the ring system, as we saw, the nitrogens and the inner part of the ring system.1127

One of them is to a histidine residue on the protein, and one is to O2.1141

Now, iron(2+), it binds O2.1164

Iron(3+) does not bind O2 or should I say binds it very badly.1174

OK, now heme, this prosthetic group, this protoporphyrin IX plus its iron center notice, 2+ and 3+.1185

There is oxidation-reduction happening; heme is associated with proteins involved in redox reactions.1198

OK, let's draw a little picture here.1217

We have our enzyme.1220

Let's go CH2; let’s go C-N, double bond, C-N, double bond C and single bond N.1225

Let’s go ahead and put an H there; put an H there.1240

I hope we have no't forgotten anything.1243

Here is our bond; there is our coordination bond.1246

I will do it in red, and I will go back to blue for our iron.1250

That is the iron center; it is in a 2+ oxidation state.1255

This is a side view looking at the protoporphyrin ring system along its edge- something like that.1263

It looks like that, and it is another coordination bound to oxygen, too.1273

That is what it looks like.1282

This, another representation of it, if you want to slightly turn it, you will end up something that looks like this.1286

Instead of looking at straight edge on, let's turn it just a little bit.1298

We end up with something that looks like this: Fe2+.1302

Let’s go to red; it is going to be bound to OO, and from the back, it is going to be attached to histidine 93, which is attached to the - not the enzyme - protein.1310

This is not an enzyme - that is it - I have just taken this and twisted it a little bit, so you are not looking it on the edge; and, of course, you have other coordination sites.1330

You have the nitrogens there, there, there so 1, 2, 3, 4, 5, 6, 6 coordination sites on the iron on this protoporphyrin IX system, on this heme system.1338

OK, now, that is OK.1350

I can go to the next page now.1358

Lets go back to blue; myoglobin, which is often abbreviated as Mb, is a single polypeptide with 153 amino acid residues- that is it.1362

153 amino acids ends up folding into some globular protein.1392

Inside of that, there is this heme; and to that heme, oxygen binds.1396

OK, now, as we said, myoglobin’s function, it depends on its ability to bind oxygen.1402

Now, let's go back to...I think I will go back to black.1411

We can describe this myoglobin oxygen interaction quantitatively.1419

That is what is nice.1447

OK, let's begin with an equilibrium expression.1451

We have protein plus ligand is going to form a protein ligand complex, protein attached to ligand- that is it.1470

Some protein, you have some ligand, and now, you have the protein and the ligand complex- that is it.1485

That is all that is going on here.1496

Let's go ahead and form the equilibrium constant; the equilibrium constant we know is products divided by reactants so we form Keq is equal to the concentration of PL/P x L.1500

Now, this forward reaction is called the association constant because the P and the L are associating to form the PL.1515

The reverse reaction would be called the dissociation constant because this PL complex is dissociating, breaking up into P and L.1523

OK, now, the forward reaction is called association, and this Keq is often symbolized as Ka or Ka.1531

Please do not confuse this with the acid dissociation constant from general chemistry when we talk about acids and bases.1579

When we talked about protein ligand interactions, when you see Ka, it is the association constant.1587

It is the reaction running in that direction.1593

OK, just be aware that that is often how they represent it.1598

It is probably like that in your books; OK, now, this - let's go back to black - Keq or Ka is a measure of the protein’s affinity for its ligand.1602

Now, of course, it is.1640

A high K value means that this numerator is high, and the denominator is low.1644

Well, if the numerator is high that means that most of the protein is going to be found attached to its ligand in this form, the form of the numerator.1649

Because it has a high affinity for its ligand, so, it wants to be attached to its ligand, which makes PL high, which makes free protein and free ligand low, which gives you a very high Keq.1659

That is what an equilibrium constant is; it is a measure of the extent to which a reaction is forward or back here.1669

It is mostly product or mostly reactant; in the case of an association of protein and ligand, your product is your protein ligand complex.1676

It is a measure of the affinity for the 2.1684

Let's write that down.1689

A high Ka means that PL is high which means a protein is mostly in the PL state.1693

This implies high affinity.1725

OK, let's rearrange this to get...we are just going to move the L concentration over to the left.1731

We end up with PL/P.1745

Notice what this is; this is just a ratio of bound protein to its ligand to unbound protein.1749

This is just a ratio; now, we noticed that it is actually a direct function of ligand concentration.1755

OK, all we have done is rearrange the Keq, move the L over here, to get an expression for bound protein over free protein.1765

This ratio here is equal to Ka/L.1772

OK, alright, let's write that again on this page.1777

Ka x L = PL/P- there we go.1784

Now, under most physio conditions/physiological conditions, the concentration of ligand is a lot higher than available binding sites.1793

As ligand binds, the ligand concentration, of course, decreases, doesn't, right?1832

As more ligand binds, the ligand concentration goes down, but because of the ligand concentrations is so high compared to the available binding sites, any reduction in ligand concentration is going to be unnoticeable, which means that its basically constant.1841

For example, if I had a cup of water and in that cup of water which has billions and billions and billions and trillions and quadrillions of molecules, I have a handful of protein molecules in there.1858

Well, if I take, let's say, the top 1 inch of water off of that, well, it is not really going to change the concentration of water relative to the protein.1870

I mean there is still so much water that even if I take a whole bunch of water, the water concentration relative to the protein concentration is going to be constant.1878

This is actually simplifies the math, I do not have to worry too much about L.1888

I can treat the ligand concentration as essentially constant; even though it does decrease relative to the protein concentration, the decrease is so small that it does not matter.1891

It is as if you do not even notice; it helps with the math.1903

As L binds, L decreases but this decrease is negligible, which means that the concentration of L is virtually constant.1912

This can help us out.1934

OK, in other words, we do not have to keep track of the ligand concentration in this expression.1939

We can just forget about it; it is going to stay constant, right?1943

When you do equilibrium constant, remember, the water concentration is essentially constant.1947

You do not put it in the equilibrium expression because it does not really change.1951

For our practical purposes, since the ligand concentration does not change, you can just ignore it from the expression.1956

It is just part of the constant; it is eaten up by the Ka.1962

That is all we are doing here.1968

Now, we want to define something.1971

Now, define this things called alpha, which is a ratio of the binding sites occupied divided by the total binding sites available.1975

I am sorry, divided by the total binding sites, not the total binding sites available.1994

OK, if I take the binding sites that are occupied divided by the total binding sites, I am getting the fraction of binding sites that are occupied, right, the part over the whole.2000

If I have 10 binding sites available and if I have 5 of those binding sites that are occupied, that means that I have 1/2 of the binding sites occupied.2015

That is all this is; this expression here, alpha is the fraction of bindings sites occupied- fraction.2027

This is equal to, well, PL which is the binding sites occupied divided by PL + P, the binding sites that are occupied plus the binding sites that are not occupied free protein, protein ligand complex.2044

This is that, so alpha is equal PL/PL + P.2064

OK, now, Ka is equal to PL/P x L, which we can rearrange to be Ka x P x L is equal to PL.2069

Alpha is equal to...since PL is equal to this, I will just put PL into here, and into here let’s see what I will get.2093

I get Ka PL/Ka PL + P.2104

Well, the Ps cancel, leaving me with Ka L/Ka L + 1, right?2124

That is my alpha; now, I am going to multiply the top and the bottom by 1/alpha, 1 over the Ka - sorry, excuse me - just to, sort of, simplify and get rid of this Ka thing.2140

When I multiply the top and the bottom by 1/Ka/1/Ka, which I am just multiplying by 1, I basically end up: this and that go away.2160

This and that go away, and what you end up with is the following.2171

You get alpha is equal to the ligand concentration, divided by the ligand concentration + 1/Ka.2175

This is just mathematical manipulation- that is all it is.2184

What we have here is the fraction.2191

We started with the fraction of binding sites occupied.2199

We have rearranged and manipulated it mathematically, so the fraction of binding sites occupied is a hyperbolic function of ligand concentration.2204

Anytime you see an equation of this form, where you have Y = X/X + Z, you are going to get a hyperbola.2221

OK, the fraction of the binding sites, we started with this equation; this was the expression for it.2233

We rearranged the Ka; we substituted and did some mathematical manipulation, alpha, which is this, is now, this L/L + 1/Ka.2237

The fraction is a function of ligand concentration.2246

This is really, really great; OK, now, let’s go ahead.2252

Let's rewrite the equation, so we have it on this page: alpha = ligand concentration/ligand concentration + 1/Ka.2258

Again, this equation describes a hyperbola; now, if we plot alpha, the fraction on the Y axis and ligand concentration on the X axis, we end up something like this.2269

Let me do it over here actually.2284

OK, this is ligand concentration L.2291

This is alpha, the fraction; it is really, really great because you can never have a fraction that is bigger than 1.2295

What you end up with is this; when we try different concentrations of L-alpha, you get this behavior.2303

This is our maximum; in other words, you cannot have more than 100% of the binding sites occupied.2312

You get this.2318

You get this hyperbolic behavior; it is really, really, really great.2322

OK, now, 0.5, I will tell you what this means in just a minute2328

Now, for the special case, actually, before I continue, let's just recall what we did.2341

We have this equation.2350

When we take a particular protein, and we measure, we start with different concentrations of ligand, and then, we measure the alpha, the percentage, of sites that are occupied.2354

We get a whole bunch of data points; we plot those data points, and we see that it actually follows a hyperbolic curve.2370

Now, if we decide to take some random numbers - not random, I mean the special case of 0.5 - it is going to be something like this.2378

For the special case of the fraction of alpha equalling 0.5, I get the following.2386

We get, I put 0.5 in for alpha 0.5 = lambda - not lambda - ligand concentration/ligand concentration + 1/Ka.2394

Now, I am going to solve for the ligand concentration.2411

That is what I want; It is going to imply the following.2416

I have got 0.5 x ligand concentration + 0.5/Ka - this is just algebra, I multiplied both sides by the denominator - equals lambda.2420

I end up with 0.5/Ka = 0.5 - why do I keep saying lambda - ligand concentration.2436

The 0.5s cancel, and what I end up is the following: 1/Ka = ligand concentration.2450

At the point where half of the binding sites are occupied, it matches.2458

It happens to be - let me go back here - this is 1/Ka.2467

This gives me a way of actually finding the equilibrium constant Ka.2473

OK, 1/Ka is the concentration.2480

It happens to be units of concentration, the concentration of ligand at which 1/2 of the binding sites are occupied.2488

This is really great; I get great concentration data.2510

I run the experiment; I try a bunch of different ligand concentrations.2515

I get a bunch of different fractions; I make the graph.2519

I go half way; I go over to the graph.2520

I go down, and this number that I hit, that is equal to 1/Ka.2523

I do a little algebra, and I actually solve for the Ka.2527

This is a practical method of actually finding the Ka value; this is fantastic.2531

OK, there you go; there is that.2535

Now, this hyperbolic behavior...well, actually you know what, I do not necessarily need to write this down.2539

Let me just go ahead and redraw the graph here quickly, sort of, a qualitative version of this graph.2555

This is 1; We are going to end up something like this.2561

And again, this is going to be our 1/Ka value.2565

This hyperbolic behavior makes sense.2569

As you start to add more and more and more and more ligand, you are going to occupy more and more and more of your binding sites that are available for binding, but at some point, you are going to add so much ligand that your concentration of ligand is going to exceed the available binding sites.2573

What is going to end up happening is you are going to reach a saturation point.2589

At some point, every single binding site is occupied; you can add as much ligand as you can.2593

You are not going to get any higher fraction than 100%.2598

That is, sort of, a theoretical maximum; you are probably going to be somewhere at...for totally, totally, really, really high concentrations of ligand, you might be up at 97, 98% saturation.2604

There is always going to be some free protein that is not binding anything, but it makes sense.2613

As you add more ligand, you have already occupied all of the binding sites, so the rate at which it is actually going to bind is going to slow down.2617

That makes sense; this is typical, typical behavior for ligand protein interaction.2628

OK, now, this Ka, as we said, is the association constant.2635

Well, you remember what 1/Ka is, right?2649

It is the equilibrium constant for the reaction in the reverse direction.2653

1/Ka is the dissociation constant.2658

Remember, we had protein plus ligand going to protein ligand.2668

That is product/reactant; well, if I take the dissociation constant, protein ligand dissociating into - let's just write it out as a single arrow - free protein and ligand.2675

Now, this is the product, and this is the reactant; it is just the reciprocal of this.2687

OK, 1/Ka is the dissociation constant.2692

Let’s call it Kd; let’s call it Kd.2696

That is going to equal protein concentration, ligand concentration over protein ligand concentration.2703

That is all this says, so let’s rewrite.2713

Alpha is equal to L/L + Kd.2718

At least, this way, we do not have to deal with this 1/Ka thing, and plus, I think it makes a little bit more sense.2724

Now, again, a high affinity means that you are going to find the protein and ligand bound together in the complex form because the protein wants its ligand.2729

It is going to be mostly this; well, it is mostly this.2738

That means there is very little of this, very little of this; when this is high and this is low, this ratio is low.2742

The lower the Kd, the higher the affinity the protein has for its ligand; let me say that again.2756

The lower the Kd, the higher the affinity the protein has for its ligand; it is just a simple equilibrium, mathematical justification for it.2758

That is all that is going on here.2767

OK, A equals that, and Kd has units of molarity; but we know that already.2771

1/Ka is units of molarity because on this axis, it is ligand concentration in moles per liter or millimoles per liter or micromoles per liter.2781

It does not really matter, so 1/Ka equals the Kd.2793

Alright, now, Kd - excuse me - is the ligand concentration, which causes 1/2 of the binding sites to be occupied.2801

Let's see if we can write a little bit better here.2838

OK, the higher the affinity of a protein for its ligand, the lower the Kd.2845

Well, we just said the lower the Kd, the higher the affinity, so either direction is fine.2854

That means that you are going to have behavior; graphically, it is going to be like this.2859

The higher the affinity, it is going to end up being like this.2863

It is going to be more well-defined hyperbola because now, this Kd is going to end up shifting that way because now, a higher affinity protein will demonstrate really characteristic hyperbolic behavior.2869

A low affinity protein is going to end up being like this, something like that- that is it.2887

It is just a measure of affinity; that is all its graph really does for you.2894

OK, now, again, myoglobins binding O2, it follows this pattern, which is...we handle it generally, but now, but the problem is that O2 is a gas.2898

We do not often speak about moles per liter, when it comes to gas.2930

We often talk about partial pressure of the gas; what we are doing is we are measuring the partial pressure of the gas above the aqueous solution because that is going to be proportional to the amount of gas that has actually dissolved the concentration.2934

You remember from PV = nRT; pressure and concentration are actually the same thing.2947

It is like the same 2 sides of a coin, you have the heads, and you have tails.2953

You remember PV = nRT; well, if I rewrite this as P = nRT/V, now, if I just take the n/V part, which equals n/V x RT, well, what is n/V?2959

n is moles, and that is volume; well, moles per volume, that is molarity, so molarity RT, and this RT is just a constant.2974

Concentration and pressure or let me do it this way pressure and concentration are directly proportional.2984

As it turns out, concentration in moles per liter and pressure in atmospheres, or whatever unit you happen to be using for pressure, are just different ways of representing concentration.2994

We can do that with a gas; it is easier to measure pressure.3004

The expression for alpha becomes, well, the concentration of O2 over the concentration of O2 plus its Kd.3008

Well, for gasses, experimentally, again, we tend to work with partial pressures.3019

The equation becomes alpha equals the partial pressure of O2 over the partial pressure of O2 + Kd- that is it.3024

You will see it sometimes like this.3035

If we define Kd as the partial pressure of O2, 0.5 this is, sort of, a symbol, it is also symbolized as this way, p50, you will see it as alpha = PO2/PO2 + p50.3041

I do not like this symbolism myself personally; you will see it in your books.3065

I like this; this actually tells me something or this.3069

This is fine, too, if we are going to deal with partial pressures instead of molarities; partial pressure, I like to see the Kd in the expression.3073

This p50, it has always confused me; it always will confuse me.3080

Again, whichever you like is fine; I personally prefer that one.3084

OK, thank you so much for joining us here at Educator.com; we will see you next time for a further discussion of protein function, bye-bye.3090

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