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Raffi Hovasapian

Raffi Hovasapian

Protein Function II: Hemoglobin

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 (6)

1 answer

Last reply by: Professor Hovasapian
Sat Oct 10, 2015 8:00 PM

Post by Kenny Patel on October 10, 2015

At 17:13 did you mean to say myoglobin or am I not understanding correctly?

1 answer

Last reply by: Professor Hovasapian
Sun Jun 29, 2014 6:01 PM

Post by Sitora Muhamedova on June 29, 2014

I cannot describe how much grateful I am for your wonderful lectures!

1 answer

Last reply by: Professor Hovasapian
Sun Sep 15, 2013 6:29 AM

Post by Vinit Shanbhag on September 14, 2013

Hey Raffi,
What is the difference between alpha and (alpha/1-alpha). Alpha is the fractional occupancy as you said in the last lecture, but what does the y axis in the hill plot actually mean??

Protein Function II: Hemoglobin

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 II: Hemoglobin 0:14
    • Hemoglobin Overview
    • Hemoglobin & Its 4 Subunits
    • α and β Interactions
    • Two Major Conformations of Hb: T State (Tense) & R State (Relaxed)
    • Transition From The T State to R State
    • Binding of Hemoglobins & O₂
    • Binding Curve
    • Hemoglobin in the Lung
    • Signoid Curve
    • Cooperative Binding
    • Hemoglobin is an Allosteric Protein
    • Homotropic Allostery
    • Describing Cooperative Binding Quantitatively
    • Deriving The Hill Equation
    • Graphing the Hill Equation
    • The Slope and Degree of Cooperation
    • The Hill Coefficient
    • Hill Coefficient = 1
    • Hill Coefficient < 1
    • Where the Graph Hits the x-axis
    • Graph for Hemoglobin

Transcription: Protein Function II: Hemoglobin

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

In our last lesson, we talked about myoglobin.0004

In this lesson, we are going to start talking about hemoglobin, so let's just jump right on in.0008

OK, now, whereas myoglobin is involved in the diffusion of the oxygen/O2 in muscle tissue, hemoglobin, that is the protein which actually transports the oxygen/O2 in the blood.0015

Excuse me.0070

Now, hemoglobin has 4 subunits; hemoglobin, which is abbreviated Hb, it has 4 subunits.0082

It is not like myoglobin; myoglobin was just a single subunit protein that has a binding site for 1 molecule of oxygen.0092

It has 4 subunits, and each of these subunits has a heme group, with a heme group.0101

We have - excuse me - 4 sites to bind O2 per protein molecule.0115

Now, the interactions of the subunits, they cause conformational changes that affect hemoglobins' affinity for O2.0131

OK, the conformational changes among these subunits, as 102 binds, there is going to be a conformational change, and that conformational change is going to affect the extent to which another O2 will bind or release depending on the physiological conditions at hand.0177

You remember, we need to actually bind the O2 tightly.0196

We need to take it to another part of the body, to the tissues, and we need to be able to release it.0201

We need that flexibility, that great degree of flexibility, in fact, because the oxygen that is coming...the lungs is going to be a particular concentration of oxygen, but that is not the same concentration of oxygen that is in the tissues.0207

We do not want some molecule that just binds O2 and hangs on to it.0223

It needs to be able to deliver it, and we do not need it to...we need...well, or if we have a molecule that does not bind it very well, well, if it does not bind it very well, then, it is not going to take up the oxygen that is in the lungs.0227

We need that high degree of flexibility based on different concentrations of O2.0242

And again, since it is a gas, we are going to be talking about different partial pressures of O2.0247

OK, now, hemoglobin has alpha and beta subunits.0252

It has 2 alpha subunits, and it has 2 beta subunits, alpha and beta subunits, 2 of each.0263

We have an alpha-1, beta-1 and an alpha-2, beta-2.0275

The alpha-1, beta-1 are...they interact rather tightly, and the alpha-2, beta-2, they interact tightly.0280

Now, there is interaction between the alpha-1, beta-2 and the alpha-2, beta-1, but it is a weaker interaction.0288

The alpha, it has 141 amino acid residues, and the beta has 146 amino acid residues.0298

OK, let's go ahead and take a look at an image of hemoglobin here.0313

We have our alpha-1, beta-1.0319

We have our alpha-2 and our beta-2.0325

Here, you can see, you have your alpha-1, beta-1, that interaction.0331

That forms as 1 subunit, 2; this is the third.0337

This is the fourth; now, you can also make out in each subunit, it has its own heme group.0341

Here is the heme group for this one, and this one is a little hidden.0346

You can see the heme group right here; let me go ahead and...it is right there, and you have the heme group right there for that one, and it is right there for this one, and here it is for that.0350

Now, I do not know if you can actually see the oxygen because it does not look like oxygen is bound, or maybe it is.0366

It is hard to tell, but that is it; this is what it looks like, so alpha-1, beta-1, alpha-2, beta-2- that is it, nice and straightforward multi-subunit protein.0372

You have this gap in between, which is going to become very, very important in just a little bit.0383

OK, now, our alpha-1, beta-1 and alpha-2, beta-2 - OK - their respective interactions are quite strong.0390

You have about 30 amino acids between alpha-1, beta-1, alpha-2 and beta-2 that are interacting with each other, so 30 amino acids interacting.0412

That is pretty strong interaction; now, as far as the alpha-1, beta-2 and the alpha-2, beta-1 down here, alpha-1, beta-2, alpha-2, beta-1, the interactions in that region there, they are less strong.0423

I will put "the interactions are less strong", somewhere in the neighborhood of about 18 or 19 amino acid residues that actually end up interacting.0447

When we use chemical agents to actually separate these subunits, as it turns out, they break up not into 4 separate subunits.0465

We can do that if we want to, but from mild treatment, what ends up happening is the alpha-1 and beta-1 actually stay together, and the alpha-2 and beta-2 stay together.0473

The interactions are quite strong between those subunits.0480

Alright, hemoglobin - let's see - it has 2 major conformations.0485

One is called the T-state, and T stands for tense.0505

This is where no oxygen has bound to it, so this is deoxyhemoglobin.0513

This is deoxyhemoglobin, and then, there is something called an R-state.0519

In this case, R stands for relaxed, and this is deoxyhemoglobin.0523

When oxygen is actually bound to it, the more oxygen that is bound to it, the hemoglobin is in more of an R-state.0532

So, when we say it has 2 major conformations, we are not saying it goes from T to R, boom.0540

There is a transition; you have 4 oxygen molecules that are binding to the hemoglobin.0547

As one of them binds, there is some conformational change, and it starts to move away from the tense state; and it starts to make the transition over to the R-state.0553

Now, it makes the second molecule of oxygen a little easier to bind.0561

That second oxygen causes more conformational changes, shifts it more towards the relaxed state, which makes it more easy to bind the third oxygen.0566

By the time the fourth oxygen molecule binds, it is completely in the relaxed state.0575

The relaxed state, the R-state, has a high affinity for oxygen.0579

The T-state has a low affinity for oxygen.0584

Now, these terms high and low, these are relative terms.0588

We are not saying that this T-state hemoglobin has no oxygen attached to it.0592

That is not it at all; in fact, it is about 60% saturated with oxygen.0596

The difference is the R-state is about 96% saturated with oxygen.0600

It is not 0, 100; it is not all or nothing.0606

It is just relative degrees of saturation.0610

The R-state- very, very saturated with oxygen; that is the arterial blood.0614

That is the red blood that has all that wonderful oxygen in it.0618

The T-state, about 60% saturation for the hemoglobin, that tends to be more of a bluish-purple.0622

That is the venous blood; that is the blood that is actually coming back from the tissues because it has delivered its oxygen.0628

Now, it is depleted oxygen, so the color actually changes.0635

OK, now, the binding of O2...OK, as we just said, the binding of O2 to a subunit of T-state hemoglobin causes a conformational change toward the R-state.0640

And again, it is a transition - it is not just, boom, it goes to the R-state - which has a greater affinity for O2.0678

It begins to bind more O2, and the more O2 it binds, the more it wants to bind.0704

That is this, sort of, domino effect, if you will, of this thing called cooperative binding, which we will talk a little bit about a little bit later.0714

OK, now, the transition from the T-state to the R-state, the alpha-1, b-1 and the alpha-2, b-2, what happens is they slide past each other.0724

I mean, the biggest change that we can see on this protein, they slide past each other, and narrow the gap between the beta-1 and beta-2.0745

OK, let's see if we can take a look and see what that, kind of, looks like here.0778

Here, again, we have our alpha-1 and our beta-1, and then, we have our alpha-2 and our beta-2.0784

What is going to actually happen is this alpha-1, b-1 and this alpha-2, b-2, are actually going to slide past each other, and they are going to narrow this gap right here.0796

That gap is going to close in on itself, kind of, like this.0808

So, if I have alpha-1 and beta-1 and alpha-2 and beta-2, what is going to end up happening, they slide past each other.0813

The betas actually start to come together and narrow this gap.0825

This is beta; the thumb is beta.0828

They will slide past each other, and beta gap will actually close; and that is going to be the transition from the T-state to the R-state.0830

The more that gap closes, the more of an affinity is has for the oxygen until by the time you get to the third bound oxygen, it is almost completely in the R-state.0839

OK, now, hemoglobin/Hb must bind O2 tightly in the lungs.0851

Alright, that is where the concentration of O2 is high, and the partial pressure is about 13 kPa in the lungs.0869

Under high concentration, it needs to bind the oxygen very, very tightly in the lungs because from there, it is going to take the blood to the tissues, then, bind it loosely, in other words, release the oxygen that it has bound, release it.0880

When we say "loose binding", we are talking about releasing the O2, not just that it does not bind the O2.0909

We are talking about actually releasing the O2, release it at the tissues.0916

Now, at the tissues, the concentration is about 4 kPa.0925

Again, partial pressure, concentration, it is the same thing; the oxygen concentration at the lungs is very high.0930

Oxygen concentration at the tissues is very low.0935

In the lungs, we need it to bind oxygen; when it gets to the tissues, we need it to no longer want the oxygen.0939

We need it to give it away.0944

OK, now, a protein such a myoglobin, which we discussed previously, with a singular affinity, it cannot accomplish this task.0948

Myoglobin is a single polypeptide protein.0983

Yes, it has a heme group, and yes, it binds oxygen; but it has - you remember the binding curve - 1 affinity.0988

It has a certain Kd, but that is it.0995

It just binds the O2; it is a great place to store oxygen, but it does not really experience the kind of changes in affinity, which are required under certain physiological conditions in the lungs.1001

We need this hemoglobin to have a high affinity for oxygen so that it can actually bind them, and then, when it gets to the tissues where the situation is completely different, where pH is different, where the concentration of oxygen is different, we need it to actually let go of its oxygen so that the tissues can use it.1015

Hemoglobin will not do that; hemoglobin has 1 affinity.1033

So, it makes sense that we have this multi-subunit protein, which is very finely-tuned and can adjust its affinity for oxygen depending on the circumstance, depending on how much O2 is there to bind, which is really the key thing that drives this.1038

As an O2 binds, the conformational changes cause it to transition from the deoxy state to deoxy state, from the T-state/tense state to the relaxed state that binds more oxygen- that is it.1055

We need it to be in the R-state in the lungs so it can bind it, and when it gets to the tissues, we need it to make a transition from the R-state to the T-state; and as it gives up each oxygen, it makes the transition back from the R to the T-state, and at that point, it is just giving up its oxygen to the tissues.1068

And again, we are talking about 96% saturation versus 60% saturation.1085

We are not talking about 96 versus 3% saturation.1090

It does not give up all of its oxygen, only what is required.1095

OK, now, let's go ahead and go to - yes - the next page here.1101

As we said, if the affinity of the protein for ligand is high...well, we do not have to say ligand, we can just say O2 because we are talking about oxygen here.1112

If the affinity of the protein for O2 is high, it simply would never release the oxygen when necessary.1137

It would not release the O2.1155

Well, if the affinity were low, then, the protein would never/not bind the O2 when necessary.1160

Both of these situations are depicted diagrammatically as follows.1188

Both these situations - I should say "are shown below", excuse me - are shown below in the following binding curves.1198

And again, we have seen this binding curve; we saw it in the previous lesson, that hyperbolic binding curve.1227

It is going to look something like this; you have got here, and you have got that.1233

This is going to be ligand concentration, and as we said, this is going to be the fraction that is actually the fraction of the binding sites that are actually occupied.1239

I believe we called it alpha; different Greek letters are used.1249

I think some books will call it theta; in fact, I think theta is the standard.1253

I just happen to use alpha; it does not really matter what you use.1257

We said because this is a fraction, 1 is going to be our highest.1261

Now, low Kd is high affinity.1266

High Kd is low affinity; now, if you have a protein that has a high affinity for oxygen, its binding curve is going to look something like this.1273

Let me go ahead and mark at least the maximum here so that I have asymptote to which I can get close.1285

It is going to be something like this; it is going to show some really, really heavy hyperbolic behavior, something like that.1292

OK, and again, the 0.5 where it meets the graph, and if you go down, this is going to be your Kd.1298

Well, low Kd, high affinity.1309

A high affinity protein for its ligand demonstrates this kind of behavior.1313

OK, let me go ahead and mark some things here; I am going to go ahead and put, let's say, 4, 8, 12 and 15.1319

So,13 kPas is there, and about 4 kPas is there.1339

Remember we said this is the region; tissues are about 4 kPa than the concentration of O2.1344

The lungs are at about 13 kPa for the concentration of O2.1350

This is not just ligand; we are actually talking about O2.1358

I am going to put O2 concentration...well, you know what, that is fine.1365

We are talking about pressure; I will put PO2.1369

This is partial pressure O2 concentration; I do not know.1371

I like the bracket symbol, but that is OK; we are talking about a gas.1374

OK, now, a high affinity protein demonstrates this kind of behavior right here.1377

A low affinity protein demonstrates this kind of behavior, something like that.1385

Now, your Kd is like over here.1394

OK, we have a really high Kd, low affinity.1402

A high affinity protein, the binding curve would look like that.1409

A low affinity curve would look like that; let me go ahead and label these.1414

Let me do this in blue; this is a low affinity protein.1418

It displays this kind of behavior; this up here, this is a high affinity protein.1428

What we need is something like this; we need a protein that in the range of - let me go ahead and do this in...that is fine, I can do it in blue - somewhere in this range, 4 kPa in the tissues and about 13 kPa in the lungs.1439

We need a protein that displays the following behavior.1466

Under conditions of low concentration, we need its Kd to be low.1470

We need it to follow this trajectory; we want it to follow this trajectory, the low affinity curve.1476

We need it that way; OK, because again, in the tissues, it needs to have a low affinity for oxygen so that it can actually push away its oxygen.1483

It does not want it; it wants to release it into the tissues because the tissues need oxygen, and then, the oxygen that is there, it does not want to just grab it up.1492

So, we need it to be a low affinity protein, to behave like a low affinity protein, so we want it to follow a low affinity protein trajectory.1500

However, in the lungs, we need it to be a high affinity protein.1510

We need it to display this kind of behavior right here at 13 kPa.1515

We need for it to actually make a transition and follow that trajectory right there.1521

We need a protein that displays this kind of behavior, not up and over high affinity, not over, over, over, slowly reaching its fraction, but we need it to be at low concentrations.1532

We need it to display low affinity; at high concentrations, we need it to display high affinity.1548

We need a hybrid between a high affinity curve and a low affinity curve.1553

That is what we want; OK, that is what we would like to see.1558

This right here - let me go back to blue - this is what we would like to see, the protein display, this kind of behavior.1564

This makes sense; in the low pressure of the tissues, low affinity.1598

We do not want it to grab the oxygen; we want it to give it away.1604

In the high pressure of the lungs, we want it to display high affinity.1607

We want it to grab up as much oxygen it can, so that when it goes back to the tissues, it will give up as much oxygen as it can.1612

That is what we want; we want hybrid behavior.1620

We want this protein to make a transition from a high state to low state, not just one affinity, boom- that is it.1624

I hope this makes sense; this is something that we want the protein to display.1631

Now, let's go ahead and go over here, do a little bit more discussion.1638

In the lungs - let's see here - the hemoglobin becomes about 96% saturated with O2.1644

In blood returning from tissues, where it has delivered its O2, as we said, it is about 60% saturated.1675

Once again, high affinity curve, that is a protein that demonstrates high affinity.1710

A low affinity curve, it demonstrates low affinity; we need a protein that demonstrates both depending on the physiological conditions.1718

Under conditions of low pressure in the tissues, we need the affinity to be low.1727

We need it to follow this trajectory, but as the pressure becomes high, as it starts to move towards the lungs, the concentration of O2, the pressure of O2, is going to be high about 13.1732

At that point, we need it to make the transition from a low affinity protein to a high affinity protein.1744

When we connect these 2 in hybrid fashion, we end up getting this curve.1751

This is called a sigmoid curve; this S pattern is characteristic of this thing called cooperative binding.1756

This is what hemoglobin demonstrates; hemoglobin satisfies this.1765

When we take a hemoglobin molecule, it actually displays this kind of behavior, which is exactly the kind of behavior we need in order to fulfill the function that it actually fulfills- binding O2 tightly, not binding O2, releasing it, binding O2 tightly, releasing it.1770

We want this; we have it in hemoglobin.1790

Hemoglobin demonstrates this transition; it is not just a single binding affinity.1792

It has multiple binding affinities; very, very low under low concentration, very, very high under high concentration and everywhere in between.1796

Again, it is a transition, not just boom, boom, and that is what this graph represents.1805

Let's see here; OK, now, let's see.1812

...and there is a hybrid, so yes, as long as it finished off with this part, this section at least, this graph is a hybrid of the high affinity graph and low affinity graph and is exactly what hemoglobin demonstrates/displays.1822

In other words, hemoglobin, when we subject it to this analysis, we get a sigmoid curve.1868

We get what we want.1874

This is called a sigmoid curve.1878

OK, let's see what we have got here...a little bit about that, that, that.1889

OK, now, let's go ahead and take a look at it.1894

This is what it looks like; a sigmoid curve, notice, it is not this way, and it is not this way.1902

It is a little bit of both; it starts to go in the low direction, but then, as it rises, it starts to get a little higher, higher, higher, boom.1908

That is what you get; that is what is happening.1916

When we measure the oxygen partial pressure percent saturation, when we measure the partial pressure, this time at 26, 8, 80, low, 50.1922

That is what is happening here; the sigmoid curve under low concentrations, the affinity, it is going to actually end up being low.1932

It is going to follow this trajectory; the high concentrations, it has a very high affinity.1942

OK, that is what is going on; that combination, that hybrid curve, gives us this curve.1949

OK, now, hemoglobin does this by what is called cooperative binding.1957

Now, as hemoglobin binds 102 molecule, it begins the transition from T-state to R-state.1979

And again, it begins the transition; it does not just jump over there.2008

It begins the transition from T-state to R-state; that is why you have this S-behavior, this little concave thing here instead of just straight up or that way.2012

It brings the transition from T to R, and the R-state, which binds O2 more tightly has a greater affinity for it.2026

As we add more O2, more O2 wants to bind tightly.2043

It makes the transition from a low affinity to a high affinity.2048

And again, things in nature do not just - boom - jump; they happen slowly.2054

You get curves; you do not get sharp edges.2060

Nature does not behave that way mostly.2064

OK, now, hemoglobin is an allosteric protein.2068

We just said that the binding of 1 molecule actually affects the binding of another molecule of O2.2078

This is allosteric regulation; this is allosteric behavior.2086

It is an allosteric protein; now, it is one where the binding of 1 molecule affects the binding of the protein for its natural ligand.2091

Now, again, protein-protein reaction, the general definition of allosteric behavior is if you have some ligand that the protein binds, there might be some other molecule that attaches to another part of the protein, and by attaching, now, the protein wants to bind more of its natural ligand or less of its natural ligand.2137

The 2 things do not have to be the same; in the case of hemoglobin, the natural ligand, which is oxygen and the thing which controls the binding of its natural ligand, also happens to be oxygen.2162

It does not have to be that way.2175

OK, now, for hemoglobin, O2 is both the allosteric modulator.2179

OK, it is the molecule which controls the behavior of the protein and how well it binds its natural ligand, and it is also the natural ligand.2200

This is called homotropic allostery.2219

It is when the natural ligand and the molecule controlling the binding of the natural ligand affecting it happen to be the same molecule.2231

If the molecules are different, it is called heterotropic allostery.2238

OK, and again, the effect can be positive or negative.2244

If I have some protein and let's say the natural ligand binds here and let's say there is an allosteric site someplace else, again, if it happens to be the same as this, it is called homotropic allostery, but if it is a different molecule that binds to the protein and has an effect on how the natural ligand actually binds to the protein, changes the affinity, it is called heterotropic allostery.2250

Again, allosteric just means it binds at a different site than the natural ligand.2275

That is all that means; OK, let's see.2280

Now, the sigmoid curve is typical of cooperative binding.2287

Now, here is what is great.2311

Cooperative binding...where, do I have it on the next page?2315

Nope, not quite; now, cooperative binding can also be described quantitatively, not just regular binding like myoglobin.2322

Cooperative binding can also be described quantitatively.2333

For a protein with N binding sites - in the case of hemoglobin, n is equal to 4 because it has 4 binding sites - we have the following equilibrium.2349

Protein + n ligands is in equilibrium with protein ligand complex and Ln.2370

Once all of the 4 in the case of hemoglobin, it is going to be Hb + n.2379

O2 is going to be in equilibrium with Hb O2 4, not n.2388

This is 4 because I have 4 O2 molecules bound to 1 hemoglobin molecule.2395

Again, 4 things bound to hemoglobin, this is a general case.2400

This is a specific case for hemoglobin.2404

OK, let's go ahead and do the same analysis that we did before, equilibrium constants, things like that.2408

Let's see if we can come up with something; well, the association constant here is going to be P Ln, products over reactants over P, Ln - right - because now, we have a coefficient there.2412

Well, as it turns out, when I do the same analysis, I end up with the following.2432

I end up with an expression for alpha, and alpha was the percentage of the binding sites that are actually occupied.2436

Alpha is going to equal, again, the ligand concentration this time to the nth power, over the ligand concentration to the nth power plus Kd.2445

OK, this reduces to what we had from myoglobin because myoglobin only has 1 site.2456

So, n is equal to 1, L/L + Kd.2461

Here, it is just Ln/Ln+ Kd, so it is actually the same expression.2465

Now, we have an expression for cooperative binding, a multi-subunit protein for which we can actually draw a binding curve, and the binding curve is going to be, again, kind of hyperbolic; but now, because of the n here, it is actually going to be sigmoid.2473

What this describes is the sigmoid curve.2492

It is a hybrid between a low affinity, hyperbolic curve and a high affinity, hyperbolic curve, follows the low trajectory, and then, goes to the high trajectory.2496

That is what this equation describes; let's go ahead and actually play with this a little bit.2508

Let's write it again; we have alpha is equal to Ln/Ln + Kd.2514

When I multiply this through, I am going to get alpha Ln + alpha Kd is equal to Ln.2525

I am going to move this over, so I am going to get alpha.2540

Kd is equal to Ln - alpha Ln.2545

I am going to factor out, so I am going to get alpha Kd; I am going to factor out my Ln, Ln x 1 - alpha, and now, I am going to end up doing a little bit of division here.2552

I am going to divide both sides by 1/alpha and divide both sides by Kd.2567

I get alpha/1-alpha is equal to Ln divided by Kd.2571

That is the equation that I get.2583

OK, now, I am going to end up taking the logarithm of both sides; when I take the log of this side, I am going to leave it as log of this alpha/1-alpha.2587

The log of this side is going to be n times the log of the ligand concentration minus the log of the Kd.2600

This is a Y = mx + b.2610

I am going to end up with a linear plot.2617

This thing, this is called the Hill equation, and the plot that it represents is something called a Hill plot.2621

OK, now, let's take a look at what this actually looks like when I graph this.2634

On the Y axis, again, I have log of alpha/1-alpha on the Y axis.2640

The X axis, I have log of ligand concentration, not ligand concentration.2647

I fiddled with the other one; the other equation from which this is derived is this one right here, where alpha is the percentage of binding sites that are occupied, and L on the X axis is the ligand concentration.2654

Now, the X axis is log of L, and the Y is log of alpha/1-alpha.2667

Let's take a look and see what this actually looks like.2675

OK, you are going to end up with something that ends up looking like this.2684

Let's see what we have got; here, on this axis, we have the log of the ligand, and on this axis, we have the log of alpha/1-alpha.2689

They did it this way; let me just rewrite this.2700

This is alpha/1-alpha, and this is just the ligand concentration.2703

Again, let me rewrite the equation.2710

Let me write it up here; that is fine.2715

I guess I can write it down here; we have log of alpha/1-alpha = n x the log of the ligand concentration - it was minus, right - minus the log of Kd.2717

Notice, this n right here, that is the slope.2733

The slope is going to give you, if you have 4 binding sites, n should be 4 for fully cooperative binding, but as it turns out, well, first of all, let's see.2739

First, the equation predicts that the line that we get will have a slope of n, the number of binding sites.2755

Again, all we have done is taken that binding curve and found a way to represent it in linear form by taking a logarithmic version of it.2774

That is all we have done here; there is nothing strange going on.2782

The equation predicts that the line should have a slope of n.2786

Experimentally, it is always going to be the slope ends up being less than n.2791

When we actually run the experiment, collect the data, it does not follow the theoretical.2796

So, experimentally, the slope is never n, but actually less than n.2804

It is actually not a bad thing; this is a pretty good thing.2820

Do not worry about it; OK, the reason this is the case is the following.2823

What the slope actually reflects is not the number of binding sites.2829

It represents the degree of cooperativity among the binding sites.2834

What the slope reflects...I should not say "reflects".2844

What the slope represents is not the number of binding sites, but the degree of cooperation among the binding sites.2850

OK, now, the higher the slope, the greater the degree of cooperation of those binding sites- that is it.2889

That is all it means.2915

Experimentally, if we get a slope of 1, there is no cooperation.2922

If we get a slope actually equal to the number of binding sites, and in the case of hemoglobin, let's say the slope is 4, that is full cooperation, full complete cooperation.2926

As it turns out experimentally for hemoglobin, the slope is going to be somewhere around 2.8-3.2937

There is a lot of cooperation but now complete cooperation.2944

This idea of the slope being the number of binding sites, that is a theoretical maximum.2949

It will never be more than that, but it can get up to that; and the more the slope, the more cooperative binding is taking place.2955

If the slope is 1, that means that there is no cooperation among the subunits.2965

Each subunit is just grabbing whatever ligand it can as it needs to.2970

There is no cooperation among them.2977

OK, well, now, let's see.2981

OK, the higher the slope, the greater the degree of cooperativity.2985

Yes, now, therefore, we designate the slope because it is not n as nH, and call it the Hill coefficient.2989

This Hill coefficient, the slope at any given time in the progress is a measure of how cooperative the individual subunits are being among each other to make the protein do what it is supposed to do, which I will repeat.3008

The Hill coefficient is a measure of the degree of cooperativity.3037

Hill plus can be a little strange, and they can be a little strange to interpret.3048

Hopefully, we can offset some of that bizarre nature of it because you are not really accustomed to seeing something like this especially for some multi-subunit protein, but do not worry about it.3054

We will deal with it as needed.3065

When you have a slope, when nH = 1, this means, no cooperativity.3069

If you do a Hill plot of, let's say, a myoglobin, well, myoglobin only has 1 binding site.3082

It only has 1 affinity; there are not multiple binding sites, so there is no cooperative binding.3088

If you looked at the graph, a Hill plot of myoglobin, you are going to see something like this.3095

Because myoglobin, it has a slope of 1, that is it.3105

One binding site, there is absolutely no cooperativity involved.3109

It binds O2 when it can; it releases O2 when it can- that is it.3112

There is no variation; it is just 1 straight line.3116

The binding curve is - boom - like this; the Hill plot is a straight line - that is it - with a slope of 1.3120

OK, now, notice, hemoglobin, that is what is happening in red.3128

This is the Hill plot for hemoglobin.3142

OK, let's take a very, very close look at this.3147

OK, notice, for hemoglobin, there are 2 places where the Hill coefficient does equal 1- here and here.3152

What this means, even for multi subunit proteins - I will say multi-subunit allosteric proteins - multi subunit allosteric proteins, there can be situations where the subunits do not affect each other or there is no cooperative binding.3181

There can be situations where there is no cooperative binding, where binding is just plain straight binding.3215

Now, again, these are experimental conditions.3239

Physiological conditions are not like this; it does not have this broad range of really, really low concentration, really, really high concentration.3243

It does not like that; the physiological conditions are mostly here where there actually is some transition between low state and high state, and I will talk a little bit more about that in just a minute.3250

Now, if nH = n, if the Hill constant, the slope actually equals the number of binding sites, which is the theoretical limit, this means that the protein is engaging in complete cooperativity.3262

It means complete cooperativity.3292

What this implies is that all sites bind simultaneously.3300

All sites, they bind simultaneously, and no partial saturation ever occurs.3308

No partial saturation ever occurs.3325

That means that hemoglobin, which is automatically grabbed for oxygen molecule simultaneously, and it will be 100% saturation- that is it.3329

There is no 1 bound, 2 molecules bound, 3 molecules bound.3337

There is no real cooperativity; it is complete cooperativity.3343

Boom, it is all or - boom - it is nothing- that is it.3347

That is complete cooperativity; we never see that in practice, so we do not have to worry about that, and let's see, the final situation just for the sake of completeness.3350

If nH is less than 1, this is negative cooperativity.3364

It is negative modulation- not altogether that important.3368

OK, now, here is what is important; let's see.3372

Now, where the graph hits the X axis, where it hits the X axis, right there, this is where the log of alpha/1-alpha = 0, right?3375

That is the 0 on the Y axis; well, if we get rid of the log, if we exponentiate this, 10 raised to both power, we end up with the following.3412

This implies that alpha/1-alpha, well, 100 is equal to 1.3422

Well, this is the same as alpha = 1-alpha, 2 alpha = 1, alpha = 1/2 or 0.5.3430

Where this Hill plot actually touches, that is going to be equivalent to the log of the Kd.3444

We said that the Kd was the concentration of ligand that allows for half saturation.3453

Well, here, if we set the log of alpha/1-alpha equal to 0, we end up getting the alpha = 0.5.3460

What this represents is the log of Kd.3472

OK, it represents the log of Kd.3476

Now, let me go ahead and draw an actual graph for hemoglobin and just to see some numbers to see what is going on here.3483

Let me go one more page.3493

Alright, in the case of hemoglobin, what is actually happening is this.3496

It is actually starting with 0 cooperativity.3502

If I extend this line, I end up here.3507

I end up with a high Kd; high Kd is low affinity.3511

OK, this represents the T-state of hemoglobin, its low affinity state.3516

At a certain point, at a certain range of concentration like from here to here, it demonstrates cooperative binding.3525

The sigmoid curve, it starts to behave a little differently, or it actually starts to demonstrate movement towards a higher binding.3535

So, now, this slope here has, now, gone from 1, 0 cooperativity, low binding state.3544

Now, the slope has gone up to about 2.8, 3 range high cooperativity.3551

Now, there is a lot of cooperativity going on as it is making the transition from the T-state to the R-state.3556

At a full R-state, again, if I extend this down here, notice, again, this has its 1.3564

Here, the Hill constant is 1, 0 cooperativity.3574

Now, it is fully in the R-state; well, in the R-state, it is almost fully saturated, so there is no more cooperativity to be had.3579

Again, it goes back to no cooperativity behavior, but it made the transition to the R-state.3587

If we extend this graph down here, and we find this Kd, this is going to be a low Kd, which is a high affinity.3594

This right here is the R-state.3603

In the case of myoglobin, when you have just 1 affinity, in the case of hemoglobin under very low concentrations, you have virtually no oxygen binding.3608

There is no cooperativity; at some point, that is going to change cooperativity.3618

It is going to start cooperating to bind more oxygen as the concentration of oxygen actually rises in the lung area, and at that point, it is going to make the transition; and once all of the hemoglobin are actually saturated with O2, at that point, again, it reaches a saturation point.3623

Most of the hemoglobin molecules, all of the binding sites, are occupied.3644

So, it no longer demonstrates cooperative binding.3649

There is no other oxygen to bind; there is no site for it to bind.3653

Now, it goes back to this non-cooperative behavior, but it has made the transition from the low affinity state, which is represented by extrapolating this and hitting a high Kd to the high affinity state, which is the R-state, which is represented by low Kd when we extrapolate this.3657

This is what makes this Hill plot actually very, very confusing, and it is confusing.3676

I am not going to suggest that it actually is not, but what you want to remember in a Hill plot, the important thing is the slope.3681

When a slope is 1, there is no cooperativity.3689

When a slope rises like in this range right here, the slope - boom - just jumped up, that is when you have cooperative binding.3693

That means the hemoglobin molecule, the individual subunits are starting to bind more oxygen.3700

As more oxygen binds, the affinity rises, so it is making its transition to the high affinity state.3706

Once it reaches its full high affinity rate, boom, it stops there.3712

Now, cooperativity can no longer operate its fully high affinity state, low affinity state.3716

The Hill plot represents the transition from low affinity state to high affinity state- T-state to R-state.3724

The slope of the Hill plot while it is making that transition is a measure of the degree of cooperativity.3735

If it were something like maybe 1.2, you would not see a lot of cooperativity- a little bit.3740

If you saw something like 3.8, you are seeing almost complete cooperativity.3745

What you are seeing is, sort of, a middle ground, more towards the high end.3750

Again, 2.8-3.0 which is perfect for what the hemoglobin molecule wants to do.3754

I hope this helps; again, let me repeat one last time.3763

The slope of the Hill plot tells you about the degree of cooperativity.3766

It will always be greater than or equal to 1 but less than the number of binding sites.3772

A slope of 1 means no cooperativity is active, either low state or high state- that is it.3781

They cannot cooperate anymore - the binding sites - because they are either mostly all empty or mostly all full.3787

This, the transition in between, here is where cooperativity is taking place.3795

This right here is what gives rise to the sigmoid behavior of the binding curve itself.3799

And again, this is just a variation of the sigmoid behavior binding curve.3805

I hope that makes sense; thank you so much for joining us here at Educator.com.3810

We will see you next time, bye-bye.3815

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