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Raffi Hovasapian

Raffi Hovasapian

Thermodynamics, Free Energy & Equilibrium

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 (19)

0 answers

Post by Swati Sharma on January 29 at 11:34:40 AM

Dear Dr Raffi,

If I am not wrong, this means that if K>1, there are more products that the reactants and if K<1 there are more reactants than the product at EQULIBRIUM. So k would not tell us about the direction of the reaction? K would tell us only if there are more products that the reactants?
SO to find the direction of the reaction we need to first find Q?
So for example if question says if the: Equilibrium constant of the reaction is 25, which direction the reaction would proceed? So I know that there are more products than the reaction, but what about the direction? Does that mean that if k>1 the reaction would go in the forward direction and if K<1 the reaction would go in the reverse direction?
In exam would Q be given? What if Q is not given and they tell us to find the direction of the reaction only with K. So if the Equilibrium constant of the reaction is 25, which way would the reaction proceed? So how  do I find the direction if  Q is not given in the exam? and only with K =25 or may be the question is wrong? I always loose points on these questions in exam I just wondering if K is only to know the concentrations at equilibrium , and Q is fro the direction. But what If Q is not given, only K is given and the question does not ask whether the Products are in greater concentration or the reactants, but instead asks what is the direction of the reaction?
So I thought if K = 25, K>1, there are more products at equilibrium, so the reaction would go towards reactants , since according to Le Chatliers principle  there are more products , so the excess products would be converted to reactants in order to maintain equilibrium. I am really sorry if my question is frustrating , I just want to make sure what I am thinking is right or wrong. I short K will not give us the direction? Q will give us the direction? Would I get a question in exam asking me about the direction of the reaction only with K or q would be provided?

Respectfully
Swati

2 answers

Last reply by: Swati Sharma
Mon Jan 29, 2018 10:24 AM

Post by Swati Sharma on January 28 at 11:27:05 PM

Dear Dr Raffi, I am very confused with this question

The equilibrium constant for the reaction Q ? R is 25.
(a) If 50 uM of Q is mixed with 50 uM of R, which way will the reaction proceed: to generate more Q or more R?

The answer says that the reaction would go towards the formation of products but I thought that according to Lechatliers principle when the products are in excess the reaction would go towards reactants to balance each other right?, So why does the answer says that the reaction would go towards products?
Respectfully
Swati

3 answers

Last reply by: Professor Hovasapian
Sun Jul 3, 2016 7:27 PM

Post by Kaye Lim on June 13, 2016

At 30:25 where you said as rxn move forward to reach equilibrium, rxn spend its free Energy and delG is risen as reactant is gone.
-->At this point, I dont understand how delG is risen when you take a new measurement of G reactant and G product. I thought for 1 mole of reactant go to product, the process release for example -50kJ of free Energy. So as rxn moves toward equilibrium, x amount of reactant got used, and there are still some reactant unreacted.

Basically, I dont understand how delG risen to 0 as rxn reach equilibrium.
This is my interpretation for delG=0 at equil, please tell me if Im correct. DelG=0 at equilibrium because rate of forward and rate of reverse rxn are equals at equilibrium. Thus, the Energy released for the forward reaction also got used at the same time by the reverse rxn to form reactant. Therefore, overall, change in free E =0 as the Energy released also got used at equilibrium. Is it correct?

1 answer

Last reply by: Professor Hovasapian
Wed Oct 8, 2014 6:04 PM

Post by leala aljehane on October 8, 2014

Hello, Prof.Hovasapian
I just have a question. you said that when   Delta G is positive value that means the product has more energy than the reactants; therefore, we need to input energy to drive the reaction. How can we know that the products have more energy than reactants before we actually start the reaction and get the product? because we just have reactants which group of substances react to form product? I just get confused how can I know the energy for something that I have not yet have it. I hope that I clear my question.

1 answer

Last reply by: Professor Hovasapian
Sat Nov 9, 2013 2:09 AM

Post by Razia Chowdhry on November 8, 2013

Also, where does the concept of ICE come from? And why would the equilibrium concentration be initial conc. + change conc.?

2 answers

Last reply by: Professor Hovasapian
Sat Nov 9, 2013 2:06 AM

Post by Razia Chowdhry on November 8, 2013

For the reaction you did aA+bB-->cC+dD. I don't understand what these small letters stand for? I know the capital stands  for concentration of that species but what about the small letters

1 answer

Last reply by: Professor Hovasapian
Mon May 27, 2013 5:48 PM

Post by marsha prytz on May 27, 2013

so when i put this keq equation into my calculator it does not equal to 20.97. i come up with a completely different number in the 200s. how do i put this calculation into my calculator?

1 answer

Last reply by: Professor Hovasapian
Mon May 27, 2013 5:41 PM

Post by marsha prytz on May 27, 2013

what does the "e" stand for in = e^3.043?

Thermodynamics, Free Energy & Equilibrium

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
  • Thermodynamics, Free Energy and Equilibrium 1:03
    • Reaction: Glucose + Pi → Glucose 6-Phosphate
    • Thermodynamics & Spontaneous Processes
    • In Going From Reactants → Product, a Reaction Wants to Release Heat
    • A Reaction Wants to Become More Disordered
    • ∆H < 0
    • ∆H > 0
    • ∆S > 0
    • ∆S <0
    • ∆G = ∆H - T∆S at Constant Pressure
    • Gibbs Free Energy
    • ∆G < 0
    • ∆G > 0
    • Reference Frame For Thermodynamics Measurements
    • More On BioChemistry Standard
    • Spontaneity
    • Keq
    • Example: Glucose + Pi → Glucose 6-Phosphate
  • Example Problem 1 40:25
    • Question
    • Solution

Transcription: Thermodynamics, Free Energy & Equilibrium

Hello and welcome to Educator.com and welcome back to biochemistry.0000

Today, we are going to start our discussion of a profoundly important topic- bioenergetics.0004

The energy transfers that take place in biological systems.0013

Today, we are going to be discussing the thermodynamics, free energy and equilibrium.0017

I cannot overestimate how important this topic is.0021

In a biochemistry course, you are going to see a lot of information.0026

It is a ton of information, as you already know, and there is certainly a lot more to come.0031

If you do not walk away with anything else from this course, an understanding of bioenergetics will serve you for many years to come, particularly those of you that go on to graduate school and are looking for research careers.0037

Understanding what is happening energetically will allow you to understand pretty much everything that is happening.0050

In any case, let’s just go ahead and jump right on in and get started, and see what we can do with this magnificent, magnificent, beautiful topic.0058

OK, another comment that I want to make really quickly, the problems, as far as this unit is concerned, this bioenergetics, there are going to be several lessons.0067

I will be doing some occasional examples and problems during the lessons, of course, but I am going to save the bulk of the problems that I actually do to the end.0076

In a series of, maybe 1, 2, 3 lessons, I would like to do them all at once, one after the other, one after the other.0085

If there is something that is not exactly clear, do not worry.0091

When we actually do the problems, it is a great way to consolidate; and in this particular case, I thought it would be great to do a whole bunch of them at the end.0095

That way, we deal with concepts; and it gives us a chance to actually review as we do the problems.0101

With that, let’s get started; let’s start with a reaction.0108

You know what, I think I will do blue; blue is always nice.0113

Let’s start with a reaction, and the glucose - I am sorry - the reaction we are going to start with is going to be glucose plus an inorganic phosphate goes to glucose-6-phosphate.0119

OK, let’s go ahead and draw this out real quickly.0140

We have got our glucose molecule; that is that.0144

Let’s go ahead and make it beta here; so, this is down.0149

This is up; this is down, and, of course, we have our CH2OH.0154

Now, plus inorganic phosphate, phosphate, so POOH, I will go ahead and put the H on there; and it goes to glucose 6-phosphate.0159

It looks like this; that is that.0173

That is that; that is here, glucose-6-phosphate.0178

This is the 6 carbon, and, of course, it is going to look like that.0184

That is a structural representation of the reaction.0192

Now, this happens to be the first step of glycolysis; well, you know what, I do not need to write that part down.0195

This happens to be the first step of glycolysis, and this is a reaction that we definitely want to move forward - very, very, important - that this reaction move forward and move forward easily.0201

OK, here is the interesting thing; we can write down any reaction we want.0212

We can put anything on the reactant side, and if it is reasonable or seems to make sense, we can put anything on the product side; but just because we write down a reaction - excuse me - just because we write an equation, it does not mean that it happens.0218

Just because we write it down, it does not mean that it is actually going to happen.0249

OK, in discussing thermodynamics, we speak of spontaneous processes, or more specifically, spontaneous reactions.0253

OK, now, spontaneous does not have the same meaning as in normal daily speech.0287

Spontaneous means it wants to happen; that is the important thing.0297

It wants to happen naturally, and if circumstances are right, it does happen naturally and easily.0305

It does happen naturally, in other words, without external pressure.0331

So, when we talk about a spontaneous process, we are making a thermodynamic statement.0346

We are saying that this reaction, all else being equal, it wants to happen; and if the reaction actually starts, and the circumstances are good for it to happen, it will happen without us doing anything about it.0350

A spontaneous does not refer to speed; it does not talk about how fast this reaction is going to take place.0362

That falls under the domain of kinetics; thermodynamics just speaks about the potential for something happening, the extent to which it wants to happen.0367

Kinetics is the domain that discusses whether we can make it happen and how fast we can make it happen; so those are two different things.0376

OK, now, our thermo is a study of the extent to which a reaction wants to happen and can happen naturally; that is all thermodynamics is.0385

Alright, now, in any reaction, nature - maybe I should capitalize nature and be respectful - in any reaction, nature wants 2 things.0400

All of our observations, all of the things that we have done, all of the things that we have observed, all the data we have put together, has led us to a couple of conclusions.0421

One of those conclusions regarding natural processes is the following regarding reactions.0429

In going from reactants to products, a reaction wants to release heat.0435

It wants to release heat; in other words, the bonds in a molecule represent a certain amount of energy.0459

Ideally, if it can move, if the reactants can move and become a product where the bonds are more tightly held together and in that process, more stable, its energy is reduced.0471

So, it actually wants to release heat naturally; that is what it would like to do under normal, ideal circumstances.0485

Now, ΔH of the reaction, the enthalpy of reaction, that is the quantitative measure of this tendency.0494

OK, ΔH reaction is the quantitative measure of this tendency at constant pressure.0511

At constant pressure, the heat that reaction releases or gains is called the enthalpy- that is all it is.0530

It is a quantitative measure of the release or the gain of heat in a reaction, but under ideal conditions, it wants to release heat.0542

Now, 2- the reaction wants to become more disordered; things fall apart.0551

Things do not just naturally go from a state of disorder to order without some external help, but things will naturally go from a state of order to disorder, naturally, without us doing anything about it.0570

That is the nature of the universe that is the second law of thermodynamics.0582

That entropy always increases in a natural process, has to.0586

So, under ideal conditions, a reaction would like to become more disordered as it moves from reactant to product.0591

That favors the forward movement of the reaction, wants to become more disordered.0599

OK, ΔS entropy - I will just put rxn of the reaction - is the quantitative measure of this tendency.0605

OK, now, when we have a ΔH, which is less than 0, which is negative, the enthalpy of the products minus the enthalpy of the reactants, when it ends up being negative, that means it has given up heat.0630

This is 'releases heat"; these are ideal conditions for a reaction to easily move forward.0645

OK, so I will just call it that; these are ideal conditions.0655

When the ΔH is greater than 0, it requires heat, or it absorbs heat from its surroundings, absorbs energy- these are less than ideal conditions.0658

Notice, I am calling something ideal, but I am not excluding the other.0670

When I say that the ΔH is greater than 0, I am not saying that it does not happen.0675

I am saying that it is less than ideal conditions, so we will leave it at that for the moment.0679

Now, ΔS, when ΔS of a reaction is greater than 0, OK, when disorder increases as you go from product, those are ideal conditions.0684

In other words, the entropy, the measure of disorder of the products is greater than the measure of the disorder of the reactants.0700

Product minus reactants, you get a positive number.0706

Those are ideal conditions for a reaction to move forward naturally, without any help, and ΔS less than 0, well the disorder decreases.0710

Those are less than ideal conditions; those are less than ideal.0725

OK, now, let’s go ahead and go to red.0732

These 2 properties, the enthalpy and the entropy, these 2 properties, ΔH and ΔS plus the third property, which is temperature, they contribute, they combine and they compete in such a way as to give rise to a single - I am not going to use that one - to give rise to a single number that tells us whether a reaction wants to move forward naturally, whether a reaction wants to and can move forward naturally.0737

OK, property of ΔH and ΔS plus this third property, temperature, they contribute, they combine and they do compete in such a way as to give rise to a single number that tells us whether a reaction wants to and can move forward naturally.0842

That number is the ΔG, and I will write the equation first.0856

ΔG is equal to ΔH - T, Δ-S- profoundly, profoundly, profoundly important relation in thermodynamics.0864

If I have a reaction, I can measure its enthalpy, the change in the enthalpy.0873

I can measure the change in entropy, and at a given temperature, these 3 things, the enthalpy, the temperature, they combine; and we call this combination the Gibbs free energy.0878

It is a single number that tells us whether a reaction will move forward spontaneously under the ideal conditions, under the right circumstances, or whether it cannot; and if it cannot, that means that we have to do something to make it happen- that is it.0888

ΔG is called the Gibbs free energy.0901

Oh, I should say at constant pressure - that is important - and under physiological conditions, the pressure is going to be constant.0913

So ΔG is called the Gibbs free energy, and it tells us if a reaction as written - and when we say as written, we mean left to right, reactants to products - as written is thermodynamically favorable.0926

It does not tell us that it is going to happen; it tells us that it is favorable, that all else being equal, it will happen- that is all that it says.0956

It does not say about how fast or if it actually does happen.0964

If I put hydrogen and oxygen into a tank and I just let it sit there, it is not going to do anything.0968

The hydrogen and oxygen are not going to combine to form water.0975

The thermodynamic says they really, really, really want to form water very badly, but it is not going to do just because I want it to be, just because it is thermodynamically favorable.0978

There is something else I have to do to make it happen; I have to ignite it with a spark.0987

Put a little bit of energy in to it just to get it over that hump, that activation energy, then everything will be fine.0992

The reaction will sustain itself, and it will go very, very far forward and release a hell of a lot of energy; but it does not mean it is going to happen.0998

So, this thermodynamic just speaks about its tendency to happen.1006

OK, now, ΔG less than 0, so a negative ΔG, that is favorable.1010

OK, that is favorable; it is natural.1018

That is called spontaneous; now, if the Δ G happens to be greater than 0, it is not favourable.1023

It is not, well, yes, it is not favorable, what we say, that it is spontaneous in reverse.1038

You remember when you switch directions, if you go from left to right and like ΔG or ΔH are just positive, if you go from right to left, you just switch the sign; it is negative.1045

If ΔG is greater than 0 for a reaction as written on the page, well, that means it is negative in the other direction.1054

That means it is spontaneous in other direction, so spontaneous in reverse direction.1060

OK, let’s see; now, OK, whenever we do anything in science, we need a reference frame for all comparative measurements.1071

If we are going to make a bunch of measurements of a bunch of different reactions, we need conditions.1101

We need to set up conditions, so that we run these reactions under the same conditions, so that we can actually compare one reaction to another or one circumstance to another.1107

We cannot just have the temperature be one thing in one experiment and then the temperature be another thing in another experiment, the pressure be different, concentrations be different.1116

In science, we need a reference frame for all comparative measurements; this is profoundly important.1123

OK, in thermodynamics, OK these properties are calculated according to a standard, according to the following standards.1131

When we run these reactions to measure these quantities, this is the standard that we follow.1159

OK, 25°C or 298K, that is the temperature standard.1166

All aqueous reagents - I will not say reagents, I will say all aqueous species - are at 1M concentration.1174

All gaseous species are at 1 atmosphere pressure, and the super script that we use is this little circle there like a little degree sign on top of the thermodynamic quantities; and that lets us know that these numbers are under standard conditions.1194

Under standard conditions of temperature and pressure, our equation becomes ΔG 0 = Δ H 0 - or whatever you want to call that thing, it is up to you - -T ΔS 0.1220

That just means that we are doing these things under standard conditions.1251

When you look in a chemistry book of the tables, on the back, the thermodynamic tables, you are going to see these.1256

Those numbers, they were all done under standard conditions because we need a common frame of reference, so that we can make some intelligent choices about what it that is going on- that is it.1260

Now, let’s talk about some units, so ΔG is in kJ/mol.1272

ΔH is also kJ/mol; usually, we will not write out the Joule, we just say kJ.1288

ΔS is J/mol-K, so it is very, very important to watch your units.1298

Remember, if you are using this equation, ΔH is going to be in kJ/mol; that is going to be the number most often reported.1307

That is the unit; ΔS is going to be J/mol-K.1315

So, either you covert this to kilojoules or you convert this to Joules, whichever is more convenient.1318

I tend to just convert the ΔH to Joules; it just depends on the unit that you are interested in.1323

You will get an answer in Joules, the delta for the ΔG, and then you can just go back to kilojoules if you want to; it is up to you.1328

Remember to convert- very, very important in all of these things.1335

Watch your units; remember to convert kJ to J or J to kJ, as necessary.1339

OK, now, a little bit more about standards.1354

Now, many biochemical reactions, they involve hydrogen ion, involve H+.1359

That is an aqueous species, and we said that aqueous species, under standard conditions are 1M.1372

Now, well, 1M H+ means that the pH is 1.1378

When running a particular reaction under standard conditions, the hydrogen ion concentration for a reaction that involves hydrogen ion, which is the majority of biochemical reactions, the pH is going to be 1.1395

However, in biochemistry or physiological conditions, the pH is not 1.1405

The pH hovers around 7, 7 to 7.3, 7.4- something like that1409

There is a transformed standard - a biochemical standard, if you will, not a chemical standard - where what we do is we set the concentration of the hydrogen ion to pH7.1414

The concentration of - we set the pH to 7 - the concentration of hydrogen ion is 10-7M, so it is a slightly modified standard.1424

Let me see, so many biochemical reactions involve H+, and 1M H+ means pH1, but physio pH = 7.1434

The transformed biochem standard calls for a hydrogen ion concentration equal to 10-7.1452

So we set the pH to 7, as well as, and since many reactions, we are going to be talking about bioenergetics, which means we are going to be talking about adenosine triphosphate.1480

Adenosine triphosphate tends to require magnesium.1492

In addition to the hydrogen ion concentration being 10-7 as well as the magnesium ion concentration, we usually set to 1mM.1497

This is called the biochemical transformed standard, whatever it is you want to call it; and you will see it written like this.1510

Instead of ΔG 0, we will go ahead and write it as ΔG 0 that.1519

When we do our numbers, the numbers that you see in biochem texts, they are under the transformed biochem standard.1525

Those are the numbers that we are going to be using in our problems.1531

OK, now that we have talked about standards a little bit, let's go ahead and discuss what it is that we actually mean by spontaneous.1534

Let me do black, now; just really briefly, let's discuss spontaneity, and we are going to use an energy diagram- our favorite thing.1543

We said ΔG less than 0, it is spontaneous as written.1560

We have ΔG greater than 0; it is spontaneous in the reverse direction.1571

OK, here is what this means; I have an energy diagram like this, energy on the Y axis.1580

This is the reaction coordinate; let's go ahead and put reactants there, products there- something like that.1589

This difference right here, this is going to be the ΔG.1597

OK, in this particular case, ΔG, which is G final minus G initial, that is going to be less than 0.1600

This, right here, from this point to this point, this is the activation energy; that is the domain of kinetics.1608

OK, that is it, so this is the energy diagram for a spontaneous reaction.1617

It releases energy and exactly what you think, exactly what you have seen before.1621

I am sure you have seen it 100 times; we will make it 101.1628

Excuse me, and something like that, let's go here.1634

Our ΔG, this is going to be a +ΔG because the energy content of the products is higher than the energy content of the reactants.1640

And again, you have your activation energy- that is it.1648

This is the energy diagram for spontaneous and non-spontaneous or spontaneous in reverse.1652

Now, again, we had mentioned that the term spontaneous refers to thermodynamic potential and tendency.1660

It says nothing about how fast it does or if it actually does so.1671

So, let me go ahead and just draw one more little energy diagram.1675

Now, I do not want it to be even; let's go ahead and make it exergonic.1681

Exothermic, endothermic, heat in, heat out- in the case of ΔG, when we are talking about ΔG, it is exergonic, endergonic.1688

OK, now, these 2 places right here, energy of the reactants and energy of the products, that is the domain of thermodynamics.1697

This right here, the activation energy and the particular path that the reaction takes in order to go from reactants to products, that is the domain of kinetics, not the same thing.1712

Again, when we talk about ΔG, we are talking about the tendency to go.1721

We are not talking about the fact that it is actually going to go and how it is going to go or how fast; that is kinetics.1726

OK, alright, now, let's go ahead and go back to blue.1733

Now, say a reaction, a particular reaction has a ΔG that is less than 0 - I will go ahead and use that little standard - and starts to move forward.1742

So, let's say we have a reaction, ΔG is favorable, and it starts to move forward.1753

OK, we know from general chemistry that as a reaction starts to move forward, eventually, the reaction will reach equilibrium, right?1763

All systems tend toward equilibrium, or the forward and the reverse reaction are the same rate.1773

OK, now, as the reaction moves forward - excuse me - as the reaction moves forward, it spends this free energy.1779

Remember, free energy is a measure of the tendency to move forward.1796

It is telling me that the reaction wants to be on the right, not on the left, a -ΔG.1799

Well, when it starts to actually move forward, well, now, it is spending that free energy.1805

Now, at any given moment, as the reaction is moving forward, if you are to measure the G of the products and the G of the reactants, the ΔG, again, the ΔG will have risen.1809

Now, you are losing free energy; that is what you are doing as you are tending toward equilibrium.1819

As the reaction moves forward, it spends this free energy as it moves toward equilibrium.1824

ΔG is also a measure of the extent to which a reaction as written is not yet at equilibrium.1842

So, the lower your ΔG, let’s say you have a ΔG of -10, let’s say you have a ΔG of -50, that reaction that has a ΔG of -50, that means it is further away from equilibrium.1878

It has more energy to spend as it makes its way toward equilibrium.1890

Once it reaches equilibrium, you are done; the reaction has done all the work that it is going to do for you.1894

It is giving you all the energy that is going to give you; now, the ΔG is 0.1899

We will talk more about that later, of course; now, let’s go to red.1904

We also know another quantitative measure of equilibrium, quantitative measure related to equilibrium, I should say.1912

We have the Keq, the equilibrium constant; it is another quantitative measure of where a reaction wants to be at equilibrium.1938

That is what the number tells you; is the reaction really far forward to the right at equilibrium?1946

Is it mostly product, virtually no reactant?1951

Is it to the left, a lot of reactant, no product; or is it somewhere in between?1954

That is what the Keq does; that is what the ΔG does.1959

OK, just a quick recap; for the reaction AA + BB goes to CC + DD, we know that the Keq is equal to - well, reactant, law of mass action - so, AA the constant - oops - those are the reactants.1963

It is going to be products over the reactants; it is going to be CC, DD, over Aa, and it is going to be Bb.1988

So, that is the general expression for Keq.1999

These are the concentrations at equilibrium- very, very important - at equilibrium.2002

OK, now, well, ΔG is a measure of the extent it is from equilibrium.2007

The Keq is a measure of the extent to which a reaction is far from equilibrium.2014

They happen to be 2 different quantitative measures, but they are measuring the same thing.2018

There must be a relation between them- there is.2021

Here, and here it is; let me go back to black here.2024

The ΔG is equal to -RT ln Keq, where R is equal to 8.315J/mol-K, and T is equal to the temperature, the absolute temperature, which means the temperature in Kelvin- that is it; that is all it is.2030

Now, let’s return to our reaction; let’s return to our initial reaction.2055

We said we had glucose plus inorganic phosphate forming glucose 6-phosphate.2068

Well, the ΔG standard for this happens to be +13.8kJ/mol.2077

This is endergonic; this is not spontaneous as written.2087

It is spontaneous in reverse.2090

What this tells me is that glucose, that under standard conditions, 1M concentration of all these things, this reaction is not going to want to move forward naturally; it is going to want to move backward naturally.2093

The glucose 6-phophate is going to want to break up into inorganic phosphate and glucose, so this is not spontaneous as written- excuse me.2103

In other words, under standard conditions, this reaction will not go forward; we want it to go forward.2124

This is not a thermodynamically favorable reaction.2149

Let’s see what we have got; let’s go ahead and do some calculations here.2155

Once again, we have got glucose plus inorganic phosphate; the equilibrium is actually going to look like this.2159

We know we write arrows of different lengths to show us that their equilibrium here, once it comes to equilibrium, is actually going to be toward the left.2167

It is going to be a very little product; it is going to be a whole bunch of reactant.2175

Again, under standard condition, when we start with 1M concentration of each of these species, again, we need a standard to work with.2180

Well, when we go ahead and put this 13.8kJ/mol into our equation, what we end up is the following.2188

We can rearrange this equation to solve for the Keq- excuse me.2197

It is going to be E to the minus ΔG / RT = E-13,800J - I have to convert to Joules because R is in J/molK - over 8.315 x 298K, what you end up with is 3.8 x 10-3.2203

Under standard conditions, it is confirmed; this Keq is very, very small.2234

That means it is going to be to the left; that is the whole idea.2239

Small Keq means not a lot of product, a whole bunch of reactant.2246

This is just another numerical measure, and these are related by R and T; that is all that is happening here.2251

You just have 2 quantitative measurements to let you know where equilibrium lies for a reaction as written.2257

OK, let’s see; let’s go ahead and do another example here.2264

This time, we will go ahead and do the hydrolysis of adenosine triphosphate.2270

H2O goes to adenosine diphosphate plus inorganic phosphate.2275

In this particular case, the ΔG under standard conditions is -30.5kJ/mol- highly exergonic, highly thermodynamically favorable.2280

This reaction wants to take place; OK, it wants to move forward.2293

Now, this means that you have 30,500J of free energy that you can use to do some kind of work, whatever that biological work is, whether it is transporting some solute across the membrane, whether it is contracting a muscle, whether it is building a nucleic acid or building a carbohydrate polymer- whatever it is.2299

Per mole of adenosine triphosphate, I have 30500J of energy that I can use.2322

Now, when I measure this Keq, you know what, I am just going to - that is OK, that is fine - I was going to not write the eq part, but that is OK.2329

When I go ahead and put it into that equation, it is going to be E to the negative.2338

Now, the equation is -ΔG / RT, so -0ΔG is negative.2345

I have to include both of both negatives, so 30,500 all over the 8.315, 298K; and what you end up with is a very huge number 2.2 x 105.2353

The fact that the Keq is huge, that confirms the fact that there is a whole bunch of product, the numerator, very little reactant and denominator- that is all that is going on here.2374

At equilibrium, it is going to look like this: ATP + H2O, that way, that way, ADP + PI.2385

Excuse me; that is what the equilibrium is going to look like.2398

OK, let’s go ahead and finish off by doing a little bit of an example.2403

I will consolidate everything that we talked about - equilibrium, free energy - with a typical example that we are going to see, actually, several times when we get to the problem section towards the end of this particular bioenergetics unit.2408

Let’s see what we have got.2424

OK, this says when glucose 1-phosphate is incubated at 25°C with the enzyme phosphoglucomutase, the following reaction takes place.2426

Glucose 1-phosphate is converted to glucose 6-phosphate.2435

OK, the ΔG for this reaction is -7.54kJ/mol, so it is spontaneous as written.2439

The question they are asking is, if the initial concentration of the glucose 1-phosphate is 0.15M, calculate the concentrations of each species when the reaction has come to equilibrium.2446

OK, we are given our ΔG; we are given our initial concentration of glucose 1-phosphate.2457

We want to find the equilibrium concentrations; OK, let’s see what we can do here.2467

This is essentially an equilibrium problem, and as such, we are going to end up making something called an ice chart, if you remember from general chemistry.2473

The plan for this particular problem - let me do it in blue - the plan is we have the ΔG; they give us the ΔG.2482

From the ΔG, we are going to find the Keq, and then after that, we are going to do an ice chart; and ice just means initial change equilibrium, one of those charts that we used to do in general chemistry to track where things, how things start, where they end up; and then do the calculation based on the Keq.2491

Let’s go ahead and do that; we start with our equation, which is, of course, ΔG.2514

I am not going to go ahead and keep writing these super scripts over and over and over and over again.2521

You know that we do all of these calculations under the transformed biochemical standard, so I am just going to write ΔG = - RT ln Keq.2525

When I rearrange Keq = E to the -ΔG / RT, when I go ahead and put these values in, Keq = E to the minus.2538

Let's go ahead and do, we said that the ΔG was -7.54 kJ/mol, so -7540, that is kJ/mol / RT, which is 8.315, and we have 298 because we are running this under standard conditions 25°C, OK, what you end up with is E3.043, and you get 20.97.2552

Our Keq is 20.97; now that we know what the Keq is, now, we will do the equilibrium part.2586

OK, let’s go ahead and write our reaction; glucose 1-phosphate is going to reach some sort of an equilibrium with glucose 6-phosphate.2593

We are going to have an initial concentration; we are going to have the change that takes place, and then we are going to have an equilibrium concentration.2605

This is what we are concerned with ultimately.2611

Well they said we started off with 0.1M glucose 1-phosphate, and we have none of this, so that is our initial concentration2614

Well, we know that the reaction is going to move forward; there is none of this.2622

So, it is going to move forward; that means glucose 1-phosphate is going to deplete.2625

It is going to deplete by a certain amount x; well, the amount of depletion - this is a 1 to 1 ratio - is going to be exactly the amount of glucose 6-phosphate that shows up.2629

This is going to be +x; that is the change that takes place.2638

The equilibrium is the initial plus the change that took place, so 0.15 - x and x.2642

These are the values that I need, and let me go ahead and do the calculation on the next page.2651

I have Keq = x / 0.15 - x, products over reactants at equilibrium.2660

Well, this happens to equal 20.97; I know what the equilibrium constant is.2673

I go ahead and solve this equation x = 20.97 x 0.15 - x.2679

I will go ahead and put 3 dots; you guys go ahead and do the algebra.2687

What you end up with is x = 0.1432M.2692

That is going to equal the equilibrium concentration of the glucose 6-phosphate.2699

Now, x, I am sorry; the equilibrium concentration of the glucose 1-phosphate, if you go back, it said it is a 0.15 - x.2705

When we do that, we get 0.0068M equals the concentration of the glucose 1-phosphate- there you go; that is our final answer.2716

We started with the ΔG; we convert it to Keq.2729

We just did an equilibrium problem, and this confirms the fact that most of the glucose 1-phosphate has been converted to glucose 6-phosphate.2732

There is virtually no glucose-1-phosphate left over.2740

OK, that is it.2744

Thank you for joining us here at Educator.com.2748

We will see you next time, bye-bye.2750

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