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Raffi Hovasapian

Raffi Hovasapian

Citric Acid Cycle II

Slide Duration:

Table of Contents

I. Preliminaries on Aqueous Chemistry
Aqueous Solutions & Concentration

39m 57s

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

38m 53s

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

29m 1s

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

39m 11s

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

41m 33s

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

44m 19s

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

18m 45s

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

38m 19s

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

27m 14s

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

48m 28s

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

45m 18s

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

42m 47s

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

1h 2m 33s

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

49m 12s

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

54m 31s

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

50m 52s

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

51m 36s

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

1h 3m 36s

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

1h 7m 16s

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

41m 38s

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

44m 2s

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

56m 40s

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

20m 37s

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

51m 37s

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

51m 23s

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

54m 49s

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

1h 17m 46s

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

37m 6s

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

43m 32s

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

39m 25s

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

44m 15s

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

44m 23s

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

40m 22s

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

54m 55s

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

38m 51s

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

38m 20s

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

48m 36s

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

45m 51s

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

37m 6s

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

44m 32s

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

30m 8s

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

49m 46s

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

56m 34s

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

42m 12s

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

43m 32s

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

1h 1m 47s

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

59m 17s

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

39m 47s

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

41m 34s

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

34m 18s

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

42m 52s

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

36m 10s

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

49m 20s

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

44m 11s

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

48m 11s

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

45m 58s

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

33m 18s

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

40m 59s

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

39m 18s

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

36m 21s

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

47m 58s

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

41m 11s

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

36m 27s

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

3 answers

Last reply by: Vincent Bedami
Fri Mar 4, 2016 3:10 PM

Post by Vincent Bedami on February 23, 2016

Please explain this problem:

The ?G°’ for the reaction catalyzed by aconitase is 6.3 kJ/mol. However,
the ?G’ for this reaction in the mammalian mitochondria is 0 kJ/mol at 25°C. What
is the ratio of [isocitrate]/[citrate] in mammalian mitochondria?

Aconitase catalyzes this reaction: citrate  isocitrate

Citric Acid Cycle II

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

  • Intro 0:00
  • Citric Acid Cycle Reactions Overview 0:26
    • Citric Acid Cycle Reactions Overview: Part 1
    • Citric Acid Cycle Reactions Overview: Part 2
    • Things to Note
  • Citric Acid Cycle Reactions & Mechanism 13:57
    • Reaction 1: Formation of Citrate
    • Reaction 1: Mechanism
    • Reaction 2: Citrate to Cis Aconistate to Isocitrate
    • Reaction 3: Isocitrate to α-Ketoglutarate
    • Reaction 3: Two Isocitrate Dehydrogenase Enzymes
    • Reaction 3: Mechanism
    • Reaction 4: Oxidation of α-Ketoglutarate to Succinyl-CoA
    • Reaction 4: Notes

Transcription: Citric Acid Cycle II

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

In the last lesson, we talked about how the pyruvate that was formed in glycolysis is converted to acetyl-CoA in this amazing enzyme called the pyruvate dehydrogenase complex.0004

Today, we are actually going to start with the reactions of the citric acid cycle, how this acetyl-CoA enters the cycle and runs through it.0016

Let’s just jump right on in.0025

This first thing that I have here is the cycle itself but just the names of the molecules that take place.0029

In the next page, I am actually going to draw out - or it is is already drawn out - the structures themselves.0037

I wanted us to get, sort of, a big picture view of this, talk about what happens, talk about the number of reactions, what goes in, what goes out, just to get a big picture idea of what the citric acid cycle is.0044

And then, we will take a look at the structures, correlate them with the individual reactions- the 1 through 8.0055

And then, we will look at the individual reactions and their mechanisms.0061

A lot of information, so we will try to cover as much as possible.0065

And again, I encourage you to look at your books.0069

One of the things that I really, really want to stress in this particular course is that the biochemistry books are really fantastic.0073

They are an incredible resource with lots of information and lots of beautiful illustrations, and I think it is nice to be able to see it like this and then, look at the illustrations in the book and to see the correlation.0080

It, sort of, locks it in your mind; now, again, there is a difference between looking at something passively and being able to write it out actively.0090

This is something that you want to be able to write out yourself, starting with the oxaloacetate going to the citrate going to the isocitrate and so on all the way around the cycle.0099

It is very, very important to be able to produce this actively instead of just looking at it passively.0110

OK, so let’s see what is going on here.0115

Acetyl-CoA, that is the molecule that we actually formed from the pyruvate.0119

That actually enters the cycle, and what it does is it condenses with oxaloacetate.0125

In some sense, oxaloacetate, you could say, is the beginning and the end of the cycle.0131

That is where things, sort of, start; these 2 condense.0135

Water comes in; coenzyme A leaves, and you end up forming this molecule called citrate, thus, the name citric acid cycle.0139

This reaction - notice - is an arrow in one direction.0150

This particular reaction is irreversible under physiological conditions; notice, these other ones are reversible.0154

Most of these reactions are reversible.0160

Reaction 1, reaction 3 and reaction 4, under physiological conditions, are irreversible; and we will talk about that a little bit later also.0164

The first step is the conversion of oxaloacetate to citrate; that is the first reaction.0171

Now, citrate loses water, and it becomes something called cis-aconitate.0177

Now, notice, I have reaction 2 and reaction 2.0183

The conversion is actually from citrate to isocitrate.0186

That is actually reaction 2, but it takes place through an intermediate called cis-aconitate.0190

In some illustrations for the citric acid cycle, you may not see this.0195

In the individual reaction, they will show you what the intermediate passes through.0199

In this particular case, I thought it would be nice to actually include it in the citric acid cycle.0203

The conversion is citrate to isocitrate, but it passes through this thing called cis-aconitate.0208

Water leaves; water comes in again, and you get the isocitrate.0214

OK, now, here is your first oxidative step and decarboxylation step.0219

In this case, NAD+ oxidizes the isocitrate to alpha-ketoglutarate, and not only does it oxidize it, it also decarboxylates it.0224

It takes away one of the carbon dioxides; that is why you have a CO2 leaving and you have an NADH leaving.0234

The things that I have put squares around, the CO2 here, the NADH, CO2, FADH2, here and here, these are the important things that you want to concentrate on in the citric acid cycle.0239

These are the things that end up leaving and these are for example...well, we will talk about what they do in just a second.0250

Reaction number 3: isocitrate to alpha-ketoglutarate.0257

Reaction number 4: it is another decarboxylation, and it is another oxidation, and again, irreversible under physiological conditions.0260

We have alpha-ketoglutarate, which is converted to succinyl-CoA.0268

Now, the succinyl-CoA is transformed into succinate, and in this particular case, notice that GDP plus an inorganic phosphate is used to actually produce a GTP.0273

In this particular case, GDP produces the GTP, and the coenzyme A leaves.0286

ATP is also possible to produce here directly, depending on the particular isozyme that is used in this reaction.0293

It will either produce GTP directly or ATP directly.0300

But ultimately, the GTP is converted to ATP in subsequent reactions in the body.0304

OK, so now, the next reaction, the no. 6 reaction, again, we have an oxidation this time by FAD, is reduced to FADH 2, and that ends up leaving.0309

It is succinate to fumarate; water comes in, fumarate to malate, and then, the final oxidation, malate to oxaloacetate, NAD+ releasing NADH.0320

The NADH is here, these 3, and the FADH2s, those are, of course, carrying the high energy electrons from the oxidation.0331

Those ends up being funneled into the electron transport chain for oxidative phosphorylation, for complete oxidation to water.0339

OK, and there you have it, oxaloacetate, and then the cycle starts all over again.0349

Acetyl-S-CoA comes in; it condenses with the oxaloacetate, and it runs through this process.0353

What you want to learn is the sequence.0359

Acetyl-CoA + oxaloacetate or you want to start...I usually start with citrate, myself: citrate, cis-aconitate, isocitrate, alpha-ketoglutarate, succinyl-CoA, succinate, fumarate, malate, oxaloacetate to start the cycle all over again.0364

This is the big picture of what is happening; again, concentrate on the things that are leaving.0378

Reaction 1, reaction 3, reaction 4, irreversible under physiological conditions; the rest of them are reversible.0384

The formation of NADH, NADH, NADH, 3 times, the formation of FADH2 once, and the release of 2 carbon dioxides, and the formation of 1 guanosine triphosphate or adenosine triphosphate.0391

OK, now, I am going to reproduce this picture on the next page, but now, I am going to deal just with the structures.0404

I would like you to see what the structures of these molecules look like.0410

I do not have all the other information, the H2O, the CO2.0414

I just wanted you to see what the structures look like just to get a global view, and then, of course, we will deal with the individual reactions themselves- not a problem.0417

OK, here we go, oxaloacetate, again, citrate, cis-aconitate, isocitrate, alpha-ketoglutarate, succinyl-CoA, succinate, fumarate, malate and back to oxaloacetate.0424

Alright, oxaloacetate is this molecule right here, and it is going to condense with the acetyl-CoA; and what I have done is, I have written the acetyl-CoA in red.0438

OK, this is the group that is actually going to attach because coenzyme A is going to leave.0449

I have written that group in blue; now, notice, blue, blue, blue, blue, blue.0456

At this point, I did not forget to put this into blue.0460

At this point, what you end up having is a symmetrical molecule.0464

Once we get to the succinate, we are not going to be able to tell anymore which acetyl group, CH2, COO-, whether it is this one or whether it is this one because, now, the molecule becomes symmetric.0468

And now, you cannot tell which of these acetyl groups actually comes from the original acetyl-CoA.0480

Up to here, you can; that is another important point for this.0487

Again, we go to reaction no. 1; we form citrate, and again, this is the acetyl group that comes from the acetyl-CoA.0492

We have got this; a water leaves to form a double bond, the cis-aconitate intermediate, and we end up forming the isocitrate.0499

Really, all we have done is we have taken this OH group from this carbon, and we have moved it to this carbon.0505

We have switched the OH and the H.0511

Let me actually make one little change here.0515

Let me go ahead and write the H that way because that way, the OH and the OH switched0520

That is why it is citrate and isocitrate; OK, reaction no. 3.0525

This is one of the decarboxylations; I did write the CO2 leaving this one because these are important.0530

These are the 2 decarboxylation steps, 2 of the oxidation steps.0534

Isocitrate becomes alpha-ketoglutarate; notice, what has happened here.0538

A CO2 is gone, right?0541

We have taken this CO2 away, and we have taken this OH, and we have oxidized it with the dehydrogenase.0545

We have turned it into a ketone, a carbonyl, so we have oxidized that carbon.0551

OK, we lose another CO2; we lose this one.0555

The carbonyl stays, but we oxidized that carbon with an acetyl, I am sorry, with a coenzyme A group- the S, a further oxidation.0562

OK, now, you have the succinyl-CoA, and at this point, it is converted to succinate, which is your symmetrical molecule.0572

And from here, it goes to fumarate, double bond, and then here, OH is attached, malate; and then, of course, oxidized to oxaloacetate, and then, it starts again.0579

These are the structures; again, this is citrate.0590

This is the cis-aconitate; here is the isocitrate.0594

This is the alpha-ketoglutarate; this is the succinyl-CoA.0598

This is the succinate, fumarate, malate and oxaloacetate, and here is your acetyl-CoA.0603

Just, sort of, take a look at this, whether you want to use this particular diagram.0612

Again, I encourage you to take a look at the diagrams in your book.0617

I think it is always great to see multiple diagrams, not just one, because each one brings just something a little subtly different.0621

And there might be something in there that strikes you, that speaks to you, that maybe is more comfortable for you, that makes more sense to you.0626

Maybe there is more room, and maybe it is clearer; maybe the structures, somehow, make more sense to your particular eye.0634

It is not a problem; what is important is, again, the cycle, the sequence and what is going on where.0640

OK, let’s go ahead and say a couple of things about this - a couple of things to note - and then, we will start with the reactions themselves.0649

OK, things to note, let’s go ahead and do this in black.0658

Well, the first thing you want to note is that steps 1, 3 and 4 are irreversible under physiological conditions.0667

That is why they have those single arrows.0677

And again, when we see reactions that are irreversible, that should be a clue that these reactions tend to be points of regulation for the particular cycle.0688

It is difficult to regulate a reversible reaction because, again, it goes back and forth.0702

It is not difficult to regulate an irreversible reaction because we can control the extent to which it moves forward or does not move forward.0706

Irreversible reactions in biochemistry are points of regulation for that particular metabolic pathway.0715

OK, now, steps 3, 4 and 8 are oxidations that yield NADH, are oxidations yielding NADH, the high energy electrons that pass to the electron transport chain.0725

Now, step 6 is also an oxidation, but it yields FADH2 - remember that flavin adenine dinucleotide - oxidation yielding FADH2.0750

Now, step 5, can produce, as we said, ATP or GTP directly depending on the isozyme that is used.0771

You Remember isozymes, they actually catalyze the same reaction, but they do it under different circumstances, maybe a slightly different substrate, things like that; but it is the same enzyme.0792

I am sorry, it is not the same enzyme; it catalyzes the same reaction.0801

The enzymes themselves are close to being identical, but they are not quite identical.0805

They have a different primary structure, a different amino acid sequence, but they do the same thing depending on the isozyme, yes.0810

OK, and finally 2 CO2 molecules are released.0818

We have 2 decarboxylations, and they take place in steps 3 and 4.0828

Steps 3 and 4- very, very important steps in the citric acid cycle.0834

OK, now that we have a nice over view, a couple of things that we want to keep in mind.0838

Now, we can go ahead and start talking about the reactions themselves.0844

OK, so let’s go ahead and look at reaction 1; I think I will go ahead and do this in blue.0848

Reaction number 1, this is the formation of the citrate.0854

This is going to be condensation of the oxaloacetate and the acetyl-CoA for the formation of citrate.0858

Woo, biochemistry, there is a lot of molecules floating around with lots of names.0868

OK, we will say formation of citrate.0872

This is a condensation reaction, and then again, a condensation reaction just means we have taken 2 molecules and we have put them together somehow.0879

This is a condensation reaction.0886

OK, let’s go ahead and write CH3.0892

Now, let me do it this way; let me start with the hydrogens on the left; H3C, C, O, S and CoA.0897

We have acetyl-CoA is our first reactant, and then, we have, let’s go ahead and do C, C, C, C.0907

Let's go ahead and do that, and let’s put an H2 there.0917

We have a carbonyl there, and then, we have that group.0923

Let’s go ahead and number these carbons actually; I am going to go ahead and number them 1, 2, 3 and 4.0927

It is going to be important because we want to keep track of which carbon is attaching to which carbon because this is a condensation reaction.0933

It is going to be important; OK, these are the 2 reactants.0941

Let me go back to blue here, and let me go ahead and draw my little arrow, and what is going to come in is H2O, and what is going to leave is CoA, S, H.0944

What is going to leave is the coenzyme A, and the enzyme that catalyzes this is citrate synthase; and the final product that we get is the following.0957

Let me go ahead and do that one in blue also; let me go C, C, C.0972

Well, I wonder if I should do that in a different color.0982

Should I do that in a different color or not?0990

Yes, you know what, I will go ahead and do that in a different color; that is not a problem.0992

I will go ahead and put C there, but for the rest, I probably will not.0995

C, let’s just go ahead and put these on here first, H2, and this is going to be OH.1001

This is going to be that one, and now, let me do this in red.1011

Actually you know what, no, I am going to go ahead and keep it in blue.1019

This is going to be CH2, and this is going to be COO-.1023

OK, what we have here is this; oh, let me number my carbons again.1030

This is 1; this is 2.1036

This is 3, and this is 4, so 1, 2, 3, 4.1039

Now notice, this carbon right here, that is this carbon right there.1043

This acetyl group, the methyl of the acetyl group - not the carbonyl carbon - ends up attaching to the no. 2 carbon of the oxaloacetate.1050

That is what makes this really, really an interesting reaction; what we have is this one right here.1061

This acetyl group attaches to the no. 2 carbon, not the no. 1 carbon or any other.1066

You still have this CO2 group here; you still have this CO2 group, and then, you end up with this molecule that has 3 CO2 groups attached.1072

OK, now, let’s go ahead and write the ΔG for this reaction, so we have it for reference- -32.21081

This is kJ/mol- clearly, highly exergonic, irreversible under physiological conditions also, not just under the standard conditions, which is represented by that.1091

Acetyl-CoA condenses with oxaloacetate.1102

The methyl group of the carbon, I am sorry, the methyl group of the acetyl-CoA actually attaches itself to the no. 2 carbon of oxaloacetate, and we are left with this molecule right here, which is our citrate.1106

This is citrate; this molecule here is acetyl-CoA.1120

I will write acetyl-S-CoA, and this right here, is our oxaloacetate- there you go.1127

That is the entry into the citric acid cycle.1137

Now, let’s go ahead and talk about the mechanism for this reaction- very, very interesting mechanism.1141

Let’s do that on the next page, and I think I am going to go to black ink for this one.1149

This is going to be the mechanism, and again, some of your teachers will have you memorize this mechanism and know it and be able to reproduce it.1153

Some of them, perhaps, just want you to see it; some of them will not really care about the mechanism at all, but it is important to be able to present it.1161

I would like you to see it; it is very, very important to get used to this, particularly those of you who will go on to graduate school, pharmacy school, things like that.1168

You have to get comfortable with these organic mechanisms- very, very important.1176

It will put you way ahead of the crowd if you can handle, at a very least, understand and follow a mechanism without confusion.1181

OK, let’s go ahead and draw out some molecules here; let’s draw out our oxaloacetate, C.1188

I am going to draw out this way; I am going to put just so we have a clear idea of what is reacting with what, and I will go ahead and put the C, H, H, H, and then, this is a C, our carbonyl, our S and our CoA.1196

OK, now, let’s go ahead and see if we cannot...you know what, let me draw out this down a little bit.1217

Yes, let me draw it down just a little, C, O, O, S and CoA.1232

Now, let me go ahead and draw something like that.1243

OK, so let me go ahead and let me do these enzymes in blue.1253

C, O, O, this is going to be Asp 3,75, that particular amino acid .1259

This is the enzyme right here. and this is the active site of the enzyme.1271

This is the citric synthase enzyme, and over here, we are going to have...let me see; let’s go 1, 2, 3, 4, 5.1276

This is going to be our histidine 3,20.1292

We have an N, and we have an N.1297

This is an H; that is an H.1301

And, of course, we have a little positive charge there because you have Hs attached to this histidine.1303

And let’s go ahead and do the same right here.1308

Let’s go that way, that way, that way, that way, that way.1312

Let’s go ahead and put an N there, an N there.1315

We have an H, and we have an H; there is a positive charge that is distributed between these 2.1319

That is why I wrote it that way, and this is going to be histidine 2,74.1325

This histidine residue on the enzyme, this histidine residue and this ASP residue, now, we have the active site; and, of course, this is the enzyme right here.1331

Let me do this in black.1341

This is the enzyme; that is the active site.1348

OK, here is what happens; let me make this H a little clearer.1352

OK, this, let me do the mechanism in red.1357

It is nice to have all these colors available.1363

That takes that, pushes these electrons here, pushes these electrons here, pushes those electrons onto nitrogen.1367

What you end up with is the following; now, let’s go back.1375

Let’s go ahead and draw the enzyme like that.1380

Now, what we have are the following molecules; let’s go ahead and draw our oxaloacetate again.1386

This is going to be C, COO-.1390

We have our carbonyl; we have our CH2.1394

We have our carbonyl again, and now, over here, this has rearranged itself.1398

Now, we have a C double bonded to a C.1403

We have an H; we have an H because we lost that H.1410

We still have our S, and we have our coenzyme A, and now, of course, we have OH - right - because it ended up taking up an H.1412

Now, we are looking at this particular molecule; let me put a couple of the electrons on there.1421

That is going to be important; now, down here, let me go ahead and go to blue and take a look at my enzymes.1426

Again, we took this H; this is our Asp 3,75, and over here, we still have our 1, 2, 3, 4.1433

Let me just draw it like this; we still have our H.1446

We have our H, and we have our histidine- still positive charge there.1452

Over here, now, what we have is - let me draw it a little further this way - here, this is N.1457

This is N; now, this is there.1467

Now, we have that - OK - and we have our H there.1469

This is our His 2,74; alright, now, what happens is the following.1478

Oh, let me do this in red - right - we are doing our mechanisms in red.1488

These electrons come and take that, push the electrons back down to there to reform the carbonyl.1490

Reformation of a carbonyl is, it wants to form; the carbonyl is a very, very stable molecule.1498

Now, it pushes these electrons over here, not onto the electrons, onto that carbon; and it pushes it, electrons there and there.1503

This N from the histidine takes this H, reforms the carbonyl.1520

OK, the electrons come back down to reform the carbonyl here, pushes these electrons out to here, so that this carbon is, now, going to attach to this carbon.1525

It is going to push these electrons out to here to grab an H that is available, and these electrons in the NH bond are going to jump onto the nitrogen to stabilize that.1536

What you end up with is the following.1547

Now, you end up with this thing attached to this thing at that carbon.1552

These 2 carbons, that carbon and that carbon, are going to be attached now because that is what this is.1559

These electrons are moving there, and they are bringing this carbon with it to attach it to this.1566

It is a condensation reaction; OK, so what you end up with is this following molecule.1571

Let me go ahead and just leave it in red; actually no, let me go back to black because we are doing this in black.1578

What you end up with is this C; now, you have the OH. right?1584

COO-, that is the oxaloacetate; now, you have the CH2, COO-S-CoA, so that carbon attached to that carbon.1592

Now, we have CH2 and COO-.1605

At this point, now, what takes place is a simple hydrolysis.1610

Water comes in; CoA-SH actually leaves.1616

Water replaces that group; what you end up with is our citrate molecule.1621

Let me draw it as C, C, C.1628

This is going to be COO-.1633

This is going to be COO-.1639

Let me go ahead and put H2 there; this has an OH.1643

This is CH2, and it is also COO-, carboxylic acid, carboxylic acid, carboxylic acid and hydroxide.1648

This is citric acid; the deprotonated, so it is citrate.1657

That is all that is, citrate, citric acid, benzoate, benzoic acid.1661

It just means that the hydrogens have been taken off.1665

OK, this oxygen right here, this oxygen actually comes from the water, just so you know.1667

I do not think it is a big deal but it is nice to know where it comes from.1674

This O, it comes from the water because of the hydrolysis.1679

This water is going to be attacking this carbon; it is going to be breaking this bond.1687

Water is going to attach; it is going to lose one of its protons.1694

It is going to lose 2 of its protons actually, and then, this S right here, that is what leaves.1697

This is that, and this comes from here.1703

This comes from here - OK - comes from the water.1708

There you go; this is citrate.1713

OK, and at this point, you just have release by the enzyme- that is it.1717

That is the mechanism; OK, now, let’s move on to reaction no. 2.1727

Now that we have our citrate molecule, let’s go ahead and go back to black.1735

Now, let’s go ahead and write our citrate, CH2, COO-.1741

We have C, C.1749

Let me draw it a little bit over to the right here, so C, C, C and C.1753

I have got CH2 - woo, these carbons, oxygens, hydrogens, they are making me crazy - COO-.1764

I have got COO-, and I have got my OH, - right - and I have got my...let me go ahead and draw both hydrogens individually, and, of course, I have my COO-.1772

This is our citrate.1783

OK, now, let’s do this.1790

The citrate is going to pass through an intermediate; we are going to go from citrate to isocitrate, and we are going to pass to an intermediate called cis-aconitate.1794

OK, it is going to go like this.1802

I wonder if I should do it as 3 here and here.1807

Well, let’s see if I can get this actually all in one line.1813

The enzyme that catalyzes this is the aconitase, and H2O is going to leave.1820

It is going to be this H2O that is going to leave; well, let me write the reaction, and then we will see what happens.1827

So, C, C, C, C, C, and this is actually a double bond.1835

This is CH2, COO-, and this is going to be COO-; and this is going to be COO-, and this is 1 to - oh no, this is, wait - 1, 2, 3, 1, 2, 3.1842

No, this is H not C; there we go, the way you, sort of, draw it, and then, what happens is, water comes back in.1862

This is our cis-aconitate, and then, water comes back in; and you end up with C, C, C and C.1873

You know what, I am going to do it over here.1892

This is our cis-aconitate; now, it is going to end up over here, and water is actually going to be coming in here and what you end up with is the final molecule 1, 2, 3 and 4.1897

We have CH2, COO-, and then, we have our COO- there.1915

Now, we have our H and our OH here, and we have our OO- here.1922

Basically, all we have done is we have taken this OH and H, and we have switched places- that is it.1928

We first removed the water to form the double bond and then, we added the water back to the double bond except in the other order- that is it.1936

Aconitase, that enzyme is what accomplishes this particular reaction- that is it.1945

OK, now, let’s go to reaction no. 3.1954

OK, this is another one of the irreversible reactions, and this is the isocitrate to alpha-ketoglutarate.1963

Reaction 3 is isocitrate to alpha-ketoglutarate, and this is an oxidative decarboxylation.1971

Let me go ahead and write that in blue; this is an oxidative decarboxylation.1986

Decarboxylation means we are going to lose CO2, and oxidative means that one of the carbons, either that one or another one, its oxidation state is going to rise.1997

It is going to be oxidized; let me go back to black here.2008

Let’s see, we have isocitrate.2013

Let’s go ahead and do C, C, C and C.2018

Let’s go a little bit higher up here, C, C, C, C.2024

This is going to be CH2, COO-.2032

This is COO-, and the H is here.2036

The OH is here, and the H is here and COO-.2040

OK, that is our isocitrate, and let me see.2045

Are we going to actually go through...yes, we will go through the mechanism for this one.2053

Alright, we have our NADH, so this is our oxidation.2059

This is our decarboxylation, so CO2 leaves.2063

NAD+ comes in; NADH leaves.2068

It is actually NADH + H+ - right - 2 hydrogens that we are actually removing, and this is isocitrate dehydrogenase that catalyzes this reaction, and our final product is our alpha-ketoglutarate.2072

We have got C, C, C - still a 4-carbon - CH2, COO-.2096

We have decarboxylated, so now, we have lost a CO2 group, and let me go ahead and write the carbonyl over on this side, COO-, so alpha-ketoglutarate.2107

What you have lost is this; let’s go ahead and do red.2122

You have lost this; let’s try this in red- there we go.2125

We have lost this; that is our CO2 that is left.2133

The NAD oxidized, so it took this hydrogen and this hydrogen away leaving just the carbonyl; and what you are left with is your alpha-ketoglutarate.2138

That is what is happening.2146

A handful of reactions, NAD+ oxidizing something, NAD+ oxidizing something, it takes the electrons.2152

It takes the 2 hydrogens; it is a handful of reactions that show up over and over and over again.2158

The body does not have 15 different ways of doing the same thing.2163

It usually just has 1 or 2 ways of doing the same thing, and it does it over and over and over again in different circumstances.2167

OK, this is our isocitrate.2174

OK, there you go; that is reaction no. 3.2179

A couple of things to note about this particular reaction.2187

Notes: there are 2 isocitrate dehydrogenase enzymes.2192

OK, one uses the NAD+.2213

The other uses the NADP+, and the other, not a big deal.2225

It is just the NAD+ with an extra phosphate group attached, otherwise, they are identical.2234

Now, also, the enzyme requires manganese.2241

OK, now, let’s go ahead and talk about the mechanism here.2253

Let me see, 1, 2, 3, 4, yes, it is fine; I can do it on this page.2257

Let me go ahead and do the mechanism in blue; we will start in blue.2263

Hello blue, blue; there we go.2269

Now, we have blue; alright, we have got C, C.2272

We have got C, C, C, C.2280

This is CH2, COO-, and we have C.2284

I will go ahead and write this one as that, and this is an H over here; and we have our H, and we have our OH over here, and we have our COO-2290

OK, the first step is going to be the...yes, the dehydrogenation, the oxidation.2308

This one goes that way.2314

The first step is going to be the NAD+ to the NADH2318

I will not go ahead and talk about that mechanism- dehydrogenation2323

This is the oxidation; this is the first part that is going to take place before the decarboxylation, and what you are going to end up is the following.2329

This H and this H are actually going to be taken away, and it is going to be turned into the ketone.2335

We have C, C, C and CH2, COO-, and this is going to be C.2340

I am going to go ahead and do it this way, and this is a carbonyl now; and this is COO-.2352

Now, the Mn2+ is actually going to be coordinated with those.2360

Electrons on the oxygens, they sort of coordinate with metal ions.2371

OK, now, here is where we have our decarboxylation.2375

Let’s see, we are going to have... let me go ahead and draw an arrow going out what is going to happen.2379

Here is what happens; let me do this in red.2386

These electrons come here to form CO2.2389

These electrons get pushed there.2395

These electrons get pushed onto oxygen.2400

What you end up getting at this point is the following.2404

I will go ahead and do it right over here; let me go back to blue.2410

OK, I have got C, C.2415

I have got C, C, C and C.2422

I have got CH2 and COO-.2426

Now, I have an H group, and I have a double bond here.2430

Now, I have a single bond with the electrons there, and I have COO-.2435

Now, what happens is these electrons come back down to form the carbonyl, and it pushes these electrons to go ahead and grab an H+ from solution, from an environment; and what you end up with is your final molecule, which is C, C, C, C, CH2, COO-.2440

Now, we have an H here and an H here.2468

It has been decarboxylated there; it is now a ketone group there, and you have a carboxylic acid there.2473

That is our alpha-ketoglutarate; this is alpha-ketoglutarate.2479

That is our mechanism for that particular conversion, so dehydrogenation first, the oxidation and then the decarboxylation.2486

Again, it is just the movement of electrons.2494

OK, now, let’s take a look at reaction no. 4.2498

Let’s go back to black.; let’s go ahead and draw a little line here, so reaction no. 4.2503

This is going to be the oxidation of the alpha-ketoglutarate to the succinyl-CoA, coenzyme A, releasing CO2.2512

Now, we are going to release another molecule of CO2.2537

This is another oxidative decarboxylation.2542

OK, and again, this step, irreversible under physiological conditions.2562

Let’s go ahead and do this in blue here for the molecules.2567

This one is going to look like this.2572

We have C, C, C and C.2576

We have CH2 and COO-.2581

I will go ahead and put the Hs here like that.2587

We have our ketone, and we have that, so this is our alpha-ketoglutarate.2591

Now, what happens is the following: what comes in, comes in and leaves and what leaves.2595

What comes in is coenzyme A.2605

What also comes in is, of course, the NAD+.2614

What leaves is the NADH, and what ends up leaving is CO2.2618

CoA comes in; CO2 leaves.2622

That is the decarboxylation; NAD+ comes in.2626

NADH leaves; that is the dehydrogenation.2629

That is the oxidation; what you end up with is the following molecule.2631

Let’s go back to blue, which is succinate; you have C, C and C.2635

Let’s go ahead and write it this way: H2, COO-.2643

This is H; this is H.2648

And then, over here, what we have is - yes, it is fine, I will just go ahead and write it this way - S-CoA.2652

This is the CO2 group that ends up leaving.2667

The CoA-SH is attached, now, to the carbonyl, so all I have done is that I have written this ketone vertically instead of horizontally, so here.2673

Now, the decarboxylation is the loss of the CO2.2680

The oxidative decarboxylation, the oxidation part is...well, what we have done is this carbon is double bonded to an electronegative atom.2684

Now, it is double bonded to oxygen but also single bonded to S, so it has been oxidized further.2692

That is the oxidative part of the oxidative decarboxylation; OK, now, the enzyme that catalyzes this - let me go ahead and do this in red - this is called the alpha-ketoglutarate dehydrogenase complex.2699

This is not a single enzyme; this alpha-ketoglutarate dehydrogenase complex is very, very, very similar to the pyruvate dehydrogenase complex that we talked about previously for the conversion of the pyruvate to the acetyl-CoA.2723

It also consists of its own E1, E2, E3 in multiple copies.2739

It also uses all 5 of those coenzymes that that enzyme used.2745

They are very, very similar; they are not the same enzyme, but they do have a common ancestor.2751

So, evolutionary, they are from the same place; they do the same thing.2756

They do it the same way; I am not going to go through the mechanism for this one.2760

If you want to see the mechanism for this one, just go back one lesson, and take a look at that mechanism.2764

Remember when we had that arm swinging around, E1 to E2 to E3, and that is what is going on there.2768

OK, alpha-ketoglutarate dehydrogenase complex converts the alpha-ketoglutarate to our succinyl-CoA.2776

Let’s go ahead and say a couple of words about this - just some notes here - and we will go ahead and close out this lesson with this reaction and pick up the rest of the citric acid cycle in the next lesson.2790

This reaction is essentially the same as the PDH reaction, the pyruvate dehydrogenase.2808

Again, it is decarboxylation + oxidation of the carbonyl of the ketone to a thioester-S-CoA.2825

That is what you are doing.2851

This enzyme is very much like the PDH.2856

I am sorry; this complex is very much like the PDH complex in both structure and function.2868

OK, it has its own enzyme 1, enzyme 2, enzyme 3 in multiple copies.2888

It uses the same 5 coenzymes.2906

They are not the same enzyme, but they do come from a same evolutionary ancestor because they do the same thing.2920

They do it the same way; they are arranged the same way, but they catalyze, sort of, the same reaction as far as the class of reaction, but of, course, they have a different substrate, but we do not call the isozymes or isozymal complexes.2926

It is just a different complex; the alpha-ketoglutarate dehydrogenase complex, the pyruvate dehydrogenase complex.2940

Those are the first 4 reactions of the citric acid cycle; we will see you next time for a discussion of the final 4 reactions of the citric acid cycle.2950

Take care; thank you for joining us here at Educator.com, bye-bye.2958

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