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Raffi Hovasapian

Raffi Hovasapian

Citric Acid Cycle III

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 (8)

1 answer

Last reply by: Professor Hovasapian
Tue Nov 15, 2016 3:46 AM

Post by Akouvi Ognodo on November 14, 2016

Good evening Sir,

Do you have any lecture about how these pathways, from Glycolysis to the citric acid cycle are controlled?

Thanks!

1 answer

Last reply by: Professor Hovasapian
Fri Feb 26, 2016 4:08 AM

Post by Vincent Bedami on February 23, 2016

I am having a problem starting a question and I am hoping you can help.

If you have a solution that contains the pyruvate dehydrogenase complex and all of
the enzymes of the citric acid cycle, but none of the intermediates of the citric acid.
If you add 3.0 mM each of pyruvate, coenzyme A, NAD+
, FAD, GDP, and Pi
(inorganic phosphate), how much CO2 would be produced?
Assume all of the enzymes are 100% active.

1 answer

Last reply by: Professor Hovasapian
Mon Dec 9, 2013 5:02 AM

Post by Jennifer Parkinson on December 7, 2013

Once again you have helped understand difficult concepts with ease - thank you for the great videos. My biochemistry exam is on Monday and I think I will pass thanks to these lectures.

1 answer

Last reply by: Professor Hovasapian
Sun Nov 24, 2013 7:09 AM

Post by tiffany yang on November 23, 2013

I remember that oxaloacetate uses PEP carboxykinase to be PEP in gluconeogenesis, so for PEP to become oxaloacetate, do we also use carboxykinase like the arrow listed in the slide? or should the arrow be the other way around for enzyme two? Thanks Raffi This is amazing. you are amazing.

Citric Acid Cycle III

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 & Mechanism 0:21
    • Reaction 5: Succinyl-CoA to Succinate
    • Reaction 5: Reaction Sequence
    • Reaction 6: Oxidation of Succinate to Fumarate
    • Reaction 7: Fumarate to Malate
    • Reaction 8: Oxidation of L-Malate to Oxaloacetate
  • More On The Citric Acid Cycle 17:17
    • Energy from Oxidation
    • How Can We Transfer This NADH Into the Mitochondria
    • Citric Cycle is Amphibolic - Works In Both Anabolic & Catabolic Pathways
    • Biosynthetic Processes
    • Anaplerotic Reactions Overview
    • Anaplerotic: Reaction 1

Transcription: Citric Acid Cycle III

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

Today, we are going to continue our discussion of the citric acid cycle.0004

Excuse me; in the last lesson, we talked about the first 4 reactions of the citric acid cycle.0008

Today, we are going to talk about the last 4, close out the cycle, and then say some final words about...well, fill in some of the gaps about what is going on.0012

Let's just jump right on in with reaction no. 5.0021

We left it off at reaction no. 4 with the formation of the succinyl-CoA.0025

Now, we are going to go ahead and start with reaction no. 5.0030

Let me go ahead and do this one; let's go ahead and just start with blue today, why not?0034

Reaction no. 5, this is going to be the conversion of the succinyl-CoA to succinate, and the reaction looks like this.0039

We have 1, 2, 3, and we have our 4, COO-.0057

We have a CH2, CH2, and I will go ahead and put the carbonyl here, S-CoA.0067

And this one in walls, this is the reaction where we actually form our guanosine triphosphate or our adenosine triphosphate.0079

I will just go ahead and write is as the GDP + PI that actually comes in, and what leaves is the GTP; and another thing that actually ends up leaving is the coenzyme A.0090

OK, and what you end up with is the following molecule.0108

You have C, C, C and C.0112

Now, we have our symmetric molecule; now, it is at this point where we can no longer tell which one of these carboxyl groups actually is the one that came from the original acetyl-CoA.0117

At this point, we cannot tell anymore.0130

OK, let's take a look.0134

Let me go ahead and write what they are; this is succinyl-CoA, and this is our succinate.0141

OK, let me go back to blue.0152

Now, the hydrolysis, if you remember from the bioenergetics chapter, a thioester, the carbonyl and this bond right here between the carbon and the sulfur, it is a very high-energy bond.0158

So, when you break that bond, there is a lot of energy that is released.0172

It is the energy released upon breaking that bond that has enough to actually form GTP, which in and of itself, is a highly endergonic reaction.0179

Again, we are attaching an endergonic reaction to a highly exergonic reaction using that energy to form the triphosphate.0187

OK, the hydrolysis of the high-energy thioester bond of succinyl-CoA drives the synthesis of GTP, and I will just put ATP in parentheses.0197

You know what, no, let me just go ahead and leave it as GTP.0236

We will talk about the ATP in just a little bit; here is the reaction sequence.0240

OK, we have our C, C, C, C.0251

This is OO-; this is H2.0257

This is H2; we have our carbonyl.0261

We have our S-CoA, and this is, of course, attached to the particular enzyme.0265

OK, and this enzyme...what ends up coming in and leaving...inorganic phosphate ends up coming in, and the CoA enzyme actually ends up leaving.0278

This inorganic phosphate ends up phosphorylating this thing.0294

They just switched places, so what you end up with is the following molecule.0299

You end up with C, C, C and C.0303

This is OO-; this is H2.0307

This is H2, and what you end up with is O and PO32-.0310

This CoA group is replaced by this phosphoryl group.0317

Yes, that is exactly right, and it is still attached to the enzyme; and let me go ahead and put that there.0324

Now, at this point, we will rewrite that.0335

We have C, C, C, C, COO-, H2, H2.0343

We have the carbonyl; we have the S-CoA, and we have its attachment to the enzyme and a histidine residue on the enzyme.0350

What ends up happening is...what you end up with is actually not the CoA.0363

Sorry about that; we just phosphorylated that.0369

We actually have an O, and we have a PO32-.0375

That is what we have; what we end up getting is we actually end up transferring this phosphoryl group to the histidine residue, and we actually end up spitting out what is left over.0381

What you end up spitting out is the molecule COO-, H2, H2 and COO-.0391

Though this is our succinate molecule, this is what is produced.0404

What you end up with is an enzyme attached to a histidine residue that has a phosphoryl group attached to it.0410

Now, at this point, here is where the GDP comes in, and it actually takes this to become GTP reforming the enzyme histidine, which can, now, continue on doing what it does.0420

That is it; that is all that happens.0442

Now, the GTP that is formed, actually, the GTP that is formed, it can react as follows.0445

GTP + ADP, they can actually switch the phosphoryls to form ATP + GDP, and the enzyme that catalyzes this is called nucleoside diphosphate kinase.0452

Here is our nucleoside diphosphate kinase; we are attaching a phosphoryl group to it to produce the ATP.0481

So, even if it produces ATP, one of the isozymes actually produces ATP directly instead of GTP, well, that is fine.0487

It can do it directly, but if it produces the GTP, well, a GTP ends up reacting with the ADP to ultimately form adenosine triphosphate.0494

The ultimate effect is you are still forming adenosine triphosphate.0503

OK, now, we are almost there, so reaction no. 6.0508

Let's go ahead and go back to black here, so reaction no. 6: oxidation of succinate to fumarate.0512

We have got C, C, C, C.0536

We have that, and this time, I am going to actually write the individual Hs so that we see it, OO-; and what you end up with is...OK.0543

Here is where FAD actually comes in, and what leaves is the FADH2.0557

This is an oxidation by flavin adenine dinucleotide.0563

This is succinate dehydrogenase.0569

It is going to end up pulling off a couple of these hydrogens here- this one and this one or this one and this one, depending on how you look at it - and what you end up with is this very, very interesting molecule, double bond, and it is actually a trans, not a cis.0574

You remember alkene nomenclature - trans - the main groups are opposite each other.0594

This is the fumarate, and this is the succinate.0600

We pulled off a couple of these hydrogens - either this one and this one, or this one and this one, or this one and this one, it does not matter how you look at it - to produce this trans molecule, which is fumarate.0606

OK, now, reaction no. 7: fumarate to malate.0619

Now, what happens is the following; you take this one and you add water.0632

I will do it as HOH, just so you can see what actually happens; this is catalyzed by fumarase, and what you end up with is the following: C, C.0652

I will go ahead and write is this way, and I will just put H here and H here.0678

Because there are 2 Hs attached to the same carbon, there is no chirality at that molecule, so I am not going to actually represent any of it with the dashes and wedges.0683

What you end up forming actually here is the L-malate from the fumarate, and here is what it actually passes through.0691

What actually ends up happening is the following; it passes through, apparently, a carbanion intermediate.0703

So, what you have is C; you have the C, the OH, the H, the COO-.0711

There is a minus charge there, COO- and H.0722

Apparently, what happens is that the hydroxy actually comes in, and it attacks this carbon pushing these electrons on the carbon to form a carbanion - a carbon that is actually carrying a negative charge - and at that point, what you have is an H+ come in.0726

This will actually grab an H+ from some source, and then, it produces the L-malate.0743

Apparently, it does pass through this carbanion intermediate, but that is it- OK, nice and straightforward.0750

Now, notice something about this, this is the trans isomer.0757

Fumarase is highly stereo-specific.0760

There is another isomer, this; there is this cis isomer, right?0763

There is this one.0767

Fumarase will not take that and convert it to L-malate.0775

It is highly stereo-specific; that is what enzymes are.0780

They are very, very, very specific about what they want and what they will react with.0783

Fumarase is highly stereo-specific meaning it only will deal with a specific stereo isomer of the molecule, and only catalyzes the conversion of trans isomer, which happens to be the - we are going from...yes - fumarate, the trans isomer.0787

Yes, not the cis isomer, which is actually called maleate, in case you wanted to know.0840

OK, reaction no. 8: this is going to be the oxidation of malate to oxaloacetate.0856

This is the final reaction, the oxidation of L-malate to oxaloacetate to begin the cycle again.0865

We have got...let's see, C, C, C, C.0879

This is OO-; this is H2.0886

Let's go ahead and put the OH here; let's go ahead and put the H here.0891

Let's go there; OK, and again, the oxidation here is the electron carriers NAD+ releasing NADH, and this is catalyzed by malate dehydrogenase, and by now, we are very, very, very familiar with what dehydrogenases do.0896

They take hydrogens away across bonds, so we are left with C, C, C and C.0919

That is OO-; that is H2.0927

This is that, and this is that.0932

This is the L-malate.0936

This is our oxaloacetate, final.0942

This is not an infinity sign; this is a carboxyl group.0948

OK, the ΔG for this particular reaction equals 29.7kJ/mol.0955

How is it that I have this highly endergonic reaction, and yet I have this reversible condition here?0963

How is it that this reaction even actually moves forward?0969

That does not make sense; well, here is how it makes sense.0972

Under physiological conditions, the product, which is the oxaloacetate, is removed by reaction 1 of the citric acid cycle, right?0977

Oxaloacetate now condenses with acetyl-CoA; that is a highly exergonic reaction.1003

Everytime the oxaloacetate is actually formed in this circumstance, the oxaloacetate is pulled forward.1008

It is used; it is pushed forward in this citric acid cycle leaving an emptiness here.1015

Le Chatelier’s principle pushes this reaction forward, even though, thermodynamically, it might be unfavorable.1021

Under cellular conditions, it is favorable- highly favorable, in fact.1027

Reaction 1 of the cycle, that is what is going on there.1030

OK, now, let's talk a little bit about all the energy from all of these oxidations.1040

We have all of this oxidation taking place.1047

We had glycolysis that ends up producing some NADH.1050

We had the conversion of the pyruvate to the acetyl-CoA.1054

We had the citric acid cycle; we produced a whole bunch of NADH.1062

We produced FADH2; what is happening with all of these?1064

Where is all of this energy going?1069

Let's do a little bit of an energy accounting and see what we can find out.1071

OK, let me go ahead and do this one in red.1075

What happens to the energy?1085

You know, I do not think I want to do this in red.1088

I think I want to do this in black.1093

Our question is "what happens to the energy form all these oxidations?".1098

Well, here is what happens.1116

NADH gives its electrons to the electron transport chain to form 2.5 ATP molecules per 2 electrons because NAD+, it pulls 2 electrons.1121

It is a hydride; the NADH, when it delivers its electrons, it is delivering 2 electrons.1147

For every 2 electrons that it delivers into the transport chain, oxidative phosphorylation, the final step, actually produces 2 1/2 ATP molecules.1151

4 electrons produces 5 ATP molecules.1160

OK, now, the FADH2, it produces 1.5 ATP per 2 electrons.1165

Now, let's start counting electrons and seeing what we have.1180

Now, we are going to count the amount of ATP that we produce in 1 turn through the entire pathway - glycolysis, citric acid cycle, electron transport chain - in other words, the complete conversion of 1 molecule of glucose to CO2 and water.1187

Oh, where is all this energy going?1206

From glycolysis to pyruvate to acetyl - well, from glucose, not glycolysis - from glucose to pyruvate to acetyl-CoA through the citric acid cycle to the electron transport chain, here is the accounting.1210

OK, the reaction of glucose to glucose 6-phosphate, we used up 1 ATP.1247

Remember, in glycolysis, 2 molecules of ATP were used up.1261

4 were produced for a net gain of 2.1266

So, we need to account for every ATP; that is what we are doing here.1270

1 ATP, I will write 1 ATP here.1273

Now, the fructose 6-phosphate to the fructose 1,6-biphosphate also uses up 1 ATP.1277

We are going to lose another ATP; again, we are just keeping a track of ATPs.1290

Now, the glyceraldehyde-3-phosphate reaction, upon its conversion in glycolysis to 1,3-biphosphoglycerate, remember, 1 molecule of glucose produces 2 molecules of the glyceraldehyde-3-phosphate, so what we end up with is, it ends up producing 2 NADHs.1296

OK, well, we said that 1 NADH actually produces 2.5 ATP per 2 electrons.1319

In this particular case, I am going to write, it is going to be either 5 ATP or +3 ATP, and I will explain the difference between these 2 in just a minute after I have actually done the accounting.1328

Now, the conversion of the 1,3-biphosphoglycerate to the 3-phosphoglycerate, that actually ends up producing 2 ATPs.1343

So, we get to add 2 ATPs.1357

It produces the ATP directly from substrate level phosphorylation.1364

OK, now, the reaction of phosphoenolpyruvate to pyruvate in glycolysis also produces 2 ATPs - each reaction, right - because we have 2 molecules of the glyceraldehyde-3-phosphate, 2 molecules of the 1,3-biphosphoglycerate, 2 molecules of the PEP.1370

Each molecule produces an ATP, so PEP to pyruvate - the overall reaction - were producing 2 ATPs, so let's add 2 ATPs to our list.1391

Now, the pyruvate to the acetyl-CoA, this one produces 2 NADHs.1400

Well, 2 NADHs produces 5 ATPs.1412

Now, we had our isocitrate reaction going to alpha-ketoglutarate.1418

That one also produced 2 NADHs.1430

That is going to produce another 5 ATPs down the line during oxidative phosphorylation.1434

OK, now, we had our alpha-ketoglutarate reaction that goes to succinyl-CoA.1444

That produces also 2 NADHs, so that is another 5 ATP molecules produced in the electron transport chain.1454

OK, I hope I have enough room here; I should have probably written a little smaller.1466

Also, let's see; we have our succinyl-CoA reaction going to succinate reaction.1470

That one actually ended up producing 2 ATPs directly- 2 GDPs, 2 ATPs.1477

That is another 2 adenosine triphosphates, right?1490

Because again, the pyruvate...1 glucose produces 2 pyruvate.1493

1 pyruvate produces 1 acetyl-CoA, so 2 pyruvates produce 2 acetyl-CoAs.1498

That is why you get the 2 ATP; that is why have all these 2, 2, 2s here.1502

I just wanted to make sure that that was clear, now, succinate to fumarate.1507

That produces 2 of the FADH2.1515

Well, 1 FADH2 or 2 electrons produces 1.5 ATP, so we have a net gain of 3 ATP for that one.1519

Now, our last one, malate to oxaloacetate that also produces 2 molecules of NADH, which accounts for 5 ATPs.1527

When I add all of the positive ATPs and negative ATPs that we used up in glycolysis, when I add all of these, my grand total is going to be - I will put it over here - 30 or 32 ATP total.1544

One pass through the entire oxidation from glycolysis, through the citric acid cycle, through the electron transport chain, actually produces a total of 30 or 32 ATP.1563

The 30 or 32 comes from that +3 or +5 that I am going to talk about in just a second.1578

That is extraordinary; 1 sugar molecule, 1 glucose molecule, 1 monomer, ends up having enough energy to produce 30 - let's just say 30, let's take the lower number - molecules of adenosine triphosphate.1584

That is a hell of a lot of energy; that should give you an idea of the amount of energy it actually takes to run the human body.1598

It is extraordinary; it is inordinate.1605

OK, now, let's go ahead and talk about this 3,5.1608

How is it that all of a sudden the 2 NADHs...why is it that we said that 1 NADH produces 2.5 adenosine triphosphates?1613

So, that is 2 NADHs produces 5 adenosine triphosphates.1621

Where is the 3 coming from; where is the little ambivalence there?1625

Here is where it comes from; we saw that the glyceraldehyde-3-phosphate to the 1,3-biphosphoglycerate reaction, that produces NADH.1629

OK, well, the NADH takes its electrons, and it gives it over to the electron transport chain.1654

The problem is, this particular reaction of glycolysis - excuse me - it takes place in the cytosol, the electron - excuse me - transport chain that takes place in the mitochondria.1660

Somehow, the cell has to find a way to get this NADH, which is outside of the mitochondria inside the mitochondria, so that it can actually deliver its electrons.1673

Well, there are 2 ways that it can do that.1682

Let's write this out, but this NADH is produced in the cytosol because the glycolysis reaction takes place in the cytosol.1688

How can we transfer this NADH into the mitochondrion, so that it can actually deliver its electrons?1712

OK, well, there are actually 2 possible ways that the cell does this.1736

There are 2 shuttle systems, a way of taking this NADH from outside the mitochondrion to inside the mitochondrion, so it can deliver its electrons.1741

The answer is: there are 2 shuttle systems exist to accomplish this.1750

Now, I am not going to go ahead and go through the shuttle systems now.1771

Later, when we talk about oxidative phosphorylation directly, we will actually draw out the shuttle system, but I just want to name them here, so that you understand, so that they are available to you, so that you know what is happening here.1777

The first one is called the malate aspartate shuttle.1790

This particular one actually produces...when the malate aspartate shuttle brings the NADH from the cytosol to the mitochondrion, this particular process actually produces the 2.5 ATP per 2 electrons, which ultimately yields 5 adenosine triphosphates.1801

The 5 comes from the transfer via the malate aspartate shuttle.1828

OK, the liver, the kidney and the heart muscles, the heart cell, the liver, kidney and the heart- that uses primarily the malate aspartate shuttle.1833

The other one is called the glycerol 3-phosphate shuttle, and this particular one, when the body uses this one, it produces the 1.5 ATP per 2 electrons; and this is where the 3 ATP comes from.1850

Now, you know where those 3 and 5 come from.1879

In liver, heart and kidney, it is going to end up producing the 32 ATP per glucose molecule.1883

In other parts of the body, where it uses the glycerol 3-phosphate shuttle to actually bring it in from the cytosol to the mitochondrion, it is going to end up producing 30 ATP per glucose molecule.1889

OK, brain uses the glycerol 3-phosphate shuttle and skeletal muscle.1901

OK, now, let's talk a little bit more...final words on the citric acid cycle up here, let's see what we can come up with.1912

Let me go back to black here; for aerobic organisms, in other words, organisms that require O2, the citric cycle is something called amphibolic, and basically, that just means it works in both directions.1928

It works in the anabolic pathways, and it works in the catabolic pathways.1956

So, it is a very, very central hub.1961

Basically, it just means it works in both anabolic and catabolic pathways.1966

What we have seen is a catabolic pathway, the breakdown of glucose.1979

OK, now, the intermediates of the citric acid cycle - in other words, all of these molecules, the citrate, the isocitrate, the alpha-ketoglutarate, the succinyl-CoA - are used as precursors for many biosynthetic processes.1988

What happens is that as this citric acid cycle is proceeding, let's say somewhere along the way, it is going to produce the alpha-ketoglutarate, well, the body will take that alpha-ketoglutarate.2032

It will siphon it off, so instead of it actually continuing on the cycle, the body will take some of it to go do what it does for some biosynthetic processes.2045

So, many of the intermediates of the cycle are actually pulled away from the cycle for anabolic pathways.2053

The citric acid cycle is very, very central.2059

It participates in catabolic pathways, as well as anabolic pathways - OK - for many biosynthetic processes.2064

Let's list some of these processes.2071

The alpha-ketoglutarate is one of the intermediates that is actually pulled away, and it can be used to produce glutamate; and glutamate can be used to form some amino acids - glutamine, proline, arginine - and it can also be used to form some of the purines.2075

OK, oxaloacetate is a very, very, very important biosynthetic precursor, and it is used to actually synthesize aspartate, which can go on to form the amino acids asparagine and the pyrimidines.2117

OK, oxaloacetate again, it can actually go on to form PEP, which can go on to form glucose if necessary; or the PEP can be used to form things like serine, glycine, cysteine and a host of other amino acids.2142

Succinyl-CoA is another one of the intermediates that can actually be siphoned off from the citric acid cycle for some biosynthetic processes- very, very important.2170

It is used to actually form the phorphorines and heme for hemoglobin and myoglobin- very, very important.2183

OK, now, here is the issue.2192

As these intermediates are siphoned off, are pulled out of the cycle to be used for these particular biosynthetic processes, whatever they happen to be, they have to be replenished somehow.2197

As these intermediates are pulled out of the cycle, they must somehow be replenished in order for the cycle to continue, otherwise, if it comes to a stop, bad things happen.2220

They must be replenished, and the body has ways of replenishing.2232

They must be replenished, so the cycle can continue.2237

Well, these reactions that actually replenish things that are taken away from a particular biosynthetic pathway, they are called anaplerotic reactions.2247

Let's go ahead and write this in blue.2259

The anaplerotic reactions, that is what they do.2264

The anaplerotic reactions, they actually replace what has been taken away.2272

OK, let me go ahead and draw a little diagram here - just like before - of the basic anaplerotic reactions.2276

We are going to start off with pyruvate to acetyl-CoA.2284

OK, what I am drawing here is the citric acid cycle version, so one of the reactions and one of the reactions.2291

One of the things that we form is oxaloacetate, of course, and another one of the intermediates is malate.2301

Now, let me go ahead and go oxaloacetate and PEP.2311

One of the reactions that actually takes place, one of the anaplerotic reactions, as oxaloacetate is pulled out of the cycle, is this one, reaction no. 1, which actually takes acetyl-CoA, and it converts it to oxaloacetate.2317

As the oxaloacetate concentration drops or is pulled away, acetyl-CoA, instead of going directly into the citric acid cycle, it directly forms the oxaloacetate.2336

OK, let me write it over here.2347

This is catalyzed by a pyruvate carboxylase reaction, pyruvate carboxylase enzyme.2352

That is the one that actually catalyzes reaction no. 1.2362

OK, again, we do not have to replace these other intermediates like the succinyl-CoA or the alpha-ketoglutarate directly.2366

We just need to make sure that the cycle does not stop.2374

So, by producing oxaloacetate, the cycle will continue and produce the alpha-ketoglutarate, the succinyl-CoA, the malate, the fumarate- whatever is necessary.2378

These are very, very important reactions, in fact, the first one is probably the most important that you should know that acetyl-CoA converted to the oxaloacetate via pyruvate carboxylase.2387

OK, this one is reaction no. 2; that is another one of the anaplerotic reactions, and this is phosphoenolpyruvate carboxykinase.2399

I need to write PEP carboxykinase.2415

Another reaction is no. 3.2425

It takes phosphoenolpyruvate, another enzyme.2429

It uses PEP under another set of reactions, again, to produce oxaloacetate.2432

It has more than one way of producing the oxaloacetate.2438

This is the PEP carboxylase reaction, and no. 4: free pyruvate.2443

This is reaction 4: malic enzyme.2458

This thing called malic enzyme will actually take free pyruvate and convert it directly to malate, so that it will actually go on and keep the citric acid cycle going.2463

OK, now, let's see; pyruvate...no wait, I am sorry.2473

A little bit of a mistake here, sorry; I have my arrows mixed up.2485

All these names are making me a little...it is not acetyl-CoA to oxaloacetate.2489

It is pyruvate to oxaloacetate because it is the pyruvate carboxylase.2492

Yes, that is one of our first bypass reactions from gluconeogenesis, if you remember right.2498

OK, reaction 1 - OK - is an important one to know.2502

I think if there is any reaction that your teacher may actually ask you to know, as far as the anaplerotics, it is going to be this one- the conversion of pyruvate directly to oxaloacetate.2521

Reaction 1 is an important one to know and to recall.2530

Recall, it is the first bypass reaction of gluconeogenesis that we talked about a couple of lessons ago.2538

We said that pyruvate + bicarbonate + adenosine triphosphate, under the action of the coenzyme biotin, which is a coenzyme for this pyruvate carboxylase, actually produces our oxaloacetate.2556

Remember, in the second bypass reaction was the oxaloacetate to phosphoenolpyruvate.2588

So, this anaplerotic reaction actually takes the free pyruvate, converts it to oxaloacetate, to replenish all of the intermediates that have been pulled away from the citric acid cycle.2593

This is the reaction: pyruvate + bicarbonate + ATP under the action of pyruvate carboxylase via the biotin - remember that biotin, that arm that swings over - to oxaloacetate.2604

If you want to take a look at the mechanism of this reaction, we talked about it back when we talked about it in gluconeogenesis.2617

OK, now, there you have it.2625

These 4 reactions, the primary ones that you probably want to concern yourself with.2631

More than any other, this is probably the one that you want to know because it happens to be the first bypass reaction of gluconeogenesis.2636

With that, we will go ahead and close out our discussion of the citric acid cycle.2644

Thank you so much for joining us here at Educator.com; we will see you next time.2647

Take care.2651

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