Enter your Sign on user name and password.

Forgot password?
Sign In | Subscribe
Start learning today, and be successful in your academic & professional career. Start Today!

Use Chrome browser to play professor video
Raffi Hovasapian

Raffi Hovasapian

Amino Acid Catabolism

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
Loading...
This is a quick preview of the lesson. For full access, please Log In or Sign up.
For more information, please see full course syllabus of Biochemistry
  • Discussion

  • Download Lecture Slides

  • Table of Contents

  • Transcription

  • Related Books & Services

Lecture Comments (5)

2 answers

Last reply by: Sally Reina
Thu Sep 7, 2017 2:07 PM

Post by Sally Reina on September 6, 2017

Hi Professor Raffi Hovasapian! Thanks for the helpful and well explained lecture :) !!

Isn't Threonine also both ketogenic and glucogenic? I was confused because my own biochemistry professor's powerpoint slides did not match up. In one slide it is glucogenic and in another it is both ketogenic and glucogenic. Then, I checked in a different biochemistry textbook were is it classified as both ketogenic and glucogenic.

Can you please confirm or clarify this for me?

Thanks so much :)!

1 answer

Last reply by: Professor Hovasapian
Tue Oct 29, 2013 5:35 PM

Post by Jennifer Parkinson on October 29, 2013

I can't tell you how much your lectures have helped me with my studies. I wish all lecturers explained things as well as you do! Thank you Professor H!

Amino Acid Catabolism

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
  • Amino Acid Catabolism 0:10
    • Common Amino Acids and 6 Major Products
    • Ketogenic Amino Acid
    • Glucogenic Amino Acid
    • Amino Acid Catabolism Diagram
    • Cofactors That Play a Role in Amino Acid Catabolism
    • Biotin
    • Tetrahydrofolate
    • S-Adenosylmethionine (AdoMet)
    • Tetrahydrobiopterin
    • S-Adenosylmethionine & Tetrahydrobiopterin Molecules
  • Catabolism of Phenylalanine 18:30
    • Reaction 1: Phenylalanine to Tyrosine
    • Reaction 2: Tyrosine to p-Hydroxyphenylpyruvate
    • Reaction 3: p-Hydroxyphenylpyruvate to Homogentisate
    • Reaction 4: Homogentisate to Maleylacetoacetate
    • Reaction 5: Maleylacetoacetate to Fumarylacetoacetate
    • Reaction 6: Fumarylacetoacetate to Fumarate & Succinyl-CoA
    • Reaction 7: Fate of Fumarate & Succinyl-CoA
  • Phenylalanine Hydroxylase 33:33
    • The Phenylalanine Hydroxylase Reaction
    • Mixed-Function Oxidases
    • When Phenylalanine Hydoxylase is Defective: Phenylketonuria (PKU)

Transcription: Amino Acid Catabolism

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

In today's lesson, we are going to be discussing amino acid catabolism, so let's just jump right on in.0004

OK, we know that we have about 20 common amino acids.0011

Now, all 20 of the pathways for amino acid catabolism, for breakdown, all converge to 6 major products.0025

All 20 pathways converge to only 6 major products.0036

When an amino acid breaks down, all those 20, there is only 1 of 6 things that it ultimately becomes, and all of them enter the citric acid cycle.0051

OK, we have alpha-ketoglutarate.0066

We have succinyl-CoA.0076

We have fumarate, and you will recognize these as citric acid cycle intermediates.0080

We have oxaloacetate.0085

We have pyruvate, and we have acetoacetyl-CoA, which actually goes on to become the ketone bodies- not a problem.0091

We will be looking at that in just a second.0105

Now, let's go ahead and define just a couple more terms associated with amino acid breakdown.0109

One of them is something called ketogenics; we refer to a ketogenic amino acid, those that are ketogenic, well, those that degrade or break down or catabolize, degrade to acetoacetyl-CoA because they can go on to form ketone bodies in the liver.0113

Remember when we discussed ketone bodies earlier - excuse me - in the liver?0157

Those are called ketogenic amino acids; they tend to ultimately produce ketone bodies, and then, we have the glucogenic, and it is exactly what you think.0165

The glucogenic amino acids are those that degrade to oxaloacetate ultimately.0178

In other words, their final form will be oxaloacetate - OK - pyruvate or the other molecules mentioned above or the other molecules, which become oxaloacetate via the citric acid cycle because they go on to form glucose in gluconeogenesis- ketogenic amino acids, glucogenic amino acids.0194

OK, let's go ahead and take a look at a diagram of amino acid catabolism.0258

We will spend a couple of minutes on this, and just, sort of, get a sense of what is going on.0265

Let's look at the legend here; these amino acids are listed around here, and as you see, this is the citric acid cycle.0270

Here is oxaloacetate, citrate, isocitrate, alpha-ketoglutarate, succinyl-CoA.0277

Back up here, here is where acetyl-CoA from pyruvate comes in to the citric acid cycle.0284

The amino acids that are in red, those are the glucogenic amino acids right here: arginine, proline, histidine, glutamine.0290

These go break down into this; this ultimately goes to oxaloacetate.0299

Oxaloacetate here can follow this path to become glucose- glucogenic, these others, glucogenic, glucogenic, glucogenic.0304

Notice the ones in purple, I am sorry, the ones in green, those are strictly ketogenic.0306

The leucine and the lysine are strictly ketogenic.0322

When they break down, they break down to acetoacetate, acetyl-CoA, and then, they will go on to form ketone bodies.0327

These are the ones that are strictly ketogenic.0340

Now, the ones in purple, they are both glucogenic and ketogenic- the phenylalanine, tyrosine tryptophan.0344

Notice here, tyrosine, phenylalanine, phenylalanine is going to be the molecule that we are actually going to talk about specifically in a little bit.0351

We are going to follow its breakdown in detail- the isoleucine here.0359

Again, you can have amino acids that are both glucogenic and ketogenic.0366

This is a nice thing to just, sort of, try to wrap your mind around just to see where things are going.0372

And again, you have your fundamental molecules that you are breaking down into the alpha-ketoglutarate.0377

The succinyl-CoA, the fumarate, oxaloacetate, these break down into pyruvate.0383

These will break down into acetoacetate- that is it.0390

This is just a centralized picture of amino acid catabolism.0394

OK, now, before we discuss the breakdown of actually 1 or 2 of these amino acids, I wanted to look at some of the enzyme cofactors that are involved in amino acid catabolism - OK - specifically the 1-carbon transfers.0398

Let's go ahead and list some of these; let me go ahead and stay with red: cofactors that play a role in amino acid catabolism.0416

OK, there is biotin; we have come across biotin before.0445

There is tetrahydrofolate - OK - H4-folate.0450

You will often see it abbreviated that way, and there is S-adenosyl methionine.0460

OK, again, these cofactors, they are involved in the transfer of 1 carbon groups, but the carbons are in different oxidation states.0474

These cofactors, they transfer 1 carbon groups in different - well, let me actually write it over here - oxidation states.0487

OK, let's take a look at biotin here; let me go back to black, I think.0521

Biotin, we have already seen this; it transfers CO2 groups between molecules.0527

In this particular case, you have a +4 oxidation state.0537

OK, and if you remember right, there are different ways to consider oxidation state for a carbon.0548

What I call a +4 oxidation state - we talked about oxidation state back when we were discussing bioenergetics - other books might call it +8 oxidation state.0555

It just depends on when they start; some people go from 0 to 8.0568

Some people go from -4 to 4; there might be some other systems.0572

Just make sure that there is a consistency; it is not necessarily that this number is incorrect or another one is correct.0576

It is just a question of your point of reference; is your point of reference going to be 0 or is it going to be -4, depending on how you are assigning oxidation states.0582

Now, regarding biotin, recall the pyruvate carboxylase reaction.0593

This was one of the cofactors in the pyruvate carboxylase enzyme, which transfers CO2 from bicarbonate to pyruvate to form the oxaloacetate.0605

We have seen this before.0639

We have seen biotin before; now, tetrahydrofolate - OK, very, very, very important cofactor - it transfers 1 carbon groups in intermediate oxidation states.0643

An example might transfer this group, or it might transfer this group.0683

C, let's go ahead and write a double bond there, H, H- something like that, less than 4, greater than -4.0692

The intermediate oxidation states carbon fully oxidized +4, it has lost 4 electrons.0705

Carbon fully reduced like methane, it has 4 hydrogen atoms, it is in a -4 oxidation state.0712

The intermediate oxidation states some of those molecules, it is the tetrahydrofolate that facilitates that 1-carbon transfer for whatever particular enzyme happens to be under discussion.0720

Now, tetrahydrofolate, we will mention as a note, it occasionally transfers a methyl group, and a methyl group is the CH3.0732

It, occasionally, will transfer that, but most of the time no.0752

Most of the time, it is going to be the next cofactor - the S-adenosyl methionine - that does most of the transfer of methyl groups.0756

Let's go back to black here; S-adenosyl methionine, otherwise known as AdoMet, this one transfers methyl groups.0764

Excuse me.0784

This one is the one that transfers methyl groups, and there is 1 more, 1 additional cofactor.0789

It is not involved in the transfer of carbon groups; it is actually involved in oxidations, but it does play a role in amino acid catabolism, and in fact, it is going to be one of the cofactors that we see when we discuss phenylalanine in just a minute.0799

It is called tetrahydrobiopterin.0813

OK, you know what, let's try this again, shall we?0826

I am going to call it H4-biopaterine, so the tetra hydro- 4 hydrogens.0835

It is involved in oxidations.0845

OK, let's see if we can see a couple of images of some of these cofactors just to get a sense of it.0853

Biotin, we have actually dealt with before, and tetrahydrofolate.0860

Let's go ahead and take a look at S-adenosyl methionine and the tetrahydrobiopterin.0865

You know what, I think I am going to actually write this out.0873

Tetra hydro, there, how is that?0877

OK, the S-adenosyl methionine, this is your AdoMet molecule.0882

All of the chemistry takes place right here, around this S.0889

Notice this S has a positive charge; this single line here, there is this CH3 group right here.0893

Because this CH3 is attached to a sulfur atom, which is electron negative, these electrons really want to be there.0902

It makes this a really, really, really good methylating agent, an agent that puts a methyl group onto another molecule, a nucleophile.0909

If you have some nucleophile, some molecule, some substrate of the particular enzyme, I will just go ahead and call it...let me go ahead and do it in red.0918

If I have some nucleophile - OK - it is going to attack here, and it is going to push the electrons onto that.0933

That is what makes this a very powerful methylating agent.0940

If we need to transfer a methyl group, put a methyl group onto a molecule...it is funny I have never really liked the word "transfer a methyl group".0945

I guess, mostly, it is just a question of your perspective, your point of reference.0954

If we are considering a particular substrate molecule, I have always thought about it as putting a methyl group on that molecule, not necessarily a transfer.0959

A transfer implies a certain equality between 1 molecule and the other, but if it is a particular molecule that you are concerned with, it is just going to be a nucleophile.0967

This nucleophile is the one that attacks the AdoMet, but really, what we are doing is we are just putting this methyl group on the nucleophile.0977

That is ultimately what is happening; in any case, it is up to you how you want to think about it, if you like the word transfer or if you want to think about it as some nucleophilic attack.0983

Ultimately, it is just a question of moving a methyl group from 1 molecule to the other.0993

All of the chemistry takes place there, and this just happens to be a picture of the tetrahydrobiopterin, just thought you should take a look at it- that is about all.0998

The tetra hydro part comes from 1, 2.1007

There is a hydrogen here; there is a hydrogen here.1013

That is where the tetra hydro part comes from- that is all.1015

And it is the same with tetrahydrofolate.1021

It is these 4 hydrogens that are here as opposed to dihydrofolate.1025

2 of the hydrogens are actually pulled away; it becomes oxidized and reduced back and forth.1028

That is what happens to it; OK, now, let's go ahead and follow the catabolism of phenylalanine.1035

I think I am going to do this in black.1043

Now, let's follow in detail the catabolism of phenylalanine.1047

OK, now, recall that phenylalanine is both keto and glucogenic.1070

Its breakdown products go on to form glucose possibly, and they can also go on to form keto bodies in the liver.1078

Recall that phenylalanine is both gluco and ketogenic.1085

Now, let's start; I think I am actually going to start on the next page so that I can do the molecule.1106

OK, I will start over there; alright, let's go ahead and draw this out, and we are going to actually list out some of the carbons that are important because we want to keep track of the carbons, so that, that, that, C, C, C, there, there, there.1111

This is going to be C, C, COO-, and we have NH3+.1128

This is our phenylalanine, and I am going to go ahead and mark off 1, 2, 3, 4.1136

Those are going to be the carbons that we want to keep our eye on.1143

1, 2, 3, 4, let me go back to black.1148

OK, now, our first reaction is...let me...slightly longer arrow here that I think I am going to need.1152

Let's go this way, and we are going to have O2 coming in.1159

We are going to have H2O coming out, and we are also going to have NADH + H+; and we are going to have NAD+, and this is going to be...the tetrahydrobiopterin is going to be the cofactor that is involved in this particular step.1165

I will write that as H - actually, I am going to do the enzyme in blue - H4-biopaterine.1186

That is the cofactor in the enzyme, is phenylalanine hydroxylase.1199

That is the first step, and what phenylalanine hydroxylase does is convert it into this molecule, converts it into tyrosine basically- another amino acid.1211

It basically adds a hydroxyl group.1223

Actually, it puts an OH group right there, so C, C, COO-.1228

This is our amino acid; this is the alpha-carbon.1237

Here is the amino group, NH3+; here is our phenylalanine up here, and the first step is the conversion to tyrosine.1241

OK, now, when there is a problem, when there is a genetic defect in this enzyme, the phenylalanine hydroxylase, that is the cause of the disease phenylketonuria.1257

I am going to go ahead over here in blue; actually, I will just leave it in red.1271

I will write PKU.1280

There are several genetic diseases along this pathway; if there are problems with these particular enzymes, it is the cause of that particular disease.1285

Let's go ahead and go back to black; OK, now that we have tyrosine, the next step in the breakdown is the following.1294

Let me go ahead and do a little arrow here; we are going to have alpha-ketoglutarate, and we are going to have glutamate, and the enzyme is going to be tyrosine aminotransferase.1301

We have seen aminotransferases before; they basically just transfer amino groups from 1 thing to another.1323

This amino group is going to go from this tyrosine; it is going to end up on alpha-ketoglutarate to turn it into the amino acid glutamate, tyrosine amino transferase, and what we end up with is the following molecule.1329

This part stays; no worries there.1348

This is OH; this is C.1354

Now, instead of the amino group, we have a carbonyl group.1357

We have C; this is OO-.1362

This is para-hydroxyphenylpyruvate.1364

This is para...you guys should be familiar with this, para-hydroxy, para, meta, ortho, para-hydroxyphenylpyruvate.1368

OK, that is the next step in the breakdown of phenylalanine, so phenylalanine to tyrosine, tyrosine to para-hydroxyphenylpyruvate.1389

Alright, let's go ahead and see what the next breakdown is going to be.1398

Let's redraw this molecule up here: boom, boom, boom, C, C.1404

Let's put that there: C, C, and COO-.1412

This was our para-hydroxyphenylpyruvate.1420

The next step is going to be...O2 is going to come in.1430

CO2 is going to leave; the enzyme that is going to be responsible for this is para-hydroxyphenylpyruvate dioxygenase.1435

Para-hydroxy - woo, these names are just crazy - phenylpyruvate dioxygenase.1446

And again, it is going to depend on your particular teacher if they want you to know the enzymes or not know the enzymes.1455

OK, what this one does is the following; it converts it into this molecule.1468

OK, let's go ahead and draw this one out; we would draw this one a little bit differently, so 1, 2, 3.1474

I will put the C there.1480

I will put that, that, that, OH, OH.1486

This is going to be C.1493

It is going to be COO-; OK, I had 1, 2, 3, 4.1498

That was the 1, 2, 3, 4 carbon; now, these carbons, there has been a little bit of a shift, little bit of a move-around, little bit of a twist.1510

This is 1; this is 2.1517

This is 3, and that is the 4 carbon, now.1520

OK, these carbons are now these carbons.1524

OK, the name for this: homogentisate or homogentisate- depending if you want to pronounce it hard or soft.1528

It is totally up to you; OK, now, let's see what we can do to this one.1539

From here, we have O2, H+.1546

OK, we have homogentisate 1,2-dioxygenase, and you end up with the following molecule.1567

Let me write this out; I am actually going to do this one in blue: 1, 2, 3, 4.1583

And then, I am going to have my 1, 2, 3 and 4.1592

Let me see, 1, 2, 3, 4; this is my no. 1 carbon.1597

I have a carbonyl on no. 2, and, of course, I have a carboxyl over there.1601

This is my no. 1, so I have got a carbonyl over here.1607

I have a double bond over here, and I have a cis configuration on this one and a carboxyl over here.1611

This is maleylacetoacetate.1619

Let me mark off 1, 2, 3, 4, 1, 2, 3, 4.1623

We are going to break that one; this is our 1 carbon, our 2 carbon, our 3 carbon, our 4 carbon.1630

We want to keep track of the carbons to see what is going to give rise to what particular molecule.1636

OK, this is maleylacetoacetate.1640

OK, now, let's go ahead and redraw this molecule.1652

Let's go 1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4.1661

This is our 1-carbon, so we have got a carbonyl over here, a carbonyl over here, a carboxyl.1671

We have a double bond here; we have that, and this is important because that is going to be a cis configuration right there.1677

In a minute, it is actually going to become a trans configuration.1686

It is going to become our fumaryl.1690

This is our maleylacetoacetate, and now, the transformation that takes place is going to be...everything is going to stay the same.1694

Let me mark my carbons again; this is going to be the 1, the 2, the 3, the 4 carbon.1712

Everything is going to stay the same, except this cis configuration on the alkene is going to be a trans configuration.1717

Now, what we have is the following.1722

Let's do 1, 2, 3 and 4, 1, 2, 3 and 4.1726

This is the no. 1 carbon, so I have got a carbonyl there.1737

I have got a carbonyl here, double bond; I am going to leave this one down below.1741

I am going to move this one up top, this OO- there, OO- here- there we go.1745

Now, we have fumaryl or fumaryl - depending on how you want to pronounce it - acetoacetate.1753

You can see where we are going to be going from here; we are going to end up splitting this molecule up into a fumarate and an acetoacetate- that is it.1760

That is all we are going to end up doing here; let me go ahead and write the enzyme that is responsible for this.1768

It is blue; it is maleylacetoacetate isomerase or isomerase.1775

It does not really matter; OK, now, let's go ahead and make our final products here.1790

Basically, water is going to come in, and it is going to split.1798

So, we have 1, 2, 3, 4; let's go ahead and break this particular bond right here, and we are going to create the following.1802

We are going to create fumarate.1808

Actually, you know what, I will just do this in blue for the fumarate, so 1, 2, 3, 4.1814

Let me go ahead and wait a minute, 1, 2.1824

Wait, yes, that is fine.1829

OK, I have got that; I have got that.1836

I have got that, and I have got that.1841

I have got this, and let me see.1848

I have got plus; now, let me go ahead and do this one in red.1853

This is going to be C, COO, C.1858

Let me see if I have got this right here.1865

It is going to be...yes, that is right, C and then COO-.1869

OK, here, we have our acetoacetate, and here we have our fumarate.1875

This fumarate here, this is going to go on into the citric acid cycle.1883

This is the part that makes it phenylalanine glucogenic.1898

This one is going to do the following, do it in red.1903

What this one is going to do...actually we will keep it in blue; that is fine.1909

We have succinyl-CoA.1914

We have succinate, and we are going to end up with our...let me do this in red.1923

We are going to be C, C, C, C, S-CoA.1935

The coenzyme A is going to be transferred from the succinyl-CoA to this acetoacetate.1941

It is going to become acetoacetyl-CoA.1947

Let me go ahead and finish off with the carbonyls here; I will go ahead and put the hydrogens here.1951

I will go ahead and put an H there, put an H there.1958

This one, it ends up either becoming acetyl-CoA and entering the citric acid cycle - this is one possibility this way - or it could go on to form ketone bodies.1961

This particular molecule can go in either direction.1975

The phenylalanine breaks down through his process, breaks down into acetoacetate and fumarate.1980

Fumarate will go on to the citric acid cycle, and then, the acetoacetate can either go on and become acetyl-CoA, which will enter the citric acid cycle, or it will go on to the liver and form ketone bodies- glucogenic, gluco, ketogenic.1989

OK, now, let's actually go back and talk about what happens in the first step, the phenylalanine hydroxylase reaction.2007

I just wanted to talk a little bit about the cofactor, the biopterin, the tetrahydrobiopterin.2017

OK, let's take a look at that again.2023

We are going to look a little bit more at the phenylalanine hydroxylase reaction, which is the first step of the breakdown.2028

That was reaction no. 1; OK, the reaction that we had was the following.2044

We had phenylalanine; I am not going to go ahead and draw these out again.2050

I am just going to write what is going on actually; let me give myself a little bit more room here.2053

OK, that was where it went from phenylalanine to tyrosine.2070

We had O2 coming in; we had H2O leaving.2075

We had NADH+ leaving to form NADH + H+, and this is the enzyme.2083

I will not list the enzyme; the enzyme is the phenylalanine hydroxylase.2095

The cofactor was the H4-biopterin.2100

Let me do it in blue; this was the cofactor.2106

We had the tetrahydrobiopterin, H4-biopterin.2109

That was the cofactor; here is what happens in this particular reaction.2116

Watch this: 5, 6, 7, 8 - OK - tetrahydrobiopterin.2123

Four hydrogens goes to 7,8-dihydrobiopaterin2137

OK, what we have is the phenylalanine.2157

Actually, you know what, I think I want to draw this one out; I am sorry.2168

I think I want to draw this one out, so I am going to actually move a couple of things around here.2172

I am going to give myself a little bit more room on the sides, so 5, 6, 7, 8 tetrahydrobiopterin goes to 7,8-dihydrobiopaterin.2179

OK, we have our phenylalanine; it is going to look like this: boom, boom, boom, boom, boom, boom, boom, C, C, COO-, NH3+.2210

I am actually going to show that particular H.2225

This is the actual reaction that takes place here; this is the O2.2229

This is the O2, and this is where the enzyme is; this is the phenylalanine hydroxylase reaction.2233

Well, I will not actually list it; the reaction that is taking place is taking place right here.2238

It is phenylalanine being converted to tyrosine.2243

I will go ahead and draw this out again; what is going to be interesting, I will write this H.2248

I will write that C, C, COO-.2254

OK, here is what is interesting about this particular reaction.2261

I specifically drew this H; that H is that H.2265

The phenylalanine hydroxylase, what it does, it attaches a hydroxy to this carbon right here, but what it does is it actually shifts.2270

It moves this particular hydrogen down one; it moves it here.2277

This is called the NIH shift- National Institute of Health; that is where it was discovered.2281

Now, let me go ahead and finish this, sort of, cyclical thing here.2287

Let me go to blue, and then, we have NADH + H+ goes to NAD+; and this particular enzyme over here is called dihydrobiopterin reductase- exactly what you think.2293

What is mentioned here, O2 coming in, H2O leaving, NADH + H+ coming in, NAD+ leaving, the actual reaction that takes place, here is the sequence.2327

This 5, 6, 7, 8 tetrahydrobiopterin, there are 4 hydrogens on this biopterin cofactor.2337

What it does is it transfers the phenylalanine hydroxylase.2344

It uses O2; OK, it attaches one of the oxygens with a hydrogen to this.2350

The other oxygen atom of the O2, it ends up reducing it to water.2357

It converts phenylalanine to tyrosine, and the process of giving up 2 of its hydrogens from 5, 6, 7, 8 tetrahydrobiopterin, it becomes 7,8-dihydrobiopaterin.2361

Now, in order to get back to its original form so that it can continue the catalytic cycle, it uses NADH.2373

OK, now, the NADH reduces the 7,8-dihydrobiopaterin to the 5, 6, 7, 8 tetrahydrobiopterin, and it is converted to NAD+.2382

Everything that you see here, this is the entire process; this is absolutely beautiful.2393

This goes here, turns into this; it uses something else to reduce so it can continue the cycle- absolutely fantastic.2397

That is what is happening in this particular reaction, the first reaction of the breakdown of the phenylalanine.2404

OK, and again, notice that the para, H, has now moved to the meta position.2412

OK, this hydrogen is this hydrogen.2416

It is not some random hydrogen; it actually moves down.2420

OK, final couple of words here about phenylalanine or actually the enzyme itself, let's go stick with blue.2425

Phenylalanine hydroxylase - OK - is one of a class of enzymes called mixed function oxidases or monooxygenases.2436

Again, with enzymes, you are going to have different names for them.2486

An oxidoreductase, we tend to call it by its more common name a dehydrogenase.2490

A monooxygenase is a more formal name; we call it a mixed function oxidase.2497

That is going to be...well, that is a really, really annoying part about biochemistry, is that multiple names for the same concept of the same enzyme especially with enzymes shows up.2502

Unfortunately, you are going to have to be aware of both; sorry.2514

OK, phenylalanine hydroxylase is one of a class of enzymes called mixed function oxidases or monooxygenases.2520

Now, what they do, they all catalyze the same thing.2527

They all catalyze the hydroxylation - like we just saw - of a substrate.2531

In other words, they attach an OH group to some carbon on the substrate.2546

They all catalyze the hydroxylation of a substrate by one of the O atoms/oxygen atoms of O2, and the other oxygen atom is reduced to water.2553

It is always going to be O2 that comes in; one atom is attached to the substrate.2583

The other is reduced to water.2590

OK, OK, now, and, of course, this particular enzyme happens to require tetrahydrobiopterin as a cofactor.2595

That is not true of all of the mixed function oxidases.2605

This one happens to require that.2609

Now, we said earlier that when phenylalanine is defective, the individual suffers from something called PKU - phenylketonuria - where phenylalanine does not follow because it cannot go through that first step of the reaction, the phenylalanine hydroxylase reaction.2613

It takes an alternative pathway for its breakdown, and it does not follow the normal degradation; but what it does is it actually exchanges its amino group with pyruvate to become phenylpyruvate, and when phenylpyruvate builds up, that is what causes the particular disease PKU.2630

Let me go ahead and just write that down really quickly, and we will finish off with that.2648

Let me go back to black; now, when phenylalanine hydroxylase is defective, the individual suffers from PKU - phenylketonuria - where phenylalanine degrades by an alternate pathway.2655

Actually, it does not really degrade; it just converts to 1 product, and that product builds up.2704

What happens is the following; I wonder if I should do it on...that is OK.2709

I guess I can do it on this page; what we have is...let's go ahead and go back to blue here.2713

We have our phenylalanine, C, C, COO-, NH3+.2720

What ends up happening is C, C, COO.2729

It ends up transferring this amino group to pyruvate.2738

The pyruvate end up turning into this, and this ends up becoming - O- - phenylpyruvate.2744

This is the phenylalanine, and this is the phenylpyruvate, which accumulates and is the cause of lots of trouble.2767

When the phenylalanine hydroxylase is defective, it takes this particular pathway, and it is the cause of PKU.2782

OK, now, in this particular lesson, in the beginning, we looked at, of course, that diagram that described the breakdown of all of the 20 common amino acids.2791

We have only looked at the specific breakdown, the details of 1 of these, the phenylalanine.2801

I urge you very, very strongly, to take a look at, at the very least, the breakdown of 2 or 3 of the other amino acids.2806

You can choose whichever ones you want; perhaps your teacher will give you a list of specific amino acids that you have to know the details of.2818

Perhaps not, but again, the idea is to...you do not necessarily have to write these down in their active form, but you should be able to follow the breakdown.2827

That is the whole idea; you want to be able to look at a particular pathway and be able to follow what is going on, not necessarily mechanistically.2839

It just depends on what it is that you have to know for your exams, but just to get a sense of the patterns that are available in all of these pathways.2846

Now, of course, each individual amino acid will break down in a different way as far as the details are concerned, but it is good to get a sense of the patterns.2856

So, I strongly urge you to take a look at, at the very least, 2 or 3 other amino acids, and just follow the path.2864

It is available in your biochemistry books.2871

Thank you for joining us here at Educator.com and Biochemistry.2874

We will see you next time, bye-bye.2878

Educator®

Please sign in for full access to this lesson.

Sign-InORCreate Account

Enter your Sign-on user name and password.

Forgot password?

Start Learning Now

Our free lessons will get you started (Adobe Flash® required).
Get immediate access to our entire library.

Sign up for Educator.com

Membership Overview

  • Unlimited access to our entire library of courses.
  • Search and jump to exactly what you want to learn.
  • *Ask questions and get answers from the community and our teachers!
  • Practice questions with step-by-step solutions.
  • Download lesson files for programming and software training practice.
  • Track your course viewing progress.
  • Download lecture slides for taking notes.

Use this form or mail us to .

For support articles click here.