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Raffi Hovasapian

Raffi Hovasapian

Acid/Base Behavior of Amino Acids

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 (23)

3 answers

Last reply by: Professor Hovasapian
Sat Apr 28, 2018 9:26 PM

Post by Swati Sharma on September 17, 2017

DR Rafi could you please explain how do you draw lines I understood the whole concept but I did not understand how do you know where the line has to go flat and where curved , I mean I understood the whole thing about deprotonation, net charge and all but I am not able to draw the curve I don't understand how to draw lines and when do they become flat and when do they jump up and when do I stop please help . In lecture you drew the curve but you did not explain how did you get that shape so it would be helpful if explain me tnx

1 answer

Last reply by: Professor Hovasapian
Fri Jun 3, 2016 8:12 PM

Post by Tammy T on May 31, 2016

Dear Prof. Hovasapian,

My questions below may look long, but it is centered around the question why pKr of the 7 AA is weaker or stronger than the pKa2 of amino group. I hope you could help me understand the chemistry of AA. I have spent a decent amount of time on them, and still have not figured out the answer. Thank you!!

-For Cysteine: Why the acidic proton in R group is more acidic than the proton in amino group? I thought the  conjugate base formed of the R group which is S- is less stable than the conjugate base formed at the amino group which is H2N: because one in charged and on is neutral. Plus, Sulfur is less Electronegative than N which should make S- conjugate base is less stable than H2N: and, in turn, make R group less acidic than amino group. What makes it the other way around?

-For Tyrosine: Why R group is weaker acid than amino group? Isn't amino group is more closer to the electron rich area COO- (the deprotonated acid), would that make amino group a weaker acid than R group since the acidic proton of amino group would less likely to leave to give a pair of electron to the area? To support that idea, the Oxygen of R group also better at stabilizing the extra lone pair of electron. Shouln't those 2 points make R group a stronger acid than amino group? Why amino group is still a stronger acid?

-For Lysine: Between the amino and the R group, why R group is a weaker acid (higher pKa) despite both have the same kind of acidic proton H3N+? I thought that since the acid was deprotonated at low pH, that would make the area around the acid electron rich already, and that would make amino group less likely to dissociate its acidic proton. Why amino group is still a stronger acid?

-For Arginine: Is the reason why the R group is such as weak acid is because the area around the acidic proton is already so electron-rich?

-For Histidine: I failed to see why the R group has such low pKa. Is it because of the ring structure which would be able to stabilize the conjugate base structure of the acidic R group?

-For Aspartate and Glutamate: Why the acid and the R group have the same kind of acidic proton which are both in the COOH group but the acid group dissociate its proton before the R group does? Is it because the acid group is closer to the EWG H3N+ (amino group)?

Thank you for your time!!

1 answer

Last reply by: Professor Hovasapian
Fri Jun 3, 2016 7:56 PM

Post by Tram T on May 28, 2016

Dear Prof. Hovasapian,

Regarding the 2 acidic protons on Amino acids, I tried to make sense of how the proton on the acid group COOH is more acidic than the proton on the amino group H3N+.

I thought that the conjugate base of the acid H3N+ which is H2N: would be more stable than the conjugate base of COOH which is COO- because neutral species would have lower Energy despite COO- has resonance structure and charge on more Electronegative atom. So that would suggest that H3N+ should be a stronger acid than COOH and H3N+ would give off its acidic H+ first. That is not the case. So what point was wrong in my reasoning?

Thank you for your amazing lecture as always. I would you could have gone into more details abt the chemistry aspect of these amino acid chemical structures.

1 answer

Last reply by: Professor Hovasapian
Sat Sep 20, 2014 8:26 PM

Post by Josh Bernier on September 19, 2014

So I'm curious, with regards to Tyrosine, why the pKr is so high? The presence of the benzene ring, allowing resonance stabilization of an anionic charge, I feel would lend itself to a much lower pKa. Am I mistaken in my thinking or is there something special occurring in the case of Tyrosine?

Much thanks!

1 answer

Last reply by: Professor Hovasapian
Wed Sep 17, 2014 10:13 PM

Post by Jenika Javier on September 12, 2014

I have another question regarding titration curve. I was just wondering, can you explain how we get the net charge?

2 answers

Last reply by: Jenika Javier
Fri Sep 12, 2014 5:54 PM

Post by Jenika Javier on September 6, 2014

Hello, I was just wondering, where did you get the PI value from in the titration curve?
Thank you!!

2 answers

Last reply by: Alex Steiner
Tue Feb 18, 2014 9:21 PM

Post by Alex Steiner on February 18, 2014

Hello, you said 8.2=8.18 so are we saying since we only have 2 significant figures for Ph that they are equal. If we knew the Ph was 8.19 then we would only have S- and no SH?

2 answers

Last reply by: Swati Sharma
Sat Apr 28, 2018 5:35 PM

Post by Alan Delez on February 1, 2014

Hi Dr. Hovasapian,

First off Great lectures!
I am coming across different pka values in my textbook. Is there a maybe a range of acceptable values? I ask this because I am expected to remember the pka table. Thank you!

1 answer

Last reply by: Professor Hovasapian
Sun Jun 9, 2013 4:53 PM

Post by Luke Frendo on June 9, 2013

Therefore, at low pH, both groups are protonated, given that there are plenty of protons in solution, now as the pH increases towards the isoelectric point, the carboxyl group will lose a proton to become negatively charged, and thus a neutral ion results. On further increasing the pH, the amino group is deprotonated. Did i get it right, because well I am still a bit confused!

Acid/Base Behavior of Amino Acids

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
  • Acid/Base Behavior of Amino Acids 0:27
    • Acid/Base Behavior of Amino Acids
    • Let's Look at Alanine
    • Titration of Acidic Solution of Alanine with a Strong Base
    • Amphoteric Amino Acids
    • Zwitterion & Isoelectric Point
    • Some Amino Acids Have 3 Ionizable Groups
    • Example: Aspartate
    • Example: Tyrosine
    • Rule of Thumb
    • Basis for the Rule
    • Example: Describe the Degree of Protonation for Each Ionizable Group
    • Histidine is Special

Transcription: Acid/Base Behavior of Amino Acids

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

Today, we're going to continue our discussion of amino acids, and we're going to talk about the acid-base behavior of amino acids.0004

This is profoundly important.0012

If you understand this, then you'll pretty much understand all of protein behavior; so let's just jump in, and see if we can completely wrap our minds around this thing.0015

OK.0028

Amino acids have two groups that are ionizable.0030

Let me go ahead and do blue here.0035

Amino acids have two groups that are ionizable.0039

OK.0055

What we mean by that is the following: that is two groups that can release and/or accept hydrogen ion depending on what the pH is.0057

In other words, an amino acid is a diprotic weak acid.0088

It has one H that it can give up, and it has another H that it can give up under different pH conditions.0093

Maybe it has already given them up, and maybe this time it will act as a weak base, and will actually take the protons- that is all this means.0100

When we say it has two groups that are ionizable, that means it has two groups that can release or accept the proton depending on what the pH happens to be.0106

In other words, it's a diprotic weak acid, weak base.0115

OK, so let's take a look at alanine.0118

Let's look at an example.0120

Let's look at alanine.0122

OK.0128

And again, the structure of alanine is: we have that, we have that, we have our amino group, and we have CH3.0129

However, I'm going to write it, fully protonated form, COOH.0141

In fact, I'm going to actually draw out the carboxyl groups so we know exactly what we're looking at - COOOH - that's it.0147

This is our first ionizable group - that's one hydrogen that can go away - and here we have our second ionizable group, so every amino acid has at least two ionizable groups.0156

One of this Hs can go away- that's all this means.0166

OK.0171

Let's follow the titration of an acidic solution of alanine with a strong base.0172

This is going to be your standard weak acid strong base titration of a weak acid with a strong base, and see what happens as we raise the pH because that's what we're doing.0200

When we're adding base to a solution, we're raising the pH; and what we're going to be doing is, we're going to be pulling off these hydrogens one at a time as the pH rises.0225

OK.0236

Again, alanine as all amino acids - I'll just write AA - are diprotic weak acids just like carbonic acid H2CO3.0239

H2CO3 releases one hydrogen to become bicarbonate, releases another one to become carbonate.0261

Amino acids, one of the Hs is released from the carboxylic acid group, another H is released from the NH3+ group- that's all that's going on here.0266

Let me see how it is that I actually wrote that weak diprotic acids, so I'm going to write it like this, then I'm going to go back to blue.0279

I'm going to use the three-letter designation, and I'm going to write the carboxyl group, and I’m going to write the NH3+ group.0289

This includes the particular R-group, so this is what we're looking at right here.0297

That's one ionizable group; that's another ionizable group.0303

Let's go ahead and see.0307

Let me go to the next page.0310

Let me redraw this so we have it on the same page: COOH, and we have NH3+- there.0311

OK.0323

Now, the carboxyl group, this one right here, the COOH group, is the stronger acid of the two groups.0325

It's the stronger acidic group of the two, and what that means is, it loses its hydrogen ion first; so it loses its H+ first- that's it - and to become COO-, right?0342

When it loses its hydrogen ion the negative charge stays back, so it becomes COO-.0376

OK.0383

The NH3+ group loses its H+ second to become NH2, so when it loses its hydrogen ion, it's taking its plus charge with it, and it leaves this one uncharged.0385

OK.0407

Now, let's go ahead and follow the titration here, so let me draw this out; and I want to make sure that I leave room at the bottom to draw a structure.0408

This axis is going to be the pH, and this axis is going to be just milliliters of OH-.0421

This is milliliters of OH-, like I'm an adding a sodium hydroxide solution or something; it’s just a volume as I add.0432

Here is what its look like.0439

I'm going to go ahead and go, something like that.0441

Here is what's happening.0451

OK.0453

I'm going to mark off a couple of points.0454

I'm going to mark an X there.0457

I'm going to mark an X there, and I'm going to mark an X there.0458

Now, I'm going to go to red- there is that, there is that, there is that, this is pKa1.0461

Here is what happens: we're going to be starting at a low pH, an acidic solution of alanine.0472

This H is attached, and this H is attached, so what we have is this particular molecule.0479

As I add hydroxide, add hydroxide, add hydroxide - well, you remember a weak acid, all of a sudden, what's going to start happening is that base is going to start pulling off this hydrogen ion from the carboxylic acid part of the amino acid, and it’s going to leave carboxylate, well, remember what we said the pKa was? - the pKa of a given weak acid of a given group, it is the pH at which the acid form and the base form are in equal concentration.0486

So, I’m just going to write a couple of things down, but I'm going to write the reaction underneath, and it will all come together.0522

The pKa1 for alanine is 2.34.0528

Well, so that's the pKa of that group.0534

This one up here, I'll call it pKa2, that is the pKa of the NH3+ group; and it happens to be 9.69 for alanine.0546

Now, I’m going to write something here called PI = 6.01, and here's the reaction that's taking place.0561

I’m going to write: ALA, COOH, NH3+.0571

OK.0586

This is going to be ALA, COO-, NH3+, and then we have ALA, COO-, and we have NH2.0588

This is a +1 charge; this is a 0 charge, and this is a -1 charge.0608

Here's what's happening: as we proceed with the titration, we start with this form, this form right here, OK; the OH is protonated, and the NH3 is protonated, we add base, we add base, we add base, were going to pull off some of this hydrogen.0621

Well, at a pH of 2.34, there is an equal amount of this form, and this form, the form with the H pulled off.0634

This is the pK1- that's this one.0643

Now, that's this right here.0650

This the first buffering region.0653

Remember, where it's flat, that's the buffering region.0657

That is when you have the base form and the acidic form.0658

In other words, the deprotonated form and the protonated form in a concentration that allows you to actually buffer.0662

It resists changes in pH, that's why it looks like this.0671

We are actually adding a hydroxide, but the hydroxide is being eaten up by this H.0675

This H is neutralizing the OH that is added, that is why the pH isn't changing, but at a certain point, this H, all of a sudden, there is no more H for the hydroxide that we add to eat up; so it actually jumps up, the pH jumps up.0680

Now, at this point, it's all in this form: negative charge on the carboxylate, positive charge here, there is a zero total charge.0695

So here, this molecule is positively charged, this is positive 1.0706

At this point it is that, and I'll talk about what the PI means in a minute.0710

I stands for isoelectric point.0714

Isoelectric means there is a zero charge- equal electricity.0715

OK, now, but notice this hydrogen is still attached.0721

I'm going to keep adding hydroxide, now, what’s going to happen is now, the hydroxy is going to pull off this hydrogen; so now, it's going to be converted to this, or this hydrogen is gone, now, this hydrogen is gone.0725

Well, during that, we have our second buffer region.0738

Now, it's the amino group that's acting as a buffer, and again, it's buffers well between about 8.69 to 10.69, here, buffers well from 1.34 to 3.34.0742

That’s the buffering region- one unit above and below the pKa;one unit above or below the pKa.0756

The reaction that's taking place is this: I'd begin with a fully protonated form, I add hydroxide, I pull off the first hydrogen, I pull it all the way off, now, I am here, now, I start pulling off the second hydrogen from the amino group, and I get to a point once I've pulled off everything, now I'm over here, now, my molecule, my amino acid has a negative 1 charge- that's all that's going on when we titrate an amino acid.0764

One hydrogen to give up, second hydrogen to give up; two buffering regions, two ionizable groups.0794

OK.0803

Now, when an amino acid exists as follows: when it exists like this C, COO-, NH3+, H, and R, I'd switched the NH3 and the R, in this particular case, this is not a Fischer projection, I wanted to see, I wanted it to be - well, you know what, actually I don’t need to do that, why don't I just stick with what we've done.0805

We have our R-group down here, and we have our NH3+ like that.0857

When it has a zero charge, when it exists in this form, it's called the zwitterion- that's it that's the name for it.0863

When the carboxyl group has been ionized but the amino group has not been ionized, negative charge, positive charge, the total molecule has a zero charge- it’s a zwitterion.0872

14:45OK.0884

In this form, the COO- group, it can, if it has to, it can accept a proton, it can accept a hydrogen ion, so the amino acid can behave as a base.0885

The amino acid, as a whole, can behave as a base because there is a group that can accept the hydrogen ion- that carboxylate group.0920

Now, the NH3+ group can give up a hydrogen ion, so the amino acid can also behave as an acid if it has to.0933

In other words, it can be both an acid or a base depending on the pH, depending on the conditions at the time, the condition surrounding the amino acid.0967

OK.0976

It is amphoteric.0979

An amphoteric substance is something that can behave as both an acid and a base depending on the environment.0981

Amphoteric is the adjective or ampholyte is the noun, so an amino acid is an ampholyte- it is an amphoteric substance.0987

OK.1003

Now, let me go to red.1004

The pH at which an amino acid is a zwitterion is called is called the PI; it’s called the isoelectric point.1008

When the first hydrogen from the carboxyl group has been completely pulled away, but none of the hydrogens from the amino group had been pulled away, the total charge on the amino acid is 0, -1, +1, they cancel the zero- it is a zwitterion.1037

The pH at which that happens, that's called the PI- the isoelectric point.1055

In the case of amino acids that have two ionizable groups, the PI is just the arithmetic mean between the two pKas- the pKa for the carboxyl group, the pKa1, and the pKa2, which is the pKa for the amino group.1061

You just add them together, divide by two, and you'll get your PI.1078

OK.1083

Now, notice how PI for alanine is 6.01.1087

Now, PIs for most amino acids or most amino acids will be in this range.1106

Now, you understand why we wrote amino acids the way that we did with the COO-, but the NH3+.1124

This is why at pH equal to about 7, we wrote our amino acids as C, H, COO-, NH3+ and R because at normal physiological pH, somewhere in the neighborhood of about 7 to 7.4 amino acids, they exist as zwitterions.1134

So, free amino acids exist in this form under normal physiological conditions.1183

OK.1188

Now, I hope that made sense.1189

You have this amino acid, it has a carboxylic acid group, it has an amino group that's protonated under conditions of low pH.1193

Both of the groups are protonated under conditions of really, really high pH.1203

Both of them are deprotonated somewhere in the middle, which is normal physiological pH.1207

The COOH group is deprotonated, but the NH3+ group is still protonated that carries positive charge to the COO- carries the negative charge.1212

Your total amino acid is zero charge zwitterion it can act as acid or base.1222

it can go both ways depending on what needs to happen in that particular environment.1226

That's what makes amino acids so incredibly powerful.1232

OK.1236

Now, some amino acids have three ionizable groups, and I'll go ahead and list them.1237

They are tyrosine, cysteine, lysine, histidine, arginine, aspartate and glutamate.1254

These amino acids have three ionizable groups because their R-group also contains something that can release or accept a proton.1281

Now, for these amino acids, you have 3 pKas.1290

We call them pK1 for the carboxylic acid group, pK2 for the amino group, and pKR, we can call it pK3, pKR.1294

They say pKR because it happens to be the group that's attached to the R-group.1305

It can be either carboxylate or it can be an amino.1310

OK.1314

Now, let's see what we've got.1316

Now, as always, the COOH that's attached to the alpha carbon, attached to alpha C, always ionizes first; so that doesn't change.1318

The pK1 always refers to the, in other words, you have an amino acid.1347

OK.1361

That particular H is the one that always ionizes first.1363

Now, well, for NH3+ and the particular R-group, it's a toss-up.1366

Sometimes the NH3 will ionize second, and then sometimes the R-group will ionize second; and then the NH3 as the pH is rising, so sometimes this will have a lower pKa than that one, ionizes first, sometimes this R-group will have a lower pKa than this group.1378

It means it ionizes first; it loses a proton first- it's just depends.1397

OK.1404

Sometimes, one or the other will ionize first, will lose its proton first.1410

A titration curve for a triprotic amino acid on that list is going to end up having three plateaus.1424

It's going to look something like this; in general, it's going to look something like this, something like that: pKa1, pK2 or pKR, depending on which one is first, and pK3 and somewhere in here you're going to have your PI.1434

Now, you can't just add them and divide by three in this case.1452

We have to experimentally determine what the isoelectric point is for these, but that's not a big deal.1455

And again, if you look in your book, you will actually see a list- all of the amino acids.1461

It will list their three letter designation, single letter designation.1468

It will give you the molar mass.1471

It will give you pK1, pK2, pKR, and then it will give you the PI and maybe some other information too.1472

OK.1480

Let's go ahead and do an example here.1481

I think this is probably the best way to do it.1483

Let me go ahead and do it on the next page.1485

So, example, we're going to take a look at aspartate.1488

In the case of aspartate, our pK1 is less than our pKR, is less than our pK2; so in this particular case, the R-group, the carboxylic acid ionizes first, releases its hydrogen, then the R-group will release its hydrogen, then the amino group the alpha-amino group will release its hydrogen as we titrate.1495

I'm going to draw out the reactions; I'm not going to do the titration curve.1519

I’m going to write out the reaction- that's what's important.1521

We want to get the structures correct: H, NH3+, we have CH2 ,and we have COOH.1526

OK.1540

We have that one, and it's going to be H3N+.1542

And again, I’m hoping that you're actually confirming all of this because there is a whole bunch of structures going on, so I might miss an H, I might miss a C, I might miss an N.1547

I hope you are confirming this.1557

OK.1560

This is C, this is COO-, and this is CH2, and this is going to be COOH, so this is pK1.1562

OK.1572

This group right here loses first.1573

Now, our second ionization is going to be pKR, so this H is going to go next1576

What we have is NH3+, alpha carbon, COO-, H, we have CH2, and we have COO-.1584

Now, we have our final equilibrium which is going to be pK2, which is going to be the amino group, and we are going to end up with a C, a COO-, an H, a COO-; and then will going to have an NH2 neutral.1597

Notice, it went from plus to neutral, because it gave up an H; that's what's happening her- an H is being lost in each case.1619

In terms of the biochemical, an H+ is leaving - actually you know what I should do it on the upper arrow, not the lower arrow, the lower arrow is the one that is coming in - so, H+ is going away, a second H+ is going away, a second H+ is going away.1631

This is pretty typical biochemical nomenclature.1660

They actually show things coming in and going out of a reaction on the arrows, but again we'll talk a little bit more about that.1663

This is pKR, now, let's do some numbers: pK1 = 1.88, the pKR = 3.65, the pK2 = 9.60, and its isoelectric point happens to be at 2.77.1669

So, at a pH of 2.77, it actually exists in this form- 0 net charge.1694

That's all that is going on here which makes sense because you're looking at 1.88 and 3.65, because each of this contributes a negative; the only positive charge comes from this thing right here, so this PI is going to be lower than you would expect.1707

Notice the PI of alanine was 6.01- this one is a lot lower.1722

OK.1727

Let's do another example.1731

This time we'll do an example where the alpha-amino group actually ionizes before the R-group does1734

Let's do tyrosine, which is actually kind of interesting in the case of tyrosine but...so pK1 is less than pK2 is less than the pK of the R-group, so tyrosine.1739

Let's go ahead and write these equilibriums.1756

We start off with COOH, everything is protonated, we have NH3+, we have CH2, we have our phenol group or benzene, then we have OH, so everything is protonated, everything is good.1760

Now, first hydrogen to go is that top hydrogen, the alpha carboxylic acid, the carboxylic acid attached to the alpha carbon.1780

We have H3N+, C, COO-, this is H, this is CH2, this is that, and we have OH, that's our first, this is pK1.1789

Now, for pK2, this time it is the amino group that ionizes next, so it becomes H2N, neutral C, we have COO-, we have H, we have CH2, we have our benzene group, and then we have our hydroxy attached to the benzene, which is still protonated.1808

That one has not been released yet.1829

And now, of course, we reach our final equilibrium, which is going to be pK of the R-group.1832

Now, the R-group is going to release its hydrogen.1838

We have C, we have COO-, we have H, we have NH2, we have CH2, we have our benzene group, and we have O-.1842

This is the equilibrium that takes place.1858

This H goes first to turn into that, then this H+ leaves to turn into that, then this H leaves to turn into that.1861

Our numbers are: our pK1 is equal to 2.20, and, of course, all of these numbers are available in your book or on the web- wherever.1875

I would encourage you to take a look at a table showing this stuff just to get a sense of what the numbers are for all the amino acids on a single page on a list.1887

It's a great way to get a sense of general behavior because there are just going to be some numbers that are just going to stand out.1895

They are just going to be totally different than all the others, and you're going to take a look and see what amino acid that is, and chances are, that amino acid is going to play a special role when we talk about metabolism later in the course.1901

OK.1913

pK2 = 9.11, and pKR = 10.07 , and PI is equal to 5.66.1915

So, at a pH of about 5.66, the majority of the amino acid exits in a neutral state- that's it.1930

OK.1939

Now, I strongly urge you to do exactly what I've done: take a couple of amino acids at random, and then just write the equilibriums for them, see what the pKa1 is, see what’s the pKa2 is, see what’s the pKR is, and then arrange them, plot the hydrogens according to the order of the pKas, and draw these out.1942

It's an absolutely fantastic way to1, familiarize yourself with the structure of the amino acids and just being able to actively draw them out, and 2, getting a sense in keeping track of which hydrogen is being ionized and where it's being ionized- very, very important.1964

OK.1984

Now, let's talk about a rule of thumb.1986

OK.1993

If you want to know whether a given group - chemical group, not amino acid group - whether a given, I should say, ionizable group is protonated, which is the acid form or deprotonated.1998

In other words, whether it’s actually has its hydrogen ion or it's lost its hydrogen ion, which is called the base form at a given pH.2037

That's often how the problems are going to present themselves.2054

We're going to say there is this particular acid and the pH of the solution is 6.7, which one of the groups is protonated, and which one is not?2057

That's how it's going to be presented, and we will do an example in a minute.2064

Here's how you do it.2068

Here's the rule of thumb: if the pH of the solution is less than the pKa of the group - and again, we're doing this for each individual group - then the group is protonated.2070

In other words, it exits in its acid form, and, of course, the other way around if the pH happens to be bigger than the pKa; and remember, the pKa is a constant.2096

These things exist for a given species for a given ionizable group in that species.2111

The pKas don't change, pHs change.2116

Then, the group is deprotonated.2128

In other words, it exists as the base form.2133

OK.2140

Now, here's the bases for this particular rule of thumb.2142

You can either learn the rule of thumb, memorize it, or you can learn this basis, which I think, is better to know the basis and to know where it comes from, because that way, you can always reason things out.2146

Well, remember the Henderson-Hasslebalch equation?2158

OK.2160

Here's the basis for the rule; let me do this in red: the pH, we said of a solution, is equal to the pKa of the acid plus the logarithm of the concentration of the base form, the unprotonated form, over the concentration of the acid form, the protonated form.2161

Now, let me rewrite that: pH = pKa plus the log of the base concentration over the acid concentration.2193

Well, if the pH is less than the pKa, if this is less than that, which is a constant, that means that this number right here, the log of B over A, is a negative number, because I have to go a certain number subtracted something to get a lower number, then log of B over A is negative - in other words, it's less than zero - so if the log of something is negative, that means that the denominator is bigger than the numerator.2206

In other words, the logarithm of a fraction is negative, the logarithm of the number bigger than one is positive.2256

If the log of B over A is negative, that means B over A is a fraction.2263

If it's a fraction, that means A is greater than B.2268

That means that the denominator is bigger than the numerator, meaning - and don't worry we’ll be doing an example in just a minute - meaning there is more A than B.2272

There is more acid form than base form.2307

There is more protonated form than non-protonated form.2309

That’s all that means.2316

OK.2318

Let's go ahead and finish off with a nice example her, see what we can do.2319

Let's go back to blue.2326

Example: the cysteine solution was prepared and buffered to a pH equal to 8.2.2332

I would like you to describe the degree of protonation for each ionizable group.2361

In other words, I'd like you to tell me does this amino acids exists in what form.2382

What's the total charge on it?2388

Which group is ionized; which group in not ionized?2390

That's what is asking.2393

OK.2394

Well, let's go ahead and take a look at - first of all this is biochemistry, it's chemistry, it's organic chemistry - draw a structure.2396

OK.2404

So, cysteine, let's go ahead and draw it out as, you want to draw out the fully protonated form first and then make your decision, NH3+, this is an H, this is a CH2, and cysteine is a SH.2406

OK.2427

Again, begin by protonating all of them.2429

In other words, that's protonated, that's protonated, that's protonated- we have three ionizable groups.2431

At pH of 8.2, which one is protonated, which one is not?2436

Well, let's see what we've got.2441

We look up the pKs.2443

Well, the pK1 is equal to 1.96; the pKR is equal to 8.18.2446

Notice, in this case, the R-group ionizes before this group does.2456

The pK2 is equal to 10.28.2460

Well, now, we just use our rule of thumb or reason it out.2466

pH is bigger than pK1, right?2476

We said that pH is 8.2, and we said the pK1 was 1.96.2478

Because the pH is bigger than pK1, that implies that the carboxylic acid group exists as a carboxylate group.2485

It's actually been ionized; it has lost its H.2502

OK.2506

The pH which is 8.2, in this particular case, it happens to equal the pKR- that's interesting.2507

This is 8.18, the pH is 8.2, and they are exactly the same.2519

This implies that - how shall I...I'm just going to write the group - CH2, SH, and the CH2, S-, they exist in equal concentrations.2525

In this case, the pH equals the pKa of the R-group.2550

When pH equals the pKa of the R-group, that means the acid form, the protonated form and the base form, the unprotonated form, exist in equal concentrations.2554

So, in this case, they're both like that- it's a little bit of this, a little bit of that, half and half exist in equal concentrations.2563

Now, the pH happens to be less than the pK2.2575

Again, the pH is 8.2, and this is 10.28.2581

Well, this implies that the alpha amino group exists as its protonated form; the pH is less than the pKa, so it has not ripped away this hydrogen; it's still H3N+, so that's it.2587

Our final answer- we have C, COO-, H, NH3+, CH2, and SH - just want to make sure if...yes - and C, COO-, NH3+, CH2, S-, H, so, this is our final answer.2613

The amino acid actually exists as an equal concentration of this thing and this thing.2649

OK.2658

This group is completely ionized; this group, the amino group is not ionized.2660

The SH group- half of it is ionized, half of it is not.2666

That's what’s going on here.2672

OK.2674

I hope that made sense, and this is strictly based on the rule of thumb.2675

Let me write and OK.2678

And again, it's based on comparison of pH and pKa; compare pH and pKa, compare pH and pKa of each R-group- that's all that's going on here.2683

OK.2695

Now, let's say one thing about one of the amino acids, and then we will go ahead and close out this particular lesson.2698

Histidine is special.2710

When I look, I see a pK1 of 1.82; I see a pKR equal to 6.00, and I see a pK2 equal to 9.17.2717

Notice.2737

OK.2742

If you take a look at a list of all of them, this is one of the numbers that will stand out- that one.2743

It is the only amino acid whose pKR, who's pKa of the R-group is close to physiological pH, is close to physio pH found in intracellular and extracellular of fluids- the fluid inside the cell, the fluid outside the cell, physiological pH.2751

This is the only amino acid whose pKR is actually close to the physio pH.2800

OK.2805

It is, therefore, it is therefore, I should say -sorry about that , let me go ahead and erase that – so, it therefore has the potential to provide good buffering capacity under physiological conditions, under physio conditions.2808

That’s it.2868

Histidine is special because its R-group has a pKa of 6.0, which is not that far from the 7.0 or 7.2.2869

As it turns out, it has the potential to actually be a pretty good buffer in that particular range.2881

As it turns out, that's exactly what it is going to do, so keep an eye out for histidine when we start talking about enzyme reactions and when we start talking about metabolism.2889

OK. That takes care of acid base behavior for amino acids.2900

Thank you for joining us here at educator.com and biochemistry.2904

We'll see you next time, bye-bye2907

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