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Raffi Hovasapian

Raffi Hovasapian

More Examples with Amino Acids & Peptides

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 (5)

1 answer

Last reply by: Professor Hovasapian
Mon May 9, 2016 3:27 AM

Post by imene hacene on May 8, 2016

How to Draw the structure of lysine that predominates at PH =5.5 and PH= 12.7 ?

0 answers

Post by Torrey Poon on January 28, 2014

Thank you Prof. Hovasapian, that explanation helped!

1 answer

Last reply by: Professor Hovasapian
Mon Jan 27, 2014 3:30 PM

Post by Torrey Poon on January 27, 2014

How did you get the value 27,166 g/mol on Example 2, part b?

More Examples with Amino Acids & Peptides

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
  • Example 1 0:22
    • Data
    • Part A: What is the pI of Serine & Draw the Correct Structure
    • Part B: How Many mL of NaOH Solution Have Been Added at This Point (pI)?
    • Part C: At What pH is the Average Charge on Serine
    • Part D: Draw the Titration Curve for This Situation
    • Part E: The 10 mL of NaOH Added to the Solution at the pI is How Many Equivalents?
    • Part F: Serine Buffer Solution
  • Example 2 23:04
    • Data
    • Part A: Calculate the Minimum Molar Mass of the Protein
    • Part B: How Many Tyr Residues in this Protein?
  • Example 3 30:08
    • Question
    • Solution
  • Example 4 48:46
    • Question
    • Solution

Transcription: More Examples with Amino Acids & Peptides

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

We just finished discussing amino acids and peptides, and what I thought we would do is just do some more example problems with amino acids and peptides just to make sure we have a complete understanding, give us a little bit of review of the things that we have done before, and just get familiar with it.0004

Let's jump on in.0020

The first example, example 1.0025

OK. Given the following data, answer the questions that follow.0033

Let me do this in blue actually.0059

We have 100mL of a 0.20M serine solution at a pH of 1.60, is titrated with a 2.0M sodium hydroxide solution.0062

We don't care about the sodium; it is the hydroxide that we are concerned about.0098

OK. The pK1 = 2.21.0100

We have a pK2, which is the pKa of the amino, that is equal to 9.15; and then I'll go ahead and give you the molar mass.0108

I'm just going to write m/m for molar mass; m/m and this happens to be 105g/mol for serine.0120

Now, the first question that we want to ask is "What is the pI of serine?", and draw the correct structure.0131

In other words, draw the correct structure at that particular pH, which is the pI.0155

Well, you have got 2 ionizable groups on serine.0162

You have the carboxyl group, and you have the amino group.0165

So, the pI, that means...let me just draw the general...so you've got N, C, C, that; and you have that.0168

Starting off at a pH of 1.6, these are both going to be protonated.0180

Well, so this serine...sorry, I'll go ahead and just do R there; we are not concerned with this serine yet.0184

This is carrying a +1 charge.0192

A pI is the isoelectric point.0194

It is the point where the net charge on the molecule is going to be 0.0196

So, the pI is going to be where the carboxyl group is full.0201

In this particular case, since you have 2 ionizable groups, it is where it is completely ionized.0206

There is no H left on there at all because then the carboxyl group is going to carry a -1.0210

The NH3+ is going to end up carrying a +1 for a net charge of 0.0217

That is the isoelectric point.0224

Well, with 2 ionizable groups, the isoelectric point takes place at the arithmetic mean of the 2 pKs.0225

So, you just add the 2.21, 9.15 and divide by 2.0232

We have pI...oops, not a capital P; this is a small P.0238

The pI, the isoelectric point is equal to pK1 plus - I'm always, always, always doing capitals - pK2 divided by 2.0245

2.21 + 9.15 / 2 gives us a pI of 5.68.0260

There we go.0270

When the pH is 5.68, that means this serine molecule has a net charge of 0.0271

The carboxyl is ionized; the amino is not ionized.0278

OK.0281

Now, let's go ahead and draw the structure of serine.0283

We have got the N; we have C, and we have C.0285

We have our ionized carboxyl group; we have this one which is not ionized.0292

Let me make my carbonyl carbon a little bit better here.0297

And then we go ahead and we have the H, and then, of course, we have CH2 and OH.0300

This is our structure at 5.68.0306

That is it. OK.0310

Let's see, part B.0316

Excuse me.0320

There we go.0324

Our pen didn't work there for a second.0327

Alright.0328

How many milliliters, specifically, of the sodium hydroxide solution, of the NaOH solution, have been added at this point, in other words, at the pI?0329

OK.0355

So, we started off with a pH of 1.6, and now, we are at a pH of 5.68- that is the isoelectric point.0357

We want to know how many milliliters of this 2M sodium hydroxide solution we've actually added to bring it to that point.0363

OK. Let's think about this.0371

First of all, we want to know how many moles of serine there is in there because it is going to depend on how many moles of ionizable groups that we have to titrate because that is what the hydroxide is doing.0374

The hydroxide is going in there, and it is pulling off the hydrogen from the carboxyl group; and when that is done, that is going to be the isoelectric point, and then it is going to go and start pulling off the hydrogens from the amino group until it's done.0386

That is the second plateau on the titration curve, which we will draw in just a minute.0402

Let's find out how many moles of serine we have.0405

Well, we have 100mL of a 0.2M solution.0409

Let me do this one in red.0415

We have 0.100L x 0.20mol/L.0418

This will give us 0.02mol of serine.0426

Well, serine has 2 ionizable groups, but 0.02mol of serine contains 2 moles of ionizable groups, right?0432

You have the carboxyl, and you have the amino.0454

With every amino acid, there is a minimum of 2 ionizable groups per mole of serine, which means that we have 0.04mol of serine cancels, 0.04mol of ionizable groups.0456

Well, the isoelectric point - in this particular case, you have 2 ionizable groups - is when one of them is completely ionized.0478

So, if you have 0.04mol of ionizable groups, when half of them have been ionized, that is your isoelectric point.0484

That means - let me write that out - one of these groups is fully ionized.0496

That is what the pI means- isoelectric point.0513

You have 0.04mol of total ionizable groups.0515

Half of them have been ionized, which mean 0.02mol.0520

Well, since we have 0.02mol of ionizable group that have been ionized, that means, and it's a 1 to 1 ratio, 1 hydroxide per 1 ionizable group, right, is pulling off 1 hydrogen, that means there are 0.02mol of the hydroxide that I have to use.0533

Let me actually, specifically write that.0557

0.02mol of OH- times, and it is 2mol/L, 2mol of hydroxide per liter.0560

What we end up with is 0.01L or 10mL of sodium hydroxide solution.0576

There we go; that's our answer.0588

I hope that made sense.0590

At the pI, we know that 1 group is fully ionized.0592

Well, I need to know how many moles there are, but each mole of serine actually brings 2 ionizable groups, so I have a total of 4 moles that can actually be ionized.0597

Half of them have been ionized at the pI, at the 5.68, so of the 0.04, 0.02mol have been ionized.0608

Well, the 0.02mol that have been ionized comes from, they have been ionized by 0.02mol of hydroxide because it is a 1 to 1 ratio, OH + H.0616

That is what forms the water.0626

This is a titration, the acid base titration.0627

That is where this comes from.0630

I take the 0.02mol of hydroxide; I multiply by the reciprocal of its molarity, and I get its volume, so, 10mL of NaOH are added.0631

That tells me that in order to fully ionize the serine completely, I would just add another 10mL, so I would need 20mL of sodium hydroxide to completely ionize it.0639

OK. Let's see, part C.0650

I hope you don't mind that I'm jumping around from color to color.0656

OK.0658

Actually, you know what, I'm going to go ahead and do this one in...I'm going to go back to black- part C.0663

Excuse me.0673

At what pH is the average charge on serine -½.0674

OK, we want to know the pH where the average charge on the whole molecule is -½.0690

OK. We have 2 ionizable groups.0696

Let me go ahead and just draw this out really quickly.0699

We have N, C, C, O-.0702

I'm just going to put an R1 here.0707

Actually, let me go ahead and put the H+.0712

OK. When both of these are protonated, the molecule is carrying a charge of +1.0716

At the pK1, right, the pK1, that is when half of the carboxyl groups have been ionized.0723

The other half is still protonated, so half protonated, half deprotonated.0730

At that point, this side is carrying a charge of -½, right?0733

Because if it were fully ionized, it would carry a charge of -1, but at the pK1 - remember we said that's when half of the groups are ionized - the protonated and deprotonated form are in equal concentration.0740

So, instead of -1 total, just a solid -1, you get a -½.0754

Well, -½ + 1 gives you a +½, and then when this is fully protonated, that is the pI, then you are going to have -1 and +1, that is going to be 0.0758

Now, at the pK2, that means half of these are going to be ionized.0773

This side of the molecule is going to carry a charge of +½, and this side is already fully ionized because we’ve passed the pK1 mark, that is a -1 charge.0781

So, -1 + ½, that gives us the negative half.0791

The pH at which the total serine molecules carrying a charge of -½ is the pK2- the 9.15.0795

Now, let me go ahead and write that out.0804

At a pH = 1.60, that implies that the charge on this molecule is +1 because nothing has been deprotonated.0808

OK. At the pK1, that implies the -½ + 1 = +½.0817

That is the charge at the pK1.0828

Well, at the pI...I didn't even write it.0832

Actually, you know what, it doesn’t matter; I'll just go ahead and do that here.0839

That is going to be -½ + 1 = +½ and then at the pI, we have, of course, -1 + 1, we have a charge of 0, and now, the pK2.0843

We have the -1 from the deprotonated carboxyl group, and then we have +½ from the half-deprotonated amino group, and that gives us a +½.0857

At a pH that is equal to the pK2; that is equal to 9.15.0869

At that pH, the serine carries a +½ charge.0875

That is it; I'm sorry, -½ charge.0880

-½- that is the one we are looking for.0882

OK, part D.0885

Draw the titration curve for this situation.0892

OK.0907

Well, we know how to do this, not a problem.0908

So, we are going to do this; we'll do something like that.0910

OK. Let's mark off some, let's do 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, I'll just go ahead and put 11, and then, so let's see, this is 1.0916

We said we started at about a 1.6, 2.12.0930

So, this 2.12, that is the pK1, and we said that the pI is 5.68.0937

I'll do 1, 2, 3, 4, 5, 5.68, so the pI is somewhere around there.0947

This is the pI.0953

You know what, let me write what these are here.0955

This is pK1; this is 2.12, 5.68, and then 9.15, 6, 7, 8, 9, 9.15.0959

So, this puts our pK2 right there, and this is 9.15.0972

Here we go.0978

We are going to start right about here.0980

We are going to plateau out.0982

We are going to plateau out, and we are going to go up, and then we are going to plateau again, and then we are going to go up.0987

So, it looks something like that.0993

That is our pK1 mark; this is our pI, the isoelectric point.0997

This is our second dissociation, the pK2, and that is it.1002

It is at this point that we've added the 10mL of sodium hydroxide.1007

We have fully ionized the carboxyl group, and then, of course, somewhere over here, we have added the 20mL.1014

This is going to be mL of OH-, and that is it.1022

The titration curve, that's what it looks like, 2 ionizable groups; you have 2 plateaus.1024

If you have 3 ionizable groups, you'll have 3 plateaus.1029

That is it, nice and simple.1032

This point, this point and this point, those are the important points- pK1, the pK2 and the pI, the isoelectric point.1034

You should be able to go back and forth.1043

If you are given a titration curve with numbers on it, you should be able to say this happens here, this happens here, this happens here; or if you are given a numerical data, you should be able to produce the titration curve.1044

OK.1056

Let's see, E.1058

The 10mL of NaOH added to the solution at the pI, so the 10mL to bring it to the pI is how many equivalents?1063

OK.1088

In general chemistry, we mentioned this thing called an equivalent.1090

We haven't really talked about it very much.1096

In biochemistry, they tend to use it a little bit more.1098

It is not really that big of a deal.1101

You are not going to see it all that often, but equivalents just means how many.1103

So, 1mol of serine, we said, has 2 ionizable groups, right?1110

It has 2mol of ionizable groups.1115

It has 2 equivalents of ionizable groups.1119

Equivalent just means how much OH do I have to add for each H that is going to be deprotonated.1123

In this particular case, in order to get to the pI, I have ionized 1 of the ionizable groups, so I've added 1 equivalent.1130

If I ionized the whole thing, I've added 2 equivalents.1140

That is it.1144

It's just, instead of talking about specific volumes like 10mL, 5.6mL, we just speak of equivalents.1147

We are speaking more globally.1153

A particular amino acid might have 3 ionizable groups.1156

Therefore, in order to fully ionize that amino acid, I have to add 3 equivalents of hydroxide: 1 for the carboxyl, 1 for the alpha-amino, and 1 for the R-group.1160

That is all that's going on.1174

So, in this particular case, 1 equivalent has been added to bring it to the pI.1175

A second equivalent would be added to bring it to full ionization- not the pK2.1181

Remember, the pK1 and the pK2 represent half deprotonation.1187

These are the buffer regions.1194

It is fully ionized here, and then the second one is fully ionized here.1197

That is the second equivalent.1201

This is really, really easy; this is just 1 equivalent, and they will often refer to it that way, qualitatively instead of quantitatively.1203

Quantitative, 10mL- they are giving you a number.1214

1 equivalent is just, they are speaking about how many ionizable groups.1216

That is all they are doing.1221

OK, F.1223

Now, would a serine buffer solution, so let's say I went ahead and had a serine solution, and I created a buffer solution out of it.1228

With a serine buffer solution, the appropriate for an experiment requiring for an experiment that needs to be maintained at a pH equal to 8.7.1242

If I am running an experiment and I need to maintain the pH at about 8.7, would it be appropriate for me to use a serine buffer solution?1280

In other words, I create a serine solution; I add enough acid or base to bring it up to this particularly.1288

Is this a good buffer solution?1294

Is serine a good buffer solution?1297

Well, the answer is yes, and the reason is, well, take a look at the pKa.1298

Where does this 8.7 fall?1303

Well, I need it to be in the buffer region, so it either needs to be here, 2.2 + or - 1, so 1.12 to 3.12- that is the range of a good buffer, or in this case 8.7.1305

Here, the pK2 is 9.15, which means our particular buffer region - let me go ahead and - this right here is going to be from 8.15 all the way to 10.15.1320

So, as long as the pH falls, if I need the pH to be in that range, this serine is actually a good buffer solution to use.1334

That is it.1342

You are just looking at the pKa.1343

That is all you are doing.1345

Note the pI; this is not the buffer region.1347

The buffer region is the horizontal region.1349

The buffer region is actually the part that resists changes in pH the more you add.1351

Notice, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, you keep adding a hydroxide; the pH doesn't go up all that much.1356

That is why.1366

So, in this particular case, experiment 8.7, yes, it falls within the range of the second pK for serine, so serine would be a perfectly good buffer solution to use in this particular experiment.1367

OK.1380

Let's go on to example no. 2.1385

OK.1394

Quantitative analysis reveals that a certain protein contains 0.60% tyrosine by mass.1396

I am going to use the...oh, that's fine; I'll just go ahead and write by mass.1427

Remember m/m, sometimes as w/w, they often say a tyrosine by weight instead of by mass- it is the same thing.1434

OK.1444

Further analysis estimates the molar mass to be about 135,800g/mol, and the molar mass of tyrosine is equal to 181g/mol.1445

This is the information that is given to you.1482

OK.1485

Quantitative analysis reveals that a certain protein, it contains, by mass, 0.60% tyrosine.1486

In other words, all of the tyrosine in there accounts for 0.6% of the total mass of protein.1493

Well, they do a little further analysis, and they are able to estimate the molar mass that is somewhere in the range of about 135,800, give or take.1498

The molar mass is 181g/mol of tyrosine.1507

So, the first question we want to ask you is...and this is the process that you will use.1511

Assuming the protein contains only 1 tyrosine residue, calculate the minimum molar mass of the protein.1520

What we are going to be doing by assuming that we actually have just 1 tyrosine residue, we have the percentage, if we assume just 1 tyrosine residue, we can place a lower limit on the molar mass; and then from there, given this other bit of information, the 135,800, then we can go ahead and find out a little bit more about it.1557

Let's go ahead and do the first part.1580

Well, let's see.1582

Let me do this one in red.1586

You remember, when we speak about a residue, it is the amino acid minus the elements of water.1591

It is minus the elements of water and the elements of water are H2O.1598

What you get is, what you end up with is 181g/mol minus the 18g/mol which is water, so a residue of tyrosine actually is 163g/mol.1607

OK.1626

Because, when we form a peptide bond, when we are forming the protein, it is a condensation reaction.1627

We are removing the elements of water, right, reverse of hydrolysis.1633

A tyrosine residue in a protein is actually missing an OH and an H from the original structure.1637

When we give the mass of the amino acid, it is a181g/mol, but when that amino acid is tied up in a peptide, in a protein, it is actually missing an oxygen and 2 hydrogens.1644

It is missing 18g/mol.1655

So, in this case, 163g/mol is the mass of the residue.1658

Well, we take the 163g/mol, divided by the total protein mass, times 100, and they already told us that this is equal to 0.60, because it’s 0.60%m/m tyrosine, part over the whole, tyrosine over the whole; and when I solve for the mass, I end up with 27,166g/mol.1663

This is the minimum per mole.1692

This is the min. molar mass, and it is based on just using 1 tyrosine residue.1696

Well, interestingly enough, I already have this, an estimation of the total molar mass, the 135,800.1702

Well, if I know that I have a minimum mass of 27,166, now, my second question to you is the following.1709

How many tyrosine residues are there in this protein?1718

Well, I have the minimum for 1 tyrosine residue- that is the relationship.1733

I have the total, so I'll just take the total, divided by the minimum, and that will give me, hopefully, somewhere near a whole number.1740

That is how many residues I have.1748

I hope that makes sense.1750

I’m going to do that on the next page, running out of room here.1751

Actually, you know what, I should be able to do it here; that’s fine.1755

I've got 135,800; that is the total estimated mass of the protein.1759

Based on this 0.6% for 1 residue, I've got 27,166g/mol, and when I divide that, I get about 4.99; so you are looking at 5 tyrosine residues.1768

There you go.1783

You use the basis of one to find the minimum, and then you work up; you divide it by the total.1785

This is not altogether different than the empirical formula, molecular formula calculation, that you do in general chemistry.1790

OK.1798

Let's go ahead and do another example here.1801

Let's go back to blue; I like blue a lot.1804

OK.1810

This is example no. 3.1811

Now, a peptide called methionine enkephalin was subjected to the following procedures with the following results.1815

OK.1853

We are going to ask you to take these results, take a look at them, and deduce the structure of the methionine enkephalin.1854

OK.1876

The first procedure that it was subjected to was 6M hydrochloric acid hydrolysis.1877

Oops...hydrolysis, there we go.1884

We basically just completely broke every single base, released every single free amino acid.1886

Let's see.1895

6M hydrochloric acid hydrolysis and we ended up with the following results: methionine to glycine to phenylalanine to tyrosine, the molar ratios were 1:2 to 1:1.1896

OK.1915

We were not able to count how many of each, but we were able to get the ratios of the amounts of the amino acids in this particular analysis, so 1:2 to 1:1, Met to Gly to Phe to Tyr.1916

OK.1928

The other procedure we subjected it to was FDNB and hydrolysis.1930

I should write FDNB then hydrolysis, then we broke it up - fluorodinitrobenzene, that is the Sanger reagent - and we ended up with the following.1942

We ended up with DNB-Tyr, this molecule's derivative of tyrosine was detected, and also, there were no free tyrosines detected.1959

OK.1985

Well, now, our third procedure, we had fragmentation.1987

We did fragmentation by pepsin, and pepsin breaks up the aromatics on the amino side.1995

OK.2013

And what we ended up was with the following.2016

We ended up with a dipeptide containing Phe and Met, and we ended up with some Tripeptide.2018

We did not sequence this; we did not know the sequence.2037

We just know that this dipeptide contains Phe and met; we don't know which one actually comes first.2039

And a tripeptide containing tyrosine and glycine in a ratio of 1:2.2044

OK.2059

We need to deduce the structure, in other words, what's the amino acid sequence.2060

OK.2066

Well, let's see what we've got.2067

Let me go ahead and go to the next page here.2070

Let me see.2074

Our glycine is the one that's 2, so I'm going to write the glycine first.2075

Glycine to methionine to phenylalanine to tyrosine- that is going to be the 2:1 to 1:1.2086

OK, so I've got this.2095

Well, they said that the FDNB gave me a DNB-Tyr.2097

OK.2108

This tells me that the tyrosine is the N-terminal residue.2109

OK.2122

So, we know that it is tyrosine.2123

Well, let me see.2124

Here is something else they said.2125

They said that there was no free tyrosine after we actually hydrolyzed it, once we reacted it with the FDNB.2128

Remember, the FDNB attaches to the N-terminal, and then once you break it up, everything comes apart, we detect this.2134

We have labeled it.2142

We detect that.2143

The others, we can also check to see what's in there, but there was no free tyrosine.2145

OK.2151

And, since there was no free tyrosine, that means there was only 1 tyrosine residue, and it happened to be the one on the end.2153

So, remember, we labeled it, the FDNB can only react with what's on the end.2180

Once that reaction is done, that's when we break up the protein, and now, you have a bunch of free acid.2188

Well, if you can have a bunch of tyrosines that are also free in addition to the one on the left, but there is no FDNB in there, so it is not going to react with those.2193

That is the whole idea.2201

It reacts with the last one first, and then if you have any other free acids, then that tells you how many that you have, but in this case, there was only 1 DNB-Tyr that was detected, but there were no free tyrosines, which means there is only 1 tyrosine, so this 2:1 to 1:1 is not just a ratio, it is exactly how much we have.2202

We have 2 glycines; we have 1 methionine, 1 phenylalanine, and we have 1 tyrosine.2221

This is going to be a pentapeptide.2228

In other words, we have 5 amino acids that make this up- really, really nice.2232

We know what the far left one is; it's going to be the tyrosine.2235

OK.2239

Now, let's go ahead and take a look at our relationship.2240

Now, pepsin cleaves, like we said, pepsin cleaves the phenylalanine, the tyrosine and tryptophan, but we don't have to worry about tryptophan on the left.2245

When it cleaves it on the left, that means, in other words, if you have, OK, if this is either phenylalanine or tyrosine, it is going to break it right there.2260

So, one of your fragments is going to have a phenylalanine or a tyrosine on the left.2277

One of the dipeptides, they said, contains phenylalanine and methionine.2282

Well, we know that that dipeptide has to have a phenylalanine on the left.2286

So, we know that we are looking at Phe and Met- that is our dipeptide.2291

Well, we also know that tyrosine...there is also a tyrosine and a glycine on a 1:2 ratio.2297

Well, I have already accounted for the phenylalanine and the methionine.2307

I know that tyrosine is on the left, so that I know that I'm looking at this- Gly and Gly.2310

I know there is nothing to the left of the tyrosine because that is the N-terminal amino, therefore, all of this information points to the following: Tyr, Gly, Gly, Phe, Met- tyrosine, glycine, glycine, phenylalanine and methionine.2318

This is the structure or the sequence of methionine enkephalin.2343

There you go; I hope that made sense.2350

You are just, sort of, putting pieces of the puzzle together.2353

There is no one way to do this; you just have to use your intuition, use the things that you know one piece at a time, put it together.2358

This one was reasonably simple because we are dealing with a pentapeptide, not going to be so simple all like that.2367

Other times, you are probably going to have to use a couple of cleaving procedures to see where you have overlaps; and, in fact, that is what we are going to do next.2373

OK.2382

Let's go ahead and take a look at another example of a sequencing of a peptide, but this one a little bit more complicated, a little bit longer.2384

Let's see what we've got.2394

OK.2397

This one I wrote out because there is a lot more analysis going on.2398

Let's take a look.2402

Glucagon is a peptide hormone that is secreted by the pancreas in response to low levels of glucose in the blood.2404

It induces the liver to convert glycogen to glucose - glycogen is a carbohydrate, glucose is a carbohydrate, glycogen is made of - and release it into the bloodstream.2411

Glucagon was subjected to several analytical procedures with the following results; use these results to deduce the - I'm sorry - amino acid sequence of glucagon.2421

So, glucagon just does the opposite of what insulin does.2431

If the blood sugar gets too high, insulin is released.2435

If the blood sugar gets too low, glucagon is released.2439

It's a way of maintaining the blood sugar level at some stable level, hopefully.2441

OK.2448

In this particular case, we did a 6M hydrochloric acid hydrolysis of the whole thing, and an amino acid separation, so we were actually able to count the number of amino acids.2449

Here are the results of the hydrolysis and the counting.2460

Histidine, serine, Gln, Gly, Try, Asn, Phe, Asp, Tyr - these are all the numbers that we have.2467

OK.2473

Now, let's see what other analyses.2475

So, we did an FDNB, and we ended up with the DNB-His.2480

OK, that's good.2485

We have that; we know that histidine, and we noticed that we have the one histidine.2486

In this particular case, that 1 histidine happens to be the N-terminal, so that's some good information.2493

We did a couple of fragmentations on this using 2 different enzymes.2498

We used the Asp-N protease, and what it does is that fragments that cleaves the Asp, the cleaves of the protein to the left of the Asp, and that is what the N means, the amino side.2503

So, when we fragment it, the fragment is going to start with an Asp.2515

Let's see here.2524

Fragmentation and Edman sequencing gave the following fragments.2526

OK, so, in this particular case, we not only fragmented but we also sequenced it; and we came up with these fragments.2529

Here, we are just using the single letter designations for the proteins, and don't worry about them if you still haven't memorized them.2535

I mean, at some point, you are going to have to; but no big deal for right now.2540

This is the first fragment; that is the second fragment, the third and the fourth.2545

So, this A1, A refers to the aspen protease, then we go ahead and take an intact protein; and we subjected it to a second fragmentation procedure with trypsin.2549

Now, trypsin, tends to break lysine and arginine.2560

It cuts them at the lysine and arginine residues, and it cuts the carboxyl sides, so to the right of it.2567

In any particular fragment, you are going to end up having an arginine or a lysine at the end.2573

OK, so let's see what we've got here.2580

And thus, fragments gave us this, and this, and this, and this.2582

Excuse me.2588

Well, OK, so, let's see if we can put this together; and let's see if we can find some overlap between these fragments and these fragments.2590

Let's see what we've got.2600

Let's see what we can do.2603

Alright.2605

Well, we know that this is what we know.2606

We know that the DNB-histidine means that histidine is the N-terminal residue.2609

Yes, so that is nice.2619

It means that His is the N-terminus of this particular protein, which is really, really great.2621

And, we have a couple of the fragments, so let's see.2630

A1 and if I take a look at T3, I notice that T3 is the one that actually has the H on the left, so we know that that fragment goes first.2634

That is fantastic.2645

We have already taken cared of about ¼ of this.2646

Let me go ahead and list this as...so, I've got H, S, E, G, T, F, T, S, D, Y, S.2650

This is the T3 fragment.2668

The T3 fragment goes there.2671

Now, let me go to blue.2673

OK.2676

I take a look at some of the fragments on the A side, and I notice that this thing, this T3 overlaps A4.2677

I'm going to go ahead and put the overlap A4 right underneath.2690

So, it is going to be D, Y, S, and then K, Y, L.2693

OK.2700

Now, let me switch colors again.2701

Now, I go back to my T, and see if there is an overlap there, turns out there is.2704

This actually overlaps the T4 fragment.2710

And again, you can switch back and forth and see that this is absolutely correct.2715

In this particular case, I write the overlap this way.2719

I just tend to do it on a stair step fashion, and then just read it off at the end.2722

You can do it anyway you like, however you want to put the pieces of the puzzle together.2725

D, S, R, OK, now, let me see.2731

I take a look at my A fragments, and yes, there is an overlap here.2735

Let me go back to red.2738

This overlaps A3, so I go ahead and write A3 underneath.2742

That is going to be D, S, R, R, A, E.2751

Let me go back to blue.2758

OK.2760

This one overlaps T1.2761

I go ahead and write T1 underneath.2767

I've got A, E, D, F, V, E, W, L, M, N, and T; and this one, it overlaps A2, and that will be my final sequence here, A2.2770

And, of course, that is the...let me do this in black.2797

This is going to be the D, F, V, E, W, L, M, N, and T; and there you go.2802

Now, I just sort of read it off, and just make sure to skip the overlap part.2811

There and there, and there, and here, and I just read it off.2817

I'm going to do this final one in...I guess I'll do it in red, how's that?2827

So, our final sequence is H, S, E, G, T, F, T, S, T, F, T, S, D, Y, S.2831

I have that overlap, so it is going to be K, Y, L, K, Y, L.2842

I have the Y, L, so it is going to be D, S, R, D, S, R, R, A, E; and then, the rest, D, F, V, E, W, L, M, N, and T.2847

There you go.2872

This is the final amino acid sequence of glucagon.2874

Again, hydrolysis- to count2878

Sanger reagent- to find out where the N-terminal is.2881

Let me go ahead and make sure that there is this little mark here.2885

Fragmentation with one enzyme or chemical procedure fragmentation with another enzyme, check for some overlaps.2890

You are just sort of putting it together.2897

Again, I like to put it together in a stair step fashion like this, and then just read it off.2899

There you go, pretty straightforward.2903

There is nothing difficult going on here.2907

It is just a question of putting the pieces together.2909

That's it.2914

OK.2915

Let's see what we've got here.2918

OK.2921

Let's close this off with one final example.2923

Excuse me.2926

Let's go ahead and do this in blue, and hopefully we can fit this in one page, so example 5.2927

I want to create as much room as possible, so I'm going to say...oh, that's fine.2941

Give a schematic for the Merrifield synthesis of the following tripeptide: Gly, Phe, Leu, so glycine, phenylalanine, and leucine; and use only the 3-letter designations.2952

You don't actually have to write out the structure, not a problem.2986

OK, so let's go ahead and do it.2990

Remember, the Merrifield synthesis, we actually synthesize from right to left, from the carboxyl end toward the amino end.2992

So, we are actually going to be starting with- oops, let's do this in red.3000

We are actually going to be starting with leucine, then phenylalanine, then glycine.3005

It is the opposite of how nature does it.3009

Nature goes amino to carboxyl; Merrifield goes carboxy to amino, because we attaching the first one to an insoluble bead.3010

OK.3019

Let's start off over here.3020

Hopefully I can do it, so let's start off with our leucine, and I'm going to react it with our Fmoc-chloride, and that is going to give me Fmoc-leucine; and then, I'm going to react this with a bead, those polymer beads.3024

What I end up with is Fmoc-leucine, and then the bead; and then I'm going to subject this to trifluoroacetic acid or mild base to deprotect that leucine, get rid of the Fmoc.3050

So, I end up with leucine and the bead.3067

OK.3072

Now, over here, I'm going to go ahead and do this in black.3073

Now, I'm going to go, and I'm going to work with my phenylalanine.3078

I'm going to take phenylalanine, and I'm going to react it with Fmoc-chloride.3082

I'm going to protect its amino group, so I get Fmoc-phenylalanine; then I'm going to react it with the DCC, dicyclohexylcarbodiimide, and I get Fmoc.3087

I get the phenylalanine, and I get my DCC, and this is what I'm actually going to take and react, goes in here; DCC comes out, and what I'm left with is Fmoc.3101

I'm left with Phe; I'm left with Leu.3122

And now, it is still attached to the bead.3125

OK.3128

I subject this to trifluoroacetic acid to release this Fmoc.3129

So, I end up with phenylalanine, leucine; and I end up with a bead.3134

Now, I'll go ahead and prepare my second amino acid; that is going to be glycine.3140

I'm going to react glycine with Fmoc-chloride.3146

I'm going to get Fmoc-Gly.3152

Notice that the Fmoc is on the N-side.3154

OK.3156

And then, I'm going to react this with the DCC to activate the carboxyl, so it'll actually react.3157

I end up with Fmoc-Gly, DCC.3164

I take this, and I react it with that; and DCC comes out, and what I'm left with here is Fmoc-Gly, Phe, Leu, and a bead.3171

OK.3193

You know what, I can keep this on 1 page; it's not a problem.3194

Well, nah, that's fine.3197

Let me go ahead and do the next page.3200

We have got Fmoc; we've got Gly.3203

We have got Phe; we've got Leu, and we've got a bead, and we want to go ahead and subject that to trifluoroacetic acid, and we end up with glycine, phenylalanine, leucine, still attached to a bead, and then we wash this with some hydrofluoric acid.3210

We end up releasing that; we end up breaking this bond, the leucine and bead bond, and we end up with our final glycine, phenylalanine and leucine.3236

There you go.3254

That is a Merrifield synthesis of that particular tripeptide.3255

OK.3261

Well, that takes care of the examples for the amino acids and peptides.3262

Thank you so much for joining us here at Educator.com and Biochemistry.3267

We'll see you next time, bye-bye.3270

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