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Raffi Hovasapian

Raffi Hovasapian

Peptides & Proteins

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 (10)

1 answer

Last reply by: Professor Hovasapian
Sat Aug 15, 2015 12:46 AM

Post by shashikanth sothuku on August 13, 2015

Hello professor
during peptide bond formation for the nitrogen to act as a nucleophile should it lose a hydrogen

1 answer

Last reply by: Professor Hovasapian
Wed Feb 5, 2014 12:22 AM

Post by Alan Delez on February 4, 2014

Hi Dr. Raffi,

You mentioned physiological conditions. What criteria does the environment have to be in order to be in those conditions?
Alan D.

1 answer

Last reply by: Professor Hovasapian
Tue Jan 28, 2014 2:49 AM

Post by crystal harnick on January 27, 2014

Hi Professor,
I believe that Tyrosine is drawn wrong in this example. One of the carbons has five bonds. I think it needs to be CH2 instead of CH3.

1 answer

Last reply by: Professor Hovasapian
Mon Sep 16, 2013 5:43 AM

Post by Yvonne Kum on September 15, 2013

Hi prof, could you please explain how many chiral centers each amino acid structure have, particularly when they form a peptide bond?
Thanks,
Yvonne

1 answer

Last reply by: Professor Hovasapian
Thu Sep 12, 2013 5:02 PM

Post by Vineet Kumar on September 10, 2013

please fix this video. I pay top dollar for this website and it doesn't work when I need it to

Peptides & Proteins

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
  • Peptides and Proteins 0:15
    • Introduction to Peptides and Proteins
    • Formation of a Peptide Bond: The Bond Between 2 Amino Acids
    • Equilibrium
    • Example 1: Build the Following Tripeptide Ala-Tyr-Ile
    • Example 1: Shape Structure
    • Example 1: Line Structure
    • Peptides Bonds
    • Terms We'll Be Using Interchangeably
    • Biological Activity & Size of a Peptide
    • Multi-Subunit Proteins
    • Proteins and Prosthetic Groups
    • Carbonic Anhydrase
    • Primary, Secondary, Tertiary, and Quaternary Structure of Proteins

Transcription: Peptides & Proteins

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

Today we are going to continue our discussion of amino acids by taking the next step.0004

We are going to put some amino acids together.0009

We are going to be talking about peptides and proteins.0011

Let's get started.0014

OK.0016

Peptides and proteins- it is just a string of different amino acids like beads on a string.0018

That's all it is- each one connected to the next.0025

Let's go; let's write that down.0029

Peptides and proteins are made up of amino acids - and again I'm just going to write AA like that - amino acids strung together- that's it.0035

Now, you’re probably wondering "Peptide, protein - what's the difference?".0053

The truth is there is no difference.0057

There are just a bunch of names that are used for proteins, amino acids that are strung together.0058

In general, if you want, you can think of a peptide as being anything less than about 10,000 atomic mass units, so molar mass of about 10,000 or less, we tend to call it a peptide.0064

A protein is 10,000 or more, and again it is not really this, you can call whatever you like.0080

We're actually going to be using several terms interchangeably.0086

So, just to sort of throw it out there, protein greater than about 10,000 atomic mass units or grams per mole, molar mass.0091

OK.0102

Now, let's go ahead and talk about the formation of a peptide bond- very, very important.0104

Bond is the bond that exists between two amino acids, and this is what holds the chain together.0114

OK....the bond between two amino acids.0124

OK.0139

Let’s go ahead and just take some generic amino acids, and see what we've got.0141

Again, when we write amino acids, I think it is the backbone that's important.0148

Yes, the R-groups are important, of course, when we're discussing them; but when we want to draw it out, it is the backbone that's connected- the peptide bond.0154

It is N, C, C, N, C, C repeating units, so if you’re going to write an amino acid, just start by writing N, C, C, and then fill in the rest.0162

We have N, C, C, I'll go ahead and put H3+ here, I'll go ahead and put the carbonyl there, and I'm going to write it in its fully protonated form just so you see that this is actually a condensation reaction.0171

The elements of water are going to be removed when we put these two amino acids together to form a dipeptide.0186

OK, so the carbonyl carbon is the second carbon.0194

The R-group goes here; the H is there, and then plus, and then, of course, we have, again, N, C, C.0197

This time I'm just going to put H there.0208

Actually, you know what, let me do it this way.0212

Let me put an H here, and let me put an H here.0215

I decided this one, I’m going to not protonate.0220

Don't worry about why, as far as where the Hs go, whether it is 3 Hs, 2 Hs, things like that, that's not what’s important right now.0221

Right now, we just want to be able to get a global sense of how these bonds form.0230

We have an H here.0237

This is the second R-group, and we have the carbonyl, and this one, I'm just going to go ahead and leave as an O-; if you want you can put an OH again.0238

Now, what happens is this.0247

I'll go ahead and do an equilibrium arrow this way and this way, so when water leaves this, the elements of water are right here.0251

Let me do this in red.0262

OK, the elements of water.0268

Basically, it is going to be, this carbon is the electrophile, and this nitrogen is going to be the nucleophile.0272

Remember the nucleophile is the one that actually has the electrons; it has the negative charge.0289

Electrophile is the one that carries the positive charge, so this thing is actually is going to attack this thing.0294

We’re not going to worry about mechanism right now, but that’s what happens.0299

What you’re going to connect is - and I’ll to do this one in blue - you’re connecting those two.0302

You’re connecting this carbon of 1 amino acid to the nitrogen of the amino group of the other amino acid.0310

OK.0320

And in this direction, it is condensation, because again, the elements of water are removed, and we're going to go ahead and write out our dipeptide; and again, we're going to go N, C, C - oops, straight lines, we definitely don't need those - N, C, C, N, C, C.0322

Now, let's go ahead and put the H3, let's leave that as plus.0348

Let's go ahead and put an R-group there; let's put the H here.0352

Here's our carbonyl, the N; let's go ahead and leave that one H that was there.0357

This is our R2 group - right? - of the other amino acid.0364

Now, we have this, and we have that.0368

The peptide bond is this thing right here; that is your peptide bond.0370

It is the carbonyl carbon attached to the nitrogen of the amino group of the amino acid to its right.0377

This is your peptide bond.0389

OK.0395

And just to let you know, in this direction, it is hydrolysis, so when we actually add water to a peptide, it actually splits this bond right here, the peptide bond; and it releases 2 free amino acids.0396

So, in this direction, two amino acids’ condensation, in this direction, it is called - got a little too much floating around here so when H2O comes in, OK, when this H2O leaves, this, well, here I will just do this - in this direction, it is called hydrolysis.0415

That's it- simple peptide formation.0440

The elements of water leave, the carbonyl carbon attaches to the nitrogen of the other amino acid, and you get your peptide bond; and it goes on like this, so N, C, C, N, C, C- it is the second carbon.0443

If this were going to attach to another amino acid, it would be this carbon that’s going to be attached.0459

If this one were going to be attached to something to its left, that would be attached.0464

That is all that’s going on here.0469

OK.0471

Under physiological conditions, under physio conditions, interestingly enough, the equilibrium of the previous reaction of peptide bond formation, the equilibrium lies to the left.0476

In other words, it lies to the formation of free amino acids, not the peptide, the left, and the reason that is so is because the hydroxy group is not a good leaving group; and you remember that from organic chemistry, just a straight hydroxy is not exactly a good leaving group.0499

It doesn't just go away to make the reaction move forward and form the peptide bond.0521

The hydroxy must be activated, and if you remember from your first year biology course or those of you who had already perhaps taken molecular biology, the amino ace will transfer RNA, ribosomes, protein synthesis, that is what is active.0537

That is activated with adenosine triphosphate and all that other stuff, so you’re welcome to look that up.0561

I'm not going to go through it here0565

It has to be activated to induce it to leave.0567

We just wanted you to know that in general, under normal physiological conditions, as is, the equilibrium tends to lie to the left, which is why you need it to be catalyzed.0577

OK. Let's do an example here.0588

Example 1: let's build the following tripeptide, so 3 amino acids, let's do Ala, Tyr and Ile, so alanine, tyrosine, isoleucine.0595

OK.0620

Let's go ahead and draw these out.0621

Again, we have N, C, C, we have N, C, C, we have N, C, C.0624

OK. I'm going to go ahead and draw them out individually so that we see- again, this is all great practice.0636

Let's see, alanine was CH3; and please, by all means, confirm that I'm actually writing the correct structures.0644

We all human; we have a bunch of carbons, nitrogens, hydrogens floating around.0652

We're going to be doing lots of structures.0657

The molecules are going to go get bigger and bigger and bigger, so, by all means, please make sure that I'm actually writing the correct structures because I get things wrong.0658

Let's see, we have that carbonyl; I'm going to go ahead and do an OH.0668

I'm going to go ahead and write an NH3+, because I'm writing them as individuals, and we said that tyrosine is the next one; so, tyrosine, CH3, I believe we have this one, the phenyl group with a hydroxy attached, and then we have the carbonyl carbon, and then, of course, we have the isoleucine, this is a plus charge, this is that, here's our carbonyl.0675

I'm going to go ahead and put an OH there, and our R-group, isoleucine - I never remember our isoleucine - this one is H, this is CH2, and I think this is CH3, yes, that is correct.0702

OK. Again, the carbonyl carbon attaches to the nitrogen.0715

The two things that we are going to connect are this and this, and we're going to connect this and this.0720

This is going to go away; this is going to go away.0730

Now, let's go ahead and draw our structure; and again, this time we go N, C, C bond, N – oops, we don't want extra straight lines because we're dealing with lines - N, C, C bond, N, C, C, OK, H3+.0734

I'm going to go ahead and put the carbonyls on first.0759

The carbonyl is on the second carbon, N, C, C.0762

The carbonyl goes on the second carbon, N, C, C, carbonyl on the second carbon, carbonyl on the second carbon.0763

This is the free end, so I'll go ahead and put that one there.0769

This is going to be alanine, so I'll do that here.0774

It is going to be tyrosine, so I'll put the OH there.0778

This one is going to be isoleucine: CH3, H, CH2, CH3.0785

I'm going to go ahead - well, you know what, that's fine - I'll go ahead and put the hydrogens.0796

In a little bit, I am probably going to start leaving off the hydrogen that's on the alpha carbon; it is there.0799

Again, from the organic chemistry, we don't always write all of the hydrogens.0809

That's it.0812

Our peptide bonds are that one - oh, you know what I should do, yes, I'm going to go ahead and put the hydrogens on the nitrogens - that's important, those are important.0813

OK.0830

Let me go back to blue.0831

That's one peptide bond right there; here is another peptide bond right here.0833

Actually, you know what, why don't we consider this whole thing a peptide bond, but that's the actual bond.0839

OK.0844

That's it.0846

This is called, if you want the name of it, basically, you just take the name of the individual acids starting from the left, you drop off the INE, and you add YL to have the "eel" sound like, remember, carbonyl, alkyl.0848

This is actually alanyl, tyrosyl, isoleucine as one word; but it is not the end of the world if you want to separate them.0866

OK.0884

This is the structure of this tripeptide, and notice, I actually use all my carbons.0887

When I do my structures, I personally like to write out every single atom; I like to write out my carbons.0893

I've never really cared for line structures myself; obviously, you want to be able to understand them, but I like to see every single carbon that I'm dealing with.0899

That is just a personal taste.0907

You have your personal taste, and by all means, don't feel compelled just because everybody else is, let's say, using line structures, that you have to use line structures, unless you have a professor that's going to take points off.0908

Understanding is more important than aesthetics at this point.0920

Later on, maybe, you can get into, maybe you’re starting to draw your line structures; but again, we want to be able to understand.0924

To this day, I actually prefer to write everything out as a straight line like this, but I'm going to go ahead and show you a couple of the other representations here, just so you know.0933

I'm going to give you the shape structure, and the shape structure is the same except it actually takes into account the angles, so it is going to look like this.0944

If you do a shape structure, it is going to be N, C, C, alternating N, C, C just like when you did alkyl change, C ,C, C, C, that little zigzag pattern, N, C, C, N, C, C, and then N, C, C.0956

Again, you just sort of fill everything in.0974

This is a plus; the carbonyl goes on the second carbon, N, C, C.0976

The carbonyl goes on the second carbonyl, N, C, C.0980

Carbonyl goes on the second carbon, something like that; and, of course, you can put your R-groups.0982

So, alanine is going to be CH3; tyrosine, it is going to be CH2.0988

Our benzene and our hydroxy and here, we have the CH, CH3, and then we have CH2, CH3, that's our isoleucine.0994

And again, let me go ahead and put the hydrogens on the nitrogen, that's important, but notice that I've left the hydrogens off the alpha carbon, so this, sort of, is another way of representing it.1010

I think it is a really nice way of doing it.1021

Again N, C, C, N, C, C, N, C, C, but notice how the carbonyls, now, they alternate, one is down one is up.1023

That's it.1030

The line structure would look like this.1031

We will go ahead and put an N, and then we’ll do that, C, C, N, C, C, then N, C, C.1041

So again, you have something that looks like this.1055

To this day, it still confuses me; it makes me crazy.1058

I really just, really like to see my carbons.1061

Carbonyl is on the second carbon, N, C, C.1064

Carbonyl is on the second carbon; that one is taken cared off.1067

Here we have CH3; here we have the CH2, the benzene, the hydroxy, and then we have the CH, we have CH3, CH2 and CH3.1070

That's it.1088

OK.1089

When you have a peptide like this- let me go ahead and put my hydrogens on, it's probably very, very important; and again, let me go ahead and do my peptide bond.1091

My peptide bond is that one right there, the carbonyl carbon and the nitrogen.1102

Where is the next one?1107

The carbonyl carbon and the nitrogen, carbonyl carbon, nitrogen, carbonyl carbon, nitrogen- that's your peptide bond, very, very important.1110

OK.1120

Traditionally, what we do- let me go ahead and put a charge on here; this is a plus charge, better not forget that, there is a minus charge.1122

OK.1129

When we write our proteins, we write them from left to right, and on the left hand side, we put the free amino group, this in red; on the right hand side, we keep the free carboxyl group.1132

This right here, this is called the N-terminal amino acid.1143

In this particular group, the N-terminal amino acid is the alanine, also called the N-terminus.1154

It is the amino terminal group, the amino terminus, so we call it the N-terminus; and this is the C-terminal amino acid or the C-terminus, C standing for carboxyl.1164

That's it.1187

We always put the amino on the left and the carboxyl on the right.1188

We read from left to right.1191

This is the alanyl, tyrosyl, isoleucine.1193

That's it.1198

OK.1200

Let's see what else we can do here.1203

All right, OK.1207

Peptide bonds are very stable once they form, having average half-lives of about 7 years.1212

So, 7 years later, you'll still have half the proteins that were made 7 years ago.1242

That's all that means- under physiological conditions, 7 years under physio conditions.1248

OK.1261

Let's go ahead and redraw our peptide here.1263

I'm going to do it as blue.1268

We've got N, C, C, N, C, C, N, C, C, 3+, carbonyl, N, C, C, carbonyl, N, C, C, carbonyl, O-.1271

We had our alanine group, and we had our tyrosine group, and we had our isoleucine group - oops, not CH2, it is CH - and then we had a CH3 out there, we had a CH2 here, and we had a CH3 there.1289

OK.1316

Now, a peptide - notice - is just like an amino acid; I mean, you've got an amino end, you've got a carboxyl end; and in this particular case, you happen to have some groups in between that also have ionizable groups.1317

That's it.1328

It is just going to behave like a long amino acid.1329

It is going to have a pKa.1332

This group is going to have a pKa; this group is going to have a pKa, and, of course, in this particular case, because this is an ionizable group, it is going to have a pKa.1334

This particular tripeptide is going to have 3 pKas.1344

The titration curve for this one is going to be exactly what you think; it is going to have 3 plateaus, 1 for each pKa.1347

That's it.1356

There is nothing strange happening here.1359

It just behaves like a really, really long amino acid.1362

Ionizable groups behave the same way they would any others.1365

Now, the pKas like for this one and this one, are not going to be the same as the pKas listed for the 3 amino acids for alanine.1369

They’re probably pretty close, but obviously, it is going to be changing a little bit because now, the environment is different.1375

OK.1382

Let's see, what shall we talk about?1385

Ionizable groups, so in this particular case, we have 3 ionizable groups.1388

OK.1392

Let's see this list: terms we'll be using interchangeably.1394

OK.1407

Let me just go ahead and write this out.1410

We talk about peptide; we talk about protein.1412

We're going to talk about polypeptide.1418

We talk about oligopeptide.1424

Again, these are just all a bunch of different terms that mean a chain of amino acids- a peptide chain.1427

As long as you specify, as long as the person that you're talking to, your audience knows what it is that you're talking about, it doesn't matter what term you use.1437

Certain teachers, they prefer you to be really, really specific, and are a little bit more pedantic about that; but for all practical purposes, again, it is understanding that matters, not little things, so we have to definitely be able to distinguish between what is important and what is not.1445

If you have a teacher that wants you to differentiate between a peptide, a protein, an oligopeptide, a polypeptide, that's fine; but other than that, don't lose any sleep over it.1461

OK.1471

Now, let's talk about some biological activity.1473

Let's see, I think I'm going to start this one on the next page, maybe.1479

Yes, here we go.1484

You know what, let me go back to blue; I really like blue very much.1492

Biological activity of a protein or a peptide, biological activity and size of a peptide or a protein have nothing to do with each other.1499

You might have a peptide that is 3 amino acids long, 6 amino acids long, or you might have one that's 417 amino acids long.1524

The size itself does not correlate to biological activity.1534

The one that is small can have incredible biological activity, and the one that's huge can have incredible biological activity; so, size doesn't mean anything.1539

It does not make it more anymore important- let's put it that way.1548

Just as an example, there is this one peptide that you know very, very well - H3, N, C, C, N, C, C.1552

This is the carbonyl here, the carbonyl here.1567

Let's go ahead and do CH2, COO-.1571

Let's go ahead and put the H on the nitrogens, and this one is going to be phenylalanine, CH2, so the tyrosine without the hydroxy, so this is called L-aspartile-L-phenylalanyl - actually, it is phenylalanine, I should say - phenylalanine methyl ester.1579

I didn't do my ester.1615

OCH3, that's an ester R-group, carbonyl, oxygen, oxygen, this oxygen connected to another carbon.1618

OK.1625

This is NutraSweet.1626

You know that NutraSweet definitely has biological activity, and it is just a dipeptide- NutraSweet, otherwise known aspartame.1628

OK.1640

Some other examples: let's see, there is a protein called cytochrome-C.1641

It has 104 amino acid residues, and it consists of just 1 chain, so one long chain of 104 amino acids.1651

OK.1665

And then, there is something like hemoglobin.1666

Yes, OK.1677

Hemoglobin- let's see, that one has 574 amino acid residues, and it actually consists of 4 different chains.1680

So, in the case of hemoglobin, you have 4 separate chains that are associated with each other.1694

OK.1709

Hemoglobin is the protein that transports oxygen in the blood, just so you know.1710

Another example would be something like a protein called hexokinase or hexokinase, depending on your pronunciation.1721

It happens to have 972 amino acid residues, but it only has 2 chains.1731

Again, just because something has more amino acid residues, doesn’t mean there are going to be more individual chains associated with each other.1740

It has almost twice as many as the hemoglobin amino acids, but it only has 2 chains instead of a 4.1750

OK.1757

And, just so you know, this one happens to be an enzyme which converts glucose - oops, and we’ll definitely be seeing this one later in the second half of the course when we talk about metabolism, when we talk about glycolysis.1758

This one converts glucose to glucose-6 phosphate, the first step in the glycolysis cycle.1821

OK.1836

Now, let's see- hemoglobin, 4 chains, hexokinase 2 chains.1839

Let's talk about this a little bit.1849

Now, proteins like hemoglobin and hexokinase - you know what, I definitely need to slow my writing down just a little bit here - which have two or more individual chains, which associate noncovalently, that's very important, noncovalently, are called multi-subunit proteins.1852

So, if you have a protein like hemoglobin or hexokinase that actually consists of more than 1 chain, well, those chains are going to fold in a certain pattern, and those chains are going to interact with each other noncovalently.1864

Those kinds of proteins, we call them multi-subunit proteins, and each individual chain is called a subunit.1878

Now, there are proteins that actually interact covalently - separate chains - insulin being an example.1903

Insulin consists of actually 2 amino acid chains, but they are actually connected covalently.1912

We don't consider those, multi-subunit, because the interaction between the chains is covalent; but when they are noncovalent, we just happen to call them multi-subunit.1919

OK.1929

Let's take a look at something.1930

This is a picture of hemoglobin; this is hemoglobin.1935

I just wanted you to see a picture of it, and see…now, don’t worry, as far as the spirals are concerned and things like that, we're going to be talking about that a little bit later- what they mean, what they represent.1944

When we talk about protein structure, specifically, we are going to get into more detail about that; but I just wanted you to see of a multi-subunit protein.1956

Notice, this red is 1 subunit; this red 1 up in here, the top right and on the bottom left, this is another subunit; and, of course, you have the 2 blues, that's a third subunit, that’s the third chain, and the fourth chain is right there.1965

So, each one of them has a series of amino acids they fold; and those 4 subunits, they come together and they form the total protein which we call hemoglobin.1981

That’s all that’s going on here.1992

OK.1995

Let's see.1996

Now, let me go back to blue.2006

Now, some proteins contain permanently associated chemical groups attached, and they're called prosthetic groups.2010

A protein could be just a long string of amino acids that has been folded into a protein, and there is nothing else that's involved with it.2045

It is a protein; it does what it does, nothing else, but there are some proteins that don’t just have the amino acid portion, but they actually have other groups that are attached to them, and these groups are called prosthetic groups.2055

Some examples would be - let's see, let's…oops…make sure these lines aren’t there - an example would be lipoproteins.2070

You know what, let me classify this a little bit better.2087

I’m going to give you the class name, and then I'm going to give you the prosthetic group.2090

So, if I talk about a particular lipoprotein, well, the prosthetic group, the thing that happens to be attached to that particular protein, is going to be a lipid, a fat, a lipid, a fat of some sort- that's it.2103

Another class is the class called glycoproteins, a huge, huge class of proteins; and the prosthetic group, a thing that happens to be attached to the protein, they're going to be carbohydrates, otherwise known as sugars.2122

There are things called hemoproteins where the thing that is attached to the prosthetic group is heme; and heme is an iron porphyrin.2144

And again, don't worry about these words; we’re going to be coming back to hemoglobin.2160

We are going to be discussing heme and iron porphyrin and things like that, so right now, I just want you to see the words and see what's going on.2164

A hemoprotein, where the prosthetic group is actually something called a heme group, and it is actually a porphyrin molecule that has an iron in the center; and this hemoglobin is actually a perfect example of a protein that has a prosthetic group, and if you look carefully, you can actually see the - let me do this one in black - you can see the heme groups right here.2170

See, they're actually inside and I know that you can see them in green.2195

There is one there; there is one in this subunit, and I think I see one in this subunit, too, right in there, if you look carefully.2199

Hemoglobin is an example of a hemoprotein.2210

It is a protein, multi-subunit, and each one of the subunits has a prosthetic group.2215

The whole protein has 4 prosthetic groups.2220

OK.2224

There is also another class, the metalloproteins, and it is exactly what you think it is.2226

The prosthetic group happens to be metal ions, for example, maybe zinc, maybe calcium, calcium 2+, maybe magnesium- whatever it happens to be.2232

Let's take an example.2250

Let's take a look at a metalloprotein to see what it might look like.2251

OK.2256

This enzyme is carbonic anhydrase; and I will write down the reaction in just a minute.2257

This is a metalloprotein.2270

This is a particular protein that has a zinc ion, actually, as its prosthetic group; and if you look really carefully, you can actually see the zinc.2272

It is right there, right in there.2283

Now, what I've done is I’ve taken this, and we’ve blown it up a little bit, so that you can actually see the interactions.2286

If we go deep inside the proteins, here is our zinc, and as you can see, its interaction is a noncovalent interaction with what looks like 3 histidine residues and this thing which looks like a hydroxy group.2291

That's what’s going on.2314

This is an example of a metalloprotein.2315

Now, carbonic anhydrase, it catalyzes the following reaction, just so you know, just to have it for information.2319

CO2, + H2O, HCO3, yes HCO3- + H+, so it catalyzes this particular equilibrium- the equilibrium between the CO2, H2O, and bicarbonate, and acid.2333

The active site of this enzyme -again, we have this as zinc ion - is coordinated to 3 histidine residues; and again, this protein has folded in on itself, but these R-groups, they are sticking out, so this particular active site, there are 3 histidine residues in different places, that have positioned themselves in such a way that they can actually trap that zinc ion, histidine resides, and what looks like a hydroxy group and NOH-.2353

That's it; that's all that's going on here.2398

OK.2400

Now, and again, as far as these little twists and turns, these arrows, these ribbons, these lines, we are going to be talking about that a little bit later.2404

Right now, what's important, I just wanted you to see some proteins, see some interactions, things like that.2414

We are going to be talking about what those mean, and they do mean specific things when we talk about protein structure- very, very important.2418

Now, let's go ahead and actually talk about protein structure just globally, real quick, and do a couple more examples of some proteins; and then later on, we'll discuss all of these in a little bit more detail.2427

OK.2445

A protein has 4 levels of structure.2446

Normally, it has 3 levels of structure, but the multi-subunits, they are the fourth level of structure.2450

The first level of structure - let me go ahead and use, that's OK, I'll go stick with black, OK - the primary structure of a protein is its amino acid sequence.2454

That's it.2465

Alanine, tyrosine, isoleucine, leusine, valine- whatever it is, that's the primary structure, the amino acid sequence.2466

Now, the amino acids, once we actually form a peptide chain, there are certain portions of that peptide chain that are going to take particular configurations.2474

Two of those configurations happen to be alpha-helix and beta-pleated sheet.2487

So, those spirals that you see, like for example over here, that means that section of the protein, the backbone, is taking on a spiral shape.2492

These flat sections like these flat sections with little arrow heads on them, that means individual amino acids have arranged themselves in something called a beta-pleated sheet; and again, we will talk in greater detail about these a little bit later.2502

This is called the secondary structure.2517

The secondary structure is where it actually folds on itself, individual portions of the amino acid chain to achieve certain basic structures that keep showing up over and over and over again; and primarily it is going to be the alpha-helix and the beta-sheet.2520

OK.2536

Now, the tertiary structure of a protein, the third level is once this is formed, and a little bit of this is formed, and whatever else is happening along the chain, that chain is going to start folding in on itself.2537

Perhaps a cysteine residue from here and a cysteine residue from there are going to bind and form a disulphide bridge.2550

Maybe there is going to be other interactions.2556

When it is actually folded, that single chain, when it has come to its final folded position, that is called the tertiary structure.2562

That is the 3-dimensional structure, and that's what we've been looking at.2567

An example of a tertiary structure protein is this one right here.2573

Notice, we have some alpha-helices; we have some beta-pleated sheets.2578

These are just regular lines; that means there is nothing is going on.2583

That is just straight amino acids, just a straight chain.2586

There is no particular uniform structure there.2590

It is just amino acid after amino acid.2593

That is this particular structure right here, just a long peptide chain.2596

So, the whole thing, this is an example of tertiary structure.2600

This happens to be the protein firefly luciferase.2604

It is an enzyme- ASE ending tells you it's an enzyme.2615

This protein is a protein that is responsible for the firefly actually being able to glow the way that it does.2617

This is an example of a tertiary structure.2625

This is a single chain.2629

It is a single chain that has folded and has taken up a particular configuration- that's the tertiary structure.2631

OK.2637

Now, when you have a multi-subunit protein, when you have, let's say, 4 chains like hemoglobin, each one takes a particular shape; and then those individual proteins actually associate noncovalently to form the entire protein.2638

When you have a multi-subunit protein, that's the fourth level of structure.2656

That is the quaternary structure.2661

So, primary, secondary, tertiary, quaternary- just wanted you to be aware of this particular setup in terms of structure; and then we are going to be talking about these in future lessons in rather great detail.2664

Let's go ahead and check out one more.2680

Again, in this particular case, this is going to be an example of quaternary structure.2684

This is hemoglobin, again, the one that we saw before.2689

You have your 1 chain right there, another chain, another chain, and another chain.2695

Each one of those represents the tertiary structure.2704

When they come together to form the entire final protein, you have your quaternary structure.2707

That's it.2711

OK.2713

Thank you for joining us here at Educator.com and Biochemistry.2714

We'll see you next time, bye-bye.2717

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