Enter your Sign on user name and password.

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

Use Chrome browser to play professor video
Raffi Hovasapian

Raffi Hovasapian

Alpha Helix & Beta Conformation

Slide Duration:

Table of Contents

I. Preliminaries on Aqueous Chemistry
Aqueous Solutions & Concentration

39m 57s

Intro
0:00
Aqueous Solutions and Concentration
0:46
Definition of Solution
1:28
Example: Sugar Dissolved in Water
2:19
Example: Salt Dissolved in Water
3:04
A Solute Does Not Have to Be a Solid
3:37
A Solvent Does Not Have to Be a Liquid
5:02
Covalent Compounds
6:55
Ionic Compounds
7:39
Example: Table Sugar
9:12
Example: MgCl₂
10:40
Expressing Concentration: Molarity
13:42
Example 1
14:47
Example 1: Question
14:50
Example 1: Solution
15:40
Another Way to Express Concentration
22:01
Example 2
24:00
Example 2: Question
24:01
Example 2: Solution
24:49
Some Other Ways of Expressing Concentration
27:52
Example 3
29:30
Example 3: Question
29:31
Example 3: Solution
31:02
Dilution & Osmotic Pressure

38m 53s

Intro
0:00
Dilution
0:45
Definition of Dilution
0:46
Example 1: Question
2:08
Example 1: Basic Dilution Equation
4:20
Example 1: Solution
5:31
Example 2: Alternative Approach
12:05
Osmotic Pressure
14:34
Colligative Properties
15:02
Recall: Covalent Compounds and Soluble Ionic Compounds
17:24
Properties of Pure Water
19:42
Addition of a Solute
21:56
Osmotic Pressure: Conceptual Example
24:00
Equation for Osmotic Pressure
29:30
Example of 'i'
31:38
Example 3
32:50
More on Osmosis

29m 1s

Intro
0:00
More on Osmosis
1:25
Osmotic Pressure
1:26
Example 1: Molar Mass of Protein
5:25
Definition, Equation, and Unit of Osmolarity
13:13
Example 2: Osmolarity
15:19
Isotonic, Hypertonic, and Hypotonic
20:20
Example 3
22:20
More on Isotonic, Hypertonic, and Hypotonic
26:14
Osmosis vs. Osmotic Pressure
27:56
Acids & Bases

39m 11s

Intro
0:00
Acids and Bases
1:16
Let's Begin With H₂O
1:17
P-Scale
4:22
Example 1
6:39
pH
9:43
Strong Acids
11:10
Strong Bases
13:52
Weak Acids & Bases Overview
14:32
Weak Acids
15:49
Example 2: Phosphoric Acid
19:30
Weak Bases
24:50
Weak Base Produces Hydroxide Indirectly
25:41
Example 3: Pyridine
29:07
Acid Form and Base Form
32:02
Acid Reaction
35:50
Base Reaction
36:27
Ka, Kb, and Kw
37:14
Titrations and Buffers

41m 33s

Intro
0:00
Titrations
0:27
Weak Acid
0:28
Rearranging the Ka Equation
1:45
Henderson-Hasselbalch Equation
3:52
Fundamental Reaction of Acids and Bases
5:36
The Idea Behind a Titration
6:27
Let's Look at an Acetic Acid Solution
8:44
Titration Curve
17:00
Acetate
23:57
Buffers
26:57
Introduction to Buffers
26:58
What is a Buffer?
29:40
Titration Curve & Buffer Region
31:44
How a Buffer Works: Adding OH⁻
34:44
How a Buffer Works: Adding H⁺
35:58
Phosphate Buffer System
38:02
Example Problems with Acids, Bases & Buffers

44m 19s

Intro
0:00
Example 1
1:21
Example 1: Properties of Glycine
1:22
Example 1: Part A
3:40
Example 1: Part B
4:40
Example 2
9:02
Example 2: Question
9:03
Example 2: Total Phosphate Concentration
12:23
Example 2: Final Solution
17:10
Example 3
19:34
Example 3: Question
19:35
Example 3: pH Before
22:18
Example 3: pH After
24:24
Example 3: New pH
27:54
Example 4
30:00
Example 4: Question
30:01
Example 4: Equilibria
32:52
Example 4: 1st Reaction
38:04
Example 4: 2nd Reaction
39:53
Example 4: Final Solution
41:33
Hydrolysis & Condensation Reactions

18m 45s

Intro
0:00
Hydrolysis and Condensation Reactions
0:50
Hydrolysis
0:51
Condensation
2:42
Example 1: Hydrolysis of Ethyl Acetate
4:52
Example 2: Condensation of Acetic Acid with Ethanol
8:42
Example 3
11:18
Example 4: Formation & Hydrolysis of a Peptide Bond Between the Amino Acids Alanine & Serine
14:56
II. Amino Acids & Proteins: Primary Structure
Amino Acids

38m 19s

Intro
0:00
Amino Acids
0:17
Proteins & Amino Acids
0:18
Difference Between Amino Acids
4:20
α-Carbon
7:08
Configuration in Biochemistry
10:43
L-Glyceraldehyde & Fischer Projection
12:32
D-Glyceraldehyde & Fischer Projection
15:31
Amino Acids in Biological Proteins are the L Enantiomer
16:50
L-Amino Acid
18:04
L-Amino Acids Correspond to S-Enantiomers in the RS System
20:10
Classification of Amino Acids
22:53
Amino Acids With Non-Polar R Groups
26:45
Glycine
27:00
Alanine
27:48
Valine
28:15
Leucine
28:58
Proline
31:08
Isoleucine
32:42
Methionine
33:43
Amino Acids With Aromatic R Groups
34:33
Phenylalanine
35:26
Tyrosine
36:02
Tryptophan
36:32
Amino Acids, Continued

27m 14s

Intro
0:00
Amino Acids With Positively Charged R Groups
0:16
Lysine
0:52
Arginine
1:55
Histidine
3:15
Amino Acids With Negatively Charged R Groups
6:28
Aspartate
6:58
Glutamate
8:11
Amino Acids With Uncharged, but Polar R Groups
8:50
Serine
8:51
Threonine
10:21
Cysteine
11:06
Asparagine
11:35
Glutamine
12:44
More on Amino Acids
14:18
Cysteine Dimerizes to Form Cystine
14:53
Tryptophan, Tyrosine, and Phenylalanine
19:07
Other Amino Acids
20:53
Other Amino Acids: Hydroxy Lysine
22:34
Other Amino Acids: r-Carboxy Glutamate
25:37
Acid/Base Behavior of Amino Acids

48m 28s

Intro
0:00
Acid/Base Behavior of Amino Acids
0:27
Acid/Base Behavior of Amino Acids
0:28
Let's Look at Alanine
1:57
Titration of Acidic Solution of Alanine with a Strong Base
2:51
Amphoteric Amino Acids
13:24
Zwitterion & Isoelectric Point
16:42
Some Amino Acids Have 3 Ionizable Groups
20:35
Example: Aspartate
24:44
Example: Tyrosine
28:50
Rule of Thumb
33:04
Basis for the Rule
35:59
Example: Describe the Degree of Protonation for Each Ionizable Group
38:46
Histidine is Special
44:58
Peptides & Proteins

45m 18s

Intro
0:00
Peptides and Proteins
0:15
Introduction to Peptides and Proteins
0:16
Formation of a Peptide Bond: The Bond Between 2 Amino Acids
1:44
Equilibrium
7:53
Example 1: Build the Following Tripeptide Ala-Tyr-Ile
9:48
Example 1: Shape Structure
15:43
Example 1: Line Structure
17:11
Peptides Bonds
20:08
Terms We'll Be Using Interchangeably
23:14
Biological Activity & Size of a Peptide
24:58
Multi-Subunit Proteins
30:08
Proteins and Prosthetic Groups
32:13
Carbonic Anhydrase
37:35
Primary, Secondary, Tertiary, and Quaternary Structure of Proteins
40:26
Amino Acid Sequencing of a Peptide Chain

42m 47s

Intro
0:00
Amino Acid Sequencing of a Peptide Chain
0:30
Amino Acid Sequence and Its Structure
0:31
Edman Degradation: Overview
2:57
Edman Degradation: Reaction - Part 1
4:58
Edman Degradation: Reaction - Part 2
10:28
Edman Degradation: Reaction - Part 3
13:51
Mechanism Step 1: PTC (Phenylthiocarbamyl) Formation
19:01
Mechanism Step 2: Ring Formation & Peptide Bond Cleavage
23:03
Example: Write Out the Edman Degradation for the Tripeptide Ala-Tyr-Ser
30:29
Step 1
30:30
Step 2
34:21
Step 3
36:56
Step 4
38:28
Step 5
39:24
Step 6
40:44
Sequencing Larger Peptides & Proteins

1h 2m 33s

Intro
0:00
Sequencing Larger Peptides and Proteins
0:28
Identifying the N-Terminal Amino Acids With the Reagent Fluorodinitrobenzene (FDNB)
0:29
Sequencing Longer Peptides & Proteins Overview
5:54
Breaking Peptide Bond: Proteases and Chemicals
8:16
Some Enzymes/Chemicals Used for Fragmentation: Trypsin
11:14
Some Enzymes/Chemicals Used for Fragmentation: Chymotrypsin
13:02
Some Enzymes/Chemicals Used for Fragmentation: Cyanogen Bromide
13:28
Some Enzymes/Chemicals Used for Fragmentation: Pepsin
13:44
Cleavage Location
14:04
Example: Chymotrypsin
16:44
Example: Pepsin
18:17
More on Sequencing Larger Peptides and Proteins
19:29
Breaking Disulfide Bonds: Performic Acid
26:08
Breaking Disulfide Bonds: Dithiothreitol Followed by Iodoacetate
31:04
Example: Sequencing Larger Peptides and Proteins
37:03
Part 1 - Breaking Disulfide Bonds, Hydrolysis and Separation
37:04
Part 2 - N-Terminal Identification
44:16
Part 3 - Sequencing Using Pepsin
46:43
Part 4 - Sequencing Using Cyanogen Bromide
52:02
Part 5 - Final Sequence
56:48
Peptide Synthesis (Merrifield Process)

49m 12s

Intro
0:00
Peptide Synthesis (Merrifield Process)
0:31
Introduction to Synthesizing Peptides
0:32
Merrifield Peptide Synthesis: General Scheme
3:03
So What Do We Do?
6:07
Synthesis of Protein in the Body Vs. The Merrifield Process
7:40
Example: Synthesis of Ala-Gly-Ser
9:21
Synthesis of Ala-Gly-Ser: Reactions Overview
11:41
Synthesis of Ala-Gly-Ser: Reaction 1
19:34
Synthesis of Ala-Gly-Ser: Reaction 2
24:34
Synthesis of Ala-Gly-Ser: Reaction 3
27:34
Synthesis of Ala-Gly-Ser: Reaction 4 & 4a
28:48
Synthesis of Ala-Gly-Ser: Reaction 5
33:38
Synthesis of Ala-Gly-Ser: Reaction 6
36:45
Synthesis of Ala-Gly-Ser: Reaction 7 & 7a
37:44
Synthesis of Ala-Gly-Ser: Reaction 8
39:47
Synthesis of Ala-Gly-Ser: Reaction 9 & 10
43:23
Chromatography: Eluent, Stationary Phase, and Eluate
45:55
More Examples with Amino Acids & Peptides

54m 31s

Intro
0:00
Example 1
0:22
Data
0:23
Part A: What is the pI of Serine & Draw the Correct Structure
2:11
Part B: How Many mL of NaOH Solution Have Been Added at This Point (pI)?
5:27
Part C: At What pH is the Average Charge on Serine
10:50
Part D: Draw the Titration Curve for This Situation
14:50
Part E: The 10 mL of NaOH Added to the Solution at the pI is How Many Equivalents?
17:35
Part F: Serine Buffer Solution
20:22
Example 2
23:04
Data
23:05
Part A: Calculate the Minimum Molar Mass of the Protein
25:12
Part B: How Many Tyr Residues in this Protein?
28:34
Example 3
30:08
Question
30:09
Solution
34:30
Example 4
48:46
Question
48:47
Solution
49:50
III. Proteins: Secondary, Tertiary, and Quaternary Structure
Alpha Helix & Beta Conformation

50m 52s

Intro
0:00
Alpha Helix and Beta Conformation
0:28
Protein Structure Overview
0:29
Weak interactions Among the Amino Acid in the Peptide Chain
2:11
Two Principals of Folding Patterns
4:56
Peptide Bond
7:00
Peptide Bond: Resonance
9:46
Peptide Bond: φ Bond & ψ Bond
11:22
Secondary Structure
15:08
α-Helix Folding Pattern
17:28
Illustration 1: α-Helix Folding Pattern
19:22
Illustration 2: α-Helix Folding Pattern
21:39
β-Sheet
25:16
β-Conformation
26:04
Parallel & Anti-parallel
28:44
Parallel β-Conformation Arrangement of the Peptide Chain
30:12
Putting Together a Parallel Peptide Chain
35:16
Anti-Parallel β-Conformation Arrangement
37:42
Tertiary Structure
45:03
Quaternary Structure
45:52
Illustration 3: Myoglobin Tertiary Structure & Hemoglobin Quaternary Structure
47:13
Final Words on Alpha Helix and Beta Conformation
48:34
IV. Proteins: Function
Protein Function I: Ligand Binding & Myoglobin

51m 36s

Intro
0:00
Protein Function I: Ligand Binding & Myoglobin
0:30
Ligand
1:02
Binding Site
2:06
Proteins are Not Static or Fixed
3:36
Multi-Subunit Proteins
5:46
O₂ as a Ligand
7:21
Myoglobin, Protoporphyrin IX, Fe ²⁺, and O₂
12:54
Protoporphyrin Illustration
14:25
Myoglobin With a Heme Group Illustration
17:02
Fe²⁺ has 6 Coordination Sites & Binds O₂
18:10
Heme
19:44
Myoglobin Overview
22:40
Myoglobin and O₂ Interaction
23:34
Keq or Ka & The Measure of Protein's Affinity for Its Ligand
26:46
Defining α: Fraction of Binding Sites Occupied
32:52
Graph: α vs. [L]
37:33
For The Special Case of α = 0.5
39:01
Association Constant & Dissociation Constant
43:54
α & Kd
45:15
Myoglobin's Binding of O₂
48:20
Protein Function II: Hemoglobin

1h 3m 36s

Intro
0:00
Protein Function II: Hemoglobin
0:14
Hemoglobin Overview
0:15
Hemoglobin & Its 4 Subunits
1:22
α and β Interactions
5:18
Two Major Conformations of Hb: T State (Tense) & R State (Relaxed)
8:06
Transition From The T State to R State
12:03
Binding of Hemoglobins & O₂
14:02
Binding Curve
18:32
Hemoglobin in the Lung
27:28
Signoid Curve
30:13
Cooperative Binding
32:25
Hemoglobin is an Allosteric Protein
34:26
Homotropic Allostery
36:18
Describing Cooperative Binding Quantitatively
38:06
Deriving The Hill Equation
41:52
Graphing the Hill Equation
44:43
The Slope and Degree of Cooperation
46:25
The Hill Coefficient
49:48
Hill Coefficient = 1
51:08
Hill Coefficient < 1
55:55
Where the Graph Hits the x-axis
56:11
Graph for Hemoglobin
58:02
Protein Function III: More on Hemoglobin

1h 7m 16s

Intro
0:00
Protein Function III: More on Hemoglobin
0:11
Two Models for Cooperative Binding: MWC & Sequential Model
0:12
MWC Model
1:31
Hemoglobin Subunits
3:32
Sequential Model
8:00
Hemoglobin Transports H⁺ & CO₂
17:23
Binding Sites of H⁺ and CO₂
19:36
CO₂ is Converted to Bicarbonate
23:28
Production of H⁺ & CO₂ in Tissues
27:28
H⁺ & CO₂ Binding are Inversely Related to O₂ Binding
28:31
The H⁺ Bohr Effect: His¹⁴⁶ Residue on the β Subunits
33:31
Heterotropic Allosteric Regulation of O₂ Binding by 2,3-Biphosphoglycerate (2,3 BPG)
39:53
Binding Curve for 2,3 BPG
56:21
V. Enzymes
Enzymes I

41m 38s

Intro
0:00
Enzymes I
0:38
Enzymes Overview
0:39
Cofactor
4:38
Holoenzyme
5:52
Apoenzyme
6:40
Riboflavin, FAD, Pyridoxine, Pyridoxal Phosphate Structures
7:28
Carbonic Anhydrase
8:45
Classification of Enzymes
9:55
Example: EC 1.1.1.1
13:04
Reaction of Oxidoreductases
16:23
Enzymes: Catalysts, Active Site, and Substrate
18:28
Illustration of Enzymes, Substrate, and Active Site
27:22
Catalysts & Activation Energies
29:57
Intermediates
36:00
Enzymes II

44m 2s

Intro
0:00
Enzymes II: Transitions State, Binding Energy, & Induced Fit
0:18
Enzymes 'Fitting' Well With The Transition State
0:20
Example Reaction: Breaking of a Stick
3:40
Another Energy Diagram
8:20
Binding Energy
9:48
Enzymes Specificity
11:03
Key Point: Optimal Interactions Between Substrate & Enzymes
15:15
Induced Fit
16:25
Illustrations: Induced Fit
20:58
Enzymes II: Catalytic Mechanisms
22:17
General Acid/Base Catalysis
23:56
Acid Form & Base Form of Amino Acid: Glu &Asp
25:26
Acid Form & Base Form of Amino Acid: Lys & Arg
26:30
Acid Form & Base Form of Amino Acid: Cys
26:51
Acid Form & Base Form of Amino Acid: His
27:30
Acid Form & Base Form of Amino Acid: Ser
28:16
Acid Form & Base Form of Amino Acid: Tyr
28:30
Example: Phosphohexose Isomerase
29:20
Covalent Catalysis
34:19
Example: Glyceraldehyde 3-Phosphate Dehydrogenase
35:34
Metal Ion Catalysis: Isocitrate Dehydrogenase
38:45
Function of Mn²⁺
42:15
Enzymes III: Kinetics

56m 40s

Intro
0:00
Enzymes III: Kinetics
1:40
Rate of an Enzyme-Catalyzed Reaction & Substrate Concentration
1:41
Graph: Substrate Concentration vs. Reaction Rate
10:43
Rate At Low and High Substrate Concentration
14:26
Michaelis & Menten Kinetics
20:16
More On Rate & Concentration of Substrate
22:46
Steady-State Assumption
26:02
Rate is Determined by How Fast ES Breaks Down to Product
31:36
Total Enzyme Concentration: [Et] = [E] + [ES]
35:35
Rate of ES Formation
36:44
Rate of ES Breakdown
38:40
Measuring Concentration of Enzyme-Substrate Complex
41:19
Measuring Initial & Maximum Velocity
43:43
Michaelis & Menten Equation
46:44
What Happens When V₀ = (1/2) Vmax?
49:12
When [S] << Km
53:32
When [S] >> Km
54:44
Enzymes IV: Lineweaver-Burk Plots

20m 37s

Intro
0:00
Enzymes IV: Lineweaver-Burk Plots
0:45
Deriving The Lineweaver-Burk Equation
0:46
Lineweaver-Burk Plots
3:55
Example 1: Carboxypeptidase A
8:00
More on Km, Vmax, and Enzyme-catalyzed Reaction
15:54
Enzymes V: Enzyme Inhibition

51m 37s

Intro
0:00
Enzymes V: Enzyme Inhibition Overview
0:42
Enzyme Inhibitors Overview
0:43
Classes of Inhibitors
2:32
Competitive Inhibition
3:08
Competitive Inhibition
3:09
Michaelis & Menten Equation in the Presence of a Competitive Inhibitor
7:40
Double-Reciprocal Version of the Michaelis & Menten Equation
14:48
Competitive Inhibition Graph
16:37
Uncompetitive Inhibition
19:23
Uncompetitive Inhibitor
19:24
Michaelis & Menten Equation for Uncompetitive Inhibition
22:10
The Lineweaver-Burk Equation for Uncompetitive Inhibition
26:04
Uncompetitive Inhibition Graph
27:42
Mixed Inhibition
30:30
Mixed Inhibitor
30:31
Double-Reciprocal Version of the Equation
33:34
The Lineweaver-Burk Plots for Mixed Inhibition
35:02
Summary of Reversible Inhibitor Behavior
38:00
Summary of Reversible Inhibitor Behavior
38:01
Note: Non-Competitive Inhibition
42:22
Irreversible Inhibition
45:15
Irreversible Inhibition
45:16
Penicillin & Transpeptidase Enzyme
46:50
Enzymes VI: Regulatory Enzymes

51m 23s

Intro
0:00
Enzymes VI: Regulatory Enzymes
0:45
Regulatory Enzymes Overview
0:46
Example: Glycolysis
2:27
Allosteric Regulatory Enzyme
9:19
Covalent Modification
13:08
Two Other Regulatory Processes
16:28
Allosteric Regulation
20:58
Feedback Inhibition
25:12
Feedback Inhibition Example: L-Threonine → L-Isoleucine
26:03
Covalent Modification
27:26
Covalent Modulators: -PO₃²⁻
29:30
Protein Kinases
31:59
Protein Phosphatases
32:47
Addition/Removal of -PO₃²⁻ and the Effect on Regulatory Enzyme
33:36
Phosphorylation Sites of a Regulatory Enzyme
38:38
Proteolytic Cleavage
41:48
Zymogens: Chymotrypsin & Trypsin
43:58
Enzymes That Use More Than One Regulatory Process: Bacterial Glutamine Synthetase
48:59
Why The Complexity?
50:27
Enzymes VII: Km & Kcat

54m 49s

Intro
0:00
Km
1:48
Recall the Michaelis–Menten Equation
1:49
Km & Enzyme's Affinity
6:18
Rate Forward, Rate Backward, and Equilibrium Constant
11:08
When an Enzyme's Affinity for Its Substrate is High
14:17
More on Km & Enzyme Affinity
17:29
The Measure of Km Under Michaelis–Menten kinetic
23:19
Kcat (First-order Rate Constant or Catalytic Rate Constant)
24:10
Kcat: Definition
24:11
Kcat & The Michaelis–Menten Postulate
25:18
Finding Vmax and [Et}
27:27
Units for Vmax and Kcat
28:26
Kcat: Turnover Number
28:55
Michaelis–Menten Equation
32:12
Km & Kcat
36:37
Second Order Rate Equation
36:38
(Kcat)/(Km): Overview
39:22
High (Kcat)/(Km)
40:20
Low (Kcat)/(Km)
43:16
Practical Big Picture
46:28
Upper Limit to (Kcat)/(Km)
48:56
More On Kcat and Km
49:26
VI. Carbohydrates
Monosaccharides

1h 17m 46s

Intro
0:00
Monosaccharides
1:49
Carbohydrates Overview
1:50
Three Major Classes of Carbohydrates
4:48
Definition of Monosaccharides
5:46
Examples of Monosaccharides: Aldoses
7:06
D-Glyceraldehyde
7:39
D-Erythrose
9:00
D-Ribose
10:10
D-Glucose
11:20
Observation: Aldehyde Group
11:54
Observation: Carbonyl 'C'
12:30
Observation: D & L Naming System
12:54
Examples of Monosaccharides: Ketose
16:54
Dihydroxy Acetone
17:28
D-Erythrulose
18:30
D-Ribulose
19:49
D-Fructose
21:10
D-Glucose Comparison
23:18
More information of Ketoses
24:50
Let's Look Closer at D-Glucoses
25:50
Let's Look At All the D-Hexose Stereoisomers
31:22
D-Allose
32:20
D-Altrose
33:01
D-Glucose
33:39
D-Gulose
35:00
D-Mannose
35:40
D-Idose
36:42
D-Galactose
37:14
D-Talose
37:42
Epimer
40:05
Definition of Epimer
40:06
Example of Epimer: D-Glucose, D-Mannose, and D-Galactose
40:57
Hemiacetal or Hemiketal
44:36
Hemiacetal/Hemiketal Overview
45:00
Ring Formation of the α and β Configurations of D-Glucose
50:52
Ring Formation of the α and β Configurations of Fructose
1:01:39
Haworth Projection
1:07:34
Pyranose & Furanose Overview
1:07:38
Haworth Projection: Pyranoses
1:09:30
Haworth Projection: Furanose
1:14:56
Hexose Derivatives & Reducing Sugars

37m 6s

Intro
0:00
Hexose Derivatives
0:15
Point of Clarification: Forming a Cyclic Sugar From a Linear Sugar
0:16
Let's Recall the α and β Anomers of Glucose
8:42
α-Glucose
10:54
Hexose Derivatives that Play Key Roles in Physiology Progression
17:38
β-Glucose
18:24
β-Glucosamine
18:48
N-Acetyl-β-Glucosamine
20:14
β-Glucose-6-Phosphate
22:22
D-Gluconate
24:10
Glucono-δ-Lactone
26:33
Reducing Sugars
29:50
Reducing Sugars Overview
29:51
Reducing Sugars Example: β-Galactose
32:36
Disaccharides

43m 32s

Intro
0:00
Disaccharides
0:15
Disaccharides Overview
0:19
Examples of Disaccharides & How to Name Them
2:49
Disaccharides Trehalose Overview
15:46
Disaccharides Trehalose: Flip
20:52
Disaccharides Trehalose: Spin
28:36
Example: Draw the Structure
33:12
Polysaccharides

39m 25s

Intro
0:00
Recap Example: Draw the Structure of Gal(α1↔β1)Man
0:38
Polysaccharides
9:46
Polysaccharides Overview
9:50
Homopolysaccharide
13:12
Heteropolysaccharide
13:47
Homopolysaccharide as Fuel Storage
16:23
Starch Has Two Types of Glucose Polymer: Amylose
17:10
Starch Has Two Types of Glucose Polymer: Amylopectin
18:04
Polysaccharides: Reducing End & Non-Reducing End
19:30
Glycogen
20:06
Examples: Structures of Polysaccharides
21:42
Let's Draw an (α1→4) & (α1→6) of Amylopectin by Hand.
28:14
More on Glycogen
31:17
Glycogen, Concentration, & The Concept of Osmolarity
35:16
Polysaccharides, Part 2

44m 15s

Intro
0:00
Polysaccharides
0:17
Example: Cellulose
0:34
Glycoside Bond
7:25
Example Illustrations
12:30
Glycosaminoglycans Part 1
15:55
Glycosaminoglycans Part 2
18:34
Glycosaminoglycans & Sulfate Attachments
22:42
β-D-N-Acetylglucosamine
24:49
β-D-N-AcetylGalactosamine
25:42
β-D-Glucuronate
26:44
β-L-Iduronate
27:54
More on Sulfate Attachments
29:49
Hylarunic Acid
32:00
Hyaluronates
39:32
Other Glycosaminoglycans
40:46
Glycoconjugates

44m 23s

Intro
0:00
Glycoconjugates
0:24
Overview
0:25
Proteoglycan
2:53
Glycoprotein
5:20
Glycolipid
7:25
Proteoglycan vs. Glycoprotein
8:15
Cell Surface Diagram
11:17
Proteoglycan Common Structure
14:24
Example: Chondroitin-4-Sulfate
15:06
Glycoproteins
19:50
The Monomers that Commonly Show Up in The Oligo Portions of Glycoproteins
28:02
N-Acetylneuraminic Acid
31:17
L-Furose
32:37
Example of an N-Linked Oligosaccharide
33:21
Cell Membrane Structure
36:35
Glycolipids & Lipopolysaccharide
37:22
Structure Example
41:28
More Example Problems with Carbohydrates

40m 22s

Intro
0:00
Example 1
1:09
Example 2
2:34
Example 3
5:12
Example 4
16:19
Question
16:20
Solution
17:25
Example 5
24:18
Question
24:19
Structure of 2,3-Di-O-Methylglucose
26:47
Part A
28:11
Part B
33:46
VII. Lipids
Fatty Acids & Triacylglycerols

54m 55s

Intro
0:00
Fatty Acids
0:32
Lipids Overview
0:34
Introduction to Fatty Acid
3:18
Saturated Fatty Acid
6:13
Unsaturated or Polyunsaturated Fatty Acid
7:07
Saturated Fatty Acid Example
7:46
Unsaturated Fatty Acid Example
9:06
Notation Example: Chain Length, Degree of Unsaturation, & Double Bonds Location of Fatty Acid
11:56
Example 1: Draw the Structure
16:18
Example 2: Give the Shorthand for cis,cis-5,8-Hexadecadienoic Acid
20:12
Example 3
23:12
Solubility of Fatty Acids
25:45
Melting Points of Fatty Acids
29:40
Triacylglycerols
34:13
Definition of Triacylglycerols
34:14
Structure of Triacylglycerols
35:08
Example: Triacylglycerols
40:23
Recall Ester Formation
43:57
The Body's Primary Fuel-Reserves
47:22
Two Primary Advantages to Storing Energy as Triacylglycerols Instead of Glycogen: Number 1
49:24
Two Primary Advantages to Storing Energy as Triacylglycerols Instead of Glycogen: Number 2
51:54
Membrane Lipids

38m 51s

Intro
0:00
Membrane Lipids
0:26
Definition of Membrane Lipids
0:27
Five Major Classes of Membrane Lipids
2:38
Glycerophospholipids
5:04
Glycerophospholipids Overview
5:05
The X Group
8:05
Example: Phosphatidyl Ethanolamine
10:51
Example: Phosphatidyl Choline
13:34
Phosphatidyl Serine
15:16
Head Groups
16:50
Ether Linkages Instead of Ester Linkages
20:05
Galactolipids
23:39
Galactolipids Overview
23:40
Monogalactosyldiacylglycerol: MGDG
25:17
Digalactosyldiacylglycerol: DGDG
28:13
Structure Examples 1: Lipid Bilayer
31:35
Structure Examples 2: Cross Section of a Cell
34:56
Structure Examples 3: MGDG & DGDG
36:28
Membrane Lipids, Part 2

38m 20s

Intro
0:00
Sphingolipids
0:11
Sphingolipid Overview
0:12
Sphingosine Structure
1:42
Ceramide
3:56
Subclasses of Sphingolipids Overview
6:00
Subclasses of Sphingolipids: Sphingomyelins
7:53
Sphingomyelins
7:54
Subclasses of Sphingolipids: Glycosphingolipid
12:47
Glycosphingolipid Overview
12:48
Cerebrosides & Globosides Overview
14:33
Example: Cerebrosides
15:43
Example: Globosides
17:14
Subclasses of Sphingolipids: Gangliosides
19:07
Gangliosides
19:08
Medical Application: Tay-Sachs Disease
23:34
Sterols
30:45
Sterols: Basic Structure
30:46
Important Example: Cholesterol
32:01
Structures Example
34:13
The Biologically Active Lipids

48m 36s

Intro
0:00
The Biologically Active Lipids
0:44
Phosphatidyl Inositol Structure
0:45
Phosphatidyl Inositol Reaction
3:24
Image Example
12:49
Eicosanoids
14:12
Arachidonic Acid & Membrane Lipid Containing Arachidonic Acid
18:41
Three Classes of Eicosanoids
20:42
Overall Structures
21:38
Prostagladins
22:56
Thromboxane
27:19
Leukotrienes
30:19
More On The Biologically Active Lipids
33:34
Steroid Hormones
33:35
Fat Soluble Vitamins
38:25
Vitamin D₃
40:40
Vitamin A
43:17
Vitamin E
45:12
Vitamin K
47:17
VIII. Energy & Biological Systems (Bioenergetics)
Thermodynamics, Free Energy & Equilibrium

45m 51s

Intro
0:00
Thermodynamics, Free Energy and Equilibrium
1:03
Reaction: Glucose + Pi → Glucose 6-Phosphate
1:50
Thermodynamics & Spontaneous Processes
3:31
In Going From Reactants → Product, a Reaction Wants to Release Heat
6:30
A Reaction Wants to Become More Disordered
9:10
∆H < 0
10:30
∆H > 0
10:57
∆S > 0
11:23
∆S <0
11:56
∆G = ∆H - T∆S at Constant Pressure
12:15
Gibbs Free Energy
15:00
∆G < 0
16:49
∆G > 0
17:07
Reference Frame For Thermodynamics Measurements
17:57
More On BioChemistry Standard
22:36
Spontaneity
25:36
Keq
31:45
Example: Glucose + Pi → Glucose 6-Phosphate
34:14
Example Problem 1
40:25
Question
40:26
Solution
41:12
More on Thermodynamics & Free Energy

37m 6s

Intro
0:00
More on Thermodynamics & Free Energy
0:16
Calculating ∆G Under Standard Conditions
0:17
Calculating ∆G Under Physiological Conditions
2:05
∆G < 0
5:39
∆G = 0
7:03
Reaction Moving Forward Spontaneously
8:00
∆G & The Maximum Theoretical Amount of Free Energy Available
10:36
Example Problem 1
13:11
Reactions That Have Species in Common
17:48
Example Problem 2: Part 1
20:10
Example Problem 2: Part 2- Enzyme Hexokinase & Coupling
25:08
Example Problem 2: Part 3
30:34
Recap
34:45
ATP & Other High-Energy Compounds

44m 32s

Intro
0:00
ATP & Other High-Energy Compounds
0:10
Endergonic Reaction Coupled With Exergonic Reaction
0:11
Major Theme In Metabolism
6:56
Why the ∆G°' for ATP Hydrolysis is Large & Negative
12:24
∆G°' for ATP Hydrolysis
12:25
Reason 1: Electrostatic Repulsion
14:24
Reason 2: Pi & Resonance Forms
15:33
Reason 3: Concentrations of ADP & Pi
17:32
ATP & Other High-Energy Compounds Cont'd
18:48
More On ∆G°' & Hydrolysis
18:49
Other Compounds That Have Large Negative ∆G°' of Hydrolysis: Phosphoenol Pyruvate (PEP)
25:14
Enzyme Pyruvate Kinase
30:36
Another High Energy Molecule: 1,3 Biphosphoglycerate
36:17
Another High Energy Molecule: Phophocreatine
39:41
Phosphoryl Group Transfers

30m 8s

Intro
0:00
Phosphoryl Group Transfer
0:27
Phosphoryl Group Transfer Overview
0:28
Example: Glutamate → Glutamine Part 1
7:11
Example: Glutamate → Glutamine Part 2
13:29
ATP Not Only Transfers Phosphoryl, But Also Pyrophosphoryl & Adenylyl Groups
17:03
Attack At The γ Phosphorous Transfers a Phosphoryl
19:02
Attack At The β Phosphorous Gives Pyrophosphoryl
22:44
Oxidation-Reduction Reactions

49m 46s

Intro
0:00
Oxidation-Reduction Reactions
1:32
Redox Reactions
1:33
Example 1: Mg + Al³⁺ → Mg²⁺ + Al
3:49
Reduction Potential Definition
10:47
Reduction Potential Example
13:38
Organic Example
22:23
Review: How To Find The Oxidation States For Carbon
24:15
Examples: Oxidation States For Carbon
27:45
Example 1: Oxidation States For Carbon
27:46
Example 2: Oxidation States For Carbon
28:36
Example 3: Oxidation States For Carbon
29:18
Example 4: Oxidation States For Carbon
29:44
Example 5: Oxidation States For Carbon
30:10
Example 6: Oxidation States For Carbon
30:40
Example 7: Oxidation States For Carbon
31:20
Example 8: Oxidation States For Carbon
32:10
Example 9: Oxidation States For Carbon
32:52
Oxidation-Reduction Reactions, cont'd
35:22
More On Reduction Potential
35:28
Lets' Start With ∆G = ∆G°' + RTlnQ
38:29
Example: Oxidation Reduction Reactions
41:42
More On Oxidation-Reduction Reactions

56m 34s

Intro
0:00
More On Oxidation-Reduction Reactions
0:10
Example 1: What If the Concentrations Are Not Standard?
0:11
Alternate Procedure That Uses The 1/2 Reactions Individually
8:57
Universal Electron Carriers in Aqueous Medium: NAD+ & NADH
15:12
The Others Are…
19:22
NAD+ & NADP Coenzymes
20:56
FMN & FAD
22:03
Nicotinamide Adenine Dinucleotide (Phosphate)
23:03
Reduction 1/2 Reactions
36:10
Ratio of NAD+ : NADH
36:52
Ratio of NADPH : NADP+
38:02
Specialized Roles of NAD+ & NADPH
38:48
Oxidoreductase Enzyme Overview
40:26
Examples of Oxidoreductase
43:32
The Flavin Nucleotides
46:46
Example Problems For Bioenergetics

42m 12s

Intro
0:00
Example 1: Calculate the ∆G°' For The Following Reaction
1:04
Example 1: Question
1:05
Example 1: Solution
2:20
Example 2: Calculate the Keq For the Following
4:20
Example 2: Question
4:21
Example 2: Solution
5:54
Example 3: Calculate the ∆G°' For The Hydrolysis of ATP At 25°C
8:52
Example 3: Question
8:53
Example 3: Solution
10:30
Example 3: Alternate Procedure
13:48
Example 4: Problems For Bioenergetics
16:46
Example 4: Questions
16:47
Example 4: Part A Solution
21:19
Example 4: Part B Solution
23:26
Example 4: Part C Solution
26:12
Example 5: Problems For Bioenergetics
29:27
Example 5: Questions
29:35
Example 5: Solution - Part 1
32:16
Example 5: Solution - Part 2
34:39
IX. Glycolysis and Gluconeogenesis
Overview of Glycolysis I

43m 32s

Intro
0:00
Overview of Glycolysis
0:48
Three Primary Paths For Glucose
1:04
Preparatory Phase of Glycolysis
4:40
Payoff Phase of Glycolysis
6:40
Glycolysis Reactions Diagram
7:58
Enzymes of Glycolysis
12:41
Glycolysis Reactions
16:02
Step 1
16:03
Step 2
18:03
Step 3
18:52
Step 4
20:08
Step 5
21:42
Step 6
22:44
Step 7
24:22
Step 8
25:11
Step 9
26:00
Step 10
26:51
Overview of Glycolysis Cont.
27:28
The Overall Reaction for Glycolysis
27:29
Recall The High-Energy Phosphorylated Compounds Discusses In The Bioenergetics Unit
33:10
What Happens To The Pyruvate That Is Formed?
37:58
Glycolysis II

1h 1m 47s

Intro
0:00
Glycolysis Step 1: The Phosphorylation of Glucose
0:27
Glycolysis Step 1: Reaction
0:28
Hexokinase
2:28
Glycolysis Step 1: Mechanism-Simple Nucleophilic Substitution
6:34
Glycolysis Step 2: Conversion of Glucose 6-Phosphate → Fructose 6-Phosphate
11:33
Glycolysis Step 2: Reaction
11:34
Glycolysis Step 2: Mechanism, Part 1
14:40
Glycolysis Step 2: Mechanism, Part 2
18:16
Glycolysis Step 2: Mechanism, Part 3
19:56
Glycolysis Step 2: Mechanism, Part 4 (Ring Closing & Dissociation)
21:54
Glycolysis Step 3: Conversion of Fructose 6-Phosphate to Fructose 1,6-Biphosphate
24:16
Glycolysis Step 3: Reaction
24:17
Glycolysis Step 3: Mechanism
26:40
Glycolysis Step 4: Cleavage of Fructose 1,6-Biphosphate
31:10
Glycolysis Step 4: Reaction
31:11
Glycolysis Step 4: Mechanism, Part 1 (Binding & Ring Opening)
35:26
Glycolysis Step 4: Mechanism, Part 2
37:40
Glycolysis Step 4: Mechanism, Part 3
39:30
Glycolysis Step 4: Mechanism, Part 4
44:00
Glycolysis Step 4: Mechanism, Part 5
46:34
Glycolysis Step 4: Mechanism, Part 6
49:00
Glycolysis Step 4: Mechanism, Part 7
50:12
Hydrolysis of The Imine
52:33
Glycolysis Step 5: Conversion of Dihydroxyaceton Phosphate to Glyceraldehyde 3-Phosphate
55:38
Glycolysis Step 5: Reaction
55:39
Breakdown and Numbering of Sugar
57:40
Glycolysis III

59m 17s

Intro
0:00
Glycolysis Step 5: Conversion of Dihydroxyaceton Phosphate to Glyceraldehyde 3-Phosphate
0:44
Glycolysis Step 5: Mechanism, Part 1
0:45
Glycolysis Step 5: Mechanism, Part 2
3:53
Glycolysis Step 6: Oxidation of Glyceraldehyde 3-Phosphate to 1,3-Biphosphoglycerate
5:14
Glycolysis Step 6: Reaction
5:15
Glycolysis Step 6: Mechanism, Part 1
8:52
Glycolysis Step 6: Mechanism, Part 2
12:58
Glycolysis Step 6: Mechanism, Part 3
14:26
Glycolysis Step 6: Mechanism, Part 4
16:23
Glycolysis Step 7: Phosphoryl Transfer From 1,3-Biphosphoglycerate to ADP to Form ATP
19:08
Glycolysis Step 7: Reaction
19:09
Substrate-Level Phosphorylation
23:18
Glycolysis Step 7: Mechanism (Nucleophilic Substitution)
26:57
Glycolysis Step 8: Conversion of 3-Phosphoglycerate to 2-Phosphoglycerate
28:44
Glycolysis Step 8: Reaction
28:45
Glycolysis Step 8: Mechanism, Part 1
30:08
Glycolysis Step 8: Mechanism, Part 2
32:24
Glycolysis Step 8: Mechanism, Part 3
34:02
Catalytic Cycle
35:42
Glycolysis Step 9: Dehydration of 2-Phosphoglycerate to Phosphoenol Pyruvate
37:20
Glycolysis Step 9: Reaction
37:21
Glycolysis Step 9: Mechanism, Part 1
40:12
Glycolysis Step 9: Mechanism, Part 2
42:01
Glycolysis Step 9: Mechanism, Part 3
43:58
Glycolysis Step 10: Transfer of a Phosphoryl Group From Phosphoenol Pyruvate To ADP To Form ATP
45:16
Glycolysis Step 10: Reaction
45:17
Substrate-Level Phosphorylation
48:32
Energy Coupling Reaction
51:24
Glycolysis Balance Sheet
54:15
Glycolysis Balance Sheet
54:16
What Happens to The 6 Carbons of Glucose?
56:22
What Happens to 2 ADP & 2 Pi?
57:04
What Happens to The 4e⁻ ?
57:15
Glycolysis IV

39m 47s

Intro
0:00
Feeder Pathways
0:42
Feeder Pathways Overview
0:43
Starch, Glycogen
2:25
Lactose
4:38
Galactose
4:58
Manose
5:22
Trehalose
5:45
Sucrose
5:56
Fructose
6:07
Fates of Pyruvate: Aerobic & Anaerobic Conditions
7:39
Aerobic Conditions & Pyruvate
7:40
Anaerobic Fates of Pyruvate
11:18
Fates of Pyruvate: Lactate Acid Fermentation
14:10
Lactate Acid Fermentation
14:11
Fates of Pyruvate: Ethanol Fermentation
19:01
Ethanol Fermentation Reaction
19:02
TPP: Thiamine Pyrophosphate (Functions and Structure)
23:10
Ethanol Fermentation Mechanism, Part 1
27:53
Ethanol Fermentation Mechanism, Part 2
29:06
Ethanol Fermentation Mechanism, Part 3
31:15
Ethanol Fermentation Mechanism, Part 4
32:44
Ethanol Fermentation Mechanism, Part 5
34:33
Ethanol Fermentation Mechanism, Part 6
35:48
Gluconeogenesis I

41m 34s

Intro
0:00
Gluconeogenesis, Part 1
1:02
Gluconeogenesis Overview
1:03
3 Glycolytic Reactions That Are Irreversible Under Physiological Conditions
2:29
Gluconeogenesis Reactions Overview
6:17
Reaction: Pyruvate to Oxaloacetate
11:07
Reaction: Oxaloacetate to Phosphoenolpyruvate (PEP)
13:29
First Pathway That Pyruvate Can Take to Become Phosphoenolpyruvate
15:24
Second Pathway That Pyruvate Can Take to Become Phosphoenolpyruvate
21:00
Transportation of Pyruvate From The Cytosol to The Mitochondria
24:15
Transportation Mechanism, Part 1
26:41
Transportation Mechanism, Part 2
30:43
Transportation Mechanism, Part 3
34:04
Transportation Mechanism, Part 4
38:14
Gluconeogenesis II

34m 18s

Intro
0:00
Oxaloacetate → Phosphoenolpyruvate (PEP)
0:35
Mitochondrial Membrane Does Not Have a Transporter for Oxaloactate
0:36
Reaction: Oxaloacetate to Phosphoenolpyruvate (PEP)
3:36
Mechanism: Oxaloacetate to Phosphoenolpyruvate (PEP)
4:48
Overall Reaction: Pyruvate to Phosphoenolpyruvate
7:01
Recall The Two Pathways That Pyruvate Can Take to Become Phosphoenolpyruvate
10:16
NADH in Gluconeogenesis
12:29
Second Pathway: Lactate → Pyruvate
18:22
Cytosolic PEP Carboxykinase, Mitochondrial PEP Carboxykinase, & Isozymes
18:23
2nd Bypass Reaction
23:04
3rd Bypass Reaction
24:01
Overall Process
25:17
Other Feeder Pathways For Gluconeogenesis
26:35
Carbon Intermediates of The Citric Acid Cycle
26:36
Amino Acids & The Gluconeogenic Pathway
29:45
Glycolysis & Gluconeogenesis Are Reciprocally Regulated
32:00
The Pentose Phosphate Pathway

42m 52s

Intro
0:00
The Pentose Phosphate Pathway Overview
0:17
The Major Fate of Glucose-6-Phosphate
0:18
The Pentose Phosphate Pathway (PPP) Overview
1:00
Oxidative Phase of The Pentose Phosphate Pathway
4:33
Oxidative Phase of The Pentose Phosphate Pathway: Reaction Overview
4:34
Ribose-5-Phosphate: Glutathione & Reductive Biosynthesis
9:02
Glucose-6-Phosphate to 6-Phosphogluconate
12:48
6-Phosphogluconate to Ribulose-5-Phosphate
15:39
Ribulose-5-Phosphate to Ribose-5-Phosphate
17:05
Non-Oxidative Phase of The Pentose Phosphate Pathway
19:55
Non-Oxidative Phase of The Pentose Phosphate Pathway: Overview
19:56
General Transketolase Reaction
29:03
Transaldolase Reaction
35:10
Final Transketolase Reaction
39:10
X. The Citric Acid Cycle (Krebs Cycle)
Citric Acid Cycle I

36m 10s

Intro
0:00
Stages of Cellular Respiration
0:23
Stages of Cellular Respiration
0:24
From Pyruvate to Acetyl-CoA
6:56
From Pyruvate to Acetyl-CoA: Pyruvate Dehydrogenase Complex
6:57
Overall Reaction
8:42
Oxidative Decarboxylation
11:54
Pyruvate Dehydrogenase (PDH) & Enzymes
15:30
Pyruvate Dehydrogenase (PDH) Requires 5 Coenzymes
17:15
Molecule of CoEnzyme A
18:52
Thioesters
20:56
Lipoic Acid
22:31
Lipoate Is Attached To a Lysine Residue On E₂
24:42
Pyruvate Dehydrogenase Complex: Reactions
26:36
E1: Reaction 1 & 2
30:38
E2: Reaction 3
31:58
E3: Reaction 4 & 5
32:44
Substrate Channeling
34:17
Citric Acid Cycle II

49m 20s

Intro
0:00
Citric Acid Cycle Reactions Overview
0:26
Citric Acid Cycle Reactions Overview: Part 1
0:27
Citric Acid Cycle Reactions Overview: Part 2
7:03
Things to Note
10:58
Citric Acid Cycle Reactions & Mechanism
13:57
Reaction 1: Formation of Citrate
13:58
Reaction 1: Mechanism
19:01
Reaction 2: Citrate to Cis Aconistate to Isocitrate
28:50
Reaction 3: Isocitrate to α-Ketoglutarate
32:35
Reaction 3: Two Isocitrate Dehydrogenase Enzymes
36:24
Reaction 3: Mechanism
37:33
Reaction 4: Oxidation of α-Ketoglutarate to Succinyl-CoA
41:38
Reaction 4: Notes
46:34
Citric Acid Cycle III

44m 11s

Intro
0:00
Citric Acid Cycle Reactions & Mechanism
0:21
Reaction 5: Succinyl-CoA to Succinate
0:24
Reaction 5: Reaction Sequence
2:35
Reaction 6: Oxidation of Succinate to Fumarate
8:28
Reaction 7: Fumarate to Malate
10:17
Reaction 8: Oxidation of L-Malate to Oxaloacetate
14:15
More On The Citric Acid Cycle
17:17
Energy from Oxidation
17:18
How Can We Transfer This NADH Into the Mitochondria
27:10
Citric Cycle is Amphibolic - Works In Both Anabolic & Catabolic Pathways
32:06
Biosynthetic Processes
34:29
Anaplerotic Reactions Overview
37:26
Anaplerotic: Reaction 1
41:42
XI. Catabolism of Fatty Acids
Fatty Acid Catabolism I

48m 11s

Intro
0:00
Introduction to Fatty Acid Catabolism
0:21
Introduction to Fatty Acid Catabolism
0:22
Vertebrate Cells Obtain Fatty Acids for Catabolism From 3 Sources
2:16
Diet: Part 1
4:00
Diet: Part 2
5:35
Diet: Part 3
6:20
Diet: Part 4
6:47
Diet: Part 5
10:18
Diet: Part 6
10:54
Diet: Part 7
12:04
Diet: Part 8
12:26
Fats Stored in Adipocytes Overview
13:54
Fats Stored in Adipocytes (Fat Cells): Part 1
16:13
Fats Stored in Adipocytes (Fat Cells): Part 2
17:16
Fats Stored in Adipocytes (Fat Cells): Part 3
19:42
Fats Stored in Adipocytes (Fat Cells): Part 4
20:52
Fats Stored in Adipocytes (Fat Cells): Part 5
22:56
Mobilization of TAGs Stored in Fat Cells
24:35
Fatty Acid Oxidation
28:29
Fatty Acid Oxidation
28:48
3 Reactions of the Carnitine Shuttle
30:42
Carnitine Shuttle & The Mitochondrial Matrix
36:25
CAT I
43:58
Carnitine Shuttle is the Rate-Limiting Steps
46:24
Fatty Acid Catabolism II

45m 58s

Intro
0:00
Fatty Acid Catabolism
0:15
Fatty Acid Oxidation Takes Place in 3 Stages
0:16
β-Oxidation
2:05
β-Oxidation Overview
2:06
Reaction 1
4:20
Reaction 2
7:35
Reaction 3
8:52
Reaction 4
10:16
β-Oxidation Reactions Discussion
11:34
Notes On β-Oxidation
15:14
Double Bond After The First Reaction
15:15
Reaction 1 is Catalyzed by 3 Isozymes of Acyl-CoA Dehydrogenase
16:04
Reaction 2 & The Addition of H₂O
18:38
After Reaction 4
19:24
Production of ATP
20:04
β-Oxidation of Unsaturated Fatty Acid
21:25
β-Oxidation of Unsaturated Fatty Acid
22:36
β-Oxidation of Mono-Unsaturates
24:49
β-Oxidation of Mono-Unsaturates: Reaction 1
24:50
β-Oxidation of Mono-Unsaturates: Reaction 2
28:43
β-Oxidation of Mono-Unsaturates: Reaction 3
30:50
β-Oxidation of Mono-Unsaturates: Reaction 4
31:06
β-Oxidation of Polyunsaturates
32:29
β-Oxidation of Polyunsaturates: Part 1
32:30
β-Oxidation of Polyunsaturates: Part 2
37:08
β-Oxidation of Polyunsaturates: Part 3
40:25
Fatty Acid Catabolism III

33m 18s

Intro
0:00
Fatty Acid Catabolism
0:43
Oxidation of Fatty Acids With an Odd Number of Carbons
0:44
β-oxidation in the Mitochondrion & Two Other Pathways
9:08
ω-oxidation
10:37
α-oxidation
17:22
Ketone Bodies
19:08
Two Fates of Acetyl-CoA Formed by β-Oxidation Overview
19:09
Ketone Bodies: Acetone
20:42
Ketone Bodies: Acetoacetate
20:57
Ketone Bodies: D-β-hydroxybutyrate
21:25
Two Fates of Acetyl-CoA Formed by β-Oxidation: Part 1
22:05
Two Fates of Acetyl-CoA Formed by β-Oxidation: Part 2
26:59
Two Fates of Acetyl-CoA Formed by β-Oxidation: Part 3
30:52
XII. Catabolism of Amino Acids and the Urea Cycle
Overview & The Aminotransferase Reaction

40m 59s

Intro
0:00
Overview of The Aminotransferase Reaction
0:25
Overview of The Aminotransferase Reaction
0:26
The Aminotransferase Reaction: Process 1
3:06
The Aminotransferase Reaction: Process 2
6:46
Alanine From Muscle Tissue
10:54
Bigger Picture of the Aminotransferase Reaction
14:52
Looking Closely at Process 1
19:04
Pyridoxal Phosphate (PLP)
24:32
Pyridoxamine Phosphate
25:29
Pyridoxine (B6)
26:38
The Function of PLP
27:12
Mechanism Examples
28:46
Reverse Reaction: Glutamate to α-Ketoglutarate
35:34
Glutamine & Alanine: The Urea Cycle I

39m 18s

Intro
0:00
Glutamine & Alanine: The Urea Cycle I
0:45
Excess Ammonia, Glutamate, and Glutamine
0:46
Glucose-Alanine Cycle
9:54
Introduction to the Urea Cycle
20:56
The Urea Cycle: Production of the Carbamoyl Phosphate
22:59
The Urea Cycle: Reaction & Mechanism Involving the Carbamoyl Phosphate Synthetase
33:36
Glutamine & Alanine: The Urea Cycle II

36m 21s

Intro
0:00
Glutamine & Alanine: The Urea Cycle II
0:14
The Urea Cycle Overview
0:34
Reaction 1: Ornithine → Citrulline
7:30
Reaction 2: Citrulline → Citrullyl-AMP
11:15
Reaction 2': Citrullyl-AMP → Argininosuccinate
15:25
Reaction 3: Argininosuccinate → Arginine
20:42
Reaction 4: Arginine → Orthinine
24:00
Links Between the Citric Acid Cycle & the Urea Cycle
27:47
Aspartate-argininosuccinate Shunt
32:36
Amino Acid Catabolism

47m 58s

Intro
0:00
Amino Acid Catabolism
0:10
Common Amino Acids and 6 Major Products
0:11
Ketogenic Amino Acid
1:52
Glucogenic Amino Acid
2:51
Amino Acid Catabolism Diagram
4:18
Cofactors That Play a Role in Amino Acid Catabolism
7:00
Biotin
8:42
Tetrahydrofolate
10:44
S-Adenosylmethionine (AdoMet)
12:46
Tetrahydrobiopterin
13:53
S-Adenosylmethionine & Tetrahydrobiopterin Molecules
14:41
Catabolism of Phenylalanine
18:30
Reaction 1: Phenylalanine to Tyrosine
18:31
Reaction 2: Tyrosine to p-Hydroxyphenylpyruvate
21:36
Reaction 3: p-Hydroxyphenylpyruvate to Homogentisate
23:50
Reaction 4: Homogentisate to Maleylacetoacetate
25:42
Reaction 5: Maleylacetoacetate to Fumarylacetoacetate
28:20
Reaction 6: Fumarylacetoacetate to Fumarate & Succinyl-CoA
29:51
Reaction 7: Fate of Fumarate & Succinyl-CoA
31:14
Phenylalanine Hydroxylase
33:33
The Phenylalanine Hydroxylase Reaction
33:34
Mixed-Function Oxidases
40:26
When Phenylalanine Hydoxylase is Defective: Phenylketonuria (PKU)
44:13
XIII. Oxidative Phosphorylation and ATP Synthesis
Oxidative Phosphorylation I

41m 11s

Intro
0:00
Oxidative Phosphorylation
0:54
Oxidative Phosphorylation Overview
0:55
Mitochondrial Electron Transport Chain Diagram
7:15
Enzyme Complex I of the Electron Transport Chain
12:27
Enzyme Complex II of the Electron Transport Chain
14:02
Enzyme Complex III of the Electron Transport Chain
14:34
Enzyme Complex IV of the Electron Transport Chain
15:30
Complexes Diagram
16:25
Complex I
18:25
Complex I Overview
18:26
What is Ubiquinone or Coenzyme Q?
20:02
Coenzyme Q Transformation
22:37
Complex I Diagram
24:47
Fe-S Proteins
26:42
Transfer of H⁺
29:42
Complex II
31:06
Succinate Dehydrogenase
31:07
Complex II Diagram & Process
32:54
Other Substrates Pass Their e⁻ to Q: Glycerol 3-Phosphate
37:31
Other Substrates Pass Their e⁻ to Q: Fatty Acyl-CoA
39:02
Oxidative Phosphorylation II

36m 27s

Intro
0:00
Complex III
0:19
Complex III Overview
0:20
Complex III: Step 1
1:56
Complex III: Step 2
6:14
Complex IV
8:42
Complex IV: Cytochrome Oxidase
8:43
Oxidative Phosphorylation, cont'd
17:18
Oxidative Phosphorylation: Summary
17:19
Equation 1
19:13
How Exergonic is the Reaction?
21:03
Potential Energy Represented by Transported H⁺
27:24
Free Energy Change for the Production of an Electrochemical Gradient Via an Ion Pump
28:48
Free Energy Change in Active Mitochondria
32:02
Loading...
This is a quick preview of the lesson. For full access, please Log In or Sign up.
For more information, please see full course syllabus of Biochemistry
  • Discussion

  • Download Lecture Slides

  • Table of Contents

  • Transcription

  • Related Books & Services

Lecture Comments (10)

2 answers

Last reply by: Swati Sharma
Sun Jan 14, 2018 10:03 PM

Post by Swati Sharma on December 22, 2017

Dear Dr Raffi


I have not at all understood the difference between left and right handed helix. Could you please explain how to find difference

Thank you

0 answers

Post by Sam Zanone on September 18, 2014

Professor Hovasapian:

Out of curiosity, could you possibly elaborate on 3D Structures of Proteins?  The Alpha Helix and Beta Sheet explanations are perfect, but our homework continually refers back to peptide chains, asking about which bonds join together to form Hydrogen bonds.  
ie:  "Which of the following peptide segments is most likely to be part of a stable alpha helix at physiological pH?" (with a multiple choice list provided of 5 different pentapeptides)

We also delve into the Ramachandran plot as well, and I was hoping you could explain that in a better organized mannerism than my professor had explained.

I'm not sure if this is too much to ask but here is my brief, or extensive depending on perspective, list of topics that I could use clarification on - and please forgive me if there are some on here that are provided further on in lectures:
1.  Ramachandran Plots
2.  Protein Chaperoning (GroEL & GroES)
3.  Beta Turns (the two common types and structural explanation)
4.  Proteostasis
5.  Example: Chris Anfinsen's Ribonuclease Refolding Experiment

I apologize if this is too many topics to amend to this lecture, but these are topics our professor is expecting us to know!

Thank you so much if you can assist in the explanation of these topics!  And keep up the fantastic lectures you are providing!  

1 answer

Last reply by: Professor Hovasapian
Wed Sep 17, 2014 10:14 PM

Post by Jenika Javier on September 14, 2014

So the amino acid that is likely to be found in the interior surface is the hydrophobic amino acid whereas the hydrophilic will be found on the surface of a globular protein?

1 answer

Last reply by: Professor Hovasapian
Sun Feb 9, 2014 3:33 AM

Post by nanette skiba on February 8, 2014

Yes, the last screen. How did you know to start at the blue string and not the red string? What did I miss?

1 answer

Last reply by: Professor Hovasapian
Sat Mar 30, 2013 5:21 PM

Post by ali aden on March 30, 2013

at the 9:11, when you draw the resonance of the peptide bond, it looks that you forget the + charge on the nitrogen atom because it has 4 bonds. Is that right?

Alpha Helix & Beta Conformation

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
  • Alpha Helix and Beta Conformation 0:28
    • Protein Structure Overview
    • Weak interactions Among the Amino Acid in the Peptide Chain
    • Two Principals of Folding Patterns
    • Peptide Bond
    • Peptide Bond: Resonance
    • Peptide Bond: φ Bond & ψ Bond
    • Secondary Structure
    • α-Helix Folding Pattern
    • Illustration 1: α-Helix Folding Pattern
    • Illustration 2: α-Helix Folding Pattern
    • β-Sheet
    • β-Conformation
    • Parallel & Anti-parallel
    • Parallel β-Conformation Arrangement of the Peptide Chain
    • Putting Together a Parallel Peptide Chain
    • Anti-Parallel β-Conformation Arrangement
    • Tertiary Structure
    • Quaternary Structure
    • Illustration 3: Myoglobin Tertiary Structure & Hemoglobin Quaternary Structure
    • Final Words on Alpha Helix and Beta Conformation

Transcription: Alpha Helix & Beta Conformation

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

Today, we are going to be talking about secondary, tertiary and quaternary structure.0004

Actually, we are only going to mention tertiary and quaternary structure towards the end.0010

I am not really going to discuss it too much; I wanted to concentrate on this lesson on the secondary structure, in particular, the alpha helix and the beta conformation or otherwise known as the beta sheet.0015

Let's just jump in and see what we can do.0026

OK, let's recap; we have talked about the primary structure of the primary structure of the protein.0030

The primary structure is its sequence of amino acids - that is it - just the lengthwise string of amino acids, alanine, glycine, leucine, isoleucine, whatever combination happens to be.0035

That is referred to as the primary sequence; now, secondary structure occurs when the protein starts to fold.0050

Now, the complete folded protein, that is the tertiary structure, but before that, as parts of this polypeptide chain starts to fold and go this way and that way, there are certain patterns that develop simply by virtue of the nature of the peptide bond and the interactions that can take place and some of the constraints on bond rotation.0059

Two of those patterns are the alpha helix and the beta-pleated sheet.0082

That is what we are going to be talking about in today's lesson; this is our primary concern.0088

Now, the tertiary structure is, of course, the complete folded polypeptide chain, once this has taken on the final shape that it is going to take in free space.0092

Now, if you have more than 1 subunit in a particular protein, 2, 3, 4, 5, however many, when you put those individual units together, that constitutes the quaternary protein structure.0104

All proteins have primary, secondary, tertiary.0117

Some proteins that have multi-subunits, they are the ones that have the quaternary structure.0122

OK, let's get started.0126

Now, let's see.0131

Weak interactions among the amino acids in the peptide chain gives rise to the secondary and tertiary structures of a protein.0136

OK, in other words, secondary and tertiary structures just means its folded state.0178

A protein does not just stay as 1 long amino acid; it actually takes on some conformation.0188

OK, and again, let's go ahead and list these interactions.0194

Again, these interactions, what we call the weak interactions are...you have a hydrogen bonding, which is probably the most important.0198

You have hydrophobic interactions probably the next most important.0215

Well, actually, you know what, I should not say that one is more important than the other; hydrogen bonding, yes, it is probably the most important, but the others, I would not necessarily classify them because they all participate.0226

We have polar interactions, and we have our ionic interactions.0236

Those account for the weak forces, the weak interactions.0250

Now, covalent interactions, there is some covalent interactions, but they are represented by only the sulfur-sulfur bond, the disulfide bond.0255

Covalent interactions, which facilitate folding, include the disulfide bond - that is about it - and we have talked about the disulfide bond when we talked about amino acids, no, primary sequence - OK - disulfide bonds.0266

OK, now, 2 principles govern the folding patterns we will discuss.0294

These are the 2 principles that you just want to keep in the back of your head.0318

Well, not necessarily just in the back of your head, but we are not going to discuss them more than just mentioning what it is that they are.0322

Two principles govern the folding patterns that we will discuss.0329

One of them is the hydrophobic amino acid side chains, they collect in the interior of a folded protein away from the aqueous solution.0333

Proteins are soluble; proteins are floating around in aqueous solution.0361

But again, hydrophobic means that they are afraid of water; they do not want to be near the water.0365

When a protein folds, it tends to have its hydrophilic amino acid side chains on the outside.0369

They can interact with the water; the hydrophobic, they tend to be on the inside as far away from the water as possible.0375

They collect in the interior of a folded protein.0381

It makes total sense; it is exactly what happens.0386

I will write "away from water".0391

OK, and 2: hydrogen bonds are maximized.0397

Again, hydrogen bonding, very, very important for protein folding, and hydrogen bonds, I will say, tend to be maximized.0402

OK, let's go ahead and recall the peptide bond.0417

The peptide bond, let me see; let me go to blue here.0422

Let's recall the peptide bond.0427

We have...remember our pattern?0438

We do N-C-C, N-C-C, right?0442

And let me see, N-C-C, the second carbon always gets...you know what, I need a little bit more room here, so let me redraw this, and in fact, I think I am going to do my resonance structure left and right instead of up and down.0450

Let me start over here on the left; let me go N-C-C, N-C-C, and the second carbon always gets the carbonyl, and let me see.0464

I will go ahead and do...well, let me see.0478

Yes, that is fine; I will go ahead and put some electrons there, and I will go ahead and just add a couple...well, you know what, that is fine.0484

I will go ahead and just leave it like that; it goes on, of course, in this direction and in that direction, but I was just concerned with a single peptide bond.0493

This is your peptide bond right here, the carbonyl connected to the nitrogen- OK, very, very important.0502

Let me go ahead and put this hydrogen in here, and I will go ahead and put my electron pair there.0510

Now, this electron pair, there is resonance going on here.0515

This electron pair actually jumps here, creates a double bond and pushes these electrons onto oxygen.0520

Another resonance structure for the peptide bond is the following: N-C-C, N-C - oops, not there - N-C-C jumping the gun a little bit.0526

So, we have something like this; we have this single-bonded between the carbonyl and the nitrogen, but it has double bond character because of this resonance structure.0545

Because of this double bond character, this peptide bond, it cannot rotate like a single bond.0555

This is fixed; this H, this N, this C and this O, they all lie in a plain.0560

H, N, C, O, they are in a plain that cannot rotate, precisely because of this resonance structure, because it has partial double bond character.0566

It is not a complete single bond; it is not a complete double bond.0576

It is a resonance; there is resonance going on.0579

Electrons can move because of resonance, the peptide bond, the bond between the carbonyl carbon and the next nitrogen, but peptide bond, itself, is not free to rotate.0583

This has profound consequences for protein structure and life and physiology, in biology.0614

OK, we have the following.0627

We have the following.0633

We have N-C-C, N-C-C, N-C-C, N-C-C, N-C-C.0642

I think I will do 1 more; I think I have 4 of them altogether, N-C-C.0654

Carbonyl is on the second of the pattern, N-C-C here, and, of course, this goes on in both directions.0660

Notice, this carbon right here, I will do it in red.0667

This is the alpha-carbon; it is the carbon that is attached to the carbonyl carbon.0672

Here, this is the alpha-carbon; here, this is the alpha-carbon.0679

OK, now, we said that the peptide bond is not free to rotate, right?0682

This is a peptide bond right here.0690

This is a peptide bond right here.0694

Sorry; this whole peptide structure, the peptide bond is actually this one right here between the carbon and the nitrogen.0698

Sorry about that.0705

There is another peptide bond right here; OK, those bonds are not free to rotate, we just said.0710

Now, the bonds that are free to rotate are the bonds to either side of the alpha-carbons.0716

In other words, carbon, this bond is free to rotate; that bond is free to rotate- that, that, that, that.0745

Those bonds are free to rotate.0754

Now, by convention, the bond, which is nitrogen carbon alpha is called the phi bond, greek letter phi.0759

OK, the bond C, alpha to the C carbonyl, it is called the psi bond or psi as you know it.0774

OK, in its fully-extended state, this one right here - if you just...N-C-C, N-C-C, N-C-C, N-C-C, fully-extended not folded - phi and psi are said to be at a 180°.0793

That is just convention.0825

This bond right here, this N-C, the phi bond, it can go like this, and this other one right here, the C, CO bond, it can go like this.0832

We have these 2 bonds that can rotate in its fully-extended state.0844

This bond is 180°; this bond is 180°.0849

Well, you can see that we can start rotating things, but eventually, things are going to bump into each other.0853

Theoretically, we can go all the way around; we can go from -180 to +180 or 180 down to 0 to -180.0858

That gives us a full 360° turn all the way around.0866

Real proteins do not do 360° turns, and the reason they do not is because of steric hindrance.0872

Things just start to bump into each other; again, these line structures, they do not give you an idea of just how closely packed these atoms are.0878

Just by convention, we said, phi and psi for a fully-extended peptide chain at 180°, that is really all you need to know.0886

OK, now, let's talk about secondary structure.0896

OK, excuse me.0900

Actually, you know what, I think I am going to go back to blue here.0909

OK, well, secondary structure by definition is the conformation of part of the peptide chain.0925

There are certain parts of the peptide chain that tend to take on certain patterns of folding, and that is what we are going to discuss.0948

That is secondary structure.0953

Not the whole peptide chain, that would be tertiary.0957

Now, given the constraints of bond rotation that we just discussed and side chain interaction - I remember we had side chains on these amino acids, they are going to interact with each other, and they are going to bump into each other - which is both good and bad.0961

There are 2 patterns of folding that tend to appear most often in proteins.0995

One of them is called the alpha helix, and the other one is called the beta conformation or the beta sheet; and I will explain the difference between beta sheet and beta conformation.1017

Most of the time, they are used synonymously; the beta sheet actually comes from several strands of the peptide chain lying next to each other to give you this thing that looks like a sheet- that is all.1036

OK, let's go ahead and talk about the alpha helix first.1049

Alpha-helix, I am going to go ahead and talk about a little bit, and then, I will go ahead and show you some images.1053

Now, the peptide backbone, and by backbone I mean the N-C-C, N-C-C, N-C-C, it wraps itself around an imaginary axis, not unlike a single-stranded DNA.1063

It wraps itself around an imaginary axis through the center of the helix, in fact, exactly like single-stranded DNA.1094

Well, I probably should not say single-stranded DNA, but you will see what we mean in just a minute.1116

OK, now, this twist is right-handed.1122

This twist is right-handed, and I will discuss what right-handed and left-handed helices mean in just a minute; and the R-groups that are on the alpha-carbons, they protrude out and away from the helix.1128

OK, let's take a look at our first image here.1159

Let's see; where is it?1163

OK, here we go; as you can see, let's take a look at this one over here on the left.1166

You see this pattern; you have got this N-C-C, N-C-C, N-C-C, N-C-C.1171

Actually, because of the constraints on the fact that the peptide bond cannot rotate, but the phi and psi bond can rotate, you end up with this pattern.1184

Well, you see the interactions, when it actually starts to curve this way, it is going around and around.1195

It is going up like this, like a spiral staircase, and that is exactly what is happening; and there is an axis right down the middle, and here, you can see the R-groups.1202

They are protruding out from the top.1212

OK, 1 complete turn accounts for about 3.5 amino acid residues.1215

Two turns for 7 complete amino acid residues, that is how they tend to arrange themselves.1222

And over here, you can see the hydrogen bonding that stabilizes this alpha helix structure- very, very common secondary structure.1230

Alpha-helices show up in a multitude of proteins.1239

Now, that is not a guarantee; we are not saying that all proteins have an alpha helix somewhere in their structure.1244

It just happens to be one of the structures that shows up in a lot of the proteins.1250

It is a motif; it is a pattern that develops, but that is no guarantee that it exists in every single protein.1254

Different proteins do different things, so some of them actually do not have alpha-helices at all so definitely distinguish that.1262

Here is another version of it; there you go.1268

You have your N-C-C, N-C-C, N-C-C, N-C-C, N-C-C pattern that wraps itself around an imaginary axis.1272

Here, you had your carbonyl, oxygen interacting with the hydrogen on the nitrogen.1282

You have got hydrogen bonding, hydrogen bonding that stabilizes this alpha helix- very, very stable arrangement, works out quite beautifully.1291

Now, let's go ahead and take a look at one more image of this.1300

Again, when you see this little ribbon-like thing and a helical structure, that is a schematic diagram of the protein.1304

What you are going to see when you see protein diagrams in most pictures is you are not going to see all these individual atoms.1314

You are not going to see ball and stick stuff; what you are going to see is individual twists.1321

That is a schematic; this twist right here, that is not part of the protein.1325

That is a schematic representation of the actual amino acid peptide chain - that is it - as you can see very clearly, this helical pattern.1330

OK, now, let's talk about this whole right-handed and left-handed helix.1340

Here is what right-handed and left-handed mean.1348

From your perspective, you are looking at this picture right now; if you take your hand and you run it away from you to the right and up, if your thumb in pointing up, it is a right-handed helix.1352

That is what this is; that is what alpha-helices are.1366

The alpha helix pattern is right-handed, notice, going away from you, going to the right away from you and up.1368

OK, notice, it is going up.1377

If your right hand follows that ribbon and if your thumb is pointing up, that is a right-handed helix.1381

If you happen to have another helix and if it is your left hand that goes to the left away from you and up and if your thumb in pointing up, then, it is going to be a left-handed helix, and that is exactly right.1390

That is all that is happening here; that is all that means.1401

OK, now, let's see.1406

I will write it on this page.1411

Interactions among the side chains can stabilize or destabilize an alpha helix.1416

Again, not all peptides have alpha-helices- very, very important.1446

OK, now, let's talk about the beta sheet, a little stranger to wrap your mind around because there is just a little bit more to keep track off in terms of what is interacting with what.1462

I am going to try my best to represent a good pattern that you can always follow, and when we actually look at some structures, we are actually going to do one by hand, do a couple by hand because it is very, very important that you would be able to do it by hand not just look at it.1480

For the most part, I think for the exams that you would take, I do not think you are going to be asked to draw out a beta conformation either parallel or anti-parallel, but at the very least, you certainly should be able to recognize it; but it is very nice to be able to draw one out because I think it helps crystalize it in your mind, solidify just what the arrangement is.1495

OK, beta sheet, OK, the peptide backbone - again, it is the backbone we are concerned with - arranges itself in a zigzag pattern resembling pleats, and if you do not know what pleats are, just think of an accordion or your pleated pants, sort of, that zigzag up and down, up, down, up, down, up, down- things like that.1517

OK, now, it is actually the beta conformation.1564

It is actually a conformation; this idea of sheet comes from the following.1575

When 2 or more peptide strands lay next to each other and interact, the structure, it begins to look like a pleated sheet.1583

Really what it is is if it is just a single strand or at most, 2 strands, what you have is something called a beta conformation.1625

OK, a single strand can actually arrange itself in this zigzag pattern, but when you lay multiple strands next to each other - let's say this is a strand, this is a strand, this is a strand - when you lay them next to each other, it looks like a sheet.1635

That is what is happening; really, what it is is when we speak about beta sheet, we are talking about beta conformation.1649

A single peptide chain can have a beta conformation.1654

Multiple strands either from the same peptide chain that is looped around or maybe a different peptide chain lying next to each other, that is what gives rise to the beta sheet.1658

You want to think in terms of beta conformation; that is what it is.1669

You do not want to think of beta sheet; you want to think conformation.1674

OK, now, the 2 or more segments/strands that are lying next to each other can be either parallel or antiparallel; and, of course, we are going to draw all of this out, so do not worry at all.1678

We are going to talk about this in a reasonable amount of detail and show you how to actually produce it yourself, not just recognize it on a sheet of paper.1712

Let's take a look here.1720

Aha, here we go; in a parallel arrangement, this right here is the peptide chain.1727

This segment of the peptide chain from here to here, all of a sudden, assumes a beta conformation.1734

In ribbon diagrams of proteins that you see, whenever you see some flat arrow, that is a beta conformation.1740

Well, this beta conformation, let's say the segment of - let's say, I do not know - 30 amino acids all of a sudden achieves a beta conformation, which we will talk about in a second.1749

I will show what it looks like, and then, you have the peptide chain that has just, sort of, random, and then, it comes around again; and then, it lays right next to this strand.1758

Now, you have, again, another beta conformation.1766

Well, if they arrange themselves like this, this we call parallel.1770

If, in fact, it ends up, let's say, having a beta conformation from here to here and then, just some random arrangement of the amino acids, but then, it loops around itself tightly; and now, it lays next to this one except going in this direction, we call that anti-parallel- that is it.1775

This is parallel, and this is anti-parallel; that is all that means.1790

That is all that means.1794

OK, now, let's see; I have got the image of the anti-parallel.1798

I have got the image of the parallel beta sheet; this is the anti-parallel beta sheet.1802

Now, let's go ahead and take a look at...aha, OK, now, this is a diagram of the parallel arrangement of the peptide chain.1810

This is 1 segment of the peptide chain; it is looped around, and this is another segment of the peptide chain.1825

See how they are next to each other; if you have, let's say, several of these, it starts to appear like an extended sheet structure- flat.1833

It is going to be like this and like that, like that, like that, like that, like that, and here is what is happening here.1842

Let's go through this very, very carefully.1850

I am going to describe what is happening on this image, and then, we are going to actually reproduce this image ourselves.1855

We want to be able to create one by hand; start at the top and repeat the N-C-C pattern, notice, N-C-C, N-C-C, N-C-C, parallel, N-C-C, N-C-C, N-C-C, again, N, C to the left, C, N, C to the left, yes, N, C to the right, C.1859

This is the parallel arrangement; all you have to do is double up the N-C-C pattern, the N-C-C pattern this way.1883

We will say start at the top, and repeat our N-C-C pattern going down in parallel.1890

OK, the carbonyl is on the second carbon, notice, N-C-C, carbonyl, N-C-C, carbonyl, N-C-C, carbonyl, and notice, they alternate, in-out, in-out; but you will get that anyway.1909

The carbonyl is the second carbon.1925

OK, now, along the inside, when you do this for 2 strands in parallel, these match, N-N, C-C, C-C, N-N, C-C, C-C.1938

They match; that is parallel.1952

Along the inside, the nH hydrogen bonds to the carbonyl, oxygen.1953

OK, that is what you have here, this nH hydrogen bonding to this carbonyl.1968

Notice, the hydrogen bonding is staggered; it is not straight across.1976

It is staggered, OK, down, up, carbonyl, the hydrogen, carbonyl, the hydrogen, carbonyl, hydrogen, carbonyl, hydrogen.1980

When you see something like this, when you see a parallel arrangement, you can recognize parallel multiple ways.1994

You can recognize the pattern of the N-C-C, N-C-C and then, the literal mirror image.1998

Actually, I am sorry, not a mirror image, just a copy of it right next to it, N-C-C, N-C-C, and you can also notice the staggered arrangement of hydrogen bonding between the carbonyl and the hydrogen on that nitrogen.2003

Now, the R-groups, they alternate - out of the page, into the page, out of the page, into the page - and last but not least, the pleats are on the alpha-carbons.2019

The pleats are here.2055

Go ahead and do this in black; that is a pleat.2060

That is a pleat; that is a pleat.2067

That is a pleat; what is happening here is these - 1, 2, 3, 4 - they are going down.2072

1, 2, 3, 4, they are coming up.2080

1, 2, 3, 4, they are going down; 1, 2, 3, 4, they are coming up.2084

If you look at it from the side, you will get something that looks like this, boom, boom, boom, boom, boom, boom, just a pleated pattern.2090

These R-groups, they are going to stick out.2100

These R-groups are going to go down; these R-groups are going to stick up.2105

These R-groups are going to go down; that is all that is going on here.2111

OK, let' see if we can actually do one of these by hand; it is really, really important.2117

We do N-C-C, N-C-C, right?2124

Let's do one more: N-C-C.2130

Carbonyl is on the second carbon; it is out, out and out.2136

OK, let's go ahead and do another one: parallel.2141

We have N-C-C.2146

We have N; we have C.2153

We have C, and we have N.2155

We have C, and we have C, N-C-C, carbonyl, N-C-C, carbonyl, N-C-C, carbonyl.2159

The nitrogen has hydrogen; the nitrogen has hydrogen.2167

Our hydrogen bonds in blue, hydrogen bonds there, hydrogen bonds there- that is it.2174

That is the pattern; you do your N-C-C.2184

You start at the top; the carbonyl is on the second carbon.2185

Along the inside, the nH, hydrogen bonds to the OH.2188

The R-groups alternate, out of the page, into the page, and the pleats are in the alpha-carbons.2191

There is an R-group out of the page; there is an R-group out of the page.2198

There is an R-group in the page; there is an R-group in the page- out of the page, out of the page and all the way down, and the pleats are along there, there, there, OK, there, there.2202

And if you were to look at this from the side, you would see that, that, that, that, and on the cusp, you would see an R sticking out here and then down here at this cusp, this.2224

You would see the R sticking out down here; that is what is going on.2235

This is the beta conformation; if you have multiple strands, you can have another strand and another strand and another strand.2239

Now, it becomes this beta sheet; this is not necessarily a beta sheet.2245

It is only 2 strands; it is a beta conformation.2250

It tends to become a beta sheet; OK, this is the parallel arrangement.2252

Alright, now, let's go ahead and take a look at an anti-parallel arrangement.2260

OK, now, the pattern for this image is actually from the bottom up.2267

So, what I am about to describe and what I actually draw is going to be from the top down.2271

The top down, this picture, we put it on this page in such a way that the particular pattern that I use, because I wanted to base on going from top to bottom, and because I wanted to maintain that N-C-C pattern just to make it easy and analogous to everything that came before, in this particular case, the way this image was arranged, is actually going to be from the bottom up.2277

Let me go ahead and just start, and we will talk about it.2303

Again, we are going to start at the top, and we are going to write our N-C-C pattern.2308

But again, for this image, it actually is going to begin from the bottom.2312

Notice, here is your N-C-C, N-C-C, N-C-C.2316

And again, the same thing, let's see, N-C-C.2321

Yes it goes down; the second C has the carbonyl.2330

Let's see, N-C-C, N-C-C, N-C.2331

OK, and then, we have...OK, now, when you arrange this one in this N-C-C pattern and then, what you do because this is anti-parallel, since you started with the N-C-C pattern, all you want to do is you want to reverse that pattern and go C-C-N, C-C-N.2339

If you were drawing this, you would go N-C-C, N-C-C, but then, you would go C-C-N, C-C-N because now, it is anti-parallel.2361

You are going to end up with the same arrangement, just keep going, just put together a second strand, put together another strand.2370

What you are going to discover is that now, again, the carbonyl, oxygen and the hydrogen on the nitrogen are going to hydrogen bond again, but this time, it is straight across- that is it, again, along the inside of the pattern.2376

Notice, we have N-C-C, N-C - I am sorry - C-C-N.2395

You are just reversing it; that is the anti-parallel part.2402

You are still going to end up with an arrangement, but this time, you are going to notice that the carbonyl and the hydrogen on the nitrogen are actually aligned with each other straight.2404

They are not going this way or this way; that is what characterizes this behavior.2412

OK, let's see what we have got here, N-C-C.2419

Let me see; what is the best way to do this?2426

N, C, should we go C-C-N?2430

Maybe, N outside, carbonyl, we have got N-C-C, C.2436

I am wondering if I should...you know what, I am actually going to describe my pattern, and I think it would actually work out best.2458

Let me go ahead and do that; let me go ahead and do it here.2469

I am going to say, start at the top.2472

Let me see, 2, C, C, C-N, C-N.2483

Yes, that is fine; OK, start at top and write the pattern N-C-C.2491

This time...actually, you know what, no, I think this is going to be a lot more confusing.2508

My apologies; we will not go ahead and do this.2515

We will just go ahead and rely on this particular picture.2517

The only thing that you need to recognize with respect to this, I think the parallel is a lot easier.2521

The anti-parallel is a little strange, but again, the only thing that you really need to know is the N-C-C, N-C-C pattern, that is the same for one of the strands.2525

Anti-parallel just means reverse that; write it as C-C-N, C-C-N.2534

And then, when you do that, like we said before, you will end up, along the inside, you will have the carbonyl oxygen directly in line with the hydrogen on the nitrogen, and this is the anti-parallel beta conformation; and when you, let's say, do another strand here, which is going to be...if this one if we say it is this direction, since this is anti-parallel, it is this direction.2540

If you have another strand, it is going to be this direction because now, this and this have to be anti-parallel, and if you add another strand, it is going to be in that direction because this and this have to be anti-parallel.2566

Well, the hydrogen bonding takes place in between the strands.2576

When you have multiple strands, now, you have something called the beta sheet, other than that, this is the anti-parallel beta conformation just for 2 strands.2580

And again, N-C-C, N-C-C, C-C-N, C-C-N, everything else is the same.2592

You are going to treat it exactly the same.2597

In the N-C-C pattern, the carbonyl appears on the second carbon.2601

In the C-C-N pattern, the carbonyl is on the first carbon because it is C-C-N, right?2605

N-C-C, the carbonyl shows up here on the second carbon if you are doing that.2609

Well, going backwards, parallel, it is C-C-N.2616

It is OK.2621

Sorry; we are going down, C-C-N because again, the carbonyl, second carbon from the nitrogen.2627

Because you have a peptide chain that has a bunch of carbon-nitrogens, carbon-nitrogens, the carbonyl carbon is attached to a nitrogen, but the alpha-carbon is attached to the carbonyl carbon; and that is also attached to the nitrogen on the other end.2639

Because you are running them together, you have to choose a place to start.2652

You have to choose your basic unit; it is up to you.2656

You can choose nitrogen-carbon-nitrogen if you want to.2658

I prefer 3 atoms, N-C-C, and when I reverse that, you have to start in 1 place and go down or go up, as long as you are consistent.2663

I prefer going up to down, so if I do N-C-C, going from up to down, my anti-parallel is going to go C-C-N from up to down- that is it.2675

And because the carbonyl is on the second carbon away from the nitrogen, here, the nitrogen, it is on the second carbon away from the nitrogen.2687

It is just a question of consistency; you just have to keep track of that.2693

That takes care of the anti-parallel beta conformation.2699

OK, now, let's go ahead and finish up with just a couple of words on tertiary and quaternary structure, and we will be all set.2703

Tertiary structure, alright, the final folded spatial arrangement of a single polypeptide chain- that is it.2712

Once it is finally achieved, once it has gone through its alpha-helices and its beta sheets and it has taken on its final shape, that is the tertiary structure.2744

Now, quaternary structure, as we said before, when a protein has 2 or more subunits - in other words, separate chains - the combined form...actually, I will say this.2754

If a protein contains 2 or more, when a protein has 2 or more subunits or separate chains, the overall combination, that is what constitutes quaternary structure- that is it, nothing too complicated.2806

Let's take a look here; I think we have an image of myoglobin here.2832

This is myoglobin.2840

Let's see where it starts; it starts here, goes through an alpha helix, a little bit of just random arrangement of the amino acids, goes through another alpha helix, turns, goes through another alpha helix, turns, alpha helix, alpha helix, and then, it ends, or you can start here and go this way.2846

It does not really matter; this is myoglobin.2863

This is tertiary structure; myoglobin is a single polypeptide chain that happens to fold, and you notice, certain segments of it, in this particular case, there are no beta sheet, you have just this, just a series of alpha-helices and free fragments that have no general discernible pattern.2867

Here, we have the hemoglobin.2886

You have 1, 2, 3, 4 subunits.2893

This would constitute quaternary structure because now, all of the subunits started to interact, so you have just this whole protein that does what it does.2898

That is quaternary structure; OK, now, let's see here, one final word.2909

This is just some random protein; it is the ribbon diagram of some random protein.2917

OK, and we have mentioned this before, but alpha-helices are represented precisely by/as helical ribbons.2923

OK, and beta conformations or beta sheet patterns, beta conformation patterns are represented as flat arrows.2944

Let's go ahead and start and see what we can do.2968

We begin here; we have some random amino acid sequence.2972

It does not really seem to strike a pattern, and then, here, it has an alpha helix; and then, it goes here.2978

The polypeptide chain continues, and then, this segment, notice, it is a flat arrow, so it is in a beta conformation, turns around.2985

It goes into, again, another beta conformation this way.2993

OK, and then, this way, another beta conformation up to here, and then, it comes around random sequence and then, a final alpha helix and then, another random sequence; and it finishes here.2997

This is the COO- end; this is the amino end.3015

This is the NH2 end; more than likely, we generally start with the NH2 and end with a COO-- that is it.3027

When you see a ribbon diagram, flat arrow is beta conformation.3036

The helix is the alpha helix, and that is it; most of the protein structures that you will see will be given to you in ribbon conformations.3040

Thank you so much for joining us here at Educator.com; we will see you next time, bye-bye.3048

Educator®

Please sign in for full access to this lesson.

Sign-InORCreate Account

Enter your Sign-on user name and password.

Forgot password?

Start Learning Now

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

Sign up for Educator.com

Membership Overview

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

Use this form or mail us to .

For support articles click here.