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Raffi Hovasapian

Raffi Hovasapian

Glycoconjugates

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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Glycoconjugates

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  • Intro 0:00
  • Glycoconjugates 0:24
    • Overview
    • Proteoglycan
    • Glycoprotein
    • Glycolipid
    • Proteoglycan vs. Glycoprotein
    • Cell Surface Diagram
    • Proteoglycan Common Structure
    • Example: Chondroitin-4-Sulfate
    • Glycoproteins
    • The Monomers that Commonly Show Up in The Oligo Portions of Glycoproteins
    • N-Acetylneuraminic Acid
    • L-Furose
    • Example of an N-Linked Oligosaccharide
    • Cell Membrane Structure
    • Glycolipids & Lipopolysaccharide
    • Structure Example

Transcription: Glycoconjugates

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

In the last lesson, we talked about polysaccharides.0004

We are going to continue our discussion of polysaccharides, and talk about something called glycoconjugates.0007

These are polysaccharides that are attached to proteins and lipids.0013

Let's just go ahead and jump in, get started.0022

OK, let's make sure we have...let's start off with black here.0026

In addition to their structural and fuel storage roles - actually, I do not think I will use the word "roles", I think I will use the word "capacities" - oligo and polysacchs - excuse me - they also carry information.0031

OK, let's go over here; they also carry information.0087

In other words, in this particular case, they are involved - as we mentioned in the previous lesson - in cell to cell and cell extracellular matrix interactions.0093

In other words, they are involved in recognition.0122

OK, in these cases, the carbohydrate, oligopolysaccharide, the carbohydrate is often joined to a protein or a lipid.0125

Lipid is just a fancy word for fat, and we are going to be discussing lipids in great detail very, very soon.0160

OK, let's talk about these things called proteoglycans.0167

Let me go to blue here, and let me see.0171

Is proteoglycan like a protein?0175

Yes, that is fine; alright, proteoglycan.0177

Our first class of glycoconjugates are these things called proteoglycans.0185

OK, they are cell surface and extracellular.0192

Extracellular means that they are just proteins that are not attached to the cell; they are actually proteins that are floating around in the cytosol.0202

That is all that means- proteins with one or more glycosaminoglycans, one or more Gags attached.0207

OK, now, these things called proteoglycans, they are the carbohydrates, but they are attached to cell surface proteins or they are attached to free proteins, secreted proteins, proteins that have been created and sent outside of the cell to sort of wander around in the matrix or wherever it is that they wander around, proteins with one or more glycosaminoglycans attached.0227

What is important here is the attachment to the protein is an actual glycosaminoglycan, and you remember from the last lesson that the glycosaminoglycan is this particular polysaccharide that has alternating, it is a linear polymer.0254

It is not branched; it is linear, but it alternates A-B, A-B, A-B with a certain collection of monomers, those monomers generally being N-acetylglucosamine or N-acetylgalactosamine and the other monomer being, more often than not, a glucuronic acid or an iduronic acid.0269

Now, other things can show up; it is not a problem, but the majority of the glycosaminoglycans are going to be those.0289

So, when that particular arrangement of polysaccharide is attached to a protein, we call that glycoconjugate; the whole thing, it is called a proteoglycan- that is all this is.0296

The carbohydrate in a proteoglycan tends to dominate the structure, and that is where the biological activity is.0306

The protein just happens to be a point of attachment.0316

OK, another family of glycoconjugate is something called a glycoprotein.0320

I know, it is kind of interesting, isn't it?0328

Glycoprotein, notice, here, proteo is first, glycan is second; here, glyco is first, protein is second.0330

Now, these are proteins with one or more oligosaccharides covalently attached, and they are also covalently attached here.0337

They can be covalently or electrostatically, but here, they are covalently attached.0364

Now, the carbohydrate portion is generally more varied in the sense that there is a greater collection of monomers to choose from, that the oligosaccharide is made of, is more varied and complex than the glycosaminoglycans on the proteoglycan, the glycosaminoglycan chains on the proteoglycans.0370

If you see a protein, and it has some carbohydrate attached, if the carbohydrate attached happens to be a glycosaminoglycan, we are talking about a proteoglycan- the whole thing.0422

If it tends to have some oligosaccharide or polysaccharide attached, but it is a lot more complex and it has branching, that is a glycoprotein.0430

That is the difference between the two; I will actually write that out in just a second.0440

Let me go ahead and just run through the list here of glycoconjugates.0445

We have proteoglycans, glycoproteins, and now, we have something called a glycolipid.0450

Now, this is just lipids in the cell membrane that have oligosaccharides attached- that is it.0461

In this particular case, the carbohydrate, the oligosaccharide, the polysaccharide, is attached to a fat, not a protein - that is it - covalently linked.0486

OK, now, proteoglycan versus glycoprotein.0496

I know this is good.0505

Now, what is the difference, proteoglycan, glycoprotein?0508

Here is the difference.0510

Proteoglycan, it has a linear glycosaminoglycan attached- that is the difference.0512

The attachment to the protein is some linear glycosaminoglycan, and we know that a glycosaminoglycan is a heteropolysaccharide.0524

It is linear, has no branching; and it consists of alternating monomers, A-B, A-B, A-B- whatever those monomers happen to be.0533

OK, linear Gag attached, and, of course, the Gags are repeating disacch units - that is how you tell - whereas a glycoprotein, it has various oligos attached, different monomers, linear, branched, all kinds of crazy things, any arrangement, high binding specificity.0542

Now, we said that these oligosaccharides attached to proteins that are on the cell surface are floating around, they serve recognition purposes.0594

Well, yes, proteoglycans are involved in recognition; glycoproteins are involved in recognition.0606

Proteoglycans are involved in sort of a global recognition - attached here, attached there.0612

Because these tend to be smaller, more complex, they have a higher binding specificity.0620

They bind specific things at specific points, whereas a proteoglycan might have some glycosaminoglycan attached; and maybe, it is sort of attached at 15 or 16 different points, just sort of like, it is attached here, attached here, attached here, sort of like a claw, whereas these glycoproteins are attached in one location.0626

So, these oligosaccharides tend to be much smaller, and they have very high binding specificity- that is the thing.0648

These glycoproteins are the ones that are involved in your body's immune response.0656

The immune cells that your body sends out to attack invaders recognize these glycoproteins on the cell surface of the bacteria and viruses and things like that.0664

OK, let's take a look at a drawing here, and OK.0675

This is a cell surface; a cell is a lipid bilayer, so that is this thing right here in blue.0681

OK, we are not going to worry about that; let's just sort of take a look and see some of these things.0690

Now, notice this particular protein here; this particular protein looks like it has a couple of things attached, so it looks linear.0697

This could be a proteoglycan; I will just say PG.0708

This could be a proteoglycan.0711

This over here, this is a membrane bound protein; part of it is in the membrane.0714

Part of it is inside the cell; part of it is outside the cell.0720

This is inside the cell here; this is outside the cell, and it has this oligosaccharide attached.0723

Notice, this is not a linear oligosaccharide; this is, it branches here.0730

It branches there, and it branches there.0735

This one is a glycoprotein- that is it.0737

That is how you tell; I mean unless you do a particular analysis, there is no way to actually tell, but this pretty much gives it away.0741

If you have some extensive branching, you are pretty much looking at something which is a glycoprotein.0749

It is going to be a very specific binding site.0754

Let's see, over here, there is another in an integral protein.0757

Integral means it is part of the cell membrane.0761

There is a part of the protein that extends inside; there is a part that extends outside, and again, we have a linear.0765

Now, this could be a glycoprotein; it just depends on what the identity of this oligosaccharide is.0770

If it happens to be a glycosaminoglycan, let's say something like chondroitin-4-sulfate, we know that this whole thing, the protein and the oligosaccharide, is a proteoglycan.0775

If it happens to be just some collection of monomers - N-acetylglucosamine, N-acetylgalactosamine, maybe a mannose, maybe a galactose, something like that - then we know we are looking at a glycoprotein.0786

It serves a more specific type of recognition site- that is all it is, and this is what it is going to look like.0800

You see, all of these proteins, they have little oligosaccharides.0807

Your cells are covered in this stuff; bacteria is covered in this stuff.0811

That is how things get recognized; in this particular case, glycoprotein, proteoglycan, I just wanted you to see what this looks like.0815

Now, over here, we have this glycolipid.0825

Here, we have a lipid molecule, some fat; and again, we will be talking about lipids specifically, but here, you have an oligosaccharide that is attached to a fat.0829

It is not attached to a protein, not a proteoglycan, not a glycoprotein, but it is in the third class; it is a glycolipid- that is it.0838

It just means it has a sugar that is attached to some fat- that is it.0846

We will return to this a little bit later in the lesson when we get into a little bit more detail about proteoglycans and glycoproteins.0851

OK, let's talk about proteoglycans first, and let's talk about their common structure.0857

Proteoglycans are alright, proteoglycan common structure, and by common structure in this particular case, what I am going to discuss is the point of attachment to a protein.0869

In this case, we said that this was our proteoglycan, so we are going to be talking about - you know, I should do this in black, this right there - how it is actually attached to the protein.0894

Well, here is how it is attached to the protein; let's go ahead, for our example.0905

I wonder if I should do this on the next page.0912

Yes, that is fine; I should have enough room here.0916

Let's go ahead and actually do a chondroitin-4-sulfate.0917

OK, chondroitin-4-sulfate, it is a glycosaminoglycan; it is linear, and its particular monomers are glucuronic acid and N-acetylgalactosamine, and I am going to write that down in just a second.0930

So, I am not going to draw these structures; I am just going to write their names connected.0949

I have got a GlcA; I have got it connected to a GalNAc- that is the N-acetylgalactosamine - and I am going to write one more GlcA, right?0953

So, we have alternating A-B, A-B, A-B, and this is going to be connected to a galactose, which is going to be connected to a galactose, which is going to be connected to a xylose sugar.0967

Remember, xylose is a 5-carbon sugar; galactose is a 6-carbon sugar, and this happens to be connected to a serine residue, which is part of the polypeptide, which makes up the protein.0980

And, that is the term Gly, Hex, Gly; and, of course, the polypeptide continues on in this direction.0999

This is going to be the N-terminus.1008

Now, when it is attached to a serine residue, what tends to be attached to the serine is another glycine, some other amino acid and some other glycine.1011

In general, this is what we tend to find more often at this point of attachment, and, of course, this polymer goes on that way, the polypeptide, and this is the C-terminus.1023

OK, this tends to be the arrangement.1033

Right there, at the protein's surface, there is some serine, glycine, some other amino acid and glycine, this arrangement, and then attached to the serine, you will have a xylose sugar, a galactose, a galactose, and then, of course, you will have your molecule.1035

Here is your molecule of your chondroitin-4-sulfate.1049

This is our chondroitin-4-sulfate, and this is our trisaccharide linker that links the protein, the amino acid serine, to our glycosaminoglycan, which is the chondroitin-4-sulfate.1058

This is our trisaccharide connector.1080

OK, let's see; all these crazy words floating around.1087

OK, and let's do this one in red.1097

This right here, this glycosidic bond is going to be beta-(1,3).1102

The anomeric carbon of the glucuronic acid is connected to galactose at its no. 3 hydroxy on the no. 3 carbon.1107

This connection right here is a beta-(1,3) glycosidic bond.1118

Now, let's go ahead and draw out serine just so you see what serine looks like as a reminder.1124

We have NCC; serine has a CH2, and it has that, and, of course, this is H.1132

This is that, and this is going to go on that way.1143

This is going to go on that way; that is serine, just as a reminder of what serine actually looks like, so that is it.1145

This is the point of attachment for a proteoglycan.1153

This is the part that is different.1160

There are going to be different glycosaminoglycans attached through a trisaccharide connector to a serine residue on a proteoglycan.1163

That is what's happening right there.1172

OK, now, let's talk about glycoproteins.1176

You know what, I think I am going to go back to blue; for some reason, I just thought I really, really like blue, and I don't know why, but there it is.1186

Now, again, the oligos are smaller and more complex, smaller and more diverse and complex than the glycosaminoglycans.1200

Now, smaller, you might think "Well, wait a minute, smaller and more complex, that doesn't make sense".1224

It does, it is referring to the branching.1229

Yes, they are smaller; you have fewer of them, but there is more complexity and there is more variation because now, you are not talking about just 2 monomers alternating A-B, A-B, A-B.1232

You are talking about maybe 5 or 6 to choose from, in general, on most of these glycoproteins; and, of course, they can have all kinds of different branching on them.1242

That is what we mean by more complex.1251

Complexity is a measure of quality; length is a measure of quantity.1254

They are smaller but they are more complex; the quality of them is different.1258

Now, OK, the first monosacch is attached to the protein by its anomeric carbon.1263

The no. 1 carbon, well, I won't say the no. 1 carbon because for ketoses, it could be the no. 2 carbon, so we will just call it the anomeric carbon, the one that originally had the carbonyl.1290

Now, the sugar is in the ring structure; now, there is a hydroxy attached to it, so that is the anomeric carbon- the one that was originally the carbonyl by its anomeric carbon.1302

OK, and now, it is attached to its anomeric carbon in 2 ways: through the hydroxy - I will draw it this way - through the hydroxy group on either serine of threonine.1314

We call this O-linked; in other words, it is an O-glycosidic bond - no worries, we will be drawing it out in just a minute - or, it could be attached through the amide nitrogen which is on asparagine, on Asn.1341

This is called N-linked because this is going to be an N-glycosidic bond.1387

So, it is either an O-linked glycoprotein or it is an N-linked glycoprotein.1393

In other words, the oligosaccharide is either attached to a serine threonine residue that is an O-linked glycoprotein, or it is attached to an asparagine residue that is going to be an N-linked.1398

So, this is an N-glycosidic bond.1409

OK, let's go ahead and draw what these things look like; let's go ahead and do an O-linked first.1417

Let me go ahead and do this in black; I think I will do it.1423

Let's use N-acetylglucosamine as our monomer that is attached to a serine residue.1429

Let's go ahead and draw our sugar unit first.1436

That is there, and let's go ahead and make it an alpha; and let's go ahead and make this, yes, NH, COO, CH3.1439

This is OH; this is OH, and this is CH2OH.1459

And now, I have got my CH2; actually, you know what, I am going to do this in 2 colors here.1466

I really want you to see this in 2 colors; I am going to do this second one in, you know what, I will do it in red.1472

O, CH2, C, this is NH; this is COO, and, of course, the polymer, the protein goes that way.1480

The protein goes that way; this right here is our serine residue.1493

OK, now, the O that is connected to the sugar that comes from the serine that is not from the hydroxy on the original sugar- that is the whole idea.1498

This is the nucleophile; it is going to get rid of that hydroxy, so it definitely comes from this serine.1509

That is important to know; that is why I did it in 2 colors.1513

I hope that is not confusing; let me see, let me write out what this is over here.1517

Let me go back to black; this is the alpha-GlcNAc.1524

Alpha, that is that; the anomeric carbon, this is alpha-1, N-acetylglucosamine, and it is attached to a serine residue.1533

This is O-linked.1542

OK, now, let's do an N-linked structure, so you see what that looks like; and this time, I am going to use the beta-N-acetylglucosamine.1546

Let me go ahead and go back to black here; let me draw my sugar that way.1556

OK, you know what, I am going to draw it a little bit lower here.1565

I need a little bit more room; excuse me.1569

I will go ahead and draw it like that, so that is that; and we said beta.1574

Let me go ahead and put in this first; this is NH.1581

I am always forgetting that H; I don't know why.1584

Well, old habits- they die hard.1587

OH, OH, and we said N-acetylglucosamine, so this is CH2OH.1591

This is a beta-GlcNAc, right?1600

Yes, and we said, now, we will go ahead and go; we have N.1607

We have COO, CH2, C, NH, COO.1614

The protein, the polypeptide is this thing right here.1628

This is the asparagine residue; this is the R-group.1632

Well, the whole thing is the asparagine residue; this is the R-group on the asparagine.1635

We have got CO, and there is also, let's go ahead and put an H on here too because there is an H there.1640

this right here is our Asn residue, and this happens to be our beta-1-carbon, and the nitrogen, this is an N-linked, right?1646

So, we have, this is N-linked, and the nitrogen comes from the protein, from the amino acid.1662

OK, so it is N-linked; this is a nucleophile.1674

This is what is nucleophilic; it is what is going to displace the hydroxy.1677

OK, there you go.1681

Now, let's talk about the monomers that commonly show up in these glycoproteins, in these oligosaccharides, monomers that commonly show up in the oligo portion of glycoproteins.1683

I wonder if I am going to have enough room here to write out all of them; yes, it is fine.1725

OK, let's do this in black.1729

Now, it is not exclusively these; these just tend to show up more often than any others.1736

GlcNAc- that is N-acetylglucosamine.1741

GlcNAc- this is N-acetylglucosamine, and we have Man.1750

This is mannose; it is a hexose.1762

We have Gal; that is galactose.1766

It is another hexose.1772

We have Neu5Ac; this is called N-acetylneuraminic acid, otherwise known as sialic acid.1774

It is actually A-sialic acid; it is a class of molecule, but we tend to call it sialic acid.1788

And, no worries, I will be drawing out the structure in just a minute, or you can look in your book- either way.1795

And, we have Fuc, which is fucose; it is just another sugar, and this one usually shows up as the L-isomer, L-fucose, instead of the D-isomer.1805

And, our last one - which I should have left room but that is OK, I will go ahead and write it over here - is GalNAc.1823

This is N-acetylgalactosamine; this is N-acetylgalactose.1832

Wooh, I mean this is exhausting.1842

You can see why biochemistry is drilled with acronyms - Gag, Gal, Man, PG, GP - all over the place, simply because we can't write everything out.1845

OK, let's go ahead and draw out a couple of the structures.1858

We have talked about most of these, but I am going to go ahead and draw out the sialic acid, the N-acetylneuraminic; and I am going to go ahead and draw out the L-fucose just so you see what the structures look like, just for the heck of it.1865

OK, let's go ahead and do this in red.1878

Actually, no, let's go ahead and do this in blue.1882

This is going to be, that is that, here, here, here.1885

Now, let me see, we have got COO-, OH.1896

This one is deoxy; we have the hydroxy here, and here, we have NCOCH3, and we have an R-group, and R happens to be equivalent to C.1904

This is OH; this is O - yes, that is right, I always forget that - CH2OH.1923

This R-group right here, that is just this thing, just not enough room; we just do that.1929

This is our N-acetylneuraminic acid.1933

This is actually the deprotonated, so it is N-acetylneuraminate.1944

This is our Neu5Ac.1951

OK, now, let's go ahead and do our other one.1957

OK, I am going to leave the stereochemistry on this one unspecified.1964

I am going to go OH; I am going to go OH, and I am going to go OH, and there is going to be a CH3 on this one, and this is L-fucose.1970

L that is the carbon, 1, 2, 3, 4; that carbon is what specifies the L.1983

OK, let me see what it is I have got here- example of an N-linked oligosaccharide.1988

Let me just give you a quick example of an N-linked oligosaccharide.1997

I will do this in red just to show you what it looks like, and I am not going to actually draw out the structure; I am just going to draw out little hexagons and put numbers in them.2004

We have Asn; that is going to be our Asn residue, and, of course, the peptide goes in that direction.2024

It goes in that direction, and it is going to have attached, let's say, I will just draw them out as hexagons.2033

Now, of course, these are sugar rings, so there is definitely an oxygen in the ring somewhere; but I do not know where that oxygen is going to be depending on what the connection is.2040

So, I am just going to draw them as little individual hexagons.2049

You will often see it like this.2053

Let's see, boom, boom, boom, boom; and let's go ahead and go here, boom, boom, boom, boom, boom, boom, and up here like this.2058

These are all in original units, so this is no. 1, 1.2071

Let's go ahead and do something like that and maybe something like that.2074

Maybe I will just go ahead and put one more for the hell of it.2081

1, 1, 1, 2, 3, 4, 2, 3, so again, 1, 2, 3, these 1, 2, 3, 4s, they are different monomers.2084

This can be N-acetylgalactosamine; this can be fucose.2096

This can be N-acetylglucosamine; this can be mannose.2099

It could be anything- that is it.2102

This is just sort of what it looks like, and again, these are all sugar hexoses, but we have not put the oxygen in there because we do not know exactly where the oxygen is in terms of connection.2105

Now, what is interesting about this, the degree of complexity that we talked about earlier has to also do what the glycosidic linkages.2117

In order to fully specify what this oligosaccharide arrangement is, I have to give the connection, that one, that one, that one, I have to specify each connection; and what is interesting about these glycoproteins, the oligosaccharide portion of these proteins, is you can have 1,4 glycosidic bond.2125

You can have 1,2 glycosidic bond, 1,3; you can have 1,6.2146

You can have 2,3- any combination.2152

As long as there is a hydroxy available to react with something else, you can have those connections.2155

That is why in order to fully specify, you have to specify the connection at each glycosidic bond.2160

We are just generally going to talk about it like this.2167

If we happen to need a specific glycoprotein that has this connection to this connection, we will deal with it like that, but this is what we mean by complexity- certainly a hell of lot more complex than a proteoglycan, which is just alternating monomers.2169

OK, let's take a look at the picture one more time- the cell membrane picture.2186

Here we go, so, again, let's say this one is a glycoprotein.2195

Let's say there is another glycoprotein; let's say this is a glycoprotein.2205

This one is a glycoprotein; this looks like a proteoglycan.2213

This one here, probably a proteoglycan attached.2217

Actually, you know what, that one looks like a glycolipid.2221

This one right here, a glycolipid- that is it.2224

You are just sort of identifying and taking a look at what the carbohydrate looks like and what it is attached to.2227

OK, now, let's go ahead and see; let's talk about glycolipids a little bit.2236

Glycolipids are lipid molecules, fat molecules, in the cell membrane.2247

I mean all of these are fat molecules.2267

These are fat molecules that are not necessarily, that make up, the things that make up the lipid bilayer of a cell membrane, it could be attached to that, but more often than not, it is attached to some lipid that is in there like a cholesterol or some other lipid that happens to be in that lipid bilayer, and the oligosaccharide is attached to that.2276

OK, are lipid molecules in the cell membrane with oligosacchs attached, and, of course, we said that already, but there is no harm in repeating ourselves.2302

OK, now, we are going to, of course, be discussing lipids, and glycolipids in much more detail when we specifically get to that chapter discussing the lipids and all the different types of lipids and certain oligosaccharides that are attached to those things.2318

We are definitely going to get more into detail about this, but just to get an idea because we are talking about glycoconjugates, and a glycolipid happens to be a glycoconjugate.2338

OK, now, I am going to talk about one particular type of glycolipid.2348

It is called a lipopolysaccharide.2353

And again, this is mostly just for your edification at this point; we will be discussing it in more detail later- lipopolysaccharide.2359

OK, a lipopolysaccharide, now the dominant feature - and when we say dominant, we definitely mean dominant - the dominant feature on the outer membrane of gram-negative bacteria for example E. coli is a gram-negative bacteria and certain salmonellas or salmonella.2370

OK, the lipopolysaccharide is the dominant feature on the outer membrane of gram-negative bacteria.2415

I mean, it is just covered with this stuff.2419

OK, it is a complex oligosaccharide, complex oligosacch units covalently attached to multiple lipids in the outer cell membrane.2423

In this particular case, a lipopolysaccharide is a specific example of a glycolipid, and it is peculiar to gram-negative bacteria; and it is where this particular oligosaccharide are, these things are attached to not just one lipid molecule in the membrane, but several different lipid molecules that are anchored in the membrane.2463

And now, we want to go ahead and take a look at one of these and what it looks like.2488

OK, this is what it looks like; let's take a look.2494

Here, we are talking about the cell interior; this bottom portion right here, this is inside the cell.2498

Inside the cell membrane, you have these lipids, OK, these long carbon chains, these are fats, these lipids that are inside the cell membrane.2507

Now, notice, these are attached to sugar units, and, of course, on the no. 6 carbon, it looks like one of these, that through and O-glycosidic bond, is attached to several other sugars.2520

So, this is going to be outside the cell; this part is the core oligosaccharide.2540

This part is always the same; this particular arrangement Kdd, Kdd, Kdo - I'm sorry, yes - Kdo, Hep, Hep, Glc, Gal, Gal, Glc, Ngc, this particular arrangement of oligosaccharide, this oligosaccharide right here is always going to be the same.2549

Do not worry, these are just different monomers: Kdo, Kdd, Hep.2566

These are just different types of sugars with different things attached to them.2569

What is different from bacteria to bacteria or different places along the bacteria, is this thing right here.2574

This is the thing that changes; this is the same.2582

This is the same, but this is the thing that changes; and depending on what this is, what collection of monomers and what glycosidic bonds are actually connecting them, that is going to be the point of recognition.2586

We call this the O-antigen; this is what your immune cells recognize when they run across the bacteria in your body.2599

That is what they attach to in order to do what the immune cells do, which is destroy these things or whatever else they plan on doing to it- that is it.2608

This is just an example of a lipopolysaccharide; it is a glycolipid.2618

It has a lipid core that is in the membrane.2623

In this particular case, certain portion of it contains an oligosaccharide, which is in variant; and then, of course, at the end, it is variant.2629

Different things happen up here; this is going to be the same.2642

This whole thing is the oligosaccharide portion plus these two, and this is the lipid portion- that is it.2644

We just wanted you to get an idea of what something like this can actually look like.2653

OK, thank you for joining us here at Educator.com2659

We will see you next time, bye-bye.2663

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