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Michael Philips

Michael Philips

Genome Editing, Synthetic Biology, & the Ethics of Modern Science

Slide Duration:

Table of Contents

I. The Beginnings of Molecular Biology
Biochemistry Review: Importance of Chemical Bonds

53m 29s

Intro
0:00
Lesson Overview
0:14
Chemical Bonds
0:41
Attractive Forces That Hold Atoms Together
0:44
Types of Bonds
0:56
Covalent Bonds
1:34
Valence Number
1:58
H O N C P S Example
2:50
Polar Bonds
7:23
Non-Polar Bond
8:46
Non-Covalent Bonds
9:46
Ionic Bonds
10:25
Hydrogen Bonds
10:52
Hydrophobic Interactions
11:34
Van Der Waals Forces
11:58
Example 1
12:51
Properties of Water
18:27
Polar Molecule
13:34
H-bonding Between Water H20 Molecules
19:29
Hydrophobic Interactions
20:30
Chemical Reactions and Free Energy
22:52
Transition State
23:00
What Affect the Rate
23:27
Forward and Reserve Reactions Occur Simultaneously But at Different Rate
23:51
Equilibrium State
24:29
Equilibrium Constant
25:18
Example 2
26:16
Chemical Reactions and Free Energy
27:49
Activation Energy
28:00
Energy Barrier
28:22
Enzymes Accelerate Reactions by Decreasing the Activation Energy
29:04
Enzymes Do Not Affect the Reaction Equilibrium or the Change in Free Energy
29:22
Gibbs Free Energy Change
30:50
Spontaneity
31:18
Gibbs Free Energy Change Determines Final Concentrations of Reactants
34:36
Endodermic vs. Exothermic Graph
35:00
Example 3
38:46
Properties of DNA
39:37
Antiparallel Orientation
40:29
Purine Bases Always Pairs Pyrimidine Bases
41:15
Structure Images
42:36
A, B, Z Forms
43:33
Major and Minor Grooves
44:09
Hydrogen Bonding and Hydrophobic Interactions Hold the Two Strands Together
44:39
Denaturation and Renaturation of DNA
44:56
Ways to Denature dsDNA
45:28
Renature When Environment is Brought Back to Normal
46:05
Hyperchromiicity
46:36
Absorbs UV Light
47:01
Spectrophotometer
48:01
Graph Example?
49:05
Example 4
51:02
Mendelian Genetics & Foundational Experiments

1h 9m 27s

Intro
0:00
Lesson Overview
0:22
Gregor Johann Mendel
1:01
Was a Biologist and Botanist
1:14
Published Seminal Paper on Hybridization and Inheritance in the Pea Plant
1:20
Results Criticized
1:28
Father of Modern Genetics
1:59
Mendel’s Laws
2:19
1st Law: Principle of Independent Segregation of Alleles
2:27
2nd Law: Principle of Independent Assortment of Genes
2:34
Principle of Independent Segregation (of Alleles)
2:41
True Breeding Lines / Homozygous
2:42
Individuals Phenotypes Determined by Genes
3:15
Alleles
3:37
Alleles Can Be Dominant or Recessive
3:50
Genotypes Can be Experimentally Determined by Mating and Analyzing the Progeny
5:36
Individual Alleles Segregate Independently Into Gametes
5:55
Example 1
6:18
Principle of Independent Segregation (of Alleles)
16:11
Individual Genes Sort Independently Into Gametes
16:22
Each Gamete Receives One Allele of Each Gene: 50/50 Chance
16:46
Genes Act Independently to Determine Unrelated Phenotypes
16:57
Example: Punnett Square
17:15
Example 2
21:36
The Chromosomal Theory of Inheritance
30:41
Walter S Sutton Linked Cytological Studies with Mendels Work
31:02
Diploid Cells Have Two Morphologically Similar Sets of Chromosomes and Each Haploid Gamete Receives One Set
31:17
Genes Are on Chromosome
31:33
Gene for Seed Color’s on a Different Chromosome Than Gene for Seed Texture
31:44
Gene Linkage
31:55
Mendel’s 2nd Law
31:57
Genes Said to Be Linked To Each Other
32:09
Linkage Between Genes
32:29
Linkage is Never 100% Complete
32:41
Genes are Found on Chromosomes
33:00
Thomas Hunt Morgan and Drosophila Melanogaster
33:01
Mutation Linked to X Chromosome
33:15
Linkage of White Gene
33:23
Eye Color of Progeny Depended on Sex of Parent
33:34
Y Chromosome Does Not Carry Copy of White Gene
33:44
X Linked Genes, Allele is Expressed in Males
33:56
Example
34:11
Example 3
35:52
Discovery of the Genetic Material of the Cell
41:52
Transforming Principle
42:44
Experiment with Streptococcus Pneumoniae
42:55
Beadle and Tatum Proposed Genes Direct the Synthesis of Enzymes
45:15
One Gene One Enzyme Hypothesis
45:46
One Gene One Polypeptide Theory
45:52
Showing the Transforming Material was DNA
46:14
Did This by Fractionating Heat-Killed “S” Strains into DNA, RNA, and Protein
46:32
Result: Only the DNA Fraction Could Transform
47:15
Leven: Tetranucleotide Hypothesis
48:00
Chargaff Showed This Was Not the Case
48:48
Chargaff: DNA of Different Species Have Different Nucleotide Composition
49:02
Hershey and Chase: DNA is the Genetic Material
50:02
Incorporate Sulfur into Protein and Phosphorous into DNA
51:12
Results: Phosphorase Entered Bacteria and Progeny Phage, But no Sulfur
53:11
Rosalind Franklin’s “Photo 51” Showing the Diffraction Pattern of DNA
53:50
Watson and Crick: Double Helical Structure of DNA
54:57
Example 4
56:56
Discovery of the Genetic Material of the Cell
58:09
Kornberg: DNA Polymerase I
58:10
Three Postulated Methods of DNA Replication
59:22
Meselson and Stahl: DNA Replication is Semi-Conservative
00:21
How DNA Was Made Denser
00:52
Discovery of RNA
03:32
Ribosomal RNA
03:48
Transfer RNA
04:00
Messenger RNA
04:30
The Central Dogma of Molecular Biology
04:49
DNA and Replication
05:08
DNA and Transcription = RNA
05:26
RNA and Translation = Protein
05:41
Reverse Transcription
06:08
Cracking the Genetic Code
06:58
What is the Genetic Code?
07:04
Nirenberg Discovered the First DNA Triplet That Would Make an Amino Acid
07:16
Code Finished in 1966 and There Are 64 Possibilities or Triplet Repeats/ Codons
07:54
Degeneracy of the Code
08:53
II. Structure of Macromolecules
Structure of Proteins

49m 44s

Intro
0:00
Lesson Overview
0:10
Amino Acids
0:47
Structure
0:55
Acid Association Constant
1:55
Amino Acids Make Up Proteins
2:15
Table of 21 Amino Acid Found in Proteins
3:34
Ionization
5:55
Cation
6:08
Zwitterion
7:51
Anion
9:15
Example 1
10:53
Amino Acids
13:11
L Alpha Amino Acids
13:19
Only L Amino Acids Become Incorporated into Proteins
13:28
Example 2
13:46
Amino Acids
18:20
Non-Polar
18:41
Polar
18:58
Hydroxyl
19:52
Sulfhydryl
20:21
Glycoproteins
20:41
Pyrrolidine
21:30
Peptide (Amide) Bonds
22:18
Levels of Organization
23:35
Primary Structure
23:54
Secondary Structure
24:22
Tertiary Structure
24:58
Quaternary Structure
25:27
Primary Structure: Specific Amino Acid Sequence
25:54
Example 3
27:30
Levels of Organization
29:31
Secondary Structure: Local 3D
29:32
Example 4
30:37
Levels of Organization
32:59
Tertiary Structure: Total 3D Structure of Protein
33:00
Quaternary Structure: More Than One Subunit
34:14
Example 5
34:52
Protein Folding
37:04
Post-Translational Modifications
38:21
Can Alter a Protein After It Leaves the Ribosome
38:33
Regulate Activity, Localization and Interaction with Other Molecules
38:52
Common Types of PTM
39:08
Protein Classification
40:22
Ligand Binding, Enzyme, DNA or RNA Binding
40:36
All Other Functions
40:53
Some Functions: Contraction, Transport, Hormones, Storage
41:34
Enzymes as Biological Catalysts
41:58
Most Metabolic Processes Require Catalysts
42:00
Most Biological Catalysts Are Proteins
43:13
Enzymes Have Specificity of Reactants
43:33
Enzymes Have an Optimum pH and Temperature
44:31
Example 6
45:08
Structure of Nucleic Acids

1h 2m 10s

Intro
0:00
Lesson Overview
0:06
Nucleic Acids
0:26
Biopolymers Essential for All Known Forms of Life That Are Composed of Nucleotides
0:27
Nucleotides Are Composed of These
1:17
Nucleic Acids Are Bound Inside Cells
2:10
Nitrogen Bases
2:49
Purines
3:01
Adenine
3:10
Guanine
3:20
Pyrimidines
3:54
Cytosine
4:25
Thymine
4:33
Uracil
4:42
Pentoses
6:23
Ribose
6:45
2' Deoxyribose
6:59
Nucleotides
8:43
Nucleoside
8:56
Nucleotide
9:16
Example 1
10:23
Polynucleotide Chains
12:18
What RNA and DNA Are Composed of
12:37
Hydrogen Bonding in DNA Structure
13:55
Ribose and 2! Deoxyribose
14:14
DNA Grooves
14:28
Major Groove
14:46
Minor Groove
15:00
Example 2
15:20
Properties of DNA
24:15
Antiparallel Orientation
24:25
Phosphodiester Linkage
24:50
Phosphate and Hydroxyl Group
25:05
Purine Bases Always Pairs Pyramidine Bases
25:30
A, B, Z Forms
25:55
Major and Minor Grooves
26:24
Hydrogen Bonding and Hydrophobic Interactions Hold Strands Together
26:34
DNA Topology - Linking Number
27:14
Linking Number
27:31
Twist
27:57
Writhe
28:31
DNA Topology - Supercoiling
31:50
Example 3
33:16
III. Maintenance of the Genome
Genome Organization: Chromatin & Nucleosomes

57m 2s

Intro
0:00
Lesson Overview
0:09
Quick Glossary
0:24
DNA
0:29
Gene
0:34
Nucleosome
0:47
Chromatin
1:07
Chromosome
1:19
Genome
1:30
Genome Organization
1:38
Physically Cellular Differences
3:09
Eukaryotes
3:18
Prokaryotes, Viruses, Proteins, Small Molecules, Atoms
4:06
Genome Variance
4:27
Humans
4:52
Junk DNA
5:10
Genes Compose Less Than 40% of DNA
6:03
Chart
6:26
Example 1
8:32
Chromosome Variance - Size, Number, and Density
10:27
Chromosome
10:47
Graph of Human Chromosomes
10:58
Eukaryotic Cell Cycle
12:07
Requirements for Proper Chromosome Duplication and Segregation
13:07
Centromeres and Telomeres
13:28
Origins of Replication
13:38
Illustration: Chromosome
13:44
Chromosome Condensation
15:52
Naked DNA to Start
16:00
Beads on a String
16:13
Mitosis
16:52
Start with Two Different Chromosomes
17:18
Split Into Two Diploid Cells
17:26
Prophase
17:42
Prometaphase
17:52
Metaphase
19:10
Anaphase
19:27
Telophase
20:11
Cytokinesis
20:31
Cohesin and Condensis
21:06
Illustration: Cohesin and Condensis
21:19
Cohesin
21:38
Condensin
21:43
Illustration of What Happens
21:50
Cohesins
27:23
Loaded During Replication and Cleaved During Mitosis
27:30
Separase
27:36
Nucleosomes
27:59
Histone Core
28:50
Eight Histone Proteins
28:57
Octamer of Core Histones Picture
29:14
Chromosome Condensation via H1
30:59
Allows Transition to Compact DNA
31:09
When Not in Mitosis
31:37
Histones Decrease Available Binding Sites
32:38
Histone Tails
33:21
Histone Code
35:32
Epigenetic Code
35:56
Phosphorylation
36:45
Acetylation
36:57
Methylation
37:01
Ubiquitnation
37:04
Example 2
38:48
Nucleosome Assembly
41:22
Duplication of DNA Requires Duplication of Histones
41:50
Old Histones Are Recycled
42:00
Parental H3-H4 Tetramers Facilitate the Inheritance of Chromatin States
44:04
Example 3
46:00
Chromatin Remodeling
48:12
Example 4
53:28
DNA Replication

1h 9m 55s

Intro
0:00
Lesson Overview
0:06
Eukaryotic Cell Cycle
0:50
G1 Growth Phase
0:57
S Phase: DNA & Replication
1:09
G2 Growth Phase
1:28
Mitosis
1:36
Normal Human Cell Divides About Every 24 Hours
1:40
Eukaryotic DNA Replication
2:04
Watson and Crick
2:05
Specific Base Pairing
2:37
DNA Looked Like Tetrinucleotide
2:55
What DNA Looks Like Now
3:18
Eukaryotic DNA Replication - Initiation
3:44
Initiation of Replication
3:53
Primer Template Junction
4:25
Origin Recognition Complex
7:00
Complex of Proteins That Recognize the Proper DNA Sequence for Initiation of Replication
7:35
Prokaryotic Replication
7:56
Illustration
8:54
DNA Helicases (MCM 2-7)
11:53
Eukaryotic DNA Replication
14:36
Single-Stranded DNA Binding Proteins
14:59
Supercoils
16:30
Topoisomerases
17:35
Illustration with Helicase
19:05
Synthesis of the RNA Primer by DNA Polymerase Alpha
20:21
Subunit: Primase RNA Polymerase That Synthesizes the RNA Primer De Navo
20:38
Polymerase Alpha-DNA Polymerase
21:01
Illustration of Primase Function Catalyzed by DnaG in Prokaryotes
21:22
Recap
24:02
Eukaryotic DNA Replication - Leading Strand
25:02
Synthesized by DNA Polymerase Epsilon
25:08
Proof Reading
25:26
Processivity Increased by Association with PCNA
25:47
What is Processivity?
26:19
Illustration: Write It Out
27:03
The Lagging Strand/ Discontinuing Strand
30:52
Example 1
31:57
Eukaryotic DNA Replication - Lagging Strand
32:46
Discontinuous
32:55
DNA Polymerase Delta
33:15
Okazaki Fragments
33:36
Illustration
33:55
Eukaryotic DNA Replication - Okazaki Fragment Processing
38:26
Illustration
38:44
When Does Okazaki Fragments Happen
40:32
Okazaki Fragments Processing
40:41
Illustration with Okazaki Fragments Process Happening
41:13
Example 2
47:42
Example 3
49:20
Telomeres
56:01
Region of Repetitive Nucleotide Sequences
56:26
Telomeres Act as Chromosome Caps by Binding Proteins
57:42
Telomeres and the End Replication Problem
59:56
Need to Use a Primer
59:57
DNA Mutations & Repairs

1h 13m 8s

Intro
0:00
Lesson Overview
0:06
Damage vs. Mutation
0:40
DNA Damage-Alteration of the Chemical Structure of DNA
0:45
DNA Mutation-Permanent Change of the Nucleotide Sequence
1:01
Insertions or Deletions (INDELS)
1:22
Classes of DNA Mutations
1:50
Spontaneous Mutations
2:00
Induced Mutations
2:33
Spontaneous Mutations
3:21
Tautomerism
3:28
Depurination
4:09
Deamination
4:30
Slippage
5:44
Induced Mutations - Causes
6:17
Chemicals
6:24
Radiation
7:46
Example 1
8:30
DNA Mutations - Tobacco Smoke
9:59
Covalent Adduct Between DNA and Benzopyrene
10:02
Benzopyrene
10:20
DNA Mutations - UV Damage
12:16
Oxidative Damage from UVA
12:30
Thymidine Dimer
12:34
Example 2
13:33
DNA Mutations - Diseases
17:25
DNA Repair
18:28
Mismatch Repair
19:15
How to Recognize Which is the Error: Recognize Parental Strand
22:23
Example 3
26:54
DNA Repair
32:45
Damage Reversal
32:46
Base-Excision Repair (BER)
34:31
Example 4
36:09
DNA Repair
45:43
Nucleotide Excision Repair (NER)
45:48
Nucleotide Excision Repair (NER) - E.coli
47:51
Nucleotide Excision Repair (NER) - Eukaryotes
50:29
Global Genome NER
50:47
Transcription Coupled NER
51:01
Comparing MMR and NER
51:58
Translesion Synthesis (TLS)
54:40
Not Really a DNA Repair Process, More of a Damage Tolerance Mechanism
54:50
Allows Replication Past DNA Lesions by Polymerase Switching
55:20
Uses Low Fidelity Polymerases
56:27
Steps of TLS
57:47
DNA Repair
00:37
Recombinational Repair
00:54
Caused By Ionizing Radiation
00:59
Repaired By Three Mechanisms
01:16
Form Rarely But Catastrophic If Not Repaired
01:42
Non-homologous End Joining Does Not Require Homology To Repair the DSB
03:42
Alternative End Joining
05:07
Homologous Recombination
07:41
Example 5
09:37
Homologous Recombination & Site-Specific Recombination of DNA

1h 14m 27s

Intro
0:00
Lesson Overview
0:16
Homologous Recombination
0:49
Genetic Recombination in Which Nucleotide Sequences Are Exchanged Between Two Similar or Identical Molecules of DNA
0:57
Produces New Combinations of DNA Sequences During Meiosis
1:13
Used in Horizontal Gene Transfer
1:19
Non-Crossover Products
1:48
Repairs Double Strand Breaks During S/Gs
2:08
MRN Complex Binds to DNA
3:17
Prime Resection
3:30
Other Proteins Bind
3:40
Homology Searching and subsequent Strand Invasion by the Filament into DNA Duplex
3:59
Holliday Junction
4:47
DSBR and SDSA
5:44
Double-Strand Break Repair Pathway- Double Holliday Junction Model
6:02
DSBR Pathway is Unique
6:11
Converted Into Recombination Products by Endonucleases
6:24
Crossover
6:39
Example 1
7:01
Example 2
8:48
Double-Strand Break Repair Pathway- Synthesis Dependent Strand Annealing
32:02
Homologous Recombination via the SDSA Pathway
32:20
Results in Non-Crossover Products
32:26
Holliday Junction is Resolved via Branch Migration
32:43
Example 3
34:01
Homologous Recombination - Single Strand Annealing
42:36
SSA Pathway of HR Repairs Double-Strand Breaks Between Two Repeat Sequences
42:37
Does Not Require a Separate Similar or Identical Molecule of DNA
43:04
Only Requires a Single DNA Duplex
43:25
Considered Mutagenic Since It Results in Large Deletions of DNA
43:42
Coated with RPA Protein
43:58
Rad52 Binds Each of the Repeated Sequences
44:28
Leftover Non-Homologous Flaps Are Cut Away
44:37
New DNA Synthesis Fills in Any Gaps
44:46
DNA Between the Repeats is Always Lost
44:55
Example 4
45:07
Homologous Recombination - Break Induced Replication
51:25
BIR Pathway Repairs DSBs Encountered at Replication Forks
51:34
Exact Mechanisms of the BIR Pathway Remain Unclear
51:49
The BIR Pathway Can Also Help to Maintain the Length of Telomeres
52:09
Meiotic Recombination
52:24
Homologous Recombination is Required for Proper Chromosome Alignment and Segregation
52:25
Double HJs are Always Resolved as Crossovers
52:42
Illustration
52:51
Spo11 Makes a Targeted DSB at Recombination Hotspots
56:30
Resection by MRN Complex
57:01
Rad51 and Dmc1 Coat ssDNA and Promote Strand Invasion and Holliday Junction Formation
57:04
Holliday Junction Migration Can Result in Heteroduplex DNA Containing One or More Mismatches
57:22
Gene Conversion May Result in Non-Mendelian Segregation
57:36
Double-Strand Break Repair in Prokaryotes - RecBCD Pathway
58:04
RecBCD Binds to and Unwinds a Double Stranded DNA
58:32
Two Tail Results Anneal to Produce a Second ssDNA Loop
58:55
Chi Hotspot Sequence
59:40
Unwind Further to Produce Long 3 Prime with Chi Sequence
59:54
RecBCD Disassemble
00:23
RecA Promotes Strand Invasion - Homologous Duplex
00:36
Holliday Junction
00:50
Comparison of Prokaryotic and Eukaryotic Recombination
01:49
Site-Specific Recombination
02:41
Conservative Site-Specific Recombination
03:10
Transposition
03:46
Transposons
04:12
Transposases Cleave Both Ends of the Transposon in Original Site and Catalyze Integration Into a Random Target Site
04:21
Cut and Paste
04:37
Copy and Paste
05:36
More Than 40% of Entire Human Genome is Composed of Repeated Sequences
06:15
Example 5
07:14
IV. Gene Expression
Transcription

1h 19m 28s

Intro
0:00
Lesson Overview
0:07
Eukaryotic Transcription
0:27
Process of Making RNA from DNA
0:33
First Step of Gene Expression
0:50
Three Step Process
1:06
Illustration of Transcription Bubble
1:17
Transcription Starting Site is +1
5:15
Transcription Unit Extends From the Promoter to the Termination Region
5:40
Example 1
6:03
Eukaryotic Transcription: Initiation
14:27
RNA Polymerase II Binds to TATA Box to Initiate RNA Synthesis
14:34
TATA Binding Protein Binds the TATA Box
14:50
TBP Associated Factors Bind
15:01
General Transcription Factors
15:22
Initiation Complex
15:30
Example 2
15:44
Eukaryotic Transcription
17:59
Elongation
18:07
FACT (Protein Dimer)
18:24
Eukaryotic Transcription: Termination
19:36
Polyadenylation is Linked to Termination
19:42
Poly-A Signals Near the End of the pre-mRNA Recruit to Bind and Cleave mRNA
20:00
Mature mRNA
20:27
Dissociate from Template DNA Strand
21:13
Example 3
21:53
Eukaryotic Transcription
25:49
RNA Polymerase I Transcribes a Single Gene That Encodes a Long rRNA Precursor
26:14
RNA Polymerase III Synthesizes tRNA, 5S rRNA, and Other Small ncRNA
29:11
Prokaryotic Transcription
32:04
Only One Multi-Subunit RNA Polymerase
32:38
Transcription and Translation Occurs Simultaneously
33:41
Prokaryotic Transcription - Initiation
38:18
Initial Binding Site
38:33
Pribnox Box
38:42
Prokaryotic Transcription - Elongation
39:15
Unwind Helix and Expand Replication Bubble
39:19
Synthesizes DNA
39:35
Sigma 70 Subunit is Released
39:50
Elongation Continues Until a Termination Sequence is Reached
40:08
Termination - Prokaryotes
40:17
Example 4
40:30
Example 5
43:58
Post-Transcriptional Modifications
47:15
Can Post Transcribe your rRNA, tRNA, mRNA
47:28
One Thing In Common
47:38
RNA Processing
47:51
Ribosomal RNA
47:52
Transfer RNA
49:08
Messenger RNA
50:41
RNA Processing - Capping
52:09
When Does Capping Occur
52:20
First RNA Processing Event
52:30
RNA Processing - Splicing
53:00
Process of Removing Introns and Rejoining Exons
53:01
Form Small Nuclear Ribonucleoproteins
53:46
Example 6
57:48
Alternative Splicing
00:06
Regulatory Gene Expression Process
00:27
Example
00:42
Example 7
02:53
Example 8
09:36
RNA Editing
11:06
Guide RNAs
11:25
Deamination
11:52
Example 9
13:50
Translation

1h 15m 1s

Intro
0:00
Lesson Overview
0:06
Linking Transcription to Translation
0:39
Making RNA from DNA
0:40
Occurs in Nucleus
0:59
Process of Synthesizing a Polypeptide from an mRNA Transcript
1:09
Codon
1:43
Overview of Translation
4:54
Ribosome Binding to an mRNA Searching for a START Codon
5:02
Charged tRNAs will Base Pair to mRNA via the Anticodon and Codon
5:37
Amino Acids Transferred and Linked to Peptide Bond
6:08
Spent tRNAs are Released
6:31
Process Continues Until a STOP Codon is Reached
6:55
Ribosome and Ribosomal Subunits
7:55
What Are Ribosomes?
8:03
Prokaryotes
8:42
Eukaryotes
10:06
Aminoacyl Site, Peptidyl tRNA Site, Empty Site
10:51
Major Steps of Translation
11:35
Charing of tRNA
11:37
Initiation
12:48
Elongation
13:09
Termination
13:47
“Charging” of tRNA
14:35
Aminoacyl-tRNA Synthetase
14:36
Class I
16:40
Class II
16:52
Important About This Reaction: It Is Highly Specific
17:10
ATP Energy is Required
18:42
Translation Initiation - Prokaryotes
18:56
Initiation Factor 3 Binds at the E-Site
19:09
Initiation Factor 1 Binds at the A-Site
20:15
Initiation Factor 2 and GTP Binds IF1
20:50
30S Subunit Associates with mRNA
21:05
N-Formyl-met-tRNA
22:34
Complete 30S Initiation Complex
23:49
IF3 Released and 50S Subunit Binds
24:07
IF1 and IF2 Released Yielding a Complete 70S Initiation Complex
24:24
Deformylase Removes Formyl Group
24:45
Example 1
25:11
Translation Initiation - Eukaryotes
29:35
Small Subunit is Already Associated with the Initiation tRNA
29:47
Formation of 43S Pre-Initiation Complex
30:02
Circularization of mRNA by eIF4
31:05
48S Pre-Initiation Complex
35:47
Example 2
38:57
Translation - Elongation
44:00
Charging, Initiation, Elongation, Termination All Happens Once
44:14
Incoming Charged tRNA Binds the Complementary Codon
44:31
Peptide Bond Formation
45:06
Translocation Occurs
46:05
tRNA Released
46:51
Example 3
47:11
Translation - Termination
55:26
Release Factors Terminate Translation When Ribosomes Come to a Stop Codon
55:38
Release Factors Are Proteins, Not tRNAs, and Do Not Carry an Amino Acid
55:50
Class I Release Factors
55:16
Class II Release Factors
57:03
Example 4
57:40
Review of Translation
01:15
Consequences of Altering the Genetic Code
02:40
Silent Mutations
03:37
Missense Mutations
04:24
Nonsense Mutations
05:28
Genetic Code
06:40
Consequences of Altering the Genetic Code
07:43
Frameshift Mutations
07:55
Sequence Example
08:07
V. Gene Regulation
Gene Regulation in Prokaryotes

45m 40s

Intro
0:00
Lesson Overview
0:08
Gene Regulation
0:50
Transcriptional Regulation
1:01
Regulatory Proteins Control Gene Expression
1:18
Bacterial Operons-Lac
1:58
Operon
2:02
Lactose Operon in E. Coli
2:31
Example 1
3:33
Lac Operon Genes
7:19
LacZ
7:25
LacY
7:40
LacA
7:55
LacI
8:10
Example 2
8:58
Bacterial Operons-Trp
17:47
Purpose is to Produce Trptophan
17:58
Regulated at Initiation Step of Transcription
18:04
Five Genes
18:07
Derepressible
18:11
Example 3
18:32
Bacteriophage Lambda
28:11
Virus That Infects E. Coli
28:24
Temperate Lifecycle
28:33
Example 4
30:34
Regulation of Translation
39:42
Binding of RNA by Proteins Near the Ribosome- Binding Site of the RNA
39:53
Intramolecular Base Pairing of mRNA to Hide Ribosome Binding Site
40:14
Post-transcriptional Regulation of rRNA
40:35
Example 5
40:08
Gene Regulation in Eukaryotes

1h 6m 6s

Intro
0:00
Lesson Overview
0:06
Eukaryotic Transcriptional Regulations
0:18
Transcription Factors
0:25
Insulator Protein
0:55
Example 1
1:44
Locus Control Regions
4:00
Illustration
4:06
Long Range Regulatory Elements That Enhance Expressions of Linked Genes
5:40
Allows Order Transcription of Downstream Genes
6:07
(Ligand) Signal Transduction
8:12
Occurs When an Extracellular Signaling Molecule Activates a Specific Receptor Located on the Cell
8:19
Examples
9:10
N F Kappa B
10:01
Dimeric Protein That Controls Transcription
10:02
Ligands
10:29
Example 2
11:04
JAK/ STAT Pathway
13:19
Turned on by a Cytokine
13:23
What is JAK
13:34
What is STAT
13:58
Illustration
14:38
Example 3
17:00
Seven-Spanner Receptors
20:49
Illustration: What Is It
21:01
Ligand Binding That Is Activating a Process
21:46
How This Happens
22:17
Example 4
24:23
Nuclear Receptor Proteins (NRPs)
28:45
Sense Steroid and Thyroid Hormones
28:56
Steroid Hormones Bind Cytoplasmic NRP Homodimer
29:10
Hormone Binds NRP Heterodimers Already Present in the Nucleus
30:11
Unbound Heterodimeric NRPs Can Cause Deacetylation of Lysines of Histone Tails
30:54
RNA Interference
32:01
RNA Induced Silencing Complex (RISC)
32:39
RNAi
33:54
RISC Pathway
34:34
Activated RISC Complex
34:41
Process
34:55
Example
39:27
Translational Regulation
41:17
Global Regulation
41:37
Competitive Binding of 5 Prime CAP of mRNA
42:34
Translation-Dependent Regulation
44:56
Nonsense Mediated mRNA Decay
45:23
Nonstop Mediated mRNA Decay
46:17
Epigenetics
48:53
Inherited Patterns of Gene Expression Resulting from Chromatin Alteration
49:15
Three Ways to Happen
50:17
DNA Sequence Does Not Act Alone in Passing Genetic Information to Future Generations
50:30
DNA Methylation
50:57
Occurs at CpG Sites Via DNA Methyltransferase Enzymes
50:58
CpG Islands Are Regions with a High Frequency of CpG Sites
52:49
Methylation of Multiple CpG Sites Silence Nearby Gene Transcription
53:32
DNA Methylation
53:46
Pattern Can Be Passed to Daughter Cells
53:47
Prevents SP1 Transcription Factors From Binding to CpG Island
54:02
MECP2
54:10
Example 5
55:27
Nucleosomes
56:48
Histone Core
57:00
Histone Protein
57:03
Chromosome Condensation Via J1
57:32
Linker Histone H1
57:33
Compact DNA
57:37
Histone Code
57:54
Post-translational Modifications of N-Terminal Histone Tails is Part of the Epigenetic Code
57:55
Phosphorylation, Acetylation, Methylation, Ubiquitination
58:09
Example 6
58:52
Nucleosome Assembly
59:13
Duplication of DNA Requires Duplication of Histones by New Protein Synthesis
59:14
Old Histones are Recycled
59:24
Parental H3-H4 Tetramers
58:57
Example 7
00:05
Chromatin Remodeling
01:48
Example 8
02:36
Transcriptionally Repressed State
02:45
Acetylation of Histones
02:54
Polycomb Repressors
03:19
PRC2 Protein Complex
03:38
PRC1 Protein Complex
04:02
MLL Protein Complex
04:09
VI. Biotechnology and Applications to Medicine
Basic Molecular Biology Research Techniques

1h 8m 41s

Intro
0:00
Lesson Overview
0:10
Gel Electraophoresis
0:31
What is Gel Electraophoresis
0:33
Nucleic Acids
0:50
Gel Matrix
1:41
Topology
2:18
Example 1
2:50
Restriction Endonucleases
8:07
Produced by Bacteria
8:08
Sequence Specific DNA Binding Proteins
8:36
Blunt or Overhanging Sticky Ends
9:04
Length Determines Approximate Cleavage Frequency
10:30
Cloning
11:18
What is Cloning
11:29
How It Works
12:12
Ampicillin Example
12:55
Example 2
13:19
Creating a Genomic DNA Library
19:33
Library Prep
19:35
DNA is Cut to Appropriate Sizes and Ligated Into Vector
20:04
Cloning
20:11
Transform Bacteria
20:19
Total Collection Represents the Whole Genome
20:29
Polymerase Chain Reaction
20:54
Molecular Biology Technique to Amplify a Small Number of DNA Molecules to Millions of Copies
21:04
Automated Process Now
21:22
Taq Polymerase and Thermocycler
21:38
Molecular Requirements
22:32
Steps of PCR
23:40
Example 3
24:42
Example 4
34:45
Southern Blot
35:25
Detect DNA
35:44
How It Works
35:50
Western Blot
37:13
Detects Proteins of Interest
37:14
How It Works
37:20
Northern Blot
39:08
Detects an RNA Sequence of Interest
39:09
How It Works
39:21
Illustration Sample
40:12
Complementary DNA (cDNA) Synthesis
41:18
Complementary Synthesis
41:19
Isolate mRNA from Total RNA
41:59
Quantitative PCR (qPCR)
44:14
Technique for Quantifying the Amount of cDNA and mRNA Transcriptions
44:29
Measure of Gene Expression
44:56
Illustration of Read Out of qPCR Machine
45:23
Analysis of the Transcriptome-Micrarrays
46:15
Collection of All Transcripts in the Cell
46:16
Microarrays
46:35
Each Spot Represents a Gene
47:20
RNA Sequencing
49:25
DNA Sequencing
50:08
Sanger Sequencing
50:21
Dideoxynucleotides
50:31
Primer Annealed to a DNA Region of Interest
51:50
Additional Presence of a Small Proportion of a ddNTPs
52:18
Example
52:49
DNA Sequencing Gel
53:13
Four Different Reactions are Performed
53:26
Each Reaction is Run in a Lane of a Denaturing Polyacrylamide Gel
53:34
Example 5
53:54
High Throughput DNA Sequencing
57:51
Dideoxy Sequencing Reactions Are Carried Out in Large Batches
57:52
Sequencing Reactions are Carried Out All Together in a Single Reaction
58:26
Molecules Separated Based on Size
59:19
DNA Molecules Cross a Laser Light
59:30
Assembling the Sequences
00:38
Genomes is Sequenced with 5-10x Coverage
00:39
Compare Genomes
01:47
Entered Into Database and the Rest is Computational
02:02
Overlapping Sequences are Ordered Into Contiguous Sequences
02:17
Example 6
03:25
Example 7
05:27
VII. Ethics of Modern Science
Genome Editing, Synthetic Biology, & the Ethics of Modern Science

45m 6s

Intro
0:00
Lesson Overview
0:47
Genome Editing
1:37
What is Genome Editing
1:43
How It Works
2:03
Four Families of Engineered Nucleases in Use
2:25
Example 1
3:03
Gene Therapy
9:37
Delivery of Nucleic Acids Into a Patient’s Cells a Treatment for Disease
9:38
Timeline of Events
10:30
Example 2
11:03
Gene Therapy
12:37
Ethical Questions
12:38
Genetic Engineering
12:42
Gene Doping
13:10
Synthetic Biology
13:44
Design and Manufacture of Biological Components That Do Not Exist in Nature
13:53
First Synthetic Cell Example
14:12
Ethical Questions
16:16
Stem Cell Biology
18:01
Use Stem Cells to Treat or Prevent Diseases
18:12
Treatment Uses
19:56
Ethical Questions
20:33
Selected Topic of Ethical Debate
21:30
Research Ethics
28:02
Application of Fundamental Ethical Principles
28:07
Examples
28:20
Declaration of Helsinki
28:33
Basic Principles of the Declaration of Helsinki
28:57
Utmost Importance: Respect for the Patient
29:04
Researcher’s Duty is Solely to the Patient or Volunteer
29:32
Incompetent Research Participant
30:09
Right Vs Wrong
30:29
Ethics
32:40
Dolly the Sheep
32:46
Ethical Questions
33:59
Rational Reasoning and Justification
35:08
Example 3
35:17
Example 4
38:00
Questions to Ponder
39:35
How to Answer
40:52
Do Your Own Research
41:00
Difficult for People Outside the Scientific Community
41:42
Many People Disagree Because They Do Not Understand
42:32
Media Cannot Be Expected to Understand Published Scientific Data on Their Own
42:43
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Lecture Comments (1)

0 answers

Post by Maryam Fayyazi on January 16 at 07:31:16 PM

Thanks for a great lecture.I was wondering if you cover cell biology as well?

Genome Editing, Synthetic Biology, & the Ethics of Modern Science

    Medium, 4 examples, 5 practice questions

  • Genome editing is the insertion or deletion of a DNA sequence from a genome using artificially engineered nucleases.
  • Gene therapy is a type of genome editing focused on the treatment of disease.
  • Synthetic biology is the design and manufacture of biological components that do not exist in nature.
  • In 1996, Dolly the sheep was the first animal to be cloned from an adult somatic cell, using the process of nuclear transfer.
  • Research ethics involves the application of ethical principles to a variety of topics involving research.

Genome Editing, Synthetic Biology, & the Ethics of Modern Science

Genetic engineering in which DNA is inserted, replaced, or removed from a genome using artificially engineered nucleases is called:
  • Genome sequencing
  • Genome editing
  • Stem cell biology
  • Synthetic biology
  • True/False: Meganucleases are a type of engineered nucleases used in genome editing.
    • True
    • False
    True/False: CRISPR is a type of adaptive immune system in prokaryotic cells to protect against infection from foreign invaders.
    • True
    • False
    The design and manufacture of biological components that do not exist in nature is called:
  • Genome sequencing
  • Genome editing
  • Stem cell biology
  • Synthetic biology
  • True/False: The Declaration of Helsinki is a set of ethical principles regarding human experimentation developed for the medical community by the World Medical Association.
    • True
    • False

    *These practice questions are only helpful when you work on them offline on a piece of paper and then use the solution steps function to check your answer.

    Answer

    Genome Editing, Synthetic Biology, & the Ethics of Modern Science

    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
    • Lesson Overview 0:47
    • Genome Editing 1:37
      • What is Genome Editing
      • How It Works
      • Four Families of Engineered Nucleases in Use
    • Example 1 3:03
    • Gene Therapy 9:37
      • Delivery of Nucleic Acids Into a Patient’s Cells a Treatment for Disease
      • Timeline of Events
    • Example 2 11:03
    • Gene Therapy 12:37
      • Ethical Questions
      • Genetic Engineering
      • Gene Doping
    • Synthetic Biology 13:44
      • Design and Manufacture of Biological Components That Do Not Exist in Nature
      • First Synthetic Cell Example
      • Ethical Questions
    • Stem Cell Biology 18:01
      • Use Stem Cells to Treat or Prevent Diseases
      • Treatment Uses
      • Ethical Questions
    • Selected Topic of Ethical Debate 21:30
    • Research Ethics 28:02
      • Application of Fundamental Ethical Principles
      • Examples
      • Declaration of Helsinki
    • Basic Principles of the Declaration of Helsinki 28:57
      • Utmost Importance: Respect for the Patient
      • Researcher’s Duty is Solely to the Patient or Volunteer
      • Incompetent Research Participant
    • Right Vs Wrong 30:29
    • Ethics 32:40
      • Dolly the Sheep
      • Ethical Questions
      • Rational Reasoning and Justification
    • Example 3 35:17
    • Example 4 38:00
    • Questions to Ponder 39:35
    • How to Answer 40:52
      • Do Your Own Research
      • Difficult for People Outside the Scientific Community
      • Many People Disagree Because They Do Not Understand
      • Media Cannot Be Expected to Understand Published Scientific Data on Their Own

    Transcription: Genome Editing, Synthetic Biology, & the Ethics of Modern Science

    Hello, and welcome back to www.educator.com, thank you for joining me.0000

    This is going to be our last lesson in this molecular biology class.0003

    What I wanted to do is talk about a few subjects that seem to be kind of glazed over,0007

    if it even touched upon it all in normal college classes because they often run at of time.0017

    There is certain information that needs to be covered.0024

    While, this is very interesting stuff, it is not of the utmost importance.0027

    It is really hard to lecture on.0032

    In no way am I going deep into this, I’m just giving a surface level view and try just to get your mind working.0035

    Try to get the topics in your head and just have you thinking about it a little bit.0042

    We are going to talk about genome editing, synthetic biology, and stem cell biology.0048

    We are going to talk about the ethical aspects of each of these, as well as just ethics of science in general.0053

    Many of you who end up going to graduate school will actually have to take seminars in research ethics.0061

    This is something that maybe will just be a starting point for you guys.0069

    For any of you who work in a lab, this is going to be something that you always have to keep in mind.0074

    It is always something that is going to surround your projects.0080

    It is good, we need to think about this.0084

    I’m going to do my job of introducing it to you and hopefully you take this upon yourselves to really think about these aspects.0088

    Genome editing, let us start with that.0099

    First of all, what is it?0101

    It is genetic engineering in which DNA is either inserted, replaced,0103

    or removed off from a genome using artificially engineered nucleases.0110

    Remember, nucleases are the enzymes that cut up nucleic acids, DNA and RNA.0116

    How do they work?0123

    Double strand breaks get introduced by the action of the nucleases, at desired locations in the genome.0124

    These double strand breaks then just get repaired by the normal mechanism0132

    that we have talked about in this molecular biology class of homologous recombination or of non-homologous end joining.0136

    Therefore, families of engineered nucleases that are in use for these processes today.0145

    We have zinc finger nucleases, we have TALENs, we have meganucleases,0152

    we have the CRISPR-Cas9 system or just the CRISPR system.0157

    Meganucleases, they usually cut on average once per genome.0160

    I'm going to focus on the CRISPR-Cas9 system because this is actually a really interesting system0167

    and really cool things can be done with this system.0177

    For genome editing, I’m just going to focus on this one.0180

    Here is our example, here is our CRISPR-Cas9 system.0184

    What is CRISPR? It stands for Clustered Regularly Interspaced Short Palindromic Repeats.0189

    Cas9, the Cas proteins, that is CRISPR associated protein.0231

    In this case Cas9, that is CRISPR associated protein 9.0250

    What is this, basically what CRISPR is a very, let us say primitive, adaptive, immune system for bacteria.0255

    If we are looking here, this is some membrane of bacteria.0280

    It is their way of defending against a bacteriophage which is a virus that infects bacteria.0283

    This is a primitive, adaptive, immune system for our prokaryotes, a bacteria.0295

    This CRISPR, it is Clustered Regularly Interspaced Short Palindromic Repeats.0302

    What it does is you have repetitions of base sequences in here, followed by spacer DNA such as this.0312

    These are spacer DNAs.0330

    Those spacers will recognize and cut, act like an endonuclease, cut up invading viral DNA.0334

    It is almost similar to RNA interference but it is a different system for doing it.0346

    How does this work?0353

    First, the virus latches onto the bacteria, injects its DNA.0354

    We have a double stranded viral DNA.0363

    It can be simplified down to a 4 step process.0367

    The invading viral DNA, double stranded DNA, or if it is an RNA virus, same thing can happen.0371

    It is cut into small fragments.0386

    From those fragments, you end up creating a novel spacer.0391

    This is in DNA sequence and this is basically a way that this is linked to this specific piece of DNA.0397

    The invading DNA or RNA is cut into small fragments, that is step 1.0407

    Step 2, a copy of that invading DNA or RNA is integrated into the CRISPR locus as a spacer.0414

    This one, this corresponded to a different piece of viral DNA.0426

    This one to a different one and to a different one, and to a different one.0435

    It is adaptive meaning it has seen that before, it keeps a piece of it so if it ever sees that DNA again,0441

    it will be able to break that down and silence it.0448

    Step 2, you make a copy of it, you put into that CRISPR locus as a spacer.0452

    3rd step, the CRISPR RNA which is called a crRNA, CRISPR RNA, they get transcribed.0459

    We will call this, this is step 1, this is step 2, this is step 3.0470

    The CRISPR RNAs are transcribed from the CRISPR locus.0485

    And then step 4, we have the crRNAs, the CRISPR RNAs, being incorporated into the CRISPR-Cas complex.0488

    And then 5, it will target viral DNA, invading viral DNA and it will degrade that.0501

    If want to call that, this is 6.0513

    The crRNA will provide specificity.0516

    It will act only, the crRNA, produced from these specific spacers, will specifically act on what is already seen.0520

    Researchers can utilize this as the crRNA, the CRISPR RNA, providing specificity for such things as,0532

    let us say gene editing for medical purposes.0543

    You can silence something, let us say if you have an overactive gene that is causing the disease,0546

    you can use the CRISPR-Cas9 complex to utilize that, you could silence that.0552

    There is plenty more in depth detail to go into this that I'm not going to go into.0563

    But I recommend you try to look this up, this is really cool, fairly cutting edge techniques being used here.0567

    Gene therapy, specifically that is our delivery in nucleic acids into a patient's cell for treatment of a disease.0579

    You can either be adding a gene, you can be knocking out a gene.0587

    You could be replacing a gene, any of that.0593

    The polymers of the nucleic acids are either expressed as proteins.0598

    Therefore, interfere with protein expression or directly correct genetic mutations by replacing the actual DNA sequence.0604

    The DNA that encodes a functional therapeutic gene will replace the mutated gene.0614

    Therefore, when it is transcribed and translated, you will get the wild type protein,0621

    instead of the mutant protein that has been causing the disease.0626

    Gene therapy, the theory on it was first published in 1972.0632

    The first experiment approved by the FDA occurred in 1990, about 18 years later.0638

    13 years after that, the first commercial gene therapy was approved at for use as a cancer treatment.0645

    The gene therapy called genidicine was approved in China in 2003.0653

    An example of a gene therapy, right here, we can see this is gene therapy using an adenovirus vector.0664

    An adenovirus is a specific type of virus, what it can do is you can manipulate the DNA inside the virus.0672

    The virus will infect the cell, bring that DNA into the nucleus of the cell.0680

    That DNA now being a good piece of DNA, not something we need to worry about of like viral DNA.0686

    But something that we plan on putting there, that will be healthy for the cell,0693

    will then make the certain proteins that we wanted to make and will help, if used properly to treat that disease.0697

    This is a little different from RNAi or from the CRISPR system, in the fact that we have something0707

    that we always need taking into consideration, when we involve a virus.0714

    Yes, it is there are plenty of research on it and plenty of ways that it has been altered,0720

    so that it should not be able to replicate and cause disease as any normal virus would.0729

    As always, something as a scientist and as the public, you keep in the back your mind.0735

    But for the most part, it does its job without infecting quote and quote, in a bad way, but infecting in a good way,0740

    getting in the cell, giving its DNA which has the good DNA that we want to make the protein of interest.0748

    Some ethical questions revolving around gene therapy is, there is always going to be problems of genetic engineering.0758

    Maybe the protein that you wanted to be sent in there.0766

    Maybe there is a mutation on the gene.0771

    Maybe you did not engineer the gene properly.0773

    Or just maybe the ethical question of just revolving around genetic engineering itself,0776

    manipulating the genome, playing god, if you want to say it that way.0784

    Another question that always is going to surround gene therapy is the aspect of gene doping,0790

    meaning, basically, if used improperly, you could almost use it as a performance enhancing drug alteRNAtive.0797

    You can do gene therapy to make you bigger, faster, stronger, have more oxygen carrying capacity, something like that.0810

    That is always a question that will be thrown around.0819

    Moving on to a different topic, synthetic biology.0827

    Synthetic biology is described as the design and manufacture of biological components that do not exist in nature.0831

    There are many ways of look at synthetic biology.0840

    I want to look at a specific one.0843

    This is an example of synthetic biology work.0847

    In 2010, scientist at the J. Craig Venter institute, if you remember J. Craig Venter,0852

    he was the entrepreneur that was involved in pushing the private funded aspect of the human genome project.0856

    Scientists at this institute had been opened, run by him, created the first synthetic cell.0869

    What they did is they started with a bacteria called mycoplasma capricolum.0876

    What they did is they took out all of the DNA, any genetic material in there,0882

    and replaced it by using the transformation technique with a brand new fully synthesized,0889

    fully synthetic, fully brand new DNA, made from their typing on a keyboard.0898

    They made it in a computer, made a bunch of DNA, you can get DNA made.0907

    They inserted their computer coded DNA into this completely empty cell.0914

    It is like a shell at this point.0922

    They obviously tried it many times until one work.0924

    And they finally found a sequence that was actually able to replicate the cell, as if it were a normal cell.0926

    In this case, they actually created a new species that they called mycoplasma mycoides.0937

    This is huge, they were able to take a manmade coded DNA sequence and put it in a shell of a bacteria, to make a living replicable organism.0944

    This is a huge, absolutely huge event.0964

    That was such a huge event like that, there is always going to be ethical questions.0971

    One of the big questions that surrounded this was, did they create new life or did they just manipulate life?0978

    You can have your own opinion on this, one of the rulings I believe it went to the court system was that,0992

    this was not actually the creation of a new life.0999

    However, this is something that will always be asked about.1002

    Some other ethical questions regarding synthetic biology is genome always are an ethical debate in and of itself.1009

    But when you start being able to computer code genes and be able put it into an organism,1016

    that brings up an entire new set of questions about gene.1024

    Finally, the fear of these synthetic bacteria that they made does not exist in nature.1030

    It was not intended to exist in nature.1039

    We have made it exist, we as a human race made it exist.1041

    What is that going to, what type of effect will that have on the current ecosystem, the currently living system?1046

    Can that bacteria infect other species?1055

    They took very good precautions to make it a non infective bacteria, in non-virulent strain.1059

    But there are ways that it can mutate or there are ways that,1066

    maybe somebody else might not take as great of care or might use this for ill purposes.1070

    That is always going to be an ethics debate.1078

    Moving on to stem cell biology, I know this is a big hot topic.1082

    This is been ethically debated, since the thoughts of stem cell biology came out.1086

    What is stem cell biology or using stem cells to treat or prevent disease.1093

    Often you have your stem cells coming from the bone marrow.1097

    When you talk about bone marrow transplant, a lot of times people with cancer,1104

    or multiple myeloma, they are one of the specific ones.1109

    You need to get bone marrow transplant and that is because cancer,1113

    as well as the chemotherapy, ravages your quickly dividing cells such as your B and T cells.1117

    Your B cells, part of your immunity that is found in your bone marrow.1124

    You need bone marrow replacement.1128

    You have what are called hematopoietic stem cells, these are stem cells that can turn into any type of white or red blood cell.1131

    Your B and T cells are a type of white blood cell.1139

    This is very useful and a very common practice nowadays.1143

    Some people do not agree with the fact of umbilical cord blood being utilized as a source of stem cells.1149

    In a huge contest or point of contention, is the fact of actually using embryonic stem cells.1157

    Stem cells from fetuses or unborn fetuses, that is a huge point of contention1166

    with many groups especially your religious focus groups.1173

    As well as even some nonreligious focus, some scientists do not agree with it.1179

    You can also have embryonic stem cells.1184

    You can also have what is called somatic cell nuclear transfer technique.1186

    But you need to start with some sort of a cell to begin with.1190

    The good thing about stem cell biology is that it can be used to treat many types of diseases.1196

    You have leukemia lymphoma, diabetes, injuries to the brain and spinal cord, deafness, anemia.1204

    Anemia is the low concentration of red blood cells which will then affect your oxygen carrying capacity.1214

    As well as stem cell biology can be used to treat organelle transplantation, to hope that goes well.1225

    Some of the ethical questions, are you destroying life?1234

    If we are talking about using embryonic stem cells, are you actually destroying a life that should have been?1239

    That is going to be a point of contention that people are going to have, a side versus the other.1247

    A lot of these decisions on ethics, you try to use as much as possible.1254

    But really, it is going to come down to belief systems and1260

    how you can manage that between yourself and the people that you have a contention with.1263

    Another one is human cloning.1270

    If we are using stem cells to make other humans, that is a huge point of contention.1272

    As of right now, human cloning is not allowed.1281

    Will it be in the future? Maybe, we do not know.1286

    Other than the ones that I had mentioned before, there are many other topics that are up for ethical debate.1292

    Some that I wanted to list here, genetically modified organisms.1299

    Vaccines, the whole vaccines, people will be thinking that they are correlated to autism.1304

    Based on a study published by a medical doctor who named Andrew Wakefield, in The Lancet,1313

    who was actually paid by competing vaccine company to falsify data1323

    and talk bad about the vaccines that are out on the market, which has spawned even though he lost his medical license.1330

    Once it was found that he falsified his data, the paper was retracted but a lot of people do not hear that part of it.1339

    They only hear the fact that the story was published years ago.1346

    This is always going to be for debate.1351

    A lot of people do not have the right facts to follow that one specifically.1353

    We have other topics for debate like save your babies.1358

    A save your baby is when a couple has a child with a condition where they are dying because they lack,1361

    let us say for example they have a kidney disease and they need a kidney transplant.1374

    Sometimes a couple will have another baby that was basically meant1379

    to use that second baby as basically an organ farm for the treatment of the first child.1385

    The second baby was born so that it can give a kidney transplant to the first child who is sick.1395

    There is always going to be ethical debate over that.1406

    There is ethical debate on genetic manipulation.1410

    Gene editing for health, you will have people on both sides.1413

    As well as the build –a-bear type baby, I want to make my baby blue eyes, 6’5, highly athletic and highly intelligent.1419

    Who is to stop somebody from picking all the best qualities to make their child, just like a freak of nature?1433

    I want to make somebody with the basketball skills and body type of Le Bron James, with the mind of Albert Einstein.1443

    It is something crazy like that.1454

    Prenatal genome sequencing, for the same reason, on being able to do that build-a-bear baby.1458

    Genome sequencing and insurance companies.1464

    If I sequence my genome because I want to know what diseases I’m susceptible for.1467

    Insurance companies are allowed to have that data, they might not offer me insurance at all.1474

    Or might have an extremely high premiums, based on my risk factors.1482

    That is a huge debate.1488

    Cloning, always a big one, specially human cloning.1490

    Animal testing, big debate.1493

    You are always going to have groups that PETA and even other scientists telling you that animal testing1495

    does not need to happen or does need happen.1503

    You do need to test on animals, if you want to pass selected drugs through the FDA, to get to the market.1507

    Like your Advil, your Tylenol, even all the way up through your chemotherapies,1518

    they have all had to have been tested on animals, before they allowed to go in the clinical trials and be tested on humans.1525

    Even though there is ethical debate on this, there is a specific way that you have to follow,1534

    to be able to get your drugs on the market.1542

    And then, one that is a different type of ethical debate is falsifying data.1547

    As a scientist or as a future scientists, this is extremely important.1558

    Falsifying data, whether it is for any reason, sometimes people falsify1565

    because it will help them get a promotion or maybe they work for a drug company and they are trying to push their product.1571

    Maybe they just want to become famous, whatever the reason.1578

    This has a huge detriment to the scientific community.1581

    Not only does it make people in the scientific community and outside the scientific community distrust the overall scientific community.1586

    But it can actually hurt the current focus of research because if someone comes out and says that1598

    this is an answer to a question that everyone has been looking for, and they falsified all your data,1612

    you do not have a lot of people able to back up their results but maybe just believe it.1621

    Then, you take that for granted that that is the correct answer.1628

    It can set you back 50 years.1633

    It can end up causing you to go down the rabbit hole.1635

    This is a huge deal that everyone needs to have high morals, when creating their research.1639

    They need to give their data, not falsified data.1647

    Do not cherry pick your results, you give all your results not just the ones that make your story look good.1652

    If you do the experiment 10 times and 9 out of 10 times it fails, but one fails does not gives you an answer you do not want.1661

    But the one time, it gives you the answer that you do want, that is the only piece of data that you share with the public, that is a problem.1670

    That is a big ethical problem.1677

    Let us talk about research ethics in general.1684

    Research ethics involves the application of fundamental ethical research principles to variety of topics involving research.1687

    Examples will include the design and implementation of research, involving both animal and human experimentation.1700

    As well as scientific misconduct, like the falsifying data falls under that.1706

    The declaration of Helsinki which is set forth in 1964 is a set of ethical principles,1713

    regarding human experimentation developed for the medical community by the WMA, the World Medical Association.1724

    This is the first fairly complete document that most countries adopted.1731

    The basic principles of this declaration of Helsinki was that, of utmost importance is the respect for the patient.1739

    Their right to self determination and their right to make an informed decision which we hear very often,1749

    informed consent, we hear that in hospitals a lot in the US.1756

    It is important that they know what they are getting themselves into in a certain research, trial, let us say.1763

    What is important is at the researchers duty is solely to the patient or volunteer,1772

    meaning they care most importantly about the patient, overall, even over the research.1778

    As hard as that is to think about, as a researcher, the patient is the most important part.1788

    Patient welfare takes precedence over both scientific and societal interests.1796

    Ethical considerations will take precedence over laws and regulations.1804

    Very importantly, same thing that we see in the hospital system as well.1810

    If a research participant is incompetent, physically and mentally incapable of giving a consent or is a minor,1816

    then you need to get surrogate consent from somebody else.1823

    The last few slides, I just want to talk about what is right vs. wrong.1833

    When we talk about ethics, you talk about right vs. wrong.1841

    The ultimate debate, ethics is the ultimate debate of right vs. wrong.1846

    There is no correct answer, there are maybe one that you favor but there is no truly correct answer, when we are talking about this.1852

    The question is going to be asked forever.1862

    Much of modern biotech has a markedly lifespan and health span focused approach.1864

    Lifespan, making people live from saying not just 80 years old to 100 years old.1871

    Health span is actually being healthy until you are 80 instead of 70, something like that.1878

    A lot of that is a morally, good morally, just goal.1888

    There are still lingering fears that exists that scientists have too much control over human evolution and destiny.1894

    Because the better we get with technology and biotechnology specifically,1902

    the more control we have over the human body, the animals, plants, and bacteria around us.1906

    It is that fear of we are becoming a godlike figure, we can affect destiny.1917

    In additional laws and regulations, both public and political opinions1928

    can affect the current and future state of research and development.1933

    This is something that we are forever going to have to work with, that is not going away.1936

    Scientists cannot just stay in a hole and do their research, without worrying or taking into consideration1945

    what politicians and the public have to say about it, for better or worse.1953

    Let us talk about a specific aspect.1963

    We will bring up Dolly the sheep, if any of us remember that.1966

    This happened in 1996 in Scotland.1969

    Dolly was the first animal to be cloned from an adult’s somatic cell, using the process of nuclear transfer.1972

    What that was is, the nucleus from an adult cell is transferred into an unfertilized, enucleated, without a nucleus zygote, which is an egg cell.1980

    You have an egg cell, you take out the nucleus.1995

    You take the nucleus from an adult cell, from a different animal.1998

    Take the nucleus out, put it into the egg.2004

    Zygote enucleated, adult cell with the nucleus.2015

    Take that out, put it into here, and then try to grow an organism.2020

    They actually did this with the sheep.2028

    That sheep lasted about 6 years, before passing away.2031

    This brought up a lot of questions and will continue to bring up a lot of questions.2037

    The fact of, is science unstoppable or can we actually limit how far we go, based on rational ethical thinking?2041

    Just because certain science is possible, does not mean that it will actually come to fruition,2054

    if we as scientists or researchers think rationally and ethically.2060

    But the public always fears that science and scientist would not.2066

    It will always be, we want to do this just because we can do it not because we think it is going to be beneficial.2072

    That is why this is kind of, just because we can, should we, type of the question.2080

    What is going to happen is that, it may fall upon the scientific community to start the ethical discussion within itself.2088

    As human biotech research progresses, as it is doing right now,2097

    ethical debates will continue to heat up and will continue to be extremely hot.2101

    Not only actions but also the intentions of the scientific community require rational reasoning and justification.2108

    An example here for ethics is the whole genome sequencing.2120

    Pretty expensive in general but it is becoming cheaper and cheaper.2126

    We have that $1000 genome insight, meaning, I might, in the near future be able to send in a sample of my DNA2130

    and for only $1000 get my entire genetic profile, which would be amazing.2138

    But whole genome sequencing differs from current prenatal genetic testing.2147

    First of all, current tests identify only serious genetic conditions in fetuses, at about moderate to high risk.2153

    Whereas prenatal whole genome sequencing could allow for the entire genetic profile.2165

    This could lead to the possibility of wanting to make that build-a-bear type kid.2173

    I can see that my kid will have brown eyes.2185

    Maybe we can use some gene therapy and give him or her, blue eyes.2188

    Or maybe, my child is going to be a boy, is it early enough to where I can change it to be a girl?2193

    Or my child will have autism or another type of disease that is not considered seriously fatal, that is not currently being tested.2201

    I think we only test for somewhere, I could be wrong, I think around 13 to 15 different genetic conditions.2221

    But this can lead to a situation where me and my child will have chondroplasia, might be a little person.2229

    Any of these things that are not perfectly in line with what the parents wanted,2240

    they can either fix that to their liking or decide to not proceed with the pregnancy.2248

    A lot of these ethical issues will come up.2256

    Also, this whole genome sequencing, as I said before, you can get your whole genome profile2259

    but maybe the insurance companies, the health Insurance companies get a hold for that.2265

    They would be able to possibly then decline you, based on your risk of a certain disease, big ethics problem.2269

    On the good side, golden rice, a genetically modified organism.2283

    This is a rice strain that was modified to contain β carotene.2288

    β carotene is a precursor of vitamin A.2293

    A single serving of this golden rice supplies 60% of the recommended dietary allowance of vitamin A.2297

    This is important because according to the World Health Organization,2308

    more than 215,000,000 preschool age children are vitamin A deficient.2313

    Over 2 million deaths in more than 500,000 cases of blindness are due to vitamin A deficiency worldwide.2321

    Just the introduction of this strain of rice can help decrease this.2332

    In fact, there have been estimates that over a million people have been saved from dying,2340

    in the several years that the golden rice has been on the market.2351

    It will just continue to rise, as year by year goes by.2359

    This is a good aspect, however, still going to be ethical debates.2364

    There is always going to be people who are for or against genetically modified organisms.2367

    I had just last two slides and I want to leave you with some questions to ponder.2377

    When thinking about research, any specific research, you want to know what is the societal impact?2383

    Are any human rights being violated?2391

    That is a big one.2393

    Do the benefits outweigh the risks?2396

    Do any means justify a good end?2400

    The means justify the end, right?2406

    Or sorry, does the end justify the means?2408

    But does any means, how you get to that result, is that okay?2410

    Does biotech ultimately advance or impede the common good of humanity, and the world as a whole?2416

    This is probably the toughest one to think about, is there anything that we have not thought about yet?2426

    That is a tough one to think about because you think about everything, and then there is always something later.2432

    This one you really have to prepare, prepare and think.2439

    How do you answer questions on ethical debates?2454

    The biggest thing that I can tell you is doing your own research, do your own literature research.2461

    You should be the expert on all the experiments that have been done before, both for and against.2471

    You want to know both sides of the argument, why it is an ethical debate, why it is bad.2482

    You need to do your literature research, that is a huge thing.2494

    You need to understand the science and you need to understand the ethical ramifications from this.2497

    This is extremely difficult, even for people in the scientific community, literature and analysis is a tough job.2504

    It is tough to do, you get better every time you do it but is really tough.2517

    It is a tough skill to master.2524

    For those of you outside of the scientific community, it is even harder because2527

    they are not strong in the subjects of biology, of genetics, of biotechnology.2532

    They do not understand it, they might not understand why you would use a certain experiment2538

    or why you might have to use animal experimentation.2544

    A lot of the disagreements come from the fact that many people are uninformed or many people do not understand the science.2550

    The media, the scientists are not usually the ones who is talking straight to the public,2561

    the media are the ones talking to the public and the politicians.2566

    The media, as much as we want them to know everything,2570

    they cannot be expected to understand published scientific data on their own.2578

    That is going to land on the scientific community.2584

    We need to educate the general public and especially those in the media who cover scientific topics.2589

    It falls on our shoulders, we need to educate the media, we need to educate the public2597

    so we can bring them up onto the knowledge level to understand much easier.2602

    But once we educate the public, especially once we educate the media,2610

    the media is responsible for taking it upon themselves, taking it upon themselves to gauge their level of understanding,2616

    before writing articles that will reach the masses and possibly promote fear mongering.2631

    The media needs to understand the science, before writing an article that could cause a huge problem in the nonscientific community.2640

    We, as scientists, can only do our best to educate the community, to educate the media.2656

    The media has to take it upon themselves that if they do not really understand what is going on,2662

    they need to reach out and do their own homework and get in touch with the scientists to prepare themselves.2668

    That is the end of the lecture, the end of the course.2676

    I wanted to say from myself, thank you so much for joining the course.2680

    I really hope you enjoyed it, and from www.educator.com, we appreciate you seeing this course.2685

    Please check out some other courses, there are plenty, from high school through the college level.2692

    From me, and www.educator.com, thanks for joining and we hope to see you again.2700

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