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Lecture Comments (12)

1 answer

Last reply by: Professor Michael Philips
Mon Apr 27, 2020 2:26 PM

Post by Monicasong on April 26, 2020

What does covalent bonds mean, professor, I can't figure out its meaning.

By the way, I like your lessons, they're quite interesting.

0 answers

Post by Mei Gill on July 6, 2018

what types of things we mainly need to know about chemical bonds?

1 answer

Last reply by: Professor Michael Philips
Wed Feb 8, 2017 3:14 PM

Post by Firebird wang on November 2, 2016

Professor, I know that AP Statistics is not your subject, but I just wonder if you are able to watch the two videos which called "Practice Test 2013 AP Statistics" and "Practice Test 2014 AP Statistics" in the AP Statistics content? Both videos showing network error, I dont know why. I already tried in different computers already.

1 answer

Last reply by: Professor Michael Philips
Tue Dec 29, 2015 1:39 PM

Post by Christoph Bader on December 16, 2015

Isn't CH4 non-polar? That is the electronegativity difference is negligible.

2 answers

Last reply by: Professor Michael Philips
Tue Dec 8, 2015 10:28 AM

Post by Professor Michael Philips on December 1, 2015

Hi Apolonia,

First of all, it is great to hear how passionate you are about science!  As for your intended undergraduate major, biochemistry, microbiology molecular biology, genetics, or immunology would all give you a great foundation of knowledge that could help you succeed.  If you truly want to do research, you would likely enter a graduate program, at which point you would then choose a more narrow focus (such as virology, genetics, etc.).  Hope that helps.  Best of luck!

1 answer

Last reply by: Professor Michael Philips
Tue Dec 1, 2015 11:25 PM

Post by Apolonia Gardner on November 24, 2015

Hello,

I am a high school senior about to send off my applications for college. I am stuck on one thing – my intended major. Biology and chemistry have been my favorite courses throughout high school, and I would like to get a college degree that will enable me to perform research with viruses. My lifetime goal is to find a cure for a disease. From your experience, what undergraduate major should I shoot for? Biochemistry? Microbiology? Molecular Biology? Immunology? Chemical Biology? Organic Chemistry? Pharmaceutical Science? Any guidance is appreciated.

Biochemistry Review: Importance of Chemical Bonds

    Medium, 4 examples, 5 practice questions

  • Chemical bonds are forces that hold atoms together.
  • Covalent bonds are very strong, and may be either polar or non-polar.
  • Water is an important part of almost all biochemical reactions.
  • Biochemical reactions flow based on the direction and magnitude of free energy.
  • ssDNA absorbs more UV light than an equal amount of dsDNA.

Biochemistry Review: Importance of Chemical Bonds

Which of the following is an example of a covalent bond?
  • Hydrogen bond
  • Ionic bond
  • van der Waals forces
  • Electric dipole
Q. Which of the following is an example of a covalent bond?

*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.

  • Hydrogen bond
  • Ionic bond
  • van der Waals forces
  • Electric dipole

Answer

Wrong answer!
Correct answer!

Biochemistry Review: Importance of Chemical Bonds

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.

Transcription: Biochemistry Review: Importance of Chemical Bonds

Michael Philips

Michael Philips

Biochemistry Review: Importance of Chemical Bonds

Slide Duration:

Table of Contents

Section 1: 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
1:00:21
How DNA Was Made Denser
1:00:52
Discovery of RNA
1:03:32
Ribosomal RNA
1:03:48
Transfer RNA
1:04:00
Messenger RNA
1:04:30
The Central Dogma of Molecular Biology
1:04:49
DNA and Replication
1:05:08
DNA and Transcription = RNA
1:05:26
RNA and Translation = Protein
1:05:41
Reverse Transcription
1:06:08
Cracking the Genetic Code
1:06:58
What is the Genetic Code?
1:07:04
Nirenberg Discovered the First DNA Triplet That Would Make an Amino Acid
1:07:16
Code Finished in 1966 and There Are 64 Possibilities or Triplet Repeats/ Codons
1:07:54
Degeneracy of the Code
1:08:53
Section 2: 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
Section 3: 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
1:00:37
Recombinational Repair
1:00:54
Caused By Ionizing Radiation
1:00:59
Repaired By Three Mechanisms
1:01:16
Form Rarely But Catastrophic If Not Repaired
1:01:42
Non-homologous End Joining Does Not Require Homology To Repair the DSB
1:03:42
Alternative End Joining
1:05:07
Homologous Recombination
1:07:41
Example 5
1:09:37
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
1:00:23
RecA Promotes Strand Invasion - Homologous Duplex
1:00:36
Holliday Junction
1:00:50
Comparison of Prokaryotic and Eukaryotic Recombination
1:01:49
Site-Specific Recombination
1:02:41
Conservative Site-Specific Recombination
1:03:10
Transposition
1:03:46
Transposons
1:04:12
Transposases Cleave Both Ends of the Transposon in Original Site and Catalyze Integration Into a Random Target Site
1:04:21
Cut and Paste
1:04:37
Copy and Paste
1:05:36
More Than 40% of Entire Human Genome is Composed of Repeated Sequences
1:06:15
Example 5
1:07:14
Section 4: 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
1:00:06
Regulatory Gene Expression Process
1:00:27
Example
1:00:42
Example 7
1:02:53
Example 8
1:09:36
RNA Editing
1:11:06
Guide RNAs
1:11:25
Deamination
1:11:52
Example 9
1:13:50
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
1:01:15
Consequences of Altering the Genetic Code
1:02:40
Silent Mutations
1:03:37
Missense Mutations
1:04:24
Nonsense Mutations
1:05:28
Genetic Code
1:06:40
Consequences of Altering the Genetic Code
1:07:43
Frameshift Mutations
1:07:55
Sequence Example
1:08:07
Section 5: 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
1:00:05
Chromatin Remodeling
1:01:48
Example 8
1:02:36
Transcriptionally Repressed State
1:02:45
Acetylation of Histones
1:02:54
Polycomb Repressors
1:03:19
PRC2 Protein Complex
1:03:38
PRC1 Protein Complex
1:04:02
MLL Protein Complex
1:04:09
Section 6: 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
1:00:38
Genomes is Sequenced with 5-10x Coverage
1:00:39
Compare Genomes
1:01:47
Entered Into Database and the Rest is Computational
1:02:02
Overlapping Sequences are Ordered Into Contiguous Sequences
1:02:17
Example 6
1:03:25
Example 7
1:05:27
Section 7: 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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