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Michael Philips

Michael Philips

Structure of Nucleic Acids

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
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
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
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
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
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
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
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
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
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
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 (4)

0 answers

Post by Paul Mcinulty on August 7, 2017

Noticed on the stem of the diagram, on the right hand side you CUU but on the other side the complimentary bases are GGA, shouldn't it be GAA?

0 answers

Post by Paul Mcinulty on August 7, 2017

The Codon - anticodon - codon clears up this problem, would you not agree?

0 answers

Post by Paul Mcinulty on August 7, 2017

Dear doctor Philips
When showing the diagram of the tRNA molecule the anticodon is GAA that would code for a GLU L Alpha Amino Acid,
However, the codon on the MRNA strand is CUU, that would code for a LEU L Alpha Amino Acid.
But on the diagram it shows a CUU codon in the acceptor stem, thst would code for a LEU L Alpha Amino acid
This important information is never emphasised in molecular cell biology text books, and again you have glossed over this fact
Don't you think it would be better to describe the TRNA molecule and MRNA strand as, for example

CUU
GAA
CUU ?
Codon
Anticodon
Codon?
Because the text books when you study this section it does not make any sense at all
The so called anticodon codes for a completely different Lamino acid from the codon
But if you go codon - anticodon - codon you would code for, for example LEU
Am I correct or am I incorrect ?
Please explain
This does not detract from the fact that your lectures have clarified so much already
And thank you so much

0 answers

Post by peter alabi on March 17, 2017

Hi, Dr. Philip. I just have to mention what a great lecturer you are, so great, you're fantastic. I also have a question... is there any significant differences between Archaean and Bacteria genome, perhaps in term of composition, organization, or topology?  Thanks for great lectures.

Structure of Nucleic Acids

    Medium, 4 examples, 5 practice questions

  • Nucleic acids are macromolecules made up of nucleotides connected by phosphodiester bonds.
  • Hydrogen bonding and hydrophobic interactions (base-stacking) hold the
    two strands of DNA together.
  • DNA is most often found as a double helix and located in the nucleus.
  • RNA is most often found as a single stranded helix and located in both the nucleus and cytoplasm.
  • RNA can be found in multiple formations with differing functions (mRNA, tRNA, and rRNA).

Structure of Nucleic Acids

Which of the following is NOT an example of a nucleic acid?
  • DNA
  • RNA
  • mRNA
  • Uracil
Nucleotides are composed of all of the following EXCEPT:
  • Hexose
  • Pentose
  • Heterocyclic nitrogen base
  • Phosphate group
Type I topoisomerases nick how many DNA strands of the helix?
  • Zero
  • One
  • Two
  • Three
The most common type of RNA in the cell is _____.
  • DNA
  • mRNA
  • tRNA
  • rRNA
RNA molecules with enzymatic activity are called:
  • Proteins
  • Telomerase
  • Ribozymes
  • Ribosomes

*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

Structure of Nucleic Acids

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 0:06
  • Nucleic Acids 0:26
    • Biopolymers Essential for All Known Forms of Life That Are Composed of Nucleotides
    • Nucleotides Are Composed of These
    • Nucleic Acids Are Bound Inside Cells
  • Nitrogen Bases 2:49
    • Purines
    • Adenine
    • Guanine
    • Pyrimidines
    • Cytosine
    • Thymine
    • Uracil
  • Pentoses 6:23
    • Ribose
    • 2' Deoxyribose
  • Nucleotides 8:43
    • Nucleoside
    • Nucleotide
  • Example 1 10:23
  • Polynucleotide Chains 12:18
    • What RNA and DNA Are Composed of
    • Hydrogen Bonding in DNA Structure
    • Ribose and 2! Deoxyribose
  • DNA Grooves 14:28
    • Major Groove
    • Minor Groove
  • Example 2 15:20
  • Properties of DNA 24:15
    • Antiparallel Orientation
    • Phosphodiester Linkage
    • Phosphate and Hydroxyl Group
    • Purine Bases Always Pairs Pyramidine Bases
    • A, B, Z Forms
    • Major and Minor Grooves
    • Hydrogen Bonding and Hydrophobic Interactions Hold Strands Together
  • DNA Topology - Linking Number 27:14
    • Linking Number
    • Twist
    • Writhe
  • DNA Topology - Supercoiling 31:50
  • Example 3 33:16

Transcription: Structure of Nucleic Acids

Welcome back to www.educator.com, today we are going to talk about the structure of nucleic acids.0000

As an overview of what we are going to talk about today, we are going to talk about nucleic acids.0008

We will talk about what they are actually composed of, the nitrogenous bases, the pentoses,0013

how they are made up of nucleotides.0019

We will talk individually about DNA and then RNA.0022

Nucleic acids are biopolymers, meaning they are on made up of monomers, multiple units making a polymer.0028

They are biological molecules.0037

These biopolymers are essential for all known forms of life.0039

DNA and RNA are composed of nucleotides.0044

Those are the monomer unit.0047

We have deoxyribonucleic acid and this would be DNA.0050

Then we have ribonucleic acid and that is RNA.0067

Nucleotides are composed of heterocyclic nitrogen bases.0077

As we are going to see later, those are A’s, T’s, G’s, C’s.0081

We are going to talk about RNA, they will also have a U.0089

Nucleotides also have pentoses, those are the ribose or deoxyribose.0096

As we can see the ribose would be for ribonucleic acid, RNA.0100

The deoxyribose is for deoxyribonucleic acid, DNA.0108

Finally, nucleotides have phosphate groups.0114

They have 1, 2, or 3 phosphate groups.0117

Remember, we have PO4 3-.0126

Nucleic acids are found inside cells.0133

If we see a eukaryotic cell right here, what we can zoom in on is the nucleus.0137

The nucleus is what houses our chromosomes.0147

Remember, our chromosomes are made up of DNA.0152

DNA is a nucleic acid.0158

Inside the nucleus, we can also find RNA.0161

As well as in the cytoplasm, we are going to find RNA as well.0165

The nitrogenous bases that we talked about, remember, I said A, G, T, and C.0172

Those can be split into two different categories.0177

We have our purines, those are our double ring, heterocyclic nitrogen structures.0181

We have adenine, adenine is our A.0189

We have guanine, our G.0199

Adenine and guanine are both going to be able to be found in DNA and they both be found in RNA.0204

They are only different, as we will see later is that, if they are in DNA, they will be attached to a deoxyribose.0221

If they are in RNA, they will be attached to a ribose.0229

Our pyrimidines are our single ring heterocyclic nitrogen structures.0236

Our heterocyclic nitrogen, that just means we have a ring structure,0241

a cyclic structure that has nitrogen to the ring, instead of all carbons.0248

That is why it is hetero, because we have nitrogen and carbon.0253

It is cyclic, we have the conjugated bonds around and it is the nitrogen we are talking about.0257

We have cytosine, it is one of our pyrimidines and that is going to be found in DNA.0264

We have thymine, another one of our pyrimidines, that is also going to be found in DNA.0273

We have uracil, it is not normally found in DNA.0281

Uracil is found in RNA.0286

Also found in RNA is cytosine.0292

What we actually have here is a switch of thymine for uracil, when we are going between DNA and RNA.0297

A good way to remember our pyrimidines, you can remember however it is useful for you.0309

What I always think of, when we have cytosine and thymine, they have a Y and so does pyrimidines.0315

If you want to think of all of them together, if you use the one letter abbreviation CU and T,0322

you could say CUT the PY, for pyrimidine.0329

CUT the PY, those are our 3 pyrimidines.0336

Then, if you know you are through pyrimidines, it is very easy to remember your two purines, your adenine and guanine.0340

As a review, what to remember, that our adenine and guanine,0348

both are going to be found in DNA and both are going to be found in RNA as well.0358

The nucleotides that we can find in DNA are A, G, T, and C.0370

The nucleotides that we will find in RNA are A, G, C, and U.0375

The other things that make up our nucleotides are our pentoses.0385

A pentose, all that is, that means 5 and the ose means a sugar.0391

It is a 5 carbon sugar.0399

Ribose occurs in RNA only, and this is ribose.0404

Deoxyribose occurs in DNA only, this is deoxyribose.0420

To be specific, it is a 2 prime deoxyribose.0429

How we can tell that this is the deoxyribose, without going into too much organic chemistry?0434

If we see right here, this is our anomeric carbon, it is the carbon bond in between two different oxygen.0445

Here is one oxygen, here is one oxygen, that is the carbon.0451

This is carbon 1, following all the way along to have the longest carbon chain, this would be carbon 2.0454

It is called the 2 prime carbon because when attached to a nitrogenous base, we count those carbons first.0468

Those would be the 1, 2, 3, 4, and so on.0477

Then, we count our sugar carbons with the prime notation.0480

This is the 2 prime carbon.0486

As we can see here, on the ribose off of the 2 prime carbon, we have an OH.0489

Off of the 2 prime carbon of the deoxyribose, all it is an H.0496

It is not shown here but I will write it in.0503

Let us write a little clearer, that is an H.0506

This is lacking in oxygen, therefore, deoxy.0513

It is a 2 prime deoxy and the whole molecule is called ribose, a 2 prime deoxyribose.0516

Important to know, is the proper terminology.0527

The difference between nucleoside and a nucleotide...0532

A nucleoside is a nitrogenous base and a pentose.0536

For example, we have ribose and guanine attached together, that is a nucleoside.0544

A nucleotide is when you have a nucleoside, therefore, a ribose and guanine, as well as a phosphate group.0556

When we say phosphate group, this is going to be either 1, 2, or 3 of them.0574

Let us say for example, one phosphate.0579

This right here will be called a nucleotide.0587

This would be called our monomeric unit that will be then added into, in this case, RNA.0590

We add the triphosphate form, if this were a 3.0602

We would add the triphosphate form into rRNA.0611

Inside the RNA, it would actually be in the monophosphate form.0614

We will talk a little more about that, as we get there.0620

For our first example, let us recognize these.0625

What bond here do we see?0630

We see adenine, right here.0633

What is adenine?0635

Adenine, if we remember back, is a nitrogenous base.0638

There is our natural base.0641

Adenosine, what do we see here.0649

Adenosine, we see that we have a sugar, a pentose, that pentose is a ribose.0654

Then, we see our adenine.0663

We have a pentose and a nitrogenous base.0669

This is considered a nucleoside.0674

Over here on the right, we have adenosine triphosphate.0687

What we can see is we have the pentose, once again, it is a ribose.0692

We then see we have the nitrogenous base, adenine.0700

Finally, we have 3 phosphate groups.0707

Therefore, this is considered a nucleotide, with a T.0712

This is how we point out the difference between a nucleoside and a nucleotide.0726

When we are going to talk about DNA and RNA, we talk about them normally in their full length chains.0740

Remember, the nucleotides make up the monomers that become the polymer of poly-ribonucleic acid ,or poly-deoxy-ribonucleic acid.0747

What these will look like, once again, we have our RNA being composed of cytosine, guanine, adenine, and uracil.0757

We have our DNA being composed of cytosine, guanine, adenine, and thymine.0771

What we see here is that most commonly, we find DNA in a double helical structure.0781

We find RNA in a single helical structure.0788

We still have the bonds between nucleotides which are phosphodiester bonds,0795

starting out between nucleotides of the same chain.0804

These are phosphodiester bonds, these are found in both DNA and RNA.0807

That is the linkage of the 5 prime phosphate.0813

The 3 prime hydroxyl will come into 5 prime phosphate.0819

In DNA, we can see that we have hydrogen bonding between base pairs.0825

Remember, the hydrogen bonding in the base stacking interactions which are a type of hydrophobic interaction,0832

are what stabilize DNA and keep it together as the double helical chain.0839

Remember, in RNA, we have ribose.0848

In DNA, we have 2prime deoxyribose.0856

Let us focus a little bit on DNA right now, and then, we will move on to a little bit of RNA specific.0871

When we talk about DNA, we have to talk about its grooves.0877

DNA has both a major groove and a minor groove.0881

The major groove is the wider of the two.0886

It is 22 angstroms wide, which is 2.2 nm.0890

In the major groove, all 4 chemical groups are visible.0895

In a minor groove which is much smaller, it is only about half the width and it is 12 angstroms or 1.2 nm wide.0901

We can only see 3 chemical groups in those grooves.0910

What does that mean, what do I mean by that?0916

To go into the next slide, I can tell you in this example.0919

In our grooves, let us say for example that this is a GC base pair, we have our 3 hydrogen bonds.0925

AT base pair on here, we have our 2 hydrogen bonds.0934

If we have our GC base pair, and we say that this is the major groove up here and the minor groove is down here.0938

I will do the minor groove in red.0950

I will do the same thing down here.0956

The minor groove is down here, the major is up here.0958

What do we mean by we can see 4 chemical groups in the major groove and only 3 in the minor.0970

Let us look at the major groove, first of all, we are looking at 4 different things.0975

First, we are looking for what are called acceptors and that is a hydrogen bond acceptor.0982

Then we have donors, and that is an H bond donor, hydrogen bond donor.1001

We then have methyl groups which is just simply a methyl group, that is a CH₃.1014

Finally, we have just hydrogen which is a non-polar hydrogen.1027

Where can we find these?1042

On a GC base pair in the major groove, we can find an acceptor which is this nitrogen.1044

This is a hydrogen bond acceptor.1056

We have another acceptor, this oxygen is making this hydrogen bond right here.1059

This hydrogen bond being made right here.1070

We have a hydrogen bond donor, which we have right there.1076

Finally, the 4th one that we can see, it is actually not written on here but I will write it for us,1084

is we have a hydrogen coming off of this carbon and that is the non-polar hydrogen.1089

We can see 4 different groups there.1110

In a minor groove, all we are able to see is 3.1112

And that is, right here, we have the acceptor, we have the hydrogen donor.1117

Then, we have the hydrogen acceptor which is this oxygen.1131

We can see that is that right there.1136

If we write this out, this is A, A, D, H and this is A, D, A.1143

In the major groove, we have a reading of acceptor, acceptor, donor, hydrogen.1171

In the minor groove, we have acceptor, donor, acceptor.1184

We can show the same thing in our AT bond.1189

Our adenine, we have an acceptor, we have a hydrogen donor coming right here.1194

We then have another hydrogen bond acceptor.1210

We can see it is already making that hydrogen bond.1217

And then, we have a methyl group.1221

Sorry, this should be an A.1236

In the minor groove, we can see the acceptor is the nitrogen.1247

We have the oxygen over here being another acceptor.1256

And then, we have the non-polar hydrogen that are not seen but it is coming off of this carbon.1262

In the major groove of an AT base pair, we can see A, D, A, N.1283

In the minor groove, we see A, H, A.1288

What is important, as I have said here, you can see in the major groove, we can see 4 different chemical groups.1293

In the minor groove, you will see 3.1301

What is important is that, in the major groove, let us draw this out.1303

In the major groove, we can see A, D, A, N, this one is in AT base pair.1309

We can see A, A, D, H, remember, acceptor, acceptor, donor, hydrogen, that is a GC base pair.1328

You are seeing both of this right here.1341

ADAN, AT, AADH, GC.1343

We can also see the reverse of that.1347

We can see a NADA, that is the reverse of this one.1349

That is going to be a TA base pair.1357

And then, we can see HDAA, the reverse of the GC base pair, therefore being a CG base pair.1360

In the minor groove, since we have less information, if we see as we have seen here, let us go this one.1373

In ADA, we know that ADA right here is a GC base pair.1384

We know that AHA down here is an AT base pair.1397

But if we look, since these are reciprocal, this ADA can also be a CG base pair.1410

This AT could be a TA base pair.1421

It is important for proteins recognizing what specific strand of DNA they want to be a part of.1427

In the minor groove, you cannot tell if it is a GC base pair or a CG base pair, or vice versa, an AT versus a TA.1434

It is important we get a lot more information from major groove and a little bit less from the minor groove,1442

that can affect the specificity of interaction between DNA binding proteins.1446

Let us move on to see more properties of DNA.1457

As this is a review from our first unit, we should know that DNA is in anti-parallel orientation,1460

meaning we have one strand going 5 prime to 3 prime, with the other strand going the opposite, 3 prime to 5 prime.1469

5 prime to 3 prime going down in this direction.1480

5 prime to 3 prime going up in the other direction.1483

It will base pair and have complimentarily.1486

There are phosphodiester linkages holding the nucleotides together on the same strand.1490

We have it right here, a phosphodiester linkages on both strands.1496

We see that the 5 prime end will have a phosphate group.1505

The 3 prime end will have a free hydroxyl group on the 3 prime, the 3rd carbon of the pentose.1516

We know very well by this point that purine base always pair with pyrimidines.1529

A’s pair with G’s, C’s pair with T’s.1536

If we are talking about RNA, we do not have a thymine.1542

In that case, adenine will pair with two hydrogen bonds to a uracil.1546

Generally, DNA is found in 3 different confirmations but the most common form is the B form.1557

The B form DNA is the one that we see in the middle.1564

B form DNA has about 10.4 base pairs per turn of the helix.1571

For simplicity sake, we often say 10 base pairs per turn.1577

As I stated in the previous couple of slides, there is a major and minor groove, as we can see.1581

As I mention one more time, hydrogen bonding between the bases ,1592

as well as base stacking interactions stabilize this interaction to keep the two strands together.1597

As we see here, we have the major groove and the minor groove.1606

We say here this would be the major groove and this would be the minor groove.1612

This is major.1627

If we are going to talk about DNA, we need to be able to talk about its topography.1638

When we talk about DNA topology, one thing that comes up is the linking number of DNA.1645

The linking number is the number of times one strand has to be passed through the other,1652

to completely separate the two strands.1660

It can be easier to find with the equation, linking number equals twist + writhe.1663

To understand that, we need to know what twist and writhe are.1672

Twist is the number of helical turns of one strand around another.1675

For example, in this up here, in this first thing on the left, the twist is 0 because1684

these two strands are not wound around each other at all.1694

If we look down here, the twist is 1 because now it is been wound around 1 time.1698

Strand A has been wound around strand B a single time.1704

Writhe is how we calculate or how we take into account super helical turns, what are called supercoils.1711

Writhe is the total number of nodes per molecule.1721

Writhe can be broken down into two separate parts.1727

We have plectonemic writhe and we have toroid writhe.1730

Plectonemic means it is just twisted around itself.1735

Toroid is when it is twisted cylindrically.1742

This is usually when the DNA is twisted around something like a protein.1745

Specifically, like something we will talk about in one of the next unit which is called a histone.1751

Let us look at this page.1759

I have already told you up here, the linking number we do not know yet.1761

But we do now right here in this first example, twist is a twist of 0 and a writhe of 0 right here, in both of these.1767

There is a linking number of however many bases it is.1785

Let us say for example, there are 360 bases in this.1788

360 base pairs in this piece of DNA.1795

For simplicity's sake, we will say that there are 10 base pairs per turn, from the previous slide.1799

Our linking number is going to be equal to 360/10 which is 36.1809

Remember, our linking number is equal to our twist + our writhe.1819

Linking number is 36, since twist and writhe do not come into play here.1826

At this point, we add 1 twist, and it is a negative twist.1834

In this case, our twist is equal to 1.1840

Our linking number, if it is equal to twist + writhe, our linking number has to decrease.1843

Our linking number is now going to be 35 because our twist is -1 and our writhe is 01853

In this case, what it would be, our linking number will be -1.1871

I will show you an example on the next slide, which will make this a lot easier.1876

As of right here, we have our single node.1880

This single node is our writhe, that is where a writhe comes into play.1889

In this case, it is a negative writhe.1895

The left side of the screen and the right side is just whether we are looking at positive twist and1897

writhe which is on the right side, or negative twist and writhe which is on the left side.1903

If we move on to the next slide, we can look at some of those extra writhe and twist.1911

Once again right here, twist is equal to 0, writhe is equal to 0.1916

If we twist this one time, we cross the strands over each other, we now have a twist.1925

Once again, right side is positive, left side is negative, in a way that this is shown.1933

Your red everything will be positive, your blue everything is going to be negative.1940

We see our super helical turn, which is once again just a supercoil.1944

This node that gives us a writhe, same thing would happen over here.1953

One more down, we can see we have a writhe of 2, 2 nodes.1961

1, 2, that is where we have a writhe.1969

Most organisms have negatively supercoil of DNA.1975

This is a way to store some energy, as well as relaxing the DNA.1980

Let us go over one example problem to try to clear this up.1985

It is a fairly simple concept but it is a little bit challenging to really understand it, at the same time.1989

If we have a linking number practice problem, let us say, if I tell you that the molecule has base pairs 360.1998

Then, if we assumed we have 10 base pair per turn then that makes our leaking number 36.2018

If this is an example of completely relaxed B form DNA, the linking number will be 36 and we would not have any writhe.2034

If linking number equals twist + writhe, we know our writhe is going to be equal to 0 and2043

our linking number is equal to 36, then our twist must be 36, since writhe is 0.2055

That is because we have turning of the strand around itself.2064

What this might look like is, I will just show you in two different colors.2069

The DNA molecules are turned around each other.2083

If I tell you that as long as we do not remove any DNA sequence, the linking number has to change.2087

If we are going to add supercoils or take out supercoils, whether it is positive or negative.2101

As long as we are not adjusting the number of base pairs, we are not taking out or adding in DNA,2105

if we add in or subtract writhe, then supercoils, we need to adjust the linking number.2111

For example, if our base pairs have not changed, they are 360.2123

Let us say in this molecule now, we have 1, 2, 3.2130

In this case, what do we see?2147

Once again, this would be a double strand of molecule.2150

We still have the proper twist.2158

If we have this molecule, what is our writhe?2166

Let us look at it, we see 1 node, 2 nodes, 3 nodes, and 4 nodes.2172

Let us write in our writhe.2183

Our writhe is going to be, in this case, we are going to call it a -4.2186

This is unwound, this is under wound.2192

If our writhe is -4 and our twist has not changed, that is still a 36, our linking number must change.2195

Remember, linking number equals twist + writhe.2207

If linking number is equal to 36 + -4, our linking number is equal to 32.2212

This is an example of how you might solve a linking number problem.2227

It is important to now, I know it is kind of hard to see on paper, but negative supercoiling,2231

negative writhe, refers to having to turn the helix to the right to remove nodes.2240

Negative supercoiling refers to having to turn the helix to the right to remove the nodes.2251

Therefore, positive supercoiling will mean you would need to turn it to the left.2286

In this case, we have a writhe of -4, meaning if you want to remove that writhe,2291

you need to turn the helix to the right 4 different times to remove those nodes.2298

As we can see, our DNA can supercoil.2308

What can be problematic with that is that DNA is not particularly flexible.2313

It can be flexible at points at times, but if you over coil things,2322

they will eventually have so much tensional stress that they break.2328

We need to have enzymes that can take care of this and relieve this tension.2334

We have what are called type 1 and type 2 topoisomerases.2340

Each one of these helps relieve torsional stress.2345

Type 1 topoisomerases, unwound DNA by making a nick in just a single strand.2350

This nick in just a single strand create a pivot point in that DNA backbone.2365

It helps swivel around, if we try to draw it out.2369

If the nick is right there, we can swivel this 360°.2383

That can help remove any torsional stress, we can go either way.2393

Action of topoisomerases 1 does not require ATP and it will change the linking number in steps of 1.2400

We have type 2 topoisomerases, they cut both strands at the same time which requires ATP energy2411

and will change the linking number in steps of 2.2421

How type 2 topoisomerases act, they separate two helixes by cutting both strand to the single helix,2426

passing it through the gap of another one while still holding onto the ends.2434

And then, re-ligating the strands together.2438

It is important because as we are going to talk about in DNA replication,2443

topoisomerases will move supercoils ahead of the replication fork.2447

Helicases which we will talk more about, generate positive supercoils ahead of the fork, the replication fork.2454

They generate negative supercoils behind the fork.2480

For every 10 base pairs that helicase unwinds, it will make 1 positive supercoil.2498

Helicase unwinds 10 base pairs, that is 1 positive supercoil.2505

We will talk more about helicase but this is important.2514

We are adding more and more supercoils.2518

Type 1 and type 2 topoisomerases are going to be able to act ahead of the fork to relieve this torsional stress.2520

If we think about it, if anyone of us ever had one of the corded phones growing up, they are normally always tangle up.2526

As they are extra tangle, those would be like writhe, the supercoils.2536

If you grab in the middle of it and pull it apart, you are basically making what we are talking about as a replication bubble.2540

If you see as you pull them apart to have a gap in the middle, you are going to increase the stress on either side of the bubble.2547

Because a phone cord is very elastic, you can do that, it is really not going to break.2557

But DNA is not as resilient, it is a little more fragile.2561

As we are opening up the DNA, we need to release torsion on either side of that bubble.2566

That is where our topoisomerases will come in to plot.2571

These are really important molecules.2574

That is the end of what we are talking about DNA for now.2579

To introduce you to RNA, I want to remind you of the central dogma of molecular biology.2584

Remember, DNA to DNA is replication, DNA to RNA is transcription, and RNA to protein is translation.2590

As we see here, this is actually transcription in action, where we have the mRNA being made from DNA.2606

As mRNA could then go to the cytoplasm and be made into a protein via translation at the ribosome.2614

RNA, remember that is ribonucleic acid.2626

It is most commonly found as a single stranded molecule, although it can be double stranded.2635

It is made up of a nucleotide, just as a DNA is, many nucleotides put together.2642

In this case, the nucleotides are attached or the nuclear bases are attached to a ribose2649

not a deoxyribose because deoxyribose is DNA.2656

Importantly, remember, uracil is found in RNA, thymine is not.2668

Whereas, uracil is not found in DNA and thymine is.2673

There are 3 major types of RNA.2678

The first is the most abundant, and that is rRNA and that is called ribosomal RNA, makes up about 75% of our total RNA.2682

Then, we have mRNA which is the smallest makeup of our RNA group and that is called messenger RNA, that makes up about 5% or less.2692

Then, we have tRNA or transfer RNA.2702

There are also things called non-coding RNA.2705

That is kind of ramped into the ribosomal RNA part.2709

We will go through in the next few slides and tell you what each one of these RNA has a function.2715

Our rRNA is the structural and catalytic constituents of the ribosome.2724

They will bind proteins and form a ribosome.2738

For eukaryotic rRNA, we have the 5S, the 5.8S, and the 28 S rRNA,2743

coming together with proteins to form this 60S subunit of the ribosome.2754

Then, we have the 18S rRNA coming together with proteins to form the 40S subunit.2761

Together, these make up the 80S eukaryotic ribosomal subunit or 80S eukaryotic full ribosome.2771

S stands for Svedberg, this is just a unit of density.2783

Yes, we do now 60 and 40 should equal 100 not 80.2796

Since this is a density unit, this is affected, 60 + 40 S does not make 100, it actually makes 80S ribosome.2803

For our prokaryotes, we have the 5S and 23S rRNA, along with proteins making it a 50S ribosomal subunit, the large subunit.2815

We have the 16S rRNA, along with proteins making up the 30 S subunit.2825

This makes a 70S prokaryotic ribosome.2832

Once again, 50 + 30 = 80, but we actually have a 70S ribosomal complex for prokaryotes.2839

Remember, Svedberg is a density unit not a weight unit.2848

This would be as an example of what an rRNA might look like.2853

The second type of RNA’s, we had mRNA or messenger RNA.2862

This is going to contain the codons for the sequence of amino acids of a polypeptide.2867

When DNA is transcribed to an mRNA, that mRNA becomes the messenger leaving the nucleus and going to the cytoplasm.2875

It will then associate with the ribosome.2887

Remember, the ribosomes are made up of rRNA and protein.2889

The mRNA will associate with ribosomes.2892

With our next RNA which is our tRNA, together that can all go through reactions to create new proteins.2896

One thing that is important to talk about is the fact that eukaryotic mRNA get post-transcriptional modified.2906

What happens is they get a 7G MTP cap - 7 methyl guanosine triphosphate cap added at the 5 prime end.2915

This is done for protection.2928

It has done that so that it cannot be eaten away from the outside by nucleuses.2932

Another way to protect it on the other side, we add a poly A tail.2938

This poly A tail is a bunch of adenosines, maybe about 200 or so.2942

Adenosine nucleotides added after all the coding sequent.2949

This would not be coded and turned into amino acids.2953

Remember, it will talk more and more about this but we have a stop codon.2957

We also have a start codon.2963

This initiation or start codon which is normally AUG which codes for methionine.2967

The start codon, in most cases, 99% or more, this is going to be an AUG codon coding for methionine.2976

Anything before the start codon, like our cap and like our 5 prime UTR2985

which means untranslated region, this does not get turned into a protein.2991

Only between the start codon and the stop codon, do we have our protein coming out, amino acids all the way through.2995

At the stop codon, that is going to be one of these 3 sequences, UAA, UAG, or UGA.3010

Anything past these stop codons, is not going to be translated as well.3023

We have a 3 prime untranslatable region, as well as our poly A tail.3028

None of these nucleotides will be turned into proteins either.3033

What is important about this stop codon is that it3038

does not actually code for any amino acid nor does any tRNA come in to bring anything to it.3040

As our last example, we will talk a little bit about the stop codon.3048

As a reminder, remember DNA is found in the nucleus.3056

Most frequently found in the nucleus.3064

Transcription occurs in the nucleus to make R, in this case we are showing mRNA.3066

MRNA can leave through a hole in the nucleus or holes in the nucleus called nuclear pores.3072

They can go to the cytoplasm where they can interact with ribosomes and tRNA’s, and3080

undergoing a process called translation to make new proteins.3086

We need that adapter molecule, we talked about rRNA which helps make up the ribosomes.3093

We talked about mRNA, the messenger.3099

What about the adapter molecule?3102

First, before we get to that adapter molecule, let us understand what is going on with RNA.3107

We have talked about the genetic code a couple times already.3112

We have our mRNA, it has a bunch of these bases.3116

It has what are called triplets or codons.3120

A codon is a 3 base pair sequence.3124

In this case, for example, if I had a UUU from 5 prime to 3 prime,3127

UUU is going to code for a phenylalanine amino acid to be added to the growing polypeptide chain.3136

If I had in AAC, that will add in a pair of gene amino acid to the growing polypeptide.3146

These amino acids have to be brought in by something and that something is going to be our tRNA.3155

The last thing before we jump in tRNA, we are going to give you this example on stop codons.3167

Our stop codons, once again, UAA, UGA, UAG, these do not code for an amino acid.3173

They do not have unassociated tRNA.3200

In fact, what they do is they signal a release factor, in eukaryote, it would be eukaryotic release factor neuron.3216

What that does is it comes in. Let us say, here is the ribosome, here is the mRNA coming through.3225

Here is the polypeptide coming out, all these amino acids.3238

tRNA’s would normally come in and add an amino acid, when it finds the proper codon.3249

Once we hit this, let us say for example, a UAA that will signal the eukaryotic release factor to come in.3255

What it does is, it acts like a pair of scissors, it will cut this chain off.3268

In which case, it is now free to float away and fold up into whatever protein it is supposed to be folded into.3280

Our tRNA, our last piece of RNA that we are going to talk about is an adapter.3294

It is the adapter between the codons in amino acids.3300

What it is, it is actually a 4 Svedberg RNA.3304

It has a form cloverleaf structure, we have hairpin loops stabilizing, intramolecular base pairs.3308

This is a single stranded RNA but it is making base pairs within itself.3315

For example, we have this is the 5 prime end and this is the 3 prime end.3336

It is a single strand but it is making intramolecular base pairs.3339

The tRNA will carry the amino acid and it will carry it at this point right here.3344

It will carry it into the ribosome during translation.3350

What is important to point out is that, there is only one tRNA for each of the 20 different amino acids inserted in the protein.3354

For example, if we go back to that UUU sequence.3364

If we had on the mRNA.3370

If this were a UUU, this is the codon on the mRNA.3380

The anticodon with tRNA would match base pairs.3395

This would be a AAA, this would only carry at this end.3400

For example, we have over here, we would have this part carrying a phenylalanine amino acid.3418

This tRNA would always have the same anticodon AAA, meaning it would only be able to carry that phenylalanine.3430

We have a phenylalanine tRNA, we have an asparagines tRNA, we have a glycine tRNA.3443

It will only match up properly its anticodon with the proper codon on mRNA and3448

only attach the single amino acid to the growing polypeptide chain.3455

One arm has that anticodon that I talked about.3464

Here would be our anticodon loop.3467

This would hydrogen bond to our codon on the mRNA.3470

Here is our mRNA, let us say again, it would hydrogen bond.3474

The CCA part on the 3 prime end carries a specific amino acid and that will be dictated by whatever this codon is.3483

For example, if this anticodon is AAA, it will match up with UUU on the mRNA.3494

Therefore, this will carry a phenylalanine amino acid.3507

That will be added to the growing polypeptide chain in the ribosome.3513

This shows it altogether, we see our messenger RNA here, our ribosome is here, our incoming tRNA are there.3521

For example, we are bringing in the phenylalanine, phenylalanine can be coded for multiple codons,3532

that is why we do not see just AAA.3537

For our purposes, we will change it and we will make it look like what we are used to.3540

We will just turn that into an A.3546

We will turn this into U, to say it is what we looked at the past few.3552

UUU matches out that codon with the AAA anticodon, and brings in phenylalanine.3560

That will make a peptide bond to the aspartate, in this case.3567

It is a growing polypeptide chain.3573

The only thing that would stop it would be our stop codons.3575

UAA, UGA, UAG, that would be our stop codons.3579

In which case no tRNA would come in but instead the eukaryotic release factor for talking about eukaryotes,3592

would come in and it would cut the chain releasing it from the loop.3600

Four our last slide, I just want to briefly talk about ribozymes.3610

I have mentioned before in proteins that a lot of them can be enzymes but not all enzymes are proteins.3615

This is where we have our exceptions.3624

Ribozymes are RNA molecules with enzymatic activity.3627

An example of those are the first one that was discovered is RNA’s P.3632

That is in the endonuclease meaning it cuts in the middle of a piece of DNA.3639

Let us say cut in here.3646

We have peptidyl transferase which is a ribozyme that is found as part of the ribosome.3649

I wrote on here telomerase but I did that to show you that, unfortunately, a lot of the times telomerase is taught as being as a ribozyme.3657

When in fact, it is not a ribozyme.3669

Telomerase is actually a ribonucleic protein.3672

That means it is a protein and ribonucleotide mixed.3689

The thing that is actually catalyzing the reaction is the protein component not the RNA component.3696

We will talk about telomerase a little more.3703

Telomerase, just in case we do not know what it is, it is the enzyme that will lengthen telomeres3706

which are the end of our DNA sequence.3713

That we do not keep shortening our sequence with every replication and how our cells die quickly.3715

That is the end of our lesson today, thank you for joining us at www.educator.com.3724

I hope to see you again.3729

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