Enter your Sign on user name and password.

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

Use Chrome browser to play professor video
Michael Philips

Michael Philips

Genome Organization: Chromatin & Nucleosomes

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
Loading...
This is a quick preview of the lesson. For full access, please Log In or Sign up.
For more information, please see full course syllabus of Molecular Biology
  • Discussion

  • Study Guides

  • Practice Questions

  • Download Lecture Slides

  • Table of Contents

  • Transcription

Start Learning Now

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

Sign up for Educator.com

Membership Overview

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

Genome Organization: Chromatin & Nucleosomes

    Medium, 4 examples, 5 practice questions

  • The genome is a highly organized structure than includes both nucleic acid and proteins.
  • Chromosomes often vary in size, number, and density between different organisms.
  • Genome size is roughly directly correlated with the complexity of an organism.
  • Genome density is roughly inversely correlated with the complexity of an organism.
  • Nucleosome and chromatin modifications can be responsible for transmitting information to future generations without changing the DNA sequence, also known as epigenetic inheritance.

Genome Organization: Chromatin & Nucleosomes

Generally, the more complex an organism, the ________ the genome.
  • More dense
  • Less dense
  • Shorter
  • Less complex
Which of the following is not one of the three requirements for proper chromosome duplication and segregation?
  • Centromere
  • Origin of replication
  • Telomeres
  • Translation
What is the first phase of Mitosis?
  • Anaphase
  • Metaphase
  • Prophase
  • Telophase
Phosphorylation of histone tails adds ______.
  • Methyl groups
  • Positive charge
  • Negative charge
  • Small peptides
Methylation of DNA and histones is often correlated, resulting in what chromatin state?
  • Repressed
  • Activated
  • Unchanged
  • Damaged

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

Answer

Genome Organization: Chromatin & Nucleosomes

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

Transcription: Genome Organization: Chromatin & Nucleosomes

Hello, and welcome back to www.educator.com, today's unit is on genome organization.0000

We will focus on chromatin and nucleosomes.0006

As an overview, we will first go over a real quick glossary of terms, just so that we are on the same page.0010

Then, we will mainly focus on our genome variance and our nucleosomes.0016

Our quick glossary, just in case we do not know any of these terms.0024

DNA, that is our genetic material that we find inside each cell.0028

A gene is going to be our molecular unit of heredity.0034

This is a piece of DNA that will encode any type of functional product, whether that is a protein or RNA.0040

We have a nucleosome and that is going to be the fundamental subunit of chromatin,0048

that is just a basic unit of DNA packaging in eukaryotes.0053

These consist of DNA wound around a histone octamer -- we will talk further about what that is.0059

We have chromatin. This is a complex of DNA protein, DNA and protein that forms chromatins and we only find this in eukaryotes.0068

Then, we have a chromosome and that is a tightly packaged and organized structure of DNA and proteins,0080

including our histone, as well as non-histone proteins.0086

Finally, a genome, that is just a complete copy of the entire sequence of DNA of an organism.0090

Let us talk about how a lot of these fit into play.0101

If we go from the most zoomed in, we have genes which consists of introns and exons.0106

We have intergenic regions, non-genes.0117

All of that is a piece of DNA, these are the smallest units.0119

If we zoom out a little bit, genes to DNA.0125

DNA, we can compact that DNA, compact it over and over and over again by winding unit around nucleosomes.0133

Nucleosomes can compact more and more, forming types of chromatin.0144

Chromatin is just DNA and protein interactions.0150

This would be an example of a type of chromatin down here.0157

As we compact even more, we have all of our chromatin compacting into chromosome.0162

If we remember, as humans, we have 23 sets of chromosomes, we are diploid so we have 46 chromosomes.0171

Remember, we have chromosomes 1 to 22 and then we have the X and Y chromosomes.0181

Let us talk about the physical cellular differences between eukaryote and prokaryote quickly.0191

Eukaryote, these are cells with nuclei, if we look down here that is a eukaryote and prokaryote.0197

The biggest one is that we have a nucleus in eukaryote.0204

In a prokaryote, they do not, they have what is called a nucleoid0210

which is very similar as to where their DNA and protein are held together but it is not enclosed in a membrane.0212

Eukaryote may also have some extra things such as mitochondria, that prokaryote do not normally have.0221

Eukaryote are the biggest, we are anywhere from 10 microns to 15 microns, which is micrometers.0229

We can be even bigger than that.0242

Smaller than eukaryote are prokaryote, a bacteria types of things.0245

Smaller than that is virus, the thing smaller than viruses are what make up all of life.0249

We have our atoms, our small molecules, our proteins, these are going to be found in all of our viruses, prokaryote, and eukaryote.0257

It is important to know that there is a variance of genomes.0268

Since, we are going to talk a lot about human stuff in this entire course.0274

We will also talk about prokaryote, bacteria, specially our E coli.0281

We want to know the relationship between all of them.0286

First, let us talk about humans, most of our genome does not code for anything.0291

It is not composed mainly of genes, it is composed mainly of intergenic regions.0298

More than 60% of the human genome does not code for a gene.0305

46% of the total genome, 46% of the total DNA is repetitive sequences and that is often referred to as junk DNA.0312

But that is a misnomer and that is not a term that we should be using because,0324

just because we do not know that it has some sort of function, it does not mean that it actually does not have a function.0329

There are studies coming out every year that is finding what normally was thought of as junk DNA or even non-coding RNA,0336

coming out as being coding for something or as being involved in some sort of gene regulation.0344

You can regulate the way that genes are expressed higher or lower, even in the non-gene sequences, the intergenic regions.0353

Genes compose less than 40% of the total DNA, and of that, less than 5% is actually the exon.0365

The exons are what is actually going to be added into the protein.0373

It has the instructions to how to make a protein.0379

The introns always cleaved out of the mRNA.0382

If we look down at this chart that I have made down here, I have four different organisms on here.0385

I have a very simple virus which is the bacteriophage virus.0392

It infects bacteria, it is called φ X174.0399

Then, we have our old friend E coli, and then drosophila melanogaster.0403

E coli is a bacterium, drosophila melanogaster is the common food fly, and then, we have us, the humans.0409

In general, genome size is roughly positively correlated with the complexity of an organism.0417

The bigger the genome size for the more complex organism.0429

The smaller the genome size for the lease complex individual.0437

This is size of DNA, in terms of mega bases, thousands of bases.0444

Also, another general thing you can talk about is that genome density, the amount of genes per base pair sequence,0454

basically, is roughly negatively correlated with the complexity of the organism.0464

A very simple organism like the bacteriophage has a much higher density of genes found in its genome than humans,0471

which we have a very a low genome density, or gene density in our genome.0480

We have about 20,000 genes but that is spread out over more than 3 billion bases,0485

whereas the bacteriophage has 11 genes but it has an extremely small genome.0494

We are talking about 5000 bases.0502

For our first example, let us talk about how big the human genome is.0514

I said, it is over three billion base pairs long and that is just the haploid genome.0520

We are a diploid organism so we have twice the amount of that.0525

L, the length of just that 3 billion base pairs, if we were to spread it all the way out, that is a meter, close to 3 feet.0529

The diploid length, the doublet, that is 2 meters, about 6 feet around of DNA.0541

The diameter of human cell is only about 10 to 15 micrometers.0550

What does that really mean?0558

Can we understand the size of that?0562

If our cell was actually the size of a basketball, if we blew it up the size of a basketball, and everything else accordingly.0565

Then, our genome would actually be able to stretch from the earth to the moon.0577

Just based on the size comparison.0586

This to me says that, we need a really good way of compacting that DNA.0591

Because we cannot have the 6 feet of DNA inside a cell, that you cannot even see with your naked eye.0598

We need to compact that really well and we need a way of uncompacting things, decondensing or condensing things,0608

based on whether we need to do things such as replication, transcription, repair, so on and so forth.0616

That is what this unit is all about.0624

First of all, let us talk about chromosome variant.0629

We are going to see the size and density variance, even in between a single cell.0634

We will have chromosome variance, in terms of number, in between different organisms.0642

Once again, a reminder, a chromosome, we have a tightly packaged and organized structure of DNA0648

and proteins including both histone and non-histone proteins.0654

Right here, we have a graph showing human chromosomes.0658

We have our total number of genes, in pink here.0663

We have the total base pairs, in green.0668

As we can see, between individual chromosomes in the same,0673

we have not only a difference or variance between chromosomes in genes, but we also have a variance in terms of base pairs.0679

If we look it to, they are fairly similar in size, such as 1 and 2.0693

We also have a difference of variance in gene density because we have so many more genes, for barely that much more base pairs.0700

This is something that we should always keep in mind, that chromosomes are going to vary by size, number,0715

and density between organisms and even within the same organism.0722

First off, let us talk about the eukaryotic cell cycle and why do I bring this out of nowhere.0729

The reason being, let us go back to this because we have talked about in one of the previous unit.0736

We will talk about it in the next unit again.0742

Remember, we have our two growth phases, G1 and G2.0746

We have S phase which is where DNA replication occurs.0750

We have mitosis, anaphase, that is where we have the splitting of our cells into two new daughter cells.0758

The reason I talk about this is that, we have to know that when we replicate DNA,0774

we are going to have to replicate a lot of other things relating to DNA.0781

One of these things that we are going to have to do is, yes, we duplicate DNA and then we segregate our DNA, or separate it.0788

In prokaryote, that happens at the same time.0796

In eukaryote, that happens at two different phases.0799

We duplicate in S phase, we segregate in anaphase.0801

Duplication, specifically segregation, relies on centromeres and telomereses.0809

Duplication is going to rely on our origins of replication.0817

If I draw out a chromosome, just a real rough drawing, we will just draw that like this.0823

We have already duplicated it, let us say that.0832

Let us start with before it is duplicated.0837

If we were on one chromosome, along the chromosome in eukaryote,0840

we are going to have multiple places where we have origins of replication.0846

That means that, that is where the DNA synthesis during replication can begin.0851

If we are talking about a bacteria, it has a single origin of replication.0857

That is because it is circular, if you replicate it at one place,0862

it will actually start replicating in both directions until it ends at the terminal point.0866

Since, eukaryote, we do not have a circular chromosomes, we have linear chromosomes.0872

We start at many different places, that way it ensures that we can finish replication before we move through S phase.0880

There is our origin of replication.0888

After we have replicated our chromosomes, we are going to have a centromere.0890

A centromere is going to be a bunch of repetitive sequent in the chromosome.0898

That is where our two chromosomes are going to bind together during our anaphase.0904

It can be in the center, it can be on one end or the other, so on and so forth, and that is fine.0910

Telomeres are always going to be at the ends of our chromosomes.0915

These are telomeres sequences and this is just repetitive sequences that capped the ends of our chromosomes and0922

allow us to have some protection from nucleolytic cleavage, as well as having adhesions,0928

binding into another chromosome which would be a very bad thing.0938

We need centromeres and telomereses, as well as origins of replication0943

to proceed through proper duplication and segregation of chromosomes.0948

Remember, I said, we need to have a way to condense our chromosomes quite a lot.0955

We have our naked duplex DNA to start with, then, we can compact it with nucleosomes.0959

We are going to talking more about nucleosomes in this lecture.0967

This is just a nice little preview.0971

This is our beads on a string or 10 nm fiber.0973

That can even more compacted, when you add in linker histone H1 to make the 30 nm solenoid fiber.0979

That can be extended even more by a chromosome scaffolding and eventually condensed in mitosis to look like the stereotypical X.0989

It looks like that X, real dark X chromosome.1001

Not X in the sex chromosome, X is in the letter X.1005

We need all this to happen.1014

I showed on the last one, we have that mitotic chromosome being extremely condensed.1016

The reason these seem to happen in mitosis is that, we need to be able to separate our daughter strands.1021

We need to make sure that everything is condensed into their individual units, their individual chromosomes,1027

so that we can properly segregate everything, that nothing gets tangled up.1034

If we remember mitosis, we start with, in this example, two different chromosomes.1038

You duplicate those chromosomes then you split that one cell into two different daughter cells.1044

Each one of which has the exact copies of that first red chromosome and that second blue chromosome.1051

Real quickly, we will go over what mitosis is, it is split into multiple phases.1059

First off, we start with prophase.1065

Prophase is when we start condensing our chromatin into chromosomes.1067

This is where we are going to start to get more and more condensed.1072

In pro metaphase, we have the nuclear envelope starting to disintegrate.1076

That nuclear envelop needs to disintegrate so that you can start moving the duplicated chromosomes away from each other.1084

Remember, once we start mitosis, we have already gone through S phase.1092

We already have twice as many chromosomes.1097

We have two times in our chromosomes that we want in every cell.1100

We have the nuclear envelope disintegrating.1105

We have microtubules coming in to grab onto those chromosomes.1107

The microtubules attached to kinetochores.1114

kinetochores bind to the centromere of the chromosome.1117

We have kinetochores binding on here.1126

Kinitocour is binding on the centromere.1130

And then, that allows the microtubules to attach to the kinitocour.1133

Eventually, they pull in either direction separating the chromosome.1140

It breaks the centromere apart.1147

In metaphase, the next step, this is all occurring throughout entire mitosis not just the pro metaphase.1151

In metaphase, we have the chromosomes aligning at the metaphase plate.1158

It is basically the midline of the cell.1162

The next part of mitosis is called anaphase and that is when the chromosome split.1169

The centromere breaks, you can break the centromere apart.1177

Or you break the chromosomes apart at the centromere.1181

The chromosome split and the kinitocour microtubules.1186

The microtubules attached to each kinitocour.1189

A kinitocour is attached to the centromere.1194

Those are being pulled in opposite directions.1197

It has to be at each pole of the cell.1201

This pole and this pole, which will eventually be two separate daughter cells.1205

In telophase, we have these decondensing chromosomes.1211

They are starting to not be as compacted, they are starting to release a little bit.1215

The get reformed, or what forms around in newly is new nuclear envelopes.1220

We start to do what is called cytokinesis.1229

The cytokinesis is the actual separation into two different daughter cells.1233

We have the cells pinching in, this is what we call a cleavage furrow.1240

The cell starts pinching in and eventually pitches off to have two separate cells.1248

In this case, each one of these cells has the exact amount of chromosomes as the original parent cell,1254

before it went through S phase.1262

We have to talk about a couple of really important protein complexes,1269

when we talk about mitosis and we talk about proper chromosome segregation.1275

We have what are called cohesin and condensins.1280

This is cohesin and this is condensin.1284

Cohesins are loaded during replication.1297

Condensins are being loaded during N phase.1303

What actually happens is, if we look at a chromosome, this is a duplicated chromosome,1308

we have cohesins using this little hinge, binding around the chromosomes.1319

This is binding our sister chromatid together.1336

This is in S phase.1344

Normally, when we go into mitosis, we have prophase, we still have our chromosomes.1350

We still have our cohesion, holding the sister chromatids together, this is prophase.1372

In prophase, we are starting to condense our chromosome.1393

How we can do that is, condensin will come in metaphase.1396

In metaphase, we will go over here.1409

We still have our condensins.1426

I will make this easier.1436

Those are our cohesions, condensins will be in red.1438

Our condensins, in metaphase, will start binding these together.1447

Our condensins, after replication, compact each sister chromatids individually, making it even more and more.1457

And then, if we move on toward anaphase.1468

In anaphase, we actually have our condensins still on there.1483

Let us write this out, anaphase.1495

But our cohesins have been cleaved, our condensins are still there.1501

Our cohesins get cleaved in anaphase.1508

What we have is, this kind of becomes a little squiggly because it is no longer bound to each other.1510

It is squiggly here too.1523

It is no longer bound there.1529

It is important that cohesins get cleaved because that allows a separation of these sisters.1530

This one can go to one cell, this one can go to another cell but we still have a little compaction.1539

Eventually, once we have separated them into different cells, the nuclear envelope starts to form,1545

these condensin can then start to be cleaved.1551

What we have, just to show us right here, SMC, all these are cohesins and condensins,1555

they are related proteins, a part of the SMC complex.1562

SMC stands for structural maintenance of chromosomes.1566

It is important that we have this compaction.1588

Cohesin and condensins play a large role in the actual condensing or compaction of DNA.1591

Remember, we have our cohesin binding sister chromatids together.1599

Condensins bind sister chromatids individually.1619

In this slide, I already talked a little bit about but I just want to reiterate.1645

We have our cohesin being loaded during replication and being cleaved during mitosis.1649

They are cleaved during anaphase.1655

They are cleaved via the enzyme separase.1657

This occurs right as we are moving into anaphase.1665

It is actually cutting up the end of metaphase and1670

separase is what then allows the sisters to be segregated into individual cells.1673

One thing that I just want to mention about the previous slide is that after replication,1686

the microtubules have attached to the kinetochores.1692

They pull in opposite directions until those cohesin proteins get cleaved.1696

Separase is in there, cleaving, as well as kinetochores are pulling apart.1702

Eventually, that allows you to proceed into anaphase.1706

Now that we talked about the mitotic chromosomes, we need to talk about what about we are not in mitosis?1713

We still need to have some sort of compaction of the chromosome, that is occurring via nucleosomes.1722

We have what is called the histone core.1730

The histone core is composed of 8 histone proteins.1736

These histone proteins are positively charged, that is great because negatively charged DNA will attract positively charged proteins.1741

What we have, if we look down here at the octamer of core histones,1754

we have two dimers of H2A and H2B, meaning there is two of each of those.1763

We have a tetramer, the H3H4 meaning we have two of each of the H3 and H4.1770

Around that, we have 147 base pairs of DNA, and that DNA is wound around that nucleosome, wound around 1.65 times.1776

The DNA wound around that histone octet 1.65 times.1796

We have what is called linker DNA and that is what will link many different nucleosomes together.1805

Remember, we are not just going to compact one little spot.1811

The linker DNA between those nucleosome is anywhere from about 20 to 60 base pairs.1814

A single nucleosome will compact DNA about 6 fold.1821

If they are just in the nucleosome, and we have a bunch of nucleosome all the way throughout.1825

Just nucleosomes, remember, we are looking at the 10nmm fiber here, a 6 fold compaction.1831

We need to compact it even more, we have 3 billion base pairs.1849

Over 2 meters of cells, when we are in diploid, 1/1 meter of cells when we are in haploid form.1853

We need to condense even more.1860

What can help with that is histone H1, also known as the linker histone.1862

That allows the transition from this 10 nm fiber which we just talked about,1868

which is just the nucleosomes and linker DNA, into the 30nm solenoid.1877

This helps compact DNA about 40 fold, from 6 fold to 40 fold between the 10 nm and the 30 nm fiber.1886

When you are not in mitosis, further compaction of DNA can be mediated by the organization of these 30 nm filament into loops.1897

These are our 30 nm filaments in loops.1909

That can consist of 40 to 90 bases per loop and that can associate with scaffolding.1915

We can get more and more compaction because we need it.1922

That is the simple aspect behind, we need all this compaction and there is an intelligent design behind this.1928

If we want talk mitosis, you can get even more condensed and eventually get to that mitotic chromosome.1938

But these, you cannot really do much with, there is no replication,1944

no transcription, none of that stuff happening during mitosis, no repair.1949

Histones, as they bind DNA to compact it, they take up available binding spots.1961

Because proteins like to bind DNA but they do not like to bind DNA when there is already something there.1968

These histones will decrease any available binding spot on the DNA.1975

Meaning, it basically makes it unavailable for anything to bind.1982

Therefore, affect whether maybe is transcribing or replicating or being repaired1988

or having interactions in bringing two pieces of DNA together.1996

Our histone tails, we have talked about the histones that are in the middle.2002

In this case, we see H2A is in yellow, H2B is in red.2007

I will write this in black, just in case you cannot see the yellow.2028

H3 is in blue and H4 is in green.2032

We have the histone octet, in the middle we have DNA wound around it, remember 1.65 times.2039

What I want to point out is, we will use a purple color.2047

Look at these coming out of the DNA, these are what are called N terminal histone tails.2054

The N terminal so the beginning part, if we think about N to C terminal.2066

These N terminal tails can interact with DNA.2070

This interaction with DNA can affect how anything, any further process may occur.2075

These histone tails can be post-translational modified.2087

Meaning, they could not have some types of groups,2091

some functional groups added to them and that will affect or alter the strength of their interaction with DNA.2095

If let us say, it strengthens the interaction of DNA, it makes it real tight, meaning it is not very available for protein to come in.2103

If the type of post-translational modification makes its interaction with DNA decrease,2111

then the DNA loosens around the nucleosome.2120

Therefore, that allows more proteins to possibly come in and maybe we can go through transcription, for instance.2124

These post-translational modifications on these N terminal tails have some sort of pattern that has been seen throughout history.2135

Scientists have theorized what is called the histone code.2149

What we see is that post-translational modifications of these N terminal histone tails,2153

somehow are related to epigenetics.2161

It is part of this epigenetic code along with, maybe DNA modifications,2164

like we have talked about methylation of DNA in other types of modifications of DNA.2170

These post-translational modifications of histone tails, maybe associated with certain modifications on DNA.2181

Together, they can be passed on to generations even though the DNA sequence itself has not been changed.2188

It is epigenetics, it is not the actual sequence is changed.2197

We have some sort of hereditary possible change.2200

This is when we are talking about the histone code.2204

Such things, such post-translational modifications of these tails,2207

such as phosphorylation which would add a negative charge.2211

Acetylation which would add a positive charge.2217

We have methylation which is the addition of methyl group.2221

Ubiquitnation which is an addition of a small protein group.2224

What we can see is that, there are very highly conserved residues in these N terminal tails.2228

We find them in many organisms throughout.2235

It shows that there is likely a common theme, a common function of this.2237

What we see is that, methylation which will increase the interaction with DNA, and recruit proteins called chromoproteins.2244

Methylation of residues on the N terminal tails such as lysines and argentines, will recruit these chromoproteins.2261

What will eventually happen is that, these chromoproteins will actually somehow figure out a way2271

to spread or propagate this methylation to neighboring nucleosomes.2278

The same thing can happen via acetylation, adding positive charge,2285

including bromodomain proteins which would neutralize the negative charges of lysines.2290

Acetylation of lysines recruit bromodomai containing proteins which can spread that,2296

can be acetylation type modification to neighboring nucleosomes.2305

As I said, down here, with ubiquitnation, that can divide a binding site for transcriptional activators or impressers.2312

It can increase the rate of transcription or decrease the rate of transcription.2319

Remember, transcription is DNA to RNA.2323

An example of histone coding, just a lot of few.2330

If we have an unmodified histone 3, that usually codes for the fact these genes are silent, wrap around this nucleosomes.2334

If we have a histone H3, the H3 histone, protein, if it has a lysine,2346

the amino acid is a K, 14 that means it is the 14th amino acid in the protein.2356

It is the 14th amino acid of the H3 protein being a lysine.2362

If it is acetylated, that often leads to increased gene expression, that is saying that transcription is active.2367

If we have the 9th amino acid which is also happens to be a lysine,2378

if that gets methylated 3 times with 3 different methyl groups, that will the silent.2383

Meaning, transcription is not going to be active.2392

There are few other traces to look at, one thing I want to point out is even the exact same histone,2396

H4, the exact same residue lysine 20, if you methylate it, you add one methyl group,2407

it will start chromosome condensation.2420

If you add a second methyl group, that will signal that DNA damage repair proteins to come in and2424

fix some sort of damage that is been found on this DNA.2434

If you methylate it one more time, you are back to chromosome condensation.2440

They wait for DNA damage repair to occur, the chromosome has to be decondensed,2445

it has to be loosened from the nucleosome so that the machinery, the damage repair machinery can come in and fix things.2452

We go from condensed to decondensed, back to condensed,2462

all by having a different modification to the same residue on the same histone.2472

We have talked about how the nucleosomes attach to DNA, how they interact.2485

We have not talked about how nucleosome are assembled or how they are replicated.2491

Remember, every time DNA gets replicated through S phase, we are getting twice the amount of DNA.2495

Therefore, we need twice the amount of nucleosomes because those DNA,2500

once put into daughter cells, are going to have to end up compacting again.2505

The duplication of DNA requires the duplication of histones.2509

This is going to occur in S phase just as the synthesis of DNA is going to occur.2513

We have all the histones being recycled.2521

We have all the H3 and H4 tetromers remain associated with one of the two DNA daughter strands.2525

And then, when we synthesize brand new H3 and H4 proteins in the tetromeric form, to bind the other daughter DNA strand.2532

And then, we have old H2A and H2B diomers completely being removed,2545

either as an old set can get back into the DNA or a brand new H2A H2B will jump in.2553

It is just a competitive interaction, it is just which one gets to be grabbed in by the DNA and added.2561

What is important to point out is that, chaperone proteins are involved in nucleosome assembly.2569

The chaperone proteins and what those are, they are just proteins that help these reaction occur.2575

We have what are called chromatin assembly factors COF1 and NAP1,2584

being necessary for the proper assembly of nucleosomes.2596

COF1 is going to be responsible for bringing in new H3H4 tetromers to nucleosomes.2599

This will say that, this response will for H3H4.2607

NAP1 is responsible for bringing in new H2A and H2B diomers into nucleosomes.2614

Without these chaperons, nucleosomes likely will fail to assemble.2626

Even if they do, it will take quite a lot of time.2632

This can affect how quickly a cell would be able to get into, let us say, anaphase.2635

One of the last things that I want to talk about nucleosome assembly is that parental H3 and H4 tetromers.2647

Remember, one of those is going to stay completely with the original strand, the parental strand.2654

You will get brand new on the daughter strand.2664

Parental H3H4 tetromers will facilitate the inheritance of chromatin state.2668

Now, we are talking back to epigenetics.2675

This will provide a template for the propagation of any preexisting histone modifications.2678

These preexisting histone modifications could signal the fact that this gene should be active2687

or this other gene should be repressed.2695

That will affect what proteins possibly are getting synthesized or at least what RNA are being made via transcription.2699

This can help restore the parental chromosome state to any of the daughter cells.2709

These modifications can actually then recruit other modification enzymes of the histones,2715

to propagate this modification along adjacent histones and throughout the region of chromatin.2722

This can allow the actual passing from replication to replication, it can pass what is called the chromatin state.2729

Maybe this is methylated or maybe this is phosphorylated.2740

You start brand new, when you add new nucleosomes.2744

You can propagate the spreading of the modifications due to the parental H3 and H4.2751

As an example, our inheritance of chromatin state, we have enzymes called histone acetyl transferase or HAT.2762

They can bind acetylated histone tails, using what is called the bromodomain.2791

That will then allow HAT to move, here is DNA, here let us say that these are wrapped around nucleosomes.2807

These are nucleosomes.2824

If HAT binds, we are just going to say HAT is this.2833

If HAT can bind, it can bind there.2841

It can actually in a billion, it will bind either this acetyl group.2850

It can move to the next nucleosome, all in there again, adding another acetyl group,2857

and propagating this inheritance of the chromatin state.2866

The same can happen with histone methyltransferases, HMT, using their chromodomain.2871

Histone acetyltransferases, remember, use their bromodomains to bind acetylated histone tails.2879

Histone metyltransferases, HMT, use their chromodomain to bind methylated histone tails.2887

They could end up propagating, as well.2924

Remember, histone acetyltransferases often loosen the interaction of the nucleus on the DNA, making it more accessible.2927

Histone methyltransferases, often compact, they increase the binding affinity of the nucleosome in DNA.2935

Therefore, compact it even more and do not allow things to come in.2945

An example of that we can see in one of the next slides, talking about chromatin remodeling.2950

Remember, we have our DNA, we have to get it into our 10 nm fiber or 30 nm fiber, we need to compact it.2958

We have our basic unit of chromatin organization being our nucleosome.2969

Each one of these is a nucleosome.2973

This might be our 10 nm fiber.2979

This is a region of 30 nm fiber.2983

The degree of our nucleosomal packaging can affect any DNA processes,2988

whether it would be transcription, repair, replication, any of that.2996

The ones that are in the less condensed state are what are called euchromatin or euchromatic regions,3002

they are more transcriptionally active.3011

They are less condensed, they are the more likely other proteins can come in and bind.3014

Our heterochromatic regions are much more condensed and much less likely to have any type of activity occurring.3021

Nucleosome positioning in chromatin compaction, where are these nucleosome are positioned, maybe there is a gene there.3032

Maybe there is a gene in there, that will affect whether a gene is active or not.3040

If it is in an open region, it can be activated.3048

If it is bound around that nucleosome, maybe it is very likely it is not going to be active.3051

The positioning and the compaction can be altered by remodeling complexes.3058

If we look at this next slide, you can see what I mean.3064

In the top one, in the presence of histone acetyl transferase and the absence of our histone methyl transferase,3069

which if we remember, usually causes the compaction of our DNA.3078

This chromatin will be much more loosely packed and it will be transcriptionally available.3085

That is due to our chromatin remodel or complex.3091

This helps move things around, maybe it is decondensing the nucleosomes or decondensing the fibers.3097

Maybe it is sliding these nucleosomes from away from this region3108

which should normally have a gene be transcriptionally repressed.3115

At this point, we want to activate it.3121

Sliding complex can move these nucleosome, maybe they were here to begin with and got moved over,3123

freeing up this part to be transcriptionally activated.3130

If we look down at the bottom, we have histone deacetylase, HDAC.3134

This is taking off acetyl groups which mean we are taking away3141

what would normally loosen our chromosomes or loosen our DNA around the nucleosome.3145

That is going to compact.3151

Histone methyl transferase, the methylation is going to compact.3153

This is going to compact this more and more and it would not allow certain machinery to come in and do whatever job it wants.3156

If you look up here, we have had around no methylation, no HMT.3164

We have these remodeller complexes, we have allowed our region to be opened up that we can actually do something with.3170

We have allowed, if we are going to do transcription, we would allow RNA polymerase 2 to come in3180

and be able to start transcribing our mRNA.3186

Whereas, we do not have any room for RNA polymerase to come in and bind in between these really tightly bound nucleosomes.3192

As our last example, we are just going to talk a little bit about what we have mentioned so far.3210

I want to give you an example that I have talked a lot about histone modifications.3219

Methylation of DNA and methylation of histones, actually seems to be correlated.3229

When both your DNA and histone tails are methylated, this usually causes that repressed states.3234

Then, we have histone metyl transferase around, maybe the HDAC, the deacetylase.3243

We are not allowed to get all this machinery into the open spaces of DNA, because it is not very open, it is very condensed.3248

I have mentioned these two words before, heterochromatin and euchromatin.3257

What we see is that heterochromatin is usually transcriptionally repressed.3264

It is in repressed state, you cannot do anything in it.3270

It stains darkly with the Giemsa, Giemsa is the way that you can visualize proteins.3273

That is spelled this way.3280

You can do Giemsa and look at it under a microscope.3284

Heterochromatins stains very darkly because your DNA are so compact.3288

The euchromatin which is transcriptionally active, remember they are going to be more loose.3293

Therefore, it is going to stain much lighter with that Giemsa.3297

Just the last thing I want to leave you with, before we end today’s lesson,3302

is that we have the acetylation of histones leading to a loosening of the DNA around the histone.3306

The reason being is our neutralizing the positive charges of our lysine residues.3316

This loosening offers a likelihood of replication or transcription.3321

When acetylation of these tails occurs, we are more likely to be in the euchromatic state.3327

When we have methylation of DNA, we are more likely to be in the heterochromatic state3340

because methylation of DNA is correlated with the methylation of histones, often.3352

That is the end of today’s lecture, I thank you for joining us.3359

Thank you for being here with www.educator.com, please come back and see me again.3363

Educator®

Please sign in for full access to this lesson.

Sign-InORCreate Account

Enter your Sign-on user name and password.

Forgot password?

Start Learning Now

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

Sign up for Educator.com

Membership Overview

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

Use this form or mail us to .

For support articles click here.