Enter your Sign on user name and password.

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

Use Chrome browser to play professor video
Michael Philips

Michael Philips

Biochemistry Review: Importance of Chemical Bonds

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

Lecture Comments (10)

0 answers

Post by Mei Gill on July 6 at 03:38:45 PM

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

1 answer

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

Post by Firebird wang on November 2, 2016

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

1 answer

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

Post by Christoph Bader on December 16, 2015

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

2 answers

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

Post by Professor Michael Philips on December 1, 2015

Hi Apolonia,

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

1 answer

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

Post by Apolonia Gardner on November 24, 2015

Hello,

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

Biochemistry Review: Importance of Chemical Bonds

    Medium, 4 examples, 5 practice questions

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

Biochemistry Review: Importance of Chemical Bonds

Which of the following is an example of a covalent bond?
  • Hydrogen bond
  • Ionic bond
  • van der Waals forces
  • Electric dipole
Which of the following molecules has a non-covalent bond?
  • O2
  • H2O
  • HCl
  • NaCl
Water is a ______molecule.
  • Non-polar
  • Polar
  • Hydrophobic
  • Lipid
A reaction will proceed toward the products when the change in free energy is_____.
  • Equal to zero
  • Less than zero
  • Greater than zero
  • Extremely small
Which two types of interactions are responsible for holding the two strands of a DNA double helix together?
  • Covalent and polar
  • Ionic and Hydrophobic interactions
  • Hydrogen bonding and hydrophobic interactions
  • van der Waals forces and hydrophilic interactions

*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

Biochemistry Review: Importance of Chemical Bonds

Lecture Slides are screen-captured images of important points in the lecture. Students can download and print out these lecture slide images to do practice problems as well as take notes while watching the lecture.

  • Intro 0:00
  • Lesson Overview 0:14
  • Chemical Bonds 0:41
    • Attractive Forces That Hold Atoms Together
    • Types of Bonds
    • Covalent Bonds
    • Valence Number
    • H O N C P S Example
    • Polar Bonds
    • Non-Polar Bond
    • Non-Covalent Bonds
    • Ionic Bonds
    • Hydrogen Bonds
    • Hydrophobic Interactions
    • Van Der Waals Forces
  • Example 1 12:51
  • Properties of Water 18:27
    • Polar Molecule
    • H-bonding Between Water H20 Molecules
    • Hydrophobic Interactions
  • Chemical Reactions and Free Energy 22:52
    • Transition State
    • What Affect the Rate
    • Forward and Reserve Reactions Occur Simultaneously But at Different Rate
    • Equilibrium State
    • Equilibrium Constant
  • Example 2 26:16
  • Chemical Reactions and Free Energy 27:49
    • Activation Energy
    • Energy Barrier
    • Enzymes Accelerate Reactions by Decreasing the Activation Energy
    • Enzymes Do Not Affect the Reaction Equilibrium or the Change in Free Energy
    • Gibbs Free Energy Change
    • Spontaneity
    • Gibbs Free Energy Change Determines Final Concentrations of Reactants
    • Endodermic vs. Exothermic Graph
  • Example 3 38:46
  • Properties of DNA 39:37
    • Antiparallel Orientation
    • Purine Bases Always Pairs Pyrimidine Bases
    • Structure Images
    • A, B, Z Forms
    • Major and Minor Grooves
    • Hydrogen Bonding and Hydrophobic Interactions Hold the Two Strands Together
    • Denaturation and Renaturation of DNA
    • Ways to Denature dsDNA
    • Renature When Environment is Brought Back to Normal
    • Hyperchromiicity
    • Absorbs UV Light
    • Spectrophotometer
    • Graph Example?
  • Example 4 51:02

Transcription: Biochemistry Review: Importance of Chemical Bonds

Hello, and welcome to www.educator.com, today is our first lecture.0000

To start with molecular biology, first we have to do a little bit of biochemistry review and0005

we are specifically going to focus on the importance of the chemical bonds.0010

As an overview, first we are going to talk about chemical bonds.0016

We are going to talk about both covalent and non-covalent bonds, and the different types of each of those.0021

We will follow that up with the properties of water, as well as chemical reactions of free energy.0026

And then, we will have just a brief intro into the properties of DNA before we finish and move on to lecture 2.0032

Chemical bonds are attractive forces that hold atoms together, thereby making molecules at least two atoms together.0043

One type of chemical bonds are covalent, which are much stronger bonds.0056

They can be either polar or non polar.0063

One other class of bonds is the non-covalent bonds, which are much weaker than the covalent bonds.0066

However, when you have many non-covalent bonds together, they can become very strong.0072

The many types of non-covalent bonds, the ones we are going to talk about, ionic bonds, hydrogen bonds,0078

hydrophobic interactions, and finally Van Der Waals forces or Van Der Waals interactions.0086

Let us start off with covalent bonds, they are very strong.0096

They involve the sharing of an electron pair between two atoms.0101

Making and breaking covalent bonds usually requires the presence of an enzyme to catalyze that reaction.0106

The valence number of an atom determines the number of covalent bonds it can form.0119

What is that mean?0124

First of all, what is the valence number?0125

That is just a number of unshared electrons in an atoms outer shell.0136

The common atoms that we are going to see in molecular biology are hydrogen, oxygen, nitrogen, carbon, phosphorus, and sulfur.0165

How many valence electrons do each of these have?0191

Hydrogen has 1 valence electron, oxygen has 6, nitrogen has 5, carbon 4, phosphorus 5, and sulfur 6.0204

I said that the valence number of an atom determines the number of covalent bonds it can form.0225

How is that true, let me show you.0233

They key here is that all atoms other than hydrogen want to have a full octet, meaning a full 8 electrons in their outermost shell.0241

That will determine how many bonds it can make.0264

Hydrogen, I said was the only one that does not want 8, that is because hydrogen, its full electron shell cannot consist of 2 electrons.0276

Every bond is a sharing of a pair of electrons.0288

With hydrogen having a valence electron, 1 valence electron, and it only liking to have 2 to fulfill it, it can make one bond.0293

Oxygen, to have its full octet, can either accept 2 electrons from similar or give up 6 of its own, but it is more likely to take 2.0309

Therefore, by taking 2 electrons, each one of those is going to participate in a bond, that is 2 bonds for oxygen.0322

Nitrogen, to get its full octet would want 3 bonds.0331

Sometimes you can actually have 4 bonds.0339

Carbon, to get its full octet wants another 4 electrons, 4 bonds.0342

Phosphorus actually is kind of a little different, in the fact that it will more likely give up its 5 than take on 3, they will have 5 bonds.0348

Sulfur is a little bit weird, in the fact that it has a little more variety, it will make a possible 2, 4, or 6 bonds.0359

The number and types of bonds ultimately determines the geometry of what the molecule will look like.0376

Single covalent bonds, that would be, let us say this, for example, a nitrogen.0384

That would be a single covalent bond which is a sharing of 2 electrons.0391

A lot of rotation of the atoms around the bond meaning this can flip upside down, flip, maybe even curl a little bit.0396

Double and triple bonds, for example a double one that is a sharing of 4 electrons,0405

or triple bond a sharing of 6 electrons between there, do not allow any rotation around that bond.0412

Bond angles are actually determined by the number of atoms.0419

The whole goal is to space out the electrons, because the electrons are negatively charged.0424

If you have ever played with a magnet, you know that two things of a like charge will not attract. They push away, they repel.0429

Two negatives or two positives repel, a negative and a positive attract.0436

Chemical bonds can be broken down into your polar and your non-polar bonds.0444

Your polar bonds also called electric dipoles.0450

This is a bond between two nonmetal atoms with differing electron negativities.0454

What that basically means is that they are not sharing the bonding, they are not sharing the electrons equally.0463

Let us say for an example, one of the examples is hydrogen chloride.0474

They have just the bond right there, what we actually find is that the chlorine atom actually has a partial negative charge,0482

whereas the hydrogen atom has a partial positive charge0496

because the electrons are being pulled by chlorine because it has a higher electron negativity.0498

If you look at the periodic table, electron negativity decreases as you go downward and as you go leftward.0505

You decrease electron negativity, as you go down into the left.0520

A non-polar bond on the other hand is a bond between two middle atoms with similar or even equal electron negativity.0527

An example of that would be, let us go back to our nitrogen.0536

That would be an example of a non-polar bond because nitrogen,0541

if we have a nitrogen with an electron negativity of 3.04 and nitrogen with an electron negativity of 3.04,0545

they are exactly the same so electrons are evenly shared.0558

Whereas, this chloride, this is a 3.16 electron negativity, hydrogen over here is a 2.20.0563

Electrons will move toward the chloride.0575

Some examples of a non-covalent bonds, or what a non-covalent bond is.0588

They are not the same as the covalent bond.0594

They do not have that real nice sharing of the actual electrons, these are not electron sharing.0598

Ionic bonds, hydrogen bonds, hydrophobic interactions, and Van Der Waals forces, are all examples of non-covalent bonds.0607

Ionic bonds being the strongest, Van Der Waals forces being the weakest.0618

Ionic bonds form between charged groups or otherwise known as ions.0627

They are the strongest of the non-covalent interactions.0633

An example, let us say, our sodium ion, our chloride ion, coming together to make sodium chloride otherwise known as table salt.0636

Hydrogen bonds are a type of dipole-dipole interaction between a hydrogen atom and a highly electron negative atom,0652

usually being your oxygen, nitrogen, sulfur, and fluorine.0664

As I mentioned before in our example of a polar bond, I used hydrogen and chlorine, hydrogen chloride as being a polar bond.0671

Hydrogen and oxygen, hydrogen and nitrogen, those are not polar bonds, those are examples of hydrogen bonds.0682

We have non-covalent bonds, the other two left, we have hydrophobic interactions and0694

those occur between non polar molecules to limit their interaction with water.0702

Think of droplets of oil in the water and how they come together to form a bigger droplet, I will explain that a little bit.0707

Finally, Van Der Waals forces, these occur between all molecules as a result of unequal distribution of electrons.0718

These can be attractive or repulsive.0727

Altogether, when we are talking about these bonds, multiple weak bonds can have an additive effect to stabilize molecules.0732

We will see that throughout this course, especially for DNA.0741

Hydrogen bonds not very strong, Van Der Waals forces not very strong,0745

hydrophobic not very strong, but those together actually hold our DNA.0750

They hold the two strands of DNA together.0756

A lot of very weak bonds, added up over the length of the molecule can be very strong.0760

Let us get some examples of covalent and non-covalent bonds.0773

Covalent, we will do in blue.0777

Let us say polar, example of a polar one.0785

An equal distribution of electrons, we said before HCl.0790

I will give you another one, CH₄.0799

CH₄ looks like this.0806

There is equal sharing between the carbon and hydrogen in all of those.0813

A non-polar, we have the one that we talked about before, N₂, we have O₂.0818

Any diatomic molecule, you put them right here, hydrogen gas, sulfide gas.0835

Or even the carbon bond in an ethane molecule.0843

This is what ethane looks like.0849

We can even draw that out to look like this.0859

All the carbon hydrogen bonds are actually covalent, polar covalent.0871

The bond between the carbon and the carbon is actually a non-polar covalent bond.0879

The non-polar, let us put in green, this is actually non-polar.0886

Let us give some examples of, what else do we have.0898

Some examples of a non-covalent.0906

Let us say ionic, I gave you one already, sodium chloride.0919

That is going to be the strongest.0926

We have hydrogen bonds, those are going to be like the ones that I shown for water.0928

They are usually longer than covalent bonds.0937

Let us see you right here, if I can draw one out.0940

By the way, water those are covalent bonds between the hydrogen and oxygen.0949

It would be a polar covalent bonds.0955

I will even draw that one up here, H₂O.0958

These are polar bonds or covalent bonds.0974

If I draw another, water, this right here, the bond between the oxygen and0984

the hydrogen of two separate molecules is a hydrogen bond.1000

Now we have hydrophobic interactions.1006

Hydrophobic interactions that would be like water and oil droplets.1013

Van Der Waals, that just says that when any two molecules come together,1020

there is a point at which they are attracted, that point is 4 to 10 angstroms.1034

There is an attraction between 4 and 10 angstroms.1049

If you go below 4 angstroms, you start to get a repulsion.1053

If you go outside of 10 angstroms then there will becomes no attraction at all.1058

One thing I want to mention about Van Der Waals is that, Van Der Waals force is actually pretty cool.1067

Van Der Waals forces, as I said, occur between any molecule.1074

Van Der Waals forces are what is responsible not only for helping DNA stay together1077

but for geckos and spiders attach into the walls.1082

That is how they stick to walls, it is different than flies and other insects.1089

That is a different way that they utilize that.1094

But geckos and spiders, specifically, the way they attach to walls is through Van Der Waals forces.1098

I think that is pretty cool.1104

Let us move on to the properties of water.1109

First thing you need to know about water is that it is a polar molecule.1112

Which means we have oxygen which is highly electron negative, bound to hydrogen which are not very electron negative.1120

Therefore, we have a partial negative charge at the oxygen because it is trying to steal the electrons.1129

We have partial positive charges with the hydrogen.1141

This symbol here is a Δ, the Greek letter Δ.1147

Water is important because it is a solvent in which everything in the cell is dissolved.1154

We have to take into account water in anything in our living system.1161

Water can hydrogen bond, you can hydrogen bond several water molecules together.1171

A single water molecule can actually make 1, 2, 3, 4 different hydrogen bonds, with 4 different water molecules.1178

The oxygen of a water molecule can hydrogen bond with two different hydrogens from different water molecules.1197

Each hydrogen of that original water molecule can hydrogen bond with an oxygen of a different water molecule.1207

If you look here on your right, this is the cubic form.1217

It is the crystal structure of the solid water which we know as ice.1223

Water also is going to undergo hydrophobic interactions.1233

Literally, what hydrophobic means is hydro water, phobic afraid.1237

It can be hydrophobic, afraid of water, hydrophilic water loving; philic - love.1245

We are going to talk about those terms, especially when we talk about proteins, later in this class.1251

Hydrophobicity, the not wanting to interact with water.1261

The hydrophobicity of non-polar molecules promotes aggregation,1265

they come in together by releasing water molecules in contact with their surfaces.1272

They released water to form more hydrogen bonds with other water molecules.1278

Imagine that this oil is in a aqueous solution of water, it is surrounded by water molecules.1284

The water wants to interact with other water molecules, we know that it did not want to interact with oil.1305

The oil desperately wants to interact with other things than water.1312

The oil wants to reduce its total surface area touching water.1319

What water will do is, it will come together to push water out.1325

It pushes all this water out to that surface area that is touching the water.1333

It will basically erase all that by becoming this big blob.1338

Of course, water still attached on the outside but it is pushed out a lot of water in the process.1345

It is better for the oil, now it is just touching less water, right.1351

It is better for the water because the water is touching more water.1357

This is a huge property of water and this is important.1361

We always think about our non polar molecules because of this.1366

Let us switch just a little bit to chemical reactions of free energy.1375

Any reaction, A + B going to C + D, there is always something called an intermediate or a transition state that we usually do not see.1380

That is the point that we call here AB, that is the point at which it is transitioning from the reactants A and B, to the products C and D.1390

It usually occurs via an enzyme.1402

The weight of the reaction is affected by the concentration of the reactant, as well as the concentration of the products.1408

The weight will also be affected by the energy barrier, the temperature,1419

as well as the pH of the solution in which the reaction is occurring.1425

When we are talking about chemical reactions, it is extremely important to know that1435

forward and reverse reactions are occurring simultaneously.1441

It is happening in both directions.1448

But the speed of reaction in the rightward direction vs. the leftward direction, differ.1452

That is what allows you to either make a bunch of products or stay with a bunch of reactants.1460

This equilibrium state is a very dynamic state, whether right of your forward and reverse reactions are equal.1470

It is important to note that forward in reverse reactions are still occurring but there is no net change of reactant or product.1480

If one reactant is being turned into a product then one product is being turned back into a reactant.1495

Forward reverse reaction is still occurring but at the same rate.1505

I have a zoomed out to macro view, nothing is changed.1509

We can measure the equilibrium because each reaction is going to have an equilibrium constant which is KEQ.1517

That is going to measure the extent to which reactants are converted into products.1527

It is a very simple measurement, it can get much more complex but I’m presenting you the simplified one.1532

Is that the KEQ is equal to the concentration of your products over the concentration of you reactants.1537

From here, you can understand that if you have your numerator bigger,1545

KEQ is going to be greater than 1, your reaction favors the products.1554

If you the denominator larger, you are going to have a number less than 1, that reaction is going to favor the reactants.1559

They are backwards.1569

As an example of these, I want to show a very cool aspect of chemical reaction.1575

In the following reaction equation, label the reactants and the products.1583

As we talked about before, I will work this through with you.1589

A + B going to C + D, you are starting with this.1593

These are going to be your reactants.1600

Your A and B you want in C and D, that is your going to be your products.1607

This is a double headed arrow that we see right here.1615

Here is a double headed arrow meaning this reaction is reversible, it can go on both directions.1628

In the other direction, C and D are your reactants, A and B are your products.1635

All 4, A, B, C, and D, are reactants and all 4 A, B, C, and D are products at one point or another, in this reaction.1650

Rightward reaction, A and B reactants.1661

Leftward reaction, C and B reactants.1664

Continuing on with our chemical reaction of free energy.1671

I want to introduce the concept of activation energy also shown as E sub a.1674

Activation energy is the minimum energy that is needed to the input to cause a chemical reaction.1680

In two reactants, let us say X + Y, clogged energy gets released.1691

It has to be greater than the energy barrier for the reaction to proceed.1696

Its energy barrier is that amount of energy required for the formation of the products.1702

This is your energy barrier or your activation energy.1708

Because this is the energy of your reactants and this is the energy of your products.1722

Even though your energy of your products are lower than your reactants,1732

you have to pass this hump, this threshold, to be able to get down to here.1735

Let us talk about enzymes, enzymes are biological catalysts.1747

They accelerate reactions by decreasing the activation energy.1753

Enzymes do not affect the reaction equilibrium, the KQ, or the change in the free energy.1762

But they can decrease this, let us say with an enzyme, my curve might look like this.1778

With, this is my activation energy with an enzyme.1802

This is my activation energy without an enzyme, which is much higher.1820

As we can see, this, the energy of the reactant and the energy of the product is unchanged.1836

Let us give a few statements about chemical reactions and free energy.1852

What is free energy, usually we talk about it as Gibbs free energy and as the change in Gibbs free energy, ΔG.1858

This is the difference between the free energy of the products - the free energy of the reactant.1868

As we saw back there on the previous slide, we had two different looking graphs.1878

This is reaction progress, this was free energy.1897

We know that the left tail, this is our reactant.1914

The right tail is our product.1922

We know that this is our activation energy or energy barrier.1927

If your products have a higher free energy, then your reactants, what do we have,1936

the difference between the free energy of the products.1945

What we are looking at is the G of our products - the G of our reactants.1948

That is our ΔG.1963

If our products have a higher energy state than our reactants, that ΔG is going to have a positive sign.1967

Meaning, you need to add in energy from the system, usually in a form of heat or ATP, to get up to this energy level.1983

That usually means that the reaction is non spontaneous.1994

It would not happen on its own, you need the input of energy.2000

This is also called an endorgonic reaction.2003

Let us look at the flip side, if our energy for our product is lower than our energy for our reactant,2013

we are going to have a -ΔG.2022

That means that it is actually going to give energy off to the system in the form of heat or ATP energy.2026

This will likely be spontaneous, meaning it can happen because you do not need to input in energy.2036

This is called an exorgonic reaction, it is likely to happen.2041

When your reactants and your products have the exact same amount of free energy,2050

That is when you are saying that that the reaction is at equilibrium.2062

You are no longer going one way or the other.2068

What is important here is that ΔG, ultimately only determines2072

the final concentrations of reactants to products but not the reaction rate.2078

The reaction rate is determined by the enzymes, by the activation energy.2090

Over here, remember, if we have the reactant, product, we have our activation energy.2103

This is endorgonic, you need to put in energy because the products have a higher energy than the reactants.2123

Meaning this is ΔG of positive, meaning endorgonic positive ΔG non spontaneous.2132

In this reaction, our reactants have a higher energy than the products.2152

Meaning they are giving energy off to the system, meaning it is exorgonic.2156

The ΔG is negative, it is likely to occur spontaneous.2162

One thing about spontaneous and not spontaneous, are –ΔG and +ΔG,2175

is that just because you have a +ΔG and it is a non-spontaneous reaction, it does not mean it will never occur.2182

Reaction coupling is what happens, meaning you can add a -ΔG to a +ΔG reaction to allow that +ΔG reaction to occur.2190

What happens is that, the second reaction consumes the products of the first reaction,2207

preventing reverse of the reaction which would otherwise be favored.2213

If you can, let say, here is our progress, here is the free energy.2217

What you could actually have here, this can be a reactant-product.2238

This can be a reaction 1, as we can see here, the products are much lower in energy.2259

The reactants, therefore, it is high -ΔG.2277

This can be coupled to another reaction where it is a +ΔG.2283

This product of reaction 1 now becomes the reactant of reaction 2.2300

That is how they can be coupled to force a +ΔG non spontaneous reaction to go forth.2317

Let us quiz you, based on the last couple of slides.2327

What information can be gained from a reaction with a –ΔG.2330

A –ΔG reaction is going to tell you that a reaction is spontaneous.2345

No energy input is needed, in fact it gives off energy to the system.2351

It will favor the formation of the products, -ΔG affects the equilibrium but not the rate.2358

It may be coupled with the +ΔG reaction to force that to proceed.2368

That is the biochemistry review that I wanted to do but I also want to introduce you to DNA.2380

We are going to go to DNA in much further detail in a few lectures but I wanted to introduce it to you first.2387

DNA stands for deoxyribonucleic acid, that is what the DNA stands for.2394

Let me write that out for you, deoxyribonucleic acid.2399

DNA is normally found in, let us call a double helix.2419

It is two stranded, as we can see over here.2423

It is in an anti parallel orientation.2428

Each strand has a 5 prime phosphate and a 3 prime hydroxyl end.2432

When it is in a double helical form, you have one strand, if we are just going to read this from top to bottom, going 5 prime to 3 prime.2448

It is bound to its complimentary strand in the opposite or2459

anti parallel orientation with 5 prime going up to the top of the page to the 3 prime hydroxyl end.2464

Purine bases and pyrimidine bases are two types of heterocyclic nitrogen bases that are parts of a nucleotide.2474

A nucleotide is the monomer of a nucleic acid.2484

Purines are two ringed heterocyclic nitrogen structures.2489

Pyrimidines are single in structure.2494

Purines and pyrimidines are always pair together.2498

Adenine is an example of a purine.2501

It will hydrogen bond to thymine which is an example of a pyrimidine.2506

Guanine is an example of a purine down here.2513

Cytosine is an example of a pyrimidine, they will hydrogen bond.2519

G’s and C’s always make 3 hydrogen bonds, as you can see here.2524

A’s and T’s always make 2 hydrogen bonds.2529

Under normal circumstances, A’s only bind with T’s in DNA.2533

G’s only bind with C’s in DNA.2539

Those bonds are on the inside.2545

On the outside is the phosphate backbone that links the nucleotides of the same chain together.2548

I said before that the bases on the inside making hydrogen bonds, 2 between A’s and T’s, 3 between G’s and C’s.2558

This right here is an example of a nucleotide.2572

These are the monomers of DNA, of the nucleic acid polymer.2579

It has to have a nitrogenous base, a purine in this case, a pyrimidine could also work.2585

Sugar, if it is DNA, it deoxyribose.2592

If it is going to be RNA, it would be an oxygen.2597

It must have a phosphate group.2609

Just a few other quick things on DNA.2615

It has several forms, A, B, and Z forms.2618

The normal is B form, that is found, there are 10.4 base pairs per turn of the helix in B DNA.2620

Let us say from here to here is one turn.2629

There are 10.4 base pairs, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10.2636

There are both major and minor grooves on the surface of the helix.2648

We of the major groove, it goes this way.2652

The major groove and the minor groove.2658

These are important because as we will talk later, you can see more of the chemicals,2662

the atoms in the DNA, that helps for DNA binding of proteins.2673

What is important and I talked about, earlier in this unit is that hydrogen bonding and2679

hydrophobic interaction is also known as base stacking interactions, hold the two strands together.2684

Our DNA can be denatured and renatured, meaning you can break and remake the hydrogen bonds,2698

kind of as if nothing ever happened.2708

You are not breaking the molecule at all, you are just separating the two chains.2711

Think of it like an ice cream sandwich, the two cookie crust are your DNA S strands, your ice cream is your hydrogen bonds.2715

If you want denature your double stranded DNA, you just melt those hydrogen bonds.2729

A couple of ways to do it is actually with heat.2737

If you microwave your ice cream sandwich, which would just be a waste of an ice cream sandwich,2740

if you did, you would be able to pull apart this cookie crust very easily.2746

Another way to denature double stranded DNA is, if you put in a high PH environment or low salt concentration.2751

Or if you add metabolic enzymes that are made to break that open.2761

A cool thing about DNA is that the same complimentary DNA strands that were denatured can renature,2766

or reheal when the environment is brought back to normal, if you decrease the temperature,2773

if you decrease the PH, if you increases the salt, certain things like that.2778

DNA strands will anneal to what it should have anneal to, what are called complimentary sequences.2783

A’s and T’s will come back, G’s and C’s will come back to each other.2790

Speaking of the ability to denature and renature, I want introduce you to a concept called hyperchromiicity.2797

What hyperchromiicity is, it is just the increase of absorbent of a substance.2806

Single stranded DNA absorbs more UV ultraviolet light, then an equal amount of double stranded DNA, almost about 20% more.2818

If single stranded DNA, if you had 10 base pairs, it would be 10 bases, because it is single stranded.2830

You had 10 base pairs of DNA, this 10 bases of RNA would absorb about 20% more UV light than double stranded DNA.2841

That is because the actual nitrogenous bases, the A’s, G’s, and T’s,2856

they are purines and pyrimidines, are what is absorbing that UV light.2862

When it is in a double stranded helix, they are compact inside on the inner portion of the double helix.2866

Single stranded DNA or single stranded RNA, those flap out in solution.2873

What we can do, we can determine at a certain point, based on the absorbents.2881

If we have microscopic DNA we cannot see in solution, we will be able to tell if it is DNA or RNA,2887

or if it is double stranded specifically or single stranded.2899

How we do that is we use a machine called a spectrophotometer.2903

We make are reading, we take a reading, when we take a sample of DNA in the water or a buffer, put into a clear tube.2907

Put it in the machine, you shine light through the one side of the cuvette.2919

You have a detector on the other side, it will calculate how much of the original light came all the way through how much is captured.2924

They do that at a wave length of 260 nm.2934

At this low wavelength, at this wavelength, we are reading absorbent values.2939

An absorbent of 0 means that it is completely translucent, all the light went all the way through.2956

An absorbent of 100% that means it is completely blocked out,2964

not a single photon of light went from the light to the capturing device.2969

At this absorbents level, we have everything being double stranded.2975

As you increase the temperature, you start to denature the DNA.2981

You start to melt those bonds.2987

As you melt the bonds, the nitrogenous bases start being able to flap around the solution,2990

meaning it catches more UV light, it absorbs more.2996

Into the point where you are completely denatured, this is double stranded DNA.3000

Until you completely denatured and this is actually single stranded DNA, where it has before absorb it.3007

Right here at the inflection point is what we call that TN or the melting point.3013

The melting point is the point at which you have 50% of your DNA as double stranded and 50% as single stranded.3024

The TM, the melting temperature, is determined by the base sequence, as well as the salt concentration.3044

That can affect the shielding, salt concentration will affect if you denature or not.3049

For our last portion of this unit, I want to leave you with a very crude method3063

to approximate a melting temperature without using any type of absorbent device or techniques.3069

For example, the crude method is that for every AT base pair, that = to 2°C.3077

For every GC base pair, that is 4°C.3090

When we usually calculate this, when we are making primers for a polymerase chain reaction PCR,3097

which is another thing we will learn in this class.3103

I wanted to give you a sample problem.3107

For example, let us say we have this sequence AT, GC, AT, GC.3109

What would be the melting temperature of this 10 base pairs sequence be?3123

We have count up how many A’s and T’s, AT bonds are 1, 2, 3, 4, 5, 6.3133

That leaves us with how G’s and C’s, 1, 2, 3, 4.3145

6 AT bonds × 2°C = 12°C.3153

4 GC bonds × 4°C = 16°C.3163

Add those together that gives us a melting temperature of this sequent at 28°C.3172

As you will be able to see is that regions with higher GC content will have higher melting temperatures.3186

Regions with higher AT content will have lower melting temperatures comparatively.3196

Thank you for joining me at www.educator.com.3203

I hope you come back and see me in lecture 2, thank you.3207

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.