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Michael Philips

Michael Philips

Structure of Proteins

Slide Duration:

Table of Contents

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

53m 29s

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

1h 9m 27s

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

49m 44s

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

1h 2m 10s

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

57m 2s

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

1h 9m 55s

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

1h 13m 8s

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

1h 14m 27s

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

1h 19m 28s

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

1h 15m 1s

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

45m 40s

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

1h 6m 6s

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

1h 8m 41s

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

45m 6s

Intro
0:00
Lesson Overview
0:47
Genome Editing
1:37
What is Genome Editing
1:43
How It Works
2:03
Four Families of Engineered Nucleases in Use
2:25
Example 1
3:03
Gene Therapy
9:37
Delivery of Nucleic Acids Into a Patient’s Cells a Treatment for Disease
9:38
Timeline of Events
10:30
Example 2
11:03
Gene Therapy
12:37
Ethical Questions
12:38
Genetic Engineering
12:42
Gene Doping
13:10
Synthetic Biology
13:44
Design and Manufacture of Biological Components That Do Not Exist in Nature
13:53
First Synthetic Cell Example
14:12
Ethical Questions
16:16
Stem Cell Biology
18:01
Use Stem Cells to Treat or Prevent Diseases
18:12
Treatment Uses
19:56
Ethical Questions
20:33
Selected Topic of Ethical Debate
21:30
Research Ethics
28:02
Application of Fundamental Ethical Principles
28:07
Examples
28:20
Declaration of Helsinki
28:33
Basic Principles of the Declaration of Helsinki
28:57
Utmost Importance: Respect for the Patient
29:04
Researcher’s Duty is Solely to the Patient or Volunteer
29:32
Incompetent Research Participant
30:09
Right Vs Wrong
30:29
Ethics
32:40
Dolly the Sheep
32:46
Ethical Questions
33:59
Rational Reasoning and Justification
35:08
Example 3
35:17
Example 4
38:00
Questions to Ponder
39:35
How to Answer
40:52
Do Your Own Research
41:00
Difficult for People Outside the Scientific Community
41:42
Many People Disagree Because They Do Not Understand
42:32
Media Cannot Be Expected to Understand Published Scientific Data on Their Own
42:43
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Lecture Comments (6)

1 answer

Last reply by: Professor Michael Philips
Fri Nov 16, 2018 12:48 PM

Post by Paul Mcinulty on August 7, 2017

Also thank you for explaining Polar Covalent bonds so clearly, I'm now looking at Mendelevs periodic table in a whole new way and it makes sense. I now understand how these molecules come together and function the way they do

1 answer

Last reply by: Professor Michael Philips
Fri Nov 16, 2018 12:48 PM

Post by Paul Mcinulty on August 7, 2017

Also AUG is the start or initiator codes is this correct?

1 answer

Last reply by: Professor Michael Philips
Fri Nov 16, 2018 12:51 PM

Post by Paul Mcinulty on August 7, 2017

Dear Mr Phillips just to make it absolutely crystal clear in my mind if, for example in a haploid gamete I have chromosome 1a all thst it contains are alleles?
Now if I take another haploid cell containing chromosome 1b that contains the same allele or an alternative allele, these two haploid cells come together to produce an offspring, will those two alleles produce a gene?
Do you get just half your alleles from one parent and the other half from your other parent and then those alleles produce your genes?
If this is correct then thank you so much, because I have spent quite a while trying to find this answer.
Thank you so much Doctor Philips you are a superb teacher

Structure of Proteins

    Medium, 6 examples, 5 practice questions

  • Proteins are macromolecules made up of amino acids connected by peptide bonds.
  • 21 different amino acids are commonly incorporated into proteins, including selenocysteine.
  • Proteins can be organized into four degrees of higher order structure.
  • Three-dimensional structure often dictates the function of proteins.
  • Some proteins, called enzymes, can catalyze biochemical reactions.

Structure of Proteins

What type of bond is formed between amino acids in a polypeptide?
  • Amine
  • Amide
  • Ester
  • Hydrophobic
Which of the following has no net charge at a physiological pH of 7.4?
  • Isoleucine
  • Aspartate
  • Lysine
  • Histidine
The sequence of amino acids, connected by peptide bonds, is what level of structure?
  • Primary
  • Secondary
  • Tertiary
  • Quaternary
An example of secondary structure is _____.
  • DNA sequence
  • Total 3D shape
  • Protein dimer
  • Alpha helix
What is the most likely be the most similar between related proteins?
  • Nucleotide sequence
  • Amino acid sequence
  • Protein structure
  • Cellular location

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

Answer

Structure of Proteins

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

Transcription: Structure of Proteins

Hello, and welcome back to www.educator.com.0000

Remember, this is our molecular biology course.0003

Today, we are going to talk about the structure of proteins.0010

As an overview, we have to first talk about amino acids, since those are the monomers of proteins.0012

We will talk about the types of bonds in proteins called peptide bonds.0019

And then, importantly, we will talk about the big types of organization of structure.0024

We will mention protein folding and briefly talk about post-translational modifications.0030

Finally, we will end with protein classification and a short introduction on enzymes being biological catalyst,0036

just as we mentioned in the first lecture.0044

Amino acids, as I said, are the monomers that make up proteins.0050

This is the general structure of an amino acid right here on the left.0056

As we see here, we have a carboxylic acid group.0060

We have a carbon bound to that, which is our α carbon.0071

Then, bound to the α carbon is our amino group.0080

The carbon, its 3rd bond, the α carbon, it makes with a hydrogen.0087

And finally, its 4th bond is to something else, what we call an R group or a side chain.0092

The amino group, the hydrogen, and the carboxylic acid group, all attach to the α carbon,0104

is going to look the same in all of our amino acids.0110

The only difference is going to be in the R group.0112

Importantly, the acid dissociation constant of the amino group is at 9.1.0116

The acid dissociation constant of the carboxylic group is 2.3.0126

Those will come into play a little later.0131

Amino acids are going to make up proteins.0135

They do this by making peptide bonds also known as amide bonds.0139

The addition of amino acid 2 to amino acid 1 is catalyzed.0146

The type of reaction is called a condensation reaction, in which case we are pushing out water.0155

This right here is our water molecule that gets pushed out.0164

As we can see here, the N terminal, the N portion of amino acid 2 always comes in and0171

make its attachment, its bond to the C terminal portion of amino acid 1.0181

That is why we have amino acids following an N to C terminal orientation.0188

A protein is N to C, it is basically like saying N is the N terminal, amino acid is the 1st amino acid it is put in.0198

The C terminal amino acid is the last one that it is put in.0208

Here is a table of the 21 amino acids that we find in proteins.0216

Many of you may have learned that there are 20 amino acids found in proteins and that is very correct.0222

The one that makes the 21st is selenocysteine.0229

That is just a cysteine molecule that has a selenium group, instead of a sulfur group.0235

This is also been found to be incorporated into proteins.0247

These are all 20 amino acids that we incorporate into proteins.0250

There are many other types of amino acids that are not incorporated into proteins.0255

Our amino acids can be broken into multiple groups.0260

We have our charged amino acids, we have our positively charged or basic amino acids.0265

We have our negatively charged or acidic amino acids.0276

Only 5 of the 21 have any type of charge.0281

We have our uncharged amino acids, right here in group B.0287

We have in group D, our hydrophobic side chains.0294

These are the ones that are going to participate in our hydrophobic bond.0299

We have our special cases, as I said before, selenocysteine, is a kind of a special case.0303

cysteine is very special, and that sulfhydryl group right here, can participate in what are called disulfide bonds.0310

These are very important for the structure of proteins.0318

Glycine is special and that it is the simplest amino acid to where it is R group is only a hydrogen.0322

Proline is specific, is a special case, it actually has a secondary amide.0333

Its R group is not free, it comes back and bind to the amino group.0342

We will know this later, being able to call this a helix breaker.0348

When we talk about our amino acids, we need to know that our ionization will vary based on the environment, the pH.0358

We have our cation, a cation is just another way of saying a positively charged ion.0367

An anion is a negatively charged ion.0382

That is what we normally think of.0389

Our cation group is when we have our amino group being proteinated.0393

It has an extra charge right here, we have this extra positive charge because it has an extra hydrogen.0400

We still have the carboxyl group having its proton.0415

This can only happen when we are at a pH below the acid dissociation constant of that carboxylic acid group,0419

as well as below the amino group.0430

If you remember, the PKA, this is 2.3 and the PKA of this is 9.1.0433

When this is below 2.3, the pH is below 2.3, we are in the cation form.0449

When we increase our pH, pass that 2.3, we are going to start getting into what is called the zwitterion form.0470

This is going to exist between the PKA of our carboxlic acid group and the PKA of our amino group.0481

This is when our pH is between 9.1 and 2.3.0491

This is when we are going to see a zwitterions form.0511

What that means is that the carboxylic acid, if we see over here, it no longer has its H over here.0520

Now it has a partial negative charge, right.0528

We have a molecule right here that has a negative charge and a positive charge.0533

Once again, this is when we are not talking about the R group at all, playing a part into it.0539

That is going to be completely separate.0545

This is what we call a zwitterion.0547

A zwitterion is a molecule that has both a positive and a negative charge on it.0550

This is going to exist until we have a pH above 9.1.0556

Right here, when the pH is greater than 9.1, we are going to move into the anionic state.0563

That is when our amino group loses this proton.0574

Right here, remember here is that proton, we no longer have it.0580

We no longer have it right here.0587

We have our negative charge, we do not have that positive charge anymore.0591

This is a negatively charged ion.0598

A negatively charge ion, we know is an anion.0602

Remember, we are not talking about the R group at this point.0604

We are just talking about the major backbone, this is important.0607

What is the physiological pH in a human cell in the human body?0613

It is about roughly 7.4, in physiological circumstances, we are always going to see our amino acids in the zwitterion form.0617

They both have the positive and the negative charge meaning it is a neutral charge.0632

The only thing that will affect whether it is a positively or negatively charged amino acid is the R group.0636

For our first example, if we can just do a little memory recall,0655

which amino acids would have a net charge at physiological pH, which as I said before is about 7.4?0660

What that is saying is, what amino acids have a negatively or positively charged side chains,0670

because that is the only thing that is going to be attributing to the charge because the zwitterionic form is a neutral charge.0677

Our acidic ones, otherwise known as negatively charged, which ones are those?0687

They are aspartate, by the way the single letter code is D.0706

And then, we have glutamate, its single letter code is E.0718

Aspartate and glutamate are also often refer to as aspartic acid and glutamic acid.0727

What about our basic amino acids, otherwise known as having a positive charge.0736

We have 3 of those, we have arginine, that was R.0753

We have histidine and we have thymine and glycine.0765

Those are the only 5 amino acids that will have a net charge at physiological pH.0782

When we talk about amino acids, we need to talk about what form they are normally found in.0794

Most of our amino acids occur as what are called L α amino acids.0800

This is a type of configuration.0805

Only L amino acids become incorporated into protein.0809

We will see that the difference between an L and a D, or an α and a β amino acid, actually look like.0815

What do they look like?0826

Here is going to be an example of an L or a D amino acid.0829

All it is, is what side the amino group is on.0834

This is an L and it also happens to be an α amino acid.0854

Let us draw a D.0872

What we are looking at is, there are plenty of other ways to see this but very simply, written out in planar form.0893

If the NH₂ is on the left, it is an L amino acid.0901

If it is on the right, it is a D amino acid.0908

What about the difference between α and β amino acids?0923

Let us do a general example, and then we will do a specific example.0929

For our α, what makes this α?0939

You are looking at where this NH₂ group is connected to.0985

This NH₂ group is connected to the carbon that is connected to the carboxylic acid group.0991

The way that we count, we would find our carboxylic group and they found the carbon that is attached to it,0998

they call that the α carbon.1006

Therefore, we have the NH₂ group attached to that carbon, being the α carbon.1011

If we go to the β, the β amino acid, if we look once again, we count a way from the carboxylic acid group.1018

This would be the α carbon, this would be the β carbon.1073

This is the carbon where we have the NH₂ group and the R group attached.1079

This makes it a β amino acid.1084

This is how we can tell between L and D, as well as between α and β amino acids.1088

It is important that we now the side chains of all of our amino acids because1102

they basically tell us what types of reactions these amino acids are going to take a part in.1108

The characteristics of our side chains, our R groups.1117

If they are non-polar, these groups are going to form or can form hydrophobic bonds.1120

These residues are often going to be buried in the interior of the proteins because they are hydrophobic.1129

In contrast, our polar groups, they can form hydrogen or ionic salt bridges, or ionic bonds which are called salt bridges.1137

They can form ionic or hydrogen bonds.1148

They often cluster on the surface of the protein because these are hydrophilic.1150

For example, we have a protein.1156

I will just make it easier, I will just make it look like this.1162

You might be more likely to see non-polar residues on the inside, and see polar residues on the outside.1171

If we get a little more specific, we can look at the hydroxyl groups are serine, threonine, and tyrosine amino acids.1192

They can be phosphorylated meaning they can get the phosphate group attached.1202

This makes them negatively charged and it can also alter their function, either on the positive or negative way.1214

The sulfhydryl group, cysteine is unique and that it can be oxidized to form a disulfide bond.1222

A disulfide bond is just a bond between two sulfur groups.1229

This is going to be important for our structure of our protein.1234

We can have covalent bonds to carbohydrate forming what are called glycoproteins.1241

They can be either O glycosylated or N glycosylated proteins.1250

All what that means is, the sugar making a bond to the amino acid via an oxygen or a nitrogen.1255

What we have here is that we can see these groups, this oxygen and hydrogen,1264

which we know as a hydroxyl group, from serine and thrinine, can participate in the O glycoscillation.1271

In the NH2 group, the amine group of a spare gene can also participate in glycoscillation.1280

In this case, it is an N glycoscillation.1287

Finally, we have proline having what it is called the pyrrolidine structure.1291

That is this big hunk of a secondary amine.1299

It has a not very nice structure.1305

In fact, it is not an open chain.1318

This is what we call helix breaker, prolines are not found in helixes because this is too bulky.1320

It is too big to be formed properly in a nice helix.1326

Often, they are found at turns because they help with the U turn type characteristic.1331

Our peptide bonds are also call amide bonds, as we stated earlier.1342

Remember, they come from a condensation reaction where water leaves.1347

The amino acid 2 makes a bond using its nitrogen, it is amine group, with the already existing amino acid ones , carboxylic acid group.1357

In this case, if we have this peptide bond forming or MI I bond between two different amino acids,1376

we would call this amino acid the N terminal amino acid.1386

We will call this amino acid the C terminal amino acid.1394

You would always add the next amino acid to the C terminal.1399

This one will always be the N terminal amino acid.1405

We will talk about other instances where we can lose those amino acids.1409

Now we have talked about the monomers of amino acids,1418

let us talk about how we can organize the actual protein molecules, the polymer of amino acids.1421

What are these levels of organization?1432

If we look in the graph over here, this is a good one to look at, follow along while I'm talking.1435

We have the primary structure, here is being the simplest sequent of the amino acids that are connected by peptide bond.1442

In this case, we have this pair of gene, glycine, phenelalanine, glutamate, adenine, so on and so forth,1450

that is very the simplest portion.1458

The next part is secondary structure.1462

This is just local 3D structure, imagine you have just a short sequence of the entire polypeptide1467

into something that we are likely going to see as in α helix or a β pleated sheet, or turns and loops.1475

This is important because it is stabilized by non covalent hydrogen bonding, not occurred between the peptide groups.1485

The next portion or the next higher order level of structure, we call tertiary structure.1498

Tertiary structure is the overall 3D structure of the protein.1507

If we look here, we are now looking at this part, just a 3D structure,1514

are not stabilized by side chain interactions between our secondary structures as well.1520

Quaternary structure can only occur when you have more than one polypeptide.1528

More than one polypeptide can come together for amino overall 3D structure that is called the quaternary structure.1541

A little more in-depth, our primary structure, that is our specific amino acid sequence.1557

We are looking back here again.1562

It is connected by a peptide bonds or amide bonds.1565

This is dictated by our mRNA codons.1569

If we remember back to the previous lesson, we know the molecular biology central dogma.1574

It is DNA to RNA, this is via transcription.1584

RNA can be made into protein via translation.1620

RNA gets turned into protein, therefore, the protein is dictated by the mRNA codons.1628

This is going to direct the subsequent organization.1635

The RNA is going to code a single codon for our cysteine amino acid, and then a serine, a leucine, a phenelalanine.1638

This is how it is dictating.1648

It is very important that even a slight change in the primary structure of a protein will affect its ability to function.1654

An example of this is found in sickle cell trait.1662

The substitution of one amino acid for another in hemoglobin causes sickle cell disease.1668

All this is, it is a single different in the 5th amino acid.1675

It is changed from a proline to a valine.1680

A normal hemoglobin which is found in red blood cells, carries oxygen very well.1684

It has no affect on the shape of our red blood cell.1693

Our red blood cells normally look like this. They look like a nice little donut shape.1702

When we have this proline to valine substitution, that causes the amino acids to chain together in an unnatural way.1706

It causes the proteins to stretch and alter the shape of the red blood cell molecules.1723

When they are looking the sickle shape, they can end up blocking blood vessels because1738

they do not flow through nice and easy like a rounded donut shaped one.1748

They can block small capillaries and veins, and it cause blockage which can cause pain or possibly even death.1752

This can come from just a single substitution in a single protein, a single amino acid substation.1762

Our levels of organization continue, the secondary structure.1773

By the way, a way to describe structure is by going like this.1777

This would be primary structure, secondary structure looks like this, tertiary, and quaternary.1783

It is just that little degree sign.1790

Our secondary structure, I will write it over here once again.1793

This one is actually secondary.1799

Our secondary structure is just our local 3D structure.1803

It includes things such as our α helix, our β pleated sheets, and even our turns and loops.1807

Our α helixes and β pleated sheets are held together specifically by hydrogen bonding.1813

If we look here, these yellow portions are hydrogen bonds.1818

These are all hydrogen bonds that are keeping this helix together .1832

What about proline in secondary structure?1839

Proline is going to look like this.1845

This is what proline is going to look like.1889

As you can see, it is very bulky secondary amine.1892

If we talk back here, this is our α carbon.1897

We have our amine group, it is all attached in one.1905

It is not free to be working around.1912

What we have is that, this is actually considered an amino acid not an actual amino.1917

What this does, this actually is not able to be fit in a nice α helix.1928

Because what do we do, if we incorporate a proline, it would break that helix.1938

What is often found in is our β pleated sheets.1943

Our β pleated sheets normally run like this, it has a nice little turn.1948

Maybe we go like this again, nice little turn.1955

Our prolines are often going to be found in the turns because they help with the U turn portion of this.1963

This is important to know, that proline is not going to be found in α helixes.1975

To continue on our levels of organization, our tertiary structure.1982

This is our overall 3D structure of a protein.1988

What is important is that 3D structure is related to function.1992

What that is saying is that, structure dictates function.2001

If it looks a certain way, it is probably going to perform a certain action.2023

We are going to talk more and more about structure dictating function, as we go throughout.2027

Our tertiary structure is stabilized by hydrogen bonds, ionic bonds, hydrophobic interactions, and our disulfide bonds.2033

If you remember correctly, our disulfide bonds are found in our cysteine residues.2045

Our quaternary structure only can occur when we have more than one polypeptide, more than one subunit.2054

We are looking at right here, the red is its own polypeptide.2064

This other multicolored one is its own polypeptide.2072

When they come together and form a complex, that now is a quaternary structure.2076

Hydrogen bonds, ionic bonds, and hydrophobic interactions, all stabilize quaternary structure.2083

What will ultimately determine a proteins native structure?2096

What do we think?2103

First of all, the proteins linear amino acid sequence is going to determine that.2105

What structure is that, what higher level order is that, primary, tertiary, quaternary, secondary?2123

Our linear amino acid sequence is primary structure.2132

What else will determine our native protein structure?2140

When we are talking about protein native structure, what we are even talking about, tertiary structure.2148

This question is asking what determines our tertiary structure.2156

What is our tertiary structure, that is the overall 3D, the total 3D depiction of it.2160

That is tertiary.2171

The answer to what ultimately determines a proteins native structure is its linear amino acid sequence, its primary structure.2174

Remember, structure dictates function.2184

Do no forget that one, we will come back to that multiple times.2221

Proteins, once they are made, once they have their tertiary structure, they can fold into a whole bunch of things.2228

They can be globular, they can look like a ball.2234

They can be fibrous, they can look like a filament or a string.2240

There is a whole bunch of ways and this is just a short small sampling of what they can look like.2245

Proteins can fold into many different shapes.2250

They are helped folding by what are called chaperones.2254

These are other types of proteins.2258

If a protein is poorly folded, sometimes you can unfold it which is called the denaturing,2261

and try to refold it again, that oftentimes does not help.2268

What you end up having to do is breakdown that protein, basically, throw it away.2273

You degrade it by sending it to either the lysosome or the peroxisome.2279

Those are basically like the cellular trash can.2294

When we have made our proteins, we can talk about what happens next.2303

We are not going to talk about the reactions right now.2310

We can alter what happens to a protein, after it leaves the ribosome.2314

That is when we are altering a protein, after its left being synthesized, after translational.2320

That is called post-translational modification.2327

These post-translational modifications can regulate a proteins activity.2332

It can regulate its localization, as well as how it interacts with other molecules.2338

It can alter its structure, it can alter its function.2344

Some common types of post-translational modifications are glycoscillation, that is the addition of sugar.2348

We can have phosphorylation which is the addition of a phosphate group.2358

We can have acetylrelation, that is the addition of acetyl group.2365

Methylation is the addition of a methyl group.2370

Lipidation that is the addition of a lipid, you know better as a type of fat.2374

Ubiquitination is the addition of a protein, a small protein called ubiquetin.2391

Proteolysis is cutting the protein.2402

Maybe the protein, you have a protein amino acids, you cutoff the first 5.2407

Proteins can be classified in many different ways.2424

One of the easiest ways to classify them is based on their function.2427

You do not necessarily want to classify them based on what they look like.2431

You want to classify them based on what they do.2433

As we can see here, a majority of our proteins are going to be ligand binding, DNA binding, enzymatic.2436

The rest of them can be broken down into many other things.2452

An enzyme is going to catalyze a reaction.2456

DNA and RNA binding, self explanatory, it is going to bind to nucleic acids.2459

Ligand binding in protein, protein interactions is going to bind to either a protein or maybe a compound in a cell.2464

We have plenty of others that serve structural purposes or make membrane proteins, things can go in and out.2472

We have transcription regulators, otherwise known as transcription factories.2480

They can either increase or decrease the speed of making in RNA, therefore, the making of a protein.2484

Some are involved in contraction, transport, some proteins are actually hormones like insulin is a peptide based hormone.2493

We have storage, some are used as protection.2505

There are many different types.2512

The majority are these 3 types.2514

Since we are talking about enzymes, we have talked about it before, in unit 1, enzymes are biological catalyst.2521

Most metabolic processes require a catalysts.2529

They need some form of catalysis.2533

Our enzymes, if you remember back from the first unit, accelerate reactions.2538

They do that by decreasing the activation energy.2546

That activation energy is the energy required to get over the energy barrier.2549

That is what allows you to get to the transition state.2554

What is very important is that, enzymes increase the velocity reaction2558

so highly that uncatalyzed reactions may never actually occur.2563

These can be increased on a hundred thousand fold to over trillion fold.2571

This actually allows you a reasonable amount of time for a reaction to occur, in the presence of the enzyme.2584

Most biological catalysts are enzymes, are proteins, but not all of them are proteins.2592

Not all of them are proteins, some enzymes can be called what are called by ribozymes,2598

that is where the active component is in RNA molecule.2607

It is important to know that enzymes have a specificity of reactant.2612

An enzyme is only going to allow a certain thing, a certain compound, combined in it.2620

For example, if my hand is an enzyme and the pen is the reactant.2627

It fits in there just fine, and now the enzyme is free to catalyze the reaction.2635

The product of the reaction is writing on this slide.2640

If my hand enzyme where to pick up my notebook, as the reactant, do I get the product of writing on the slide?2649

No, the enzyme is specific to the reactant.2662

It is only going to catalyze a reaction when it has the correct reactant in it.2665

And then finally, enzymes have an optimum pH in temperature, meaning they work in a certain environment.2671

The cells in our body at a pH around 7.4, had enzymes that are happy at about 7.4, in 98° F.2680

But if you were to throw those enzymes into our stomach acid which is around pH, anywhere from 1 to 4,2691

those enzymes would not work very well.2701

In fact, they will be denatured and then have to be degraded and thrown away.2702

This is important.2706

For our final slide, we are going to talk about just a quick example.2710

I want you to arrange the following three properties from least similar to most similar, between related proteins.2716

What I'm asking you is between two proteins that are related,2724

what is the most likely sequence that is going to be similar between any two proteins?2729

Let us say, remember we are looking at the 3D structure of a protein.2747

The structure dictates function, meaning multiple things that look alike can do the same thing.2755

We might see then that the protein structure is going to be the most similar.2774

If we remember back to the second unit, when we talked about the genetic code,2795

we have DNA being made into RNA, and RNA being made into a protein.2804

If you remember it correctly, to make a protein, we need our amino acids.2834

If we remember, multiple different codons on the RNA can be made into the same amino acid,2841

which we call the degeneracy of the genetic code.2857

Therefore, our amino acid sequent, we could get aspartate from multiple different pieces of RNA triplets.2861

123, 123, 123, 123, this is RNA codon.2878

Remember, our RNA is made from DNA.2885

This will have come from 123 of DNA, so on and so forth.2888

This should allow us to understand that, what is next most similar between related proteins would be the amino acid sequent.2899

Therefore, leaving us with the least similar being our nucleotide sequence.2919

From least similar, similarity increases as you go from left to right.2942

We could add in another one over here, that what could be either more similar, would be protein function.2958

We would go right here.2976

That ends our lesson for today, thank you for watching www.educator.com.2979

Please come back and see me again soon.2983

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