Sp​ilianakisLab

COURSE BIOL207 - MOLECULAR BIOLOGY
TYPE OF COURSE Core, Mandatory
YEAR 2nd year undergraduate Biology students
SEMESTER Winter
CREDITS 4 (ECTS=6)
DEPARTMENT Biology, University of Crete
LECTURES Biology Auditorium I, Wednesday 14:00-16:00, Friday 17:00-19:00 
COURSE MATERIAL In Google Classroom (class code: er4vfo3) you can have access to i. textbooks of the course, ii. Powerpoint presentations of the lectures, iii. pdf files of the lecture presentations, iv. previous exams questions & answers, v. Video files of ZOOM lectures, vi. educational videos.
  • Molecular Biology of the Gene, 7th Edition
  • James D. Watson, Cold Spring Harbor Laboratory
  • Tania A. Baker, Massachusetts Institute of Technology
  • Stephen P. Bell, Massachusetts Institute of Technology
  • Alexander Gann, Cold Spring Harbor Laboratory
  • Michael Levine, University of California, Berkeley
  • Richard Losick, Harvard University
  • EVDOXOS ID: 41960287
  • Principles of Molecular Biology
  • Burton E. Tropp, ​Queens College/CUNY
  • EVDOXOS ID: 41959952
  • Molecular Cell Biology
  • HARVEY LODISH, ARNOLD BERK, CHRIS KAISER, MONTY KRIEGER, ANTHONY BRETSCHER, HIDDE PLOEGH, ANGELICA AMON, KELSEY MARTIN
  • EVDOXOS ID: 771132967777113296113296
  • Lewin's Genes XII
  • Jocelyn E. Krebs, Elliott S. Goldstein, Stephen T. Kilpatrick
  • (Greek Publisher: UTOPIA)
  • EVDOXOS ID: 94674819

Lectures content and download

LECTURE 1

Nucleic acids convey genetic information. 
- AVERY’S BOMBSHELL: DNA CAN CARRY GENETIC SPECIFICITY
- Viral Genes Are Also Nucleic Acids
- THE DOUBLE HELIX
- Chargaff’s Rules
- Finding the Polymerases That Make DNA
- Experimental Evidence Favors Strand Separation during DNA Replication
- THE GENETIC INFORMATION WITHIN DNA IS CONVEYED BY THE SEQUENCE OF ITS FOUR NUCLEOTIDE BUILDING BLOCKS
- Evidence That Genes Control Amino Acid Sequences in Proteins
- DNA Cannot Be the Template That Directly Orders Amino Acids during Protein Synthesis
- RNA Is Chemically Very Similar to DNA
- THE CENTRAL DOGMA
- The Adaptor Hypothesis of Crick
- Discovery of Transfer RNA
- The Paradox of the Nonspecific-Appearing Ribosomes
- Discovery of Messenger RNA (mRNA)
- Enzymatic Synthesis of RNA upon DNATemplates
- Establishing the Genetic Code
- ESTABLISHING THE DIRECTION OF PROTEIN SYNTHESIS
- Start and Stop Signals Are Also Encoded within DNA 


LECTURE 2

Weak and strong chemical bonds. 
- CHARACTERISTICS OF CHEMICAL BONDS
- Chemical Bonds Are Explainable in Quantum-Mechanical Terms
- Chemical-Bond Formation Involves a Change in the Form of Energy
- Equilibrium between Bond Making and Breaking
- THE CONCEPT OF FREE ENERGY
- Keq Is Exponentially Related to DG
- Covalent Bonds Are Very Strong
- WEAK BONDS IN BIOLOGICAL SYSTEMS
- Weak Bonds Have Energies between 1 and 7 kcal/mol
- Weak Bonds Are Constantly Made and Broken at Physiological Temperatures
- The Distinction between Polar and Nonpolar Molecules
- van der Waals Forces
- Hydrogen Bonds
- Some Ionic Bonds Are Hydrogen Bonds
- Weak Interactions Demand Complementary Molecular Surfaces
- Water Molecules Form Hydrogen Bonds
- Weak Bonds between Molecules in Aqueous Solutions
- Organic Molecules That Tend to Form Hydrogen Bonds Are Water Soluble
- Hydrophobic “Bonds” Stabilize Macromolecules
- The Uniqueness of Molecular Shapes and the Concept of SelectiveStickiness
- The Advantage of DG between 2 and 5 kcal/mol
- Weak Bonds Attach Enzymes to Substrates
- Weak Bonds Mediate Most Protein–DNA and Protein–Protein Interactions
- HIGH-ENERGY BONDS
- MOLECULES THAT DONATE ENERGY ARE THERMODYNAMICALLY UNSTABLE
- ENZYMES LOWER ACTIVATION ENERGIES IN BIOCHEMICAL REACTIONS
- FREE ENERGY IN BIOMOLECULES
-High-Energy Bonds Hydrolyze with Large Negative ΔG 


LECTURE 3

The Structure of DNA
DNA STRUCTURE
- DNA Is Composed of Polynucleotide Chains
- Each Base Has Its Preferred Tautomeric Form
- The Two Strands of the Double Helix Are Wound around Each Other in an Antiparallel Orientation
- The Two Chains of the Double Helix Have Complementary Sequences
- The Double Helix Is Stabilized by Base Pairing and Base Stacking
- Hydrogen Bonding Is Important for the Specificity of Base Pairing
- Bases Can Flip Out from the Double Helix
- DNA Is Usually a Right-Handed Double Helix
- DNA Has 10.5 bp per Turn of the Helix in Solution: The Mica Experiment
- The Double Helix Has Minor and Major Grooves
- The Major Groove Is Rich in Chemical Information
- The Double Helix Exists in Multiple Conformations
- DNA Can Sometimes Form a Left-Handed Helix
- How Spots on an X-Ray Film Reveal the Structure of DNA
- DNA Strands Can Separate (Denature) and Reassociate- Some DNA Molecules Are Circles 

DNA TOPOLOGY
- Linking Number Is an Invariant Topological Property of Covalently Closed, Circular DNA
- Topoisomerases Can Relax Supercoiled DNA- Prokaryotes Have a Special Topoisomerase That Introduces Supercoils into DNA
- Topoisomerases Also Unknot and Disentangle DNA Molecules
- Topoisomerases Use a Covalent Protein–DNA Linkage to Cleave and Rejoin DNA Strands
- Topoisomerases Form an Enzyme Bridge and Pass DNA Segments through Each Other 


LECTURE 4

The Structure and Versatility of RNA
- RNA CONTAINS RIBOSE AND URACIL AND IS USUALLY SINGLE-STRANDED 
- RNA CHAINS FOLD BACK ON THEMSELVES TO FORM LOCAL REGIONS OF DOUBLE HELIX SIMILAR TO A-FORM DNA 
- RNA CAN FOLD UP INTO COMPLEX TERTIARY STRUCTURES 
- NUCLEOTIDE SUBSTITUTIONS IN COMBINATION WITH CHEMICAL PROBING PREDICT RNA STRUCTURE
   - An RNA Switch Controls Protein Synthesis by Murine Leukemia Virus 
- DIRECTED EVOLUTION SELECTS RNAs THAT BIND SMALL MOLECULES 
- SOME RNAs ARE ENZYMES
    - Creating an RNA Mimetic of the Green Fluorescent Protein by Directed Evolution
    - The Hammerhead Ribozyme Cleaves RNA by the Formation of a 20, 30 Cyclic Phosphate
    - A Ribozyme at the Heart of the Ribosome Acts on a Carbon Center 


LECTURE 5

The Structure of Proteins
THE BASICS
- Amino Acids
- The Peptide Bond
- Polypeptide Chains
- Three Amino Acids with Special Conformational Properties
- Ramachandran Plot: Permitted Combinations of Main
-Chain Torsion Angles f and c 

IMPORTANCE OF WATER PROTEIN STRUCTURE CAN BE DESCRIBED AT FOUR LEVELS PROTEIN DOMAINS
- Polypeptide Chains Typically Fold into One or More Domains
- Basic Lessons from the Study of Protein Structures
- Classes of Protein Domains
- Linkers and Hinges
- Post-Translational Modifications
- The Antibody Molecule as an Illustration of Protein Domains 

FROM AMINO-ACID SEQUENCE TO THREE DIMENSIONAL STRUCTURE
- Protein Folding
- Three-Dimensional Structure of a Protein Is Specified by Its Amino Acid Sequence (Anfinsen Experiment)
- Predicting Protein Structure from Amino Acid Sequence 

CONFORMATIONAL CHANGES IN PROTEINS PROTEINS AS AGENTS OF SPECIFIC MOLECULAR RECOGNITION
- Proteins That Recognize DNA Sequence
- Protein–Protein Interfaces
- Proteins That Recognize RNA 

ENZYMES: PROTEINS AS CATALYSTS 
REGULATION OF PROTEIN ACTIVITY   

LECTURE 6

Techniques of Molecular Biology
NUCLEIC ACIDS: BASIC METHODS
- Gel Electrophoresis Separates DNA and RNA Molecules according to Size
- Restriction Endonucleases Cleave DNA Molecules at Particular Sites
- DNA Hybridization Can Be Used to Identify Specific DNA Molecules
- Hybridization Probes Can Identify Electrophoretically Separated DNAs and RNAs
- Isolation of Specific Segments of DNA

DNA Cloning
- Vector DNA Can Be Introduced into Host Organisms by Transformation
- Libraries of DNA Molecules Can Be Created by Cloning
- Hybridization Can Be Used to Identify a Specific Clone in a DNA Library
- Chemical Synthesis of Defined DNA Sequences
- The Polymerase Chain Reaction Amplifies DNAs by Repeated Rounds of DNA Replication In Vitro
- Nested Sets of DNA Fragments Reveal Nucleotide Sequences
- Forensics and the Polymerase Chain Reaction
- Shotgun Sequencing a Bacterial Genome
- The Shotgun Strategy Permits a Partial Assembly of Large Genome Sequences
- Sequenators Are Used for High-Throughput Sequencing
- The Paired-End Strategy Permits the Assembly of Large-Genome Scaffolds
- The $1000 Human Genome Is within Reach 

GENOMICS
- Bioinformatics Tools Facilitate the Genome-Wide Identification of Protein-Coding Genes
- Whole-Genome Tiling ArraysAreUsed to Visualize the Transcriptome
- Regulatory DNA Sequences Can Be Identified by Using Specialized Alignment Tools
- Genome Editing Is Used to Precisely Alter Complex Genomes 

PROTEINS
- Specific ProteinsCanBePurified fromCell Extracts
- Purification of a Protein Requires a Specific Assay
- Preparation of Cell Extracts Containing Active Proteins
- Proteins Can Be Separated from One Another Using Column Chromatography
- Separation of Proteins on Polyacrylamide Gels
- Antibodies Are Used to Visualize Electrophoretically Separated Proteins
- Protein Molecules Can Be Directly Sequenced 

PROTEOMICS
- Combining Liquid Chromatography with Mass Spectrometry Identifies Individual Proteins within a Complex Extract
- Proteome Comparisons Identify Important
- Differences between Cells
- Mass Spectrometry Can Also Monitor Protein Modification States
- Protein–Protein Interactions Can Yield Information regarding Protein Function 

NUCLEIC ACID–PROTEIN INTERACTIONS
- The Electrophoretic Mobility of DNA Is Altered by Protein Binding- DNA-Bound Protein Protects the DNA from Nucleases and Chemical Modification
- Chromatin Immunoprecipitation Can Detect Protein Association with DNA in the Cell
- Chromosome Conformation Capture Assays Are Used to Analyze Long-Range Interactions
- In Vitro Selection Can Be Used to Identify a Protein’s DNA- or RNA-Binding Site 


LECTURE 7

Genome Structure, Chromatin, and the Nucleosome 
GENOME SEQUENCE AND CHROMOSOME DIVERSITY
- Chromosomes Can Be Circular or Linear
- Every Cell Maintains a Characteristic Number of Chromosomes
- Genome Size Is Related to the Complexity of the Organism
- The E. coli Genome Is Composed Almost Entirely of Genes
- More Complex Organisms Have Decreased Gene Density
- Genes Make Up Only a Small Proportion of the Eukaryotic Chromosomal DNA
- The Majority of Human Intergenic Sequences Are Composed of Repetitive DNA 

CHROMOSOME DUPLICATION AND SEGREGATION
- Eukaryotic Chromosomes Require Centromeres, Telomeres, and Origins of Replication to Be Maintained during Cell Division
- Eukaryotic Chromosome Duplication and Segregation Occur in Separate Phases of the Cell Cycle
- Chromosome Structure Changes as Eukaryotic Cells Divide
- Sister-Chromatid Cohesion and Chromosome Condensation Are Mediated by SMC Proteins
- Mitosis Maintains the Parental Chromosome Number During Gap Phases, Cells Prepare for the Next Cell Cycle Stage and Check That the Previous Stage Is Completed Correctly
- Meiosis Reduces the Parental Chromosome Number
- Different Levels of Chromosome Structure Can Be Observed by Microscopy 

THE NUCLEOSOME
- Nucleosomes Are the Building Blocks of Chromosomes
- Histones Are Small, Positively Charged Proteins
- The Atomic Structure of the Nucleosome
- Histones Bind Characteristic Regions of DNA within the Nucleosome
- Micrococcal Nuclease and the DNA Associated with the Nucleosome
- Many DNA Sequence–Independent Contacts Mediate the Interaction between the Core Histones and DNA
- The Histone Amino-Terminal Tails Stabilize DNA Wrapping around the Octamer
- Wrapping of the DNA around the Histone Protein Core Stores Negative Superhelicity 

HIGHER-ORDER CHROMATIN STRUCTURE
- Heterochromatin and Euchromatin
- Nucleosomes and Superhelical Density
- Histone H1 Binds to the Linker DNA between Nucleosomes
- Nucleosome Arrays Can Form More Complex Structures: The 30-nm Fiber
- The Histone Amino-Terminal Tails Are Required for the Formation of the 30-nm Fiber
- Further Compaction of DNA Involves Large Loops of Nucleosomal DNA
- Histone Variants Alter Nucleosome Function 

REGULATION OF CHROMATIN STRUCTURE
- The Interaction of DNA with the Histone Octamer Is Dynamic
- Nucleosome-Remodeling Complexes Facilitate Nucleosome Movement
- Some Nucleosomes Are Found in Specific Positions: Nucleosome Positioning
- The Amino-Terminal Tails of the Histones Are Frequently Modified
- Protein Domains in Nucleosome-Remodeling and -Modifying Complexes Recognize Modified Histones 
- Determining Nucleosome Position in the Cell Specific Enzymes Are Responsible for Histone Modification
- Nucleosome Modification and Remodeling Work Together to Increase DNA Accessibility 

NUCLEOSOME ASSEMBLY
- Nucleosomes Are Assembled Immediately after DNA Replication
- Assembly of Nucleosomes Requires Histone “Chaperones” 


LECTURE 8

The Replication of DNA
THE CHEMISTRY OF DNA SYNTHESIS
- DNA Synthesis Requires Deoxynucleoside Triphosphates and a Primer:Template Junction
- DNA Is Synthesized by Extending the 3' End of the Primer
- Hydrolysis of Pyrophosphate Is the Driving Force for DNA Synthesis 

THE MECHANISM OF DNA POLYMERASE
- DNA Polymerases Use a Single Active Site to Catalyze DNA Synthesis
- Incorporation Assays Can Be Used to Measure Nucleic Acid and Protein Synthesis
- DNA Polymerases Resemble a Hand That Grips the Primer:Template Junction
- DNA Polymerases Are Processive Enzymes
- Exonucleases Proofread Newly Synthesized DNA
- Anticancer and Antiviral Agents Target DNA Replication 

THE REPLICATION FORK
- Both Strands of DNA Are Synthesized Together at the Replication Fork
- The Initiation of a New Strand of DNA Requires an RNA Primer
- RNA Primers Must Be Removed to Complete DNA Replication
- DNA Helicases Unwind the Double Helix in Advance of the Replication Fork
- DNA Helicase Pulls Single-Stranded DNA through a Central Protein Pore
- Single-Stranded DNA-Binding Proteins Stabilize ssDNA before Replication
- Topoisomerases Remove Supercoils Produced by DNA Unwinding at the Replication Fork
- Replication Fork Enzymes Extend the Range of DNA Polymerase Substrates 

THE SPECIALIZATION OF DNA POLYMERASES
- DNA Polymerases Are Specialized for Different Roles in the Cell
- Sliding Clamps Dramatically Increase DNA Polymerase Processivity
- Sliding Clamps Are Opened and Placed on DNA by Clamp Loaders
- ATP Control of Protein Function: Loading a Sliding Clamp 

DNA SYNTHESIS AT THE REPLICATION FORK
- Interactions between Replication Fork Proteins Form the E. coli Replisome 

INITIATION OF DNA REPLICATION
- Specific Genomic DNA Sequences Direct the Initiation of DNA Replication
- The Replicon Model of Replication Initiation
- Replicator Sequences Include Initiator-Binding Sites and Easily Unwound DNA
- The Identification of Origins of Replication and Replicators 

BINDING AND UNWINDING: ORIGIN SELECTION AND ACTIVATION BY THE INITIATOR PROTEIN
- Protein–Protein and Protein–DNA Interactions Direct the Initiation Process
- E. coli DNA Replication Is Regulated by DnaA, ATP Levels and SeqA
- Eukaryotic Chromosomes Are Replicated Exactly Once per Cell Cycle
- Helicase Loading Is the First Step in the Initiation of Replication in Eukaryotes
- Helicase Loading and Activation Are Regulated to Allow Only a Single Round of Replication during Each Cell Cycle
- Similarities between Eukaryotic and Prokaryotic DNA Replication Initiation 

FINISHING REPLICATION
- Type II Topoisomerases Are Required to Separate Daughter DNA Molecules
- Lagging-Strand Synthesis Is Unable to Copy the Extreme Ends of Linear Chromosomes
- Telomerase Is a Novel DNA Polymerase That Does Not Require an Exogenous Template
- Telomerase Solves the End Replication Problem by Extending the 3' End of the Chromosome
- Aging, Cancer, and the Telomere Hypothesis
- Telomere-Binding Proteins Regulate Telomerase Activity and Telomere Length
- Telomere-Binding Proteins Protect Chromosome Ends 

LECTURE 9

The Mutability and Repair of DNA
REPLICATION ERRORS AND THEIR REPAIR
- The Nature of Mutations
- Some Replication Errors Escape Proofreading
- Expansion of Triple Repeats Causes Disease
- Mismatch Repair Removes Errors That Escape Proofreading 

DNA DAMAGE
- DNA Undergoes Damage Spontaneously from Hydrolysis and Deamination
- The Ames Test
- DNA Is Damaged by Alkylation, Oxidation, and Radiation
- Quantitation of DNA Damage and Its Effects on Cellular Survival and Mutagenesis
- Mutations Are Also Caused by Base Analogs and Intercalating Agents 

REPAIR AND TOLERANCE OF DNA DAMAGE
- Direct Reversal of DNA Damage
- Base Excision Repair Enzymes Remove Damaged Bases by a Base-Flipping Mechanism
- Nucleotide Excision Repair Enzymes Cleave Damaged DNA on Either Side of the Lesion
- Linking Nucleotide Excision Repair and Translesion Synthesis to a Genetic Disorder in Humans
- Recombination Repairs DNA Breaks by Retrieving Sequence Information from Undamaged DNA
- DSBs in DNA Are Also Repaired by Direct Joining of Broken Ends
- Nonhomologous End Joining
- Translesion DNA Synthesis Enables Replication to Proceed across DNA Damage 

LECTURE 10

Mechanisms of Transcription
RNA POLYMERASES AND THE TRANSCRIPTION CYCLE
- RNA Polymerases Come in Different Forms but Share Many Features
- Transcription by RNA Polymerase Proceeds in a Series of Steps
- Transcription Initiation Involves Three Defined Steps 

THE TRANSCRIPTION CYCLE IN BACTERIA
- Bacterial Promoters Vary in Strength and Sequence but Have Certain Defining Features
- Consensus Sequences
- The sigma Factor Mediates Binding of Polymerase to the Promoter
- Transition to the Open Complex Involves Structural Changes in RNA Polymerase and in the Promoter DNA
- Transcription Is Initiated by RNA Polymerase without the Need for a Primer
- During Initial Transcription, RNA Polymerase Remains Stationary and Pulls Downstream DNA into Itself
- Promoter Escape Involves Breaking Polymerase–Promoter Interactions and Polymerase Core–s Interactions
- The Elongating Polymerase Is a Processive Machine That Synthesizes and Proofreads RNA
- The Single-Subunit RNA Polymerases
- RNA Polymerase Can Become Arrested and Need RemovingTranscription Is Terminated by Signals within the RNA Sequence 

TRANSCRIPTION IN EUKARYOTES
- RNA Polymerase II Core Promoters Are Made Up of Combinations of Different Classes of Sequence Elements
- RNA Polymerase II Forms a Preinitiation Complex with General Transcription Factors at the Promoter
- Promoter Escape Requires Phosphorylation of the Polymerase “Tail"
- TBP Binds to and Distorts DNA Using a b Sheet Inserted into the Minor Groove
- The Other General Transcription Factors Also Have Specific Roles in Initiation 
- In Vivo, Transcription Initiation Requires Additional Proteins, Including the Mediator Complex
- Mediator Consists of Many Subunits, Some Conserved from Yeast to Human
- A New Set of Factors Stimulates Pol II Elongation and RNA Proofreading
- Elongating RNA Polymerase Must Deal with Histones in Its Path
- Elongating Polymerase Is Associated with a New Set of Protein Factors Required for Various Types of RNA
- ProcessingTranscription Termination Is Linked to RNA Destruction by a Highly Processive RNase 

TRANSCRIPTION BY RNA POLYMERASES I AND III
- RNA Pol I and Pol III Recognize Distinct Promoters but Still Require TBP
- Pol I Transcribes Just the rRNA Genes
- Pol III Promoters Are Found Downstream from the Transcription Start Site 

LECTURE 11

RNA Splicing
THE CHEMISTRY OF RNA SPLICING
- Sequences within the RNA Determine Where Splicing Occurs
- The Intron Is Removed in a Form Called a Lariat as the Flanking Exons Are Joined
- Adenovirus and the Discovery of Splicing 

THE SPLICEOSOME MACHINERY
- RNA Splicing Is Performed by a Large Complex Called the Spliceosome 

SPLICING PATHWAYS
- Assembly, Rearrangements, and Catalysis within the Spliceosome: The Splicing Pathway
- Spliceosome Assembly Is Dynamic and Variable and Its Disassembly Ensures That the Splicing Reaction Goes Only Forward in the Cell
- Self-Splicing Introns Reveal That RNA Can Catalyze RNA Splicing
- Group I Introns Release a Linear Intron Rather Than a Lariat
- Converting Group I Introns into Ribozymes
- How Does the Spliceosome Find the Splice Sites Reliably? 

VARIANTS OF SPLICING
- Exons from Different RNA Molecules Can Be Fused by Trans-Splicing
- A Small Group of Introns Is Spliced by an Alternative Spliceosome Composed of a Different Set of snRNPs 

ALTERNATIVE SPLICING
- Single Genes Can Produce Multiple Products by Alternative Splicing
- Several Mechanisms Exist to Ensure Mutually Exclusive Splicing
- The Curious Case of the Drosophila Dscam Gene: Mutually Exclusive Splicing on a Grand Scale
- Mutually Exclusive Splicing of Dscam Exon 6 Cannot Be Accounted for by Any Standard Mechanism and Instead Uses a Novel Strategy
- Identification of Docking Site and Selector Sequences
- Alternative Splicing Is Regulated by Activators and Repressors
- Regulation of Alternative Splicing Determines the Sex of Flies
- An Alternative Splicing Switch Lies at the Heart of Pluripotency 

EXON SHUFFLING
- Exons Are Shuffled by Recombination to Produce Genes Encoding New Proteins
- Defects in Pre-mRNA Splicing Cause Human Disease 

RNA EDITING
- RNA Editing Is AnotherWay of Altering the Sequence of an mRNAGuide RNAs Direct the Insertion and Deletion of UridinesDeaminases and HIV mRNA TRANSPORT 


LECTURE 12

Translation
MESSENGER RNA
- Polypeptide Chains Are Specified by Open Reading Frames
- Prokaryotic mRNAs Have a Ribosome-Binding Site That Recruits the Translational Machinery
- Eukaryotic mRNAs Are Modified at their 50 and 30 Ends to Facilitate Translation 

TRANSFER RNA
- tRNAs Are Adaptors between Codons and Amino Acids
- CCA-Adding Enzymes: Synthesizing RNA without a Template
- tRNAs Share a Common Secondary Structure That Resembles a Cloverleaf
- tRNAs Have an L-Shaped Three-Dimensional Structure 

ATTACHMENT OF AMINO ACIDS TO tRNA
- tRNAs Are Charged by the Attachment of an Amino Acid to the 30-Terminal Adenosine Nucleotide via a High-Energy Acyl Linkage
- Aminoacyl-tRNA Synthetases Charge tRNAs in Two Steps
- Each Aminoacyl-tRNA Synthetase Attaches a Single Amino Acid to One or More tRNAs
- tRNA Synthetases Recognize Unique Structural Features of Cognate tRNAs
- Aminoacyl-tRNA Formation Is Very Accurate
- Some Aminoacyl-tRNA Synthetases Use an Editing Pocket to Charge tRNAs with High Accuracy
- The Ribosome Is Unable to Discriminate between Correctly and Incorrectly Charged tRNAs 

THE RIBOSOME
- Selenocysteine
- The Ribosome Is Composed of a Large and a Small Subunit
- The Large and Small Subunits Undergo Association and Dissociation during Each Cycle of Translation
- New Amino Acids Are Attached to the Carboxyl Terminus of the Growing Polypeptide Chain
- Peptide Bonds Are Formed by Transfer of the Growing Polypeptide Chain from One tRNA to Another
- Ribosomal RNAs Are Both Structural and Catalytic Determinants of the Ribosome
- The Ribosome Has Three Binding Sites for tRNA
- Channels through the Ribosome Allow the mRNA and Growing Polypeptide to Enter and/or Exit the Ribosome 

INITIATION OF TRANSLATION
- Prokaryotic mRNAs Are Initially Recruited to the Small Subunit by Base Pairing to rRNA
- A Specialized tRNA Charged with a Modified Methionine Binds Directly to the Prokaryotic Small Subunit
- Three Initiation Factors Direct the Assembly of an Initiation Complex That Contains mRNA and the Initiator tRNA
- Eukaryotic Ribosomes Are Recruited to the mRNA by the 5' Cap
- Translation Initiation Factors Hold Eukaryotic mRNAs in Circles
uORFs and IRESs: Exceptions That Prove the Rule
-The Start Codon Is Found by Scanning Downstream from the 5' End of the mRNA 

TRANSLATION ELONGATION
- Aminoacyl-tRNAs Are Delivered to the A-Site by Elongation Factor EF-Tu
- The Ribosome Uses Multiple Mechanisms to Select against Incorrect Aminoacyl-tRNAs
- The Ribosome Is a Ribozyme
- Peptide-Bond Formation Initiates Translocation in the Large Subunit
- EF-G Drives Translocation by Stabilizing Intermediates in Translocation
- EF-Tu–GDP and EF-G–GDP Must Exchange GDP for GTP before Participating in a New Round of Elongation
- A Cycle of Peptide-Bond Formation Consumes Two Molecules of GTP and One Molecule of ATP 

TERMINATION OF TRANSLATION
- Release Factors Terminate Translation in Response to Stop Codons
- Short Regions of Class I Release Factors Recognize Stop Codons and Trigger Release of the Peptidyl Chain
- GTP-Binding Proteins
- Conformational Switching, and the Fidelity and Ordering of the Events of Translation
- GDP/GTP Exchange and GTP Hydrolysis Control the Function of the Class II Release Factor
- The Ribosome Recycling Factor Mimics a tRNA 

REGULATION OF TRANSLATION
- Protein or RNA Binding near the Ribosome-Binding Site Negatively Regulates Bacterial Translation Initiation
- Regulation of Prokaryotic Translation: Ribosomal Proteins Are Translational Repressors of Their Own Synthesis
- Antibiotics Arrest Cell Division by Blocking Specific Steps in Translation
- Global Regulators of Eukaryotic Translation Target Key Factors Required for mRNA Recognition and Initiator tRNA Ribosome Binding
- Spatial Control of Translation by mRNA-Specific 4E-BPs
- An Iron-Regulated, RNA-Binding Protein Controls Translation of Ferritin
- Translation of the Yeast Transcriptional Activator Gcn4 Is Controlled by Short Upstream ORFs and Ternary Complex Abundance
- Ribosome and Polysome Profiling 

TRANSLATION-DEPENDENT REGULATION OF mRNA AND PROTEIN STABILITY
- The SsrA RNA Rescues Ribosomes That Translate Broken mRNAs
- A Frontline Drug in Tuberculosis Therapy Targets SsrA Tagging
- Eukaryotic Cells Degrade mRNAs That Are Incomplete or Have Premature Stop Codons