Genes VII

ISBN: B000R0CSVM
EAN: N/A

Year: 2005
Pages: 382

Authors: Benjamin Lewin

BUY ON AMAZON

Contents
1. Introduction
2. DNA is the genetic material
3. DNA is a double helix
4. DNA replication is semiconservative
5. Nucleic acids hybridize by base pairing
6. Mutations change the sequence of DNA
7. Mutations are concentrated at hotspots
8. A cistron is a single stretch of DNA
9. The nature of multiple alleles
10. Recombination occurs by physical exchange of DNA
11. The genetic code is triplet
12. The relationship between coding sequences and proteins
13. cis-acting sites and trans-acting molecules
14. Genetic information can be provided by DNA or RNA
15. Summary
1. Introduction
2. Genes can be mapped by restriction cleavage
3. How variable are individual genomes?
4. Eukaryotic genes are often interrupted
5. Organization of interrupted genes may be conserved
6. Exon sequences are conserved but introns vary
7. Genes can be isolated by the conservation of exons
8. Genes show a wide distribution of sizes
9. Some DNA sequences code for more than one protein
10. How did interrupted genes evolve?
11. The scope of the paradigm
12. Summary
1. Introduction
2. Why are genomes so large?
3. Total gene number is known for several organisms
4. How many genes are essential?
5. How many genes are expressed?
6. Organelles have DNA
7. Organelle genomes are circular DNAs that code for organelle proteins
8. Mitochondrial DNA codes for few proteins
9. The chloroplast genome codes for 100 proteins and RNAs
10. Summary
1. Introduction
2. Gene clusters are formed by duplication and divergence
3. Sequence divergence is the basis for the evolutionary clock
4. Pseudogenes are dead ends of evolution
5. Unequal crossing-over rearranges gene clusters
6. Genes for rRNA form tandem repeats
7. The repeated genes for rRNA maintain constant sequence
8. Crossover fixation could maintain identical repeats
9. Satellite DNAs often lie in heterochromatin
10. Arthropod satellites have very short identical repeats
11. Mammalian satellites consist of hierarchical repeats
12. Minisatellites are useful for genetic mapping
13. Summary
1. Introduction
2. Transfer RNA is the adapter
3. Messenger RNA is translated by ribosomes
4. The life cycle of messenger RNA
5. Translation of eukaryotic mRNA
6. The 5 end of eukaryotic mRNA is capped
7. The 3 terminus is polyadenylated
8. Bacterial mRNA degradation involves multiple enzymes
9. Yeast mRNA degradation involves multiple activities
10. Sequence elements may destabilize mRNA
11. Nonsense mutations trigger a surveillance system
12. Summary
1. Introduction
2. The stages of protein synthesis
3. Initiation in bacteria needs 30S subunits and accessory factors
4. A special initiator tRNA starts the polypeptide chain
5. Initiation involves base pairing between mRNA and rRNA
6. Small subunits scan for initiation sites on eukaryotic mRNA
7. Eukaryotes use a complex of many initiation factors
8. Elongation factor T loads aminoacyl-tRNA into the A site
9. Translocation moves the ribosome
10. Three codons terminate protein synthesis
11. Ribosomes have several active centers
12. The organization of 16S rRNA
13. 23S rRNA has peptidyl transferase activity
14. Summary
1. Introduction
2. Codon-anticodon recognition involves wobbling
3. tRNA contains modified bases that influence its pairing properties
4. There are sporadic alterations of the universal code
5. tRNAs are charged with amino acids by synthetases
6. Accuracy depends on proofreading
7. Suppressor tRNAs have mutated anticodons that read new codons
8. The accuracy of translation
9. tRNA may influence the reading frame
10. Summary
1. Introduction
2. Chaperones may be required for protein folding
3. The Hsp70 family is ubiquitous.
4. Hsp60GroEL forms an oligomeric ring structure
5. Post-translational membrane insertion depends on leader sequences
6. A hierarchy of sequences determines location within organelles
7. Signal sequences initiate translocation
8. The translocon forms a pore
9. How do proteins enter and leave membranes?
10. Anchor signals are needed for membrane residence
11. Bacteria use both co-translational and post-translational translocation
12. Pores are used for nuclear ingress and egress
13. Nuclear pores are large symmetrical structures
14. Proteins require signals to be transported through the pore
15. Transport receptors carry cargo proteins through the pore
16. Protein degradation by proteasomes
17. Summary
1. Introduction
2. Transcription is catalyzed by RNA polymerase
3. RNA polymerase consists of multiple subunits
4. Sigma factor controls binding to DNA
5. Promoter recognition depends on consensus sequences
6. RNA polymerase binds to one face of DNA
7. Substitution of sigma factors may control initiation
8. Sigma factors may be organized into cascades
9. Bacterial RNA polymerase has two modes of termination
10. How does rho factor work?
11. Antitermination depends on specific sites
12. More subunits for RNA polymerase
13. Summary
1. Introduction
2. Structural gene clusters are coordinately controlled
3. Repressor is controlled by a small molecule inducer
4. Mutations identify the operator and the regulator gene
5. Repressor protein binds to the operator and is released by inducer
6. The specificity of protein-DNA interactions
7. Repression can occur at multiple loci
8. Distinguishing positive and negative control
9. Catabolite repression involves positive regulation at the promoter
10. Adverse growth conditions provoke the stringent response
11. Autogenous control may occur at translation
12. Alternative secondary structures control attenuation
13. Attenuation can be controlled by translation
14. Small RNA molecules can regulate translation
15. Summary
1. Introduction
2. Lytic development is controlled by a cascade
3. Functional clustering in phages T7 and T4
4. The lambda lytic cascade relies on antitermination
5. Lysogeny is maintained by an autogenous circuit
6. The DNA-binding form of repressor is a dimer
7. Repressor binds cooperatively at each operator using a helix-turn-helix motif
8. How is repressor synthesis established?
9. A second repressor is needed for lytic infection
10. A delicate balance: lysogeny versus lysis
11. Summary
1. Introduction
2. Origins can be mapped by autoradiography and electrophoresis
3. The bacterial genome is a single circular replicon
4. Each eukaryotic chromosome contains many replicons
5. Isolating the origins of yeast replicons
6. D loops maintain mitochondrial origins
7. The problem of linear replicons
8. Rolling circles produce multimers of a replicon
9. Single-stranded genomes are generated for bacterial conjugation
10. Connecting bacterial replication to the cell cycle
11. Cell division and chromosome segregation
12. The division apparatus consists of cytoskeletal and regulatory components
13. Partioning involves membrane attachment and (possibly) a motor
14. Multiple systems ensure plasmid survival in bacterial populations
15. Plasmid incompatibility is connected with copy number
16. Summary
1. Introduction
2. DNA polymerases are the enzymes that make DNA
3. DNA polymerases have various nuclease activities
4. DNA polymerases control the fidelity of replication
5. Some DNA polymerases have a common structure
6. DNA synthesis is semidiscontinuous
7. Single-stranded DNA is needed for replication
8. Priming is required to start DNA synthesis
9. The primosome is needed to restart replication
10. Coordinating synthesis of the lagging and leading strands
11. The replication apparatus of phage T4
12. Creating the replication forks at an origin
13. Common events in priming replication at the origin
14. Does methylation at the origin regulate initiation?
15. Licensing factor controls eukaryotic rereplication
16. Summary
1. Introduction
2. Breakage and reunion involves heteroduplex DNA
3. Double-strand breaks initiate recombination
4. Double-strand breaks initiate synapsis
5. The bacterial RecBCD system is stimulated by chi sequences
6. RecA catalyzes single-strand assimilation
7. The Ruv system resolves Holliday junctions
8. Gene conversion accounts for interallelic recombination
9. Topological manipulation of DNA
10. Specialized recombination involves breakage and reunion at specific sites
11. Repair systems correct damage to DNA
12. Excision repair systems in E. coli
13. Base flipping is used by methylases and glycosylases
14. Error-prone repair and mutator phenotypes
15. Controlling the direction of mismatch repair
16. Retrieval systems in E. coli
17. RecA triggers the SOS system
18. Eukaryotic repair systems
19. Summary
1. Introduction
2. Insertion sequences are simple transposition modules
3. Composite transposons have IS modules
4. Transposition occurs by both replicative and nonreplicative mechanisms
5. Transposons cause rearrangement of DNA
6. Common intermediates for transposition
7. Replicative transposition proceeds through a cointegrate
8. Nonreplicative transposition proceeds by breakage and reunion
9. TnA transposition requires transposase and resolvase
10. Transposition of Tn10 has multiple controls
11. Controlling elements in maize cause breakage and rearrangements
12. Controlling elements in maize form families of transposons
13. Spm elements influence gene expression
14. The role of transposable elements in hybrid dysgenesis
15. Summary
1. Introduction
2. The retrovirus life cycle involves transpositionVlike events
3. Retroviruses may transduce cellular sequences
4. Yeast Ty elements resemble retroviruses
5. Many transposable elements reside in D. melanogaster
6. Retroposons fall into two classes
7. Summary
1. Introduction
2. The mating pathway is triggered by signal transduction
3. Yeast can switch silent and active loci for mating type
4. Silent cassettes at HML and HMR are repressed
5. Unidirectional transposition is initiated by the recipient MAT locus
6. Regulation of HO expression
7. Trypanosomes rearrange DNA to express new surface antigens
8. Interaction of Ti plasmid DNA with the plant genome
9. Selection of amplified genomic sequences
10. Exogenous sequences can be introduced into cells and animals by transfection
11. Summary
1. Introduction
2. Condensing viral genomes into their coats
3. The bacterial genome is a nucleoid with many supercoiled loops
4. Loops, domains, and scaffolds in eukaryotic DNA
5. The contrast between interphase chromatin and mitotic chromosomes
6. The extended state of lampbrush chromosomes
7. Transcription disrupts the structure of polytene chromosomes
8. The eukaryotic chromosome as a segregation device
9. Telomeres are simple repeats that seal the ends of chromosomes
10. Telomeres are synthesized by a ribonucleoprotein enzyme
11. Summary
1. Introduction
2. The nucleosome is the subunit of all chromatin
3. DNA is coiled in arrays of nucleosomes
4. DNA structure varies on the nucleosomal surface
5. Supercoiling and the periodicity of DNA
6. The path of nucleosomes in the chromatin fiber
7. Organization of the histone octamer
8. Reproduction of chromatin requires assembly of nucleosomes
9. Do nucleosomes lie at specific positions?
10. Are transcribed genes organized in nucleosomes?
11. DNAase hypersensitive sites change chromatin structure
12. Domains define regions that contain active genes
13. Heterochromatin depends on interactions with histones
14. Global changes in X chromosomes
15. Methylation is responsible for imprinting
16. Epigenetic effects can be inherited
17. Yeast prions show unusual inheritance
18. Prions cause diseases in mammals
19. Summary
1. Introduction
2. Eukaryotic RNA polymerases consist of many subunits
3. Promoter elements are defined by mutations and footprinting
4. RNA polymerase I has a bipartite promoter
5. RNA polymerase III uses both downstream and upstream promoters
6. The startpoint for RNA polymerase II
7. TBP is a universal factor
8. The basal apparatus assembles at the promoter
9. A connection between transcription and repair
10. Promoters for RNA polymerase II have short sequence elements
11. Enhancers contain bidirectional elements that assist initiation
12. Independent domains bind DNA and activate transcription
13. Interaction of upstream factors with the basal apparatus
14. Summary
1. Introduction
2. Response elements identify genes under common regulation
3. There are many types of DNA-binding domains
4. A zinc finger motif is a DNA-binding domain
5. Steroid receptors have several independent domains
6. Homeodomains bind related targets in DNA
7. Helix-loop-helix proteins interact by combinatorial association
8. Leucine zippers are involved in dimer formation
9. Chromatin remodeling is an active process
10. Histone acetylation and deacetylation control chromatin activity
11. Polycomb and trithorax are antagonistic repressors and activators
12. Long range regulation and insulation of domains
14. Summary
1. Introduction
2. Nuclear splice junctions are interchangeable but are read in pairs
3. Nuclear splicing proceeds through a lariat
4. The spliceosome contains snRNAs
5. Group II introns autosplice via lariat formation
6. Alternative splicing involves differential use of splice junctions
7. cis-splicing and trans-splicing reactions
8. Yeast tRNA splicing involves cutting and rejoining
9. The 3 ends of polI and polIII transcripts are generated by termination
10. The 3 ends of mRNAs are generated by cleavage
11. Cleavage of the 3 end may require a small RNA
12. Production of rRNA requires cleavage and modification events
13. Small RNAs are required for rRNA processing
14. Summary
1. Introduction
2. Group I introns undertake self-splicing by transesterification
3. Group I introns form a characteristic secondary structure
4. Ribozymes have various catalytic activities
5. Some introns code for proteins that sponsor mobility
6. RNA can have ribonuclease activities
7. RNA editing utilizes information from several sources
8. Summary
1. Introduction
2. Clonal selection amplifies lymphocytes that respond to individual antigens
3. Immunoglobulin genes are assembled from their parts in lymphocytes
4. The diversity of germline information
5. Recombination between V and C gene segments generates deletions and rearrangements
6. Allelic exclusion is triggered by productive rearrangement
7. DNA recombination causes class switching
8. Somatic mutation generates additional diversity
9. B cell development and memory
10. T-cell receptors are related to immunoglobulins
11. The major histocompatibility locus codes for many genes of the immune system
12. Summary
1. Introduction
2. Oligosaccharides are added to proteins in the ER and Golgi
3. Coated vesicles transport both exported and imported proteins
4. Different types of coated vesicles exist in each pathway
5. An alternative model for protein transport
6. Budding and fusion reactions
7. Protein localization depends on further signals
8. ER proteins are retrieved from the Golgi
9. Receptors recycle via endocytosis
10. Summary
1. Introduction
2. Carriers and channels form water soluble paths through the membrane
3. G proteins may activate or inhibit target proteins
4. Protein tyrosine kinases induce phosphorylation cascades
5. The RasMAPK pathway
6. Activating MAP kinase pathways
7. Cyclic AMP and activation of CREB
8. The JAK-STAT pathway
9. TGFb signals through Smads
10. Structural subunits can be messengers
11. Summary
1. Introduction
2. Cycle progression depends on discrete control points
3. M phase kinase regulates entry into mitosis
4. Protein phosphorylation and dephosphorylation control the cell cycle
5. Cdc2 is the key regulator in yeasts
6. CDC28 acts at both START and mitosis in S. cerevisiae
7. The animal cell cycle is controlled by many cdk-cyclin complexes
8. G0G1 and G1S transitions involve cdk inhibitors
9. Protein degradation is important in mitosis
10. Reorganization of the cell at mitosis
11. Apoptosis is a property of many or all cells
12. The Fas receptor is a major trigger for apoptosis
13. A common pathway for apoptosis functions via caspases
14. Apoptosis involves changes at the mitochondrial envelope
15. There are multiple apoptotic pathways
16. Summary
1. Introduction
2. Transforming viruses carry oncogenes
3. Retroviral oncogenes have cellular counterparts
4. Ras proto-oncogenes can be activated by mutation
5. Insertion, translocation, or amplification may activate proto-oncogenes
6. Oncogenes code for components of signal transduction cascades
7. Growth factor receptor kinases and cytoplasmic tyrosine kinases
8. Oncoproteins may regulate gene expression
9. RB is a tumor suppressor that controls the cell cycle
10. Tumor suppressor p53 suppresses growth or triggers apoptosis
11. Immortalization and transformation
12. Summary
1. Introduction
2. Fly development uses a cascade of transcription factors
3. A gradient must be converted into discrete compartments
4. Maternal gene products establish gradients in early embryogenesis
5. Anterior development uses localized gene regulators
6. Posterior development uses another localized regulator
7. How are mRNAs and proteins transported and localized?
8. Dorsal-ventral development uses localized receptor-ligand interactions
9. TGFbBMPs are diffusible morphogens
10. Cell fate is determined by compartments that form by the blastoderm stage
11. The winglesswnt signaling pathway
12. Complex loci are extremely large and involved in regulation
13. The homeobox is a common coding motif in homeotic genes