Flylib.com
Contents
Table of content
Next page
Genes are DNA
Introduction
DNA is the genetic material
DNA is a double helix
DNA replication is semiconservative
Nucleic acids hybridize by base pairing
Mutations change the sequence of DNA
Mutations are concentrated at hotspots
A cistron is a single stretch of DNA
The nature of multiple alleles
Recombination occurs by physical exchange of DNA
The genetic code is triplet
The relationship between coding sequences and proteins
cis
-acting sites and
trans
-acting molecules
Genetic information can be provided by DNA or RNA
Summary
From genes to genomes
Introduction
Genes can be mapped by restriction cleavage
How variable are individual genomes?
Eukaryotic genes are often interrupted
Organization of interrupted genes may be conserved
Exon sequences are conserved but introns vary
Genes can be isolated by the conservation of exons
Genes show a wide distribution of sizes
Some DNA sequences code for more than one protein
How did interrupted genes evolve?
The scope of the paradigm
Summary
How many genes are there?
Introduction
Why are genomes so large?
Total gene number is known for several organisms
How many genes are essential?
How many genes are expressed?
Organelles have DNA
Organelle genomes are circular DNAs that code for organelle proteins
Mitochondrial DNA codes for few proteins
The chloroplast genome codes for ~100 proteins and RNAs
Summary
Clusters and repeats
Introduction
Gene clusters are formed by duplication and divergence
Sequence divergence is the basis for the evolutionary clock
Pseudogenes are dead ends of evolution
Unequal crossing-over rearranges gene clusters
Genes for rRNA form tandem repeats
The repeated genes for rRNA maintain constant sequence
Crossover fixation could maintain identical repeats
Satellite DNAs often lie in heterochromatin
Arthropod satellites have very short identical repeats
Mammalian satellites consist of hierarchical repeats
Minisatellites are useful for genetic mapping
Summary
Messenger RNA
Introduction
Transfer RNA is the adapter
Messenger RNA is translated by ribosomes
The life cycle of messenger RNA
Translation of eukaryotic mRNA
The 5′ end of eukaryotic mRNA is capped
The 3′ terminus is polyadenylated
Bacterial mRNA degradation involves multiple enzymes
Yeast mRNA degradation involves multiple activities
Sequence elements may destabilize mRNA
Nonsense mutations trigger a surveillance system
Summary
Protein synthesis
Introduction
The stages of protein synthesis
Initiation in bacteria needs 30S subunits and accessory factors
A special initiator tRNA starts the polypeptide chain
Initiation involves base pairing between mRNA and rRNA
Small subunits scan for initiation sites on eukaryotic mRNA
Eukaryotes use a complex of many initiation factors
Elongation factor T loads aminoacyl-tRNA into the A site
Translocation moves the ribosome
Three codons terminate protein synthesis
Ribosomes have several active centers
The organization of 16S rRNA
23S rRNA has peptidyl transferase activity
Summary
Using the genetic code
Introduction
Codon-anticodon recognition involves wobbling
tRNA contains modified bases that influence its pairing properties
There are sporadic alterations of the universal code
tRNAs are charged with amino acids by synthetases
Accuracy depends on proofreading
Suppressor tRNAs have mutated anticodons that read new codons
The accuracy of translation
tRNA may influence the reading frame
Summary
Protein localization
Introduction
Chaperones may be required for protein folding
The Hsp70 family is ubiquitous.
Hsp60/GroEL forms an oligomeric ring structure
Post-translational membrane insertion depends on leader sequences
A hierarchy of sequences determines location within organelles
Signal sequences initiate translocation
The translocon forms a pore
How do proteins enter and leave membranes?
Anchor signals are needed for membrane residence
Bacteria use both co-translational and post-translational translocation
Pores are used for nuclear ingress and egress
Nuclear pores are large symmetrical structures
Proteins require signals to be transported through the pore
Transport receptors carry cargo proteins through the pore
Protein degradation by proteasomes
Summary
Transcription
Introduction
Transcription is catalyzed by RNA polymerase
RNA polymerase consists of multiple subunits
Sigma factor controls binding to DNA
Promoter recognition depends on consensus sequences
RNA polymerase binds to one face of DNA
Substitution of sigma factors may control initiation
Sigma factors may be organized into cascades
Bacterial RNA polymerase has two modes of termination
How does rho factor work?
Antitermination depends on specific sites
More subunits for RNA polymerase
Summary
The Operon
Introduction
Structural gene clusters are coordinately controlled
Repressor is controlled by a small molecule inducer
Mutations identify the operator and the regulator gene
Repressor protein binds to the operator and is released by inducer
The specificity of protein-DNA interactions
Repression can occur at multiple loci
Distinguishing positive and negative control
Catabolite repression involves positive regulation at the promoter
Adverse growth conditions provoke the stringent response
Autogenous control may occur at translation
Alternative secondary structures control attenuation
Attenuation can be controlled by translation
Small RNA molecules can regulate translation
Summary
Phage strategies
Introduction
Lytic development is controlled by a cascade
Functional clustering in phages T7 and T4
The lambda lytic cascade relies on antitermination
Lysogeny is maintained by an autogenous circuit
The DNA-binding form of repressor is a dimer
Repressor binds cooperatively at each operator using a helix-turn-helix motif
How is repressor synthesis established?
A second repressor is needed for lytic infection
A delicate balance: lysogeny versus lysis
Summary
The replicon
Introduction
Origins can be mapped by autoradiography and electrophoresis
The bacterial genome is a single circular replicon
Each eukaryotic chromosome contains many replicons
Isolating the origins of yeast replicons
D loops maintain mitochondrial origins
The problem of linear replicons
Rolling circles produce multimers of a replicon
Single-stranded genomes are generated for bacterial conjugation
Connecting bacterial replication to the cell cycle
Cell division and chromosome segregation
The division apparatus consists of cytoskeletal and regulatory components
Partioning involves membrane attachment and (possibly) a motor
Multiple systems ensure plasmid survival in bacterial populations
Plasmid incompatibility is connected with copy number
Summary
DNA replication
Introduction
DNA polymerases are the enzymes that make DNA
DNA polymerases have various nuclease activities
DNA polymerases control the fidelity of replication
Some DNA polymerases have a common structure
DNA synthesis is semidiscontinuous
Single-stranded DNA is needed for replication
Priming is required to start DNA synthesis
The primosome is needed to restart replication
Coordinating synthesis of the lagging and leading strands
The replication apparatus of phage T4
Creating the replication forks at an origin
Common events in priming replication at the origin
Does methylation at the origin regulate initiation?
Licensing factor controls eukaryotic rereplication
Summary
Recombination and repair
Introduction
Breakage and reunion involves heteroduplex DNA
Double-strand breaks initiate recombination
Double-strand breaks initiate synapsis
The bacterial RecBCD system is stimulated by
chi
sequences
RecA catalyzes single-strand assimilation
The Ruv system resolves Holliday junctions
Gene conversion accounts for interallelic recombination
Topological manipulation of DNA
Specialized recombination involves breakage and reunion at specific sites
Repair systems correct damage to DNA
Excision repair systems in
E. coli
Base flipping is used by methylases and glycosylases
Error-prone repair and mutator phenotypes
Controlling the direction of mismatch repair
Retrieval systems in
E. coli
RecA triggers the SOS system
Eukaryotic repair systems
Summary
Transposons
Introduction
Insertion sequences are simple transposition modules
Composite transposons have IS modules
Transposition occurs by both replicative and nonreplicative mechanisms
Transposons cause rearrangement of DNA
Common intermediates for transposition
Replicative transposition proceeds through a cointegrate
Nonreplicative transposition proceeds by breakage and reunion
TnA transposition requires transposase and resolvase
Transposition of Tn10 has multiple controls
Controlling elements in maize cause breakage and rearrangements
Controlling elements in maize form families of transposons
Spm elements influence gene expression
The role of transposable elements in hybrid dysgenesis
Summary
Retroviruses and retroposons
Introduction
The retrovirus life cycle involves transposition Vlike events
Retroviruses may transduce cellular sequences
Yeast Ty elements resemble retroviruses
Many transposable elements reside in
D. melanogaster
Retroposons fall into two classes
Summary
Rearrangement of DNA
Introduction
The mating pathway is triggered by signal transduction
Yeast can switch silent and active loci for mating type
Silent cassettes at HML and HMR are repressed
Unidirectional transposition is initiated by the recipient MAT locus
Regulation of HO expression
Trypanosomes rearrange DNA to express new surface antigens
Interaction of Ti plasmid DNA with the plant genome
Selection of amplified genomic sequences
Exogenous sequences can be introduced into cells and animals by transfection
Summary
Chromosomes
Introduction
Condensing viral genomes into their coats
The bacterial genome is a nucleoid with many supercoiled loops
Loops, domains, and scaffolds in eukaryotic DNA
The contrast between interphase chromatin and mitotic chromosomes
The extended state of lampbrush chromosomes
Transcription disrupts the structure of polytene chromosomes
The eukaryotic chromosome as a segregation device
Telomeres are simple repeats that seal the ends of chromosomes
Telomeres are synthesized by a ribonucleoprotein enzyme
Summary
Nucleosomes
Introduction
The nucleosome is the subunit of all chromatin
DNA is coiled in arrays of nucleosomes
DNA structure varies on the nucleosomal surface
Supercoiling and the periodicity of DNA
The path of nucleosomes in the chromatin fiber
Organization of the histone octamer
Reproduction of chromatin requires assembly of nucleosomes
Do nucleosomes lie at specific positions?
Are transcribed genes organized in nucleosomes?
DNAase hypersensitive sites change chromatin structure
Domains define regions that contain active genes
Heterochromatin depends on interactions with histones
Global changes in X chromosomes
Methylation is responsible for imprinting
Epigenetic effects can be inherited
Yeast prions show unusual inheritance
Prions cause diseases in mammals
Summary
Initiation of transcription
Introduction
Eukaryotic RNA polymerases consist of many subunits
Promoter elements are defined by mutations and footprinting
RNA polymerase I has a bipartite promoter
RNA polymerase III uses both downstream and upstream promoters
The startpoint for RNA polymerase II
TBP is a universal factor
The basal apparatus assembles at the promoter
A connection between transcription and repair
Promoters for RNA polymerase II have short sequence elements
Enhancers contain bidirectional elements that assist initiation
Independent domains bind DNA and activate transcription
Interaction of upstream factors with the basal apparatus
Summary
Regulation of transcription
Introduction
Response elements identify genes under common regulation
There are many types of DNA-binding domains
A zinc finger motif is a DNA-binding domain
Steroid receptors have several independent domains
Homeodomains bind related targets in DNA
Helix-loop-helix proteins interact by combinatorial association
Leucine zippers are involved in dimer formation
Chromatin remodeling is an active process
Histone acetylation and deacetylation control chromatin activity
Polycomb and trithorax are antagonistic repressors and activators
Long range regulation and insulation of domains
Gene expression is associated with demethylation
Summary
Nuclear splicing and RNA processing
Introduction
Nuclear splice junctions are interchangeable but are read in pairs
Nuclear splicing proceeds through a lariat
The spliceosome contains snRNAs
Group II introns autosplice via lariat formation
Alternative splicing involves differential use of splice junctions
cis
-splicing and
trans
-splicing reactions
Yeast tRNA splicing involves cutting and rejoining
The 3′ ends of polI and polIII transcripts are generated by termination
The 3′ ends of mRNAs are generated by cleavage
Cleavage of the 3′ end may require a small RNA
Production of rRNA requires cleavage and modification events
Small RNAs are required for rRNA processing
Summary
Catalytic RNA
Introduction
Group I introns undertake self-splicing by transesterification
Group I introns form a characteristic secondary structure
Ribozymes have various catalytic activities
Some introns code for proteins that sponsor mobility
RNA can have ribonuclease activities
RNA editing utilizes information from several sources
Summary
Immune diversity
Introduction
Clonal selection amplifies lymphocytes that respond to individual antigens
Immunoglobulin genes are assembled from their parts in lymphocytes
The diversity of germline information
Recombination between V and C gene segments generates deletions and rearrangements
Allelic exclusion is triggered by productive rearrangement
DNA recombination causes class switching
Somatic mutation generates additional diversity
B cell development and memory
T-cell receptors are related to immunoglobulins
The major histocompatibility locus codes for many genes of the immune system
Summary
Protein trafficking
Introduction
Oligosaccharides are added to proteins in the ER and Golgi
Coated vesicles transport both exported and imported proteins
Different types of coated vesicles exist in each pathway
An alternative model for protein transport
Budding and fusion reactions
Protein localization depends on further signals
ER proteins are retrieved from the Golgi
Receptors recycle via endocytosis
Summary
Signal transduction
Introduction
Carriers and channels form water soluble paths through the membrane
G proteins may activate or inhibit target proteins
Protein tyrosine kinases induce phosphorylation cascades
The Ras/MAPK pathway
Activating MAP kinase pathways
Cyclic AMP and activation of CREB
The JAK-STAT pathway
TGFβ signals through Smads
Structural subunits can be messengers
Summary
Cell cycle and growth regulation
Introduction
Cycle progression depends on discrete control points
M phase kinase regulates entry into mitosis
Protein phosphorylation and dephosphorylation control the cell cycle
Cdc2 is the key regulator in yeasts
CDC28
acts at both START and mitosis in
S. cerevisiae
The animal cell cycle is controlled by many cdk-cyclin complexes
G0/G1 and G1/S transitions involve cdk inhibitors
Protein degradation is important in mitosis
Reorganization of the cell at mitosis
Apoptosis is a property of many or all cells
The Fas receptor is a major trigger for apoptosis
A common pathway for apoptosis functions via caspases
Apoptosis involves changes at the mitochondrial envelope
There are multiple apoptotic pathways
Summary
Oncogenes and cancer
Introduction
Transforming viruses carry oncogenes
Retroviral oncogenes have cellular counterparts
Ras proto-oncogenes can be activated by mutation
Insertion, translocation, or amplification may activate proto-oncogenes
Oncogenes code for components of signal transduction cascades
Growth factor receptor kinases and cytoplasmic tyrosine kinases
Oncoproteins may regulate gene expression
RB is a tumor suppressor that controls the cell cycle
Tumor suppressor p53 suppresses growth or triggers apoptosis
Immortalization and transformation
Summary
Gradients, cascades, and signaling pathways
Introduction
Fly development uses a cascade of transcription factors
A gradient must be converted into discrete compartments
Maternal gene products establish gradients in early embryogenesis
Anterior development uses localized gene regulators
Posterior development uses another localized regulator
How are mRNAs and proteins transported and localized?
Dorsal-ventral development uses localized receptor-ligand interactions
TGFβ/BMPs are diffusible morphogens
Cell fate is determined by compartments that form by the blastoderm stage
The wingless/wnt signaling pathway
Complex loci are extremely large and involved in regulation
The homeobox is a common coding motif in homeotic genes
Summary
Table of content
Next page
Genes VII
ISBN: B000R0CSVM
EAN: N/A
Year: 2005
Pages: 382
Authors:
Benjamin Lewin
BUY ON AMAZON
Strategies for Information Technology Governance
Assessing Business-IT Alignment Maturity
Measuring and Managing E-Business Initiatives Through the Balanced Scorecard
Technical Issues Related to IT Governance Tactics: Product Metrics, Measurements and Process Control
Governing Information Technology Through COBIT
Governance in IT Outsourcing Partnerships
Lotus Notes and Domino 6 Development (2nd Edition)
Using the Form Design Document
Writing Field Formulas
Validating Check Boxes
Writing Java Applications
The Role of the Domino Directory in Application Security
Snort Cookbook
Dynamic Rules
Detecting Binary Content
Detecting Malware
Monitoring a Network Using Policy-Based IDS
Performing Forensics Using Snort
Developing Tablet PC Applications (Charles River Media Programming)
The Tablet PC
Form Effects
Custom Grammars for Speech Recognition
Pong Game
Storing Ink in a Database
The Java Tutorial: A Short Course on the Basics, 4th Edition
Questions and Exercises
Code Samples
Example Four: LunarPhases
Code Samples
Appendix D. Deprecated Thread Methods
VBScript in a Nutshell, 2nd Edition
Common Problem Areas and How to Avoid Them
Program Flow
Windows Script Host 5.6
Section A.12. Miscellaneous
Section A.15. String Manipulation
flylib.com © 2008-2017.
If you may any questions please contact us: flylib@qtcs.net
Privacy policy
This website uses cookies. Click
here
to find out more.
Accept cookies