Transcript Viruses (4)
Viruses – Ch. 9 in Cliffs, pg. 135 The Discovery of Viruses • Tobacco mosaic disease stunts growth of tobacco plants and gives their leaves a mosaic coloration • In the late 1800s, researchers hypothesized that a particle smaller than bacteria caused the disease • In 1935, Wendell Stanley confirmed this hypothesis by crystallizing the infectious particle, now known as tobacco mosaic virus (TMV) © 2011 Pearson Education, Inc. Structure of Viruses • Viruses are not cells • A virus is a very small infectious particle consisting of nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope © 2011 Pearson Education, Inc. Viral Genomes • Viral genomes may consist of either – Double- or single-stranded DNA, or – Double- or single-stranded RNA • Depending on its type of nucleic acid, a virus is called a DNA virus or an RNA virus © 2011 Pearson Education, Inc. Capsids and Envelopes • A capsid is the protein shell that encloses the viral genome • Capsids are built from protein subunits called capsomeres • A capsid can have various structures • An envelope can incorporate phospholipids and proteins from host cell of animals © 2011 Pearson Education, Inc. Figure 19.3 Capsomere RNA DNA Membranous RNA envelope Capsid Head DNA Tail sheath Capsomere of capsid Tail fiber Glycoprotein 18 250 nm 20 nm (a) Tobacco mosaic virus Glycoproteins 70–90 nm (diameter) 80–200 nm (diameter) 50 nm (b) Adenoviruses 80 225 nm 50 nm 50 nm (c) Influenza viruses (d) Bacteriophage T4 • Bacteriophages, also called phages, are viruses that infect bacteria • They have the most complex capsids found among viruses • Phages have an elongated capsid head that encloses their DNA • A protein tail piece attaches the phage to the host and injects the phage DNA inside © 2011 Pearson Education, Inc. Host cells • Viruses are intracellular parasites, which means they can replicate only within a host cell • Each virus has a host range, a limited number of host cells that it can infect © 2011 Pearson Education, Inc. Replication • Once a viral genome has entered a cell, the cell begins to make viral proteins • The virus makes use of host enzymes, ribosomes, tRNAs, amino acids, ATP, and other molecules • Viral nucleic acid molecules and capsomeres spontaneously self-assemble into new viruses © 2011 Pearson Education, Inc. Animation: Simplified Viral Reproductive Cycle Right-click slide / select “Play” © 2011 Pearson Education, Inc. Figure 19.4 1 Entry and uncoating DNA VIRUS 3 Transcription and manufacture of capsid proteins Capsid 2 Replication HOST CELL Viral DNA mRNA Viral DNA Capsid proteins 4 Self-assembly of new virus particles and their exit from the cell Replication of Phages • Phages are the best understood of all viruses • Phages have two reproductive mechanisms: the lytic cycle and the lysogenic cycle © 2011 Pearson Education, Inc. The Lytic Cycle • The lytic cycle - lyses • The lytic cycle produces new phages and lyses (breaks open) the host’s cell wall, releasing the new viruses • A phage that reproduces only by the lytic cycle is called a virulent phage • Bacteria have defenses against phages, including restriction enzymes that recognize and cut up certain phage DNA © 2011 Pearson Education, Inc. Animation: Phage T4 Lytic Cycle Right-click slide / select “Play” © 2011 Pearson Education, Inc. Figure 19.5-5 1 Attachment 2 Entry of phage DNA and degradation of host DNA 5 Release Phage assembly 4 Assembly Head Tail Tail fibers 3 Synthesis of viral genomes and proteins The Lysogenic Cycle • The lysogenic cycle replicates the phage genome without destroying the host • The viral DNA molecule is incorporated into the host cell’s chromosome • This integrated viral DNA is known as a prophage • Every time the host divides, it copies the phage DNA and passes the copies to daughter cells © 2011 Pearson Education, Inc. Animation: Phage Lambda Lysogenic and Lytic Cycles Right-click slide / select “Play” © 2011 Pearson Education, Inc. • An environmental signal can trigger the virus genome to exit the bacterial chromosome and switch to the lytic mode • Phages that use both the lytic and lysogenic cycles are called temperate phages © 2011 Pearson Education, Inc. Figure 19.6 Phage DNA Daughter cell with prophage The phage injects its DNA. Cell divisions produce a population of bacteria infected with the prophage. Phage DNA circularizes. Phage Bacterial chromosome Occasionally, a prophage exits the bacterial chromosome, initiating a lytic cycle. Lytic cycle The cell lyses, releasing phages. Lysogenic cycle Certain factors determine whether lytic cycle is induced New phage DNA and proteins are synthesized and assembled into phages. or lysogenic cycle is entered Prophage The bacterium reproduces, copying the prophage and transmitting it to daughter cells. Phage DNA integrates into the bacterial chromosome, becoming a prophage. Figure 19.6a Phage DNA The phage injects its DNA. Phage DNA circularizes. Phage Bacterial chromosome Lytic cycle The cell lyses, releasing phages. Certain factors determine whether lytic cycle or lysogenic cycle is entered is induced New phage DNA and proteins are synthesized and assembled into phages. Figure 19.6b Daughter cell with prophage Cell divisions produce a population of bacteria infected with the prophage. Phage DNA circularizes. Occasionally, a prophage exits the bacterial chromosome, initiating a lytic cycle. Lysogenic cycle Certain factors determine whether lytic cycle or lysogenic cycle Prophage is entered is induced The bacterium reproduces, copying the prophage and transmitting it to daughter cells. Phage DNA integrates into the bacterial chromosome, becoming a prophage. Viral Envelopes • Many viruses that infect animals have a membranous envelope • Viral glycoproteins on the envelope bind to specific receptor molecules on the surface of a host cell • Some viral envelopes are formed from the host cell’s plasma membrane as the viral capsids exit © 2011 Pearson Education, Inc. Figure 19.7 Capsid Capsid and viral genome enter the cell RNA Envelope (with glycoproteins) HOST CELL Template Viral genome (RNA) mRNA ER Capsid proteins Copy of genome (RNA) Glycoproteins New virus DNA or RNA viruses • DNA serves as a template for mRNA and viral protein production • RNA viruses serve as a template for mRNA then viral protein production Retroviruses ssRNA that use reverse transcriptase (enzyme) to make DNA That DNA is then transcribed to mRNA using the cell’s machinery. RNA errors are great – mutation level is high Animal immune systems often can’t keep up. Two strains of viral genomes can recombine to form another virus. SIV to HIV Animation: HIV Reproductive Cycle Right-click slide / select “Play” © 2011 Pearson Education, Inc. Evolution of Viruses • Viruses do not fit our definition of living organisms • Since viruses can replicate only within cells, they probably evolved as bits of cellular nucleic acid • Candidates for the source of viral genomes are plasmids, circular DNA in bacteria and yeasts, and transposons, small mobile DNA segments • Plasmids, transposons, and viruses are all mobile genetic elements © 2011 Pearson Education, Inc. Prokaryotes (Bacteria) Archaea and Bacteria are prokaryotes Single circular DNA with no proteins Reproduce using binary fission DNA replicates then divides Bacteria contain plasmids which are circular pieces of DNA outside the chromosome R plasmids code for antibiotic resistance Most plasmids replicate outside the bacterial genome Episomes – plasmids that become incorporated into the host cell’s genome Metabolism controlled by operons Binary Fission Plasmids Transcription in prokaryotes is different – no introns Transcription and translation are coupled Gene transfer Horizontal gene transfer introduces genetic variation Conjugation – donating DNA through pili Transduction – introduction of new DNA by a virus Transformation – bacteria absorb DNA from surroundings (our lab) Conjugation Transduction Transformation STEM CELLS • Beginning embryological cells • Will be determined at a “later date” • As genes are turned on or off (due to the work of repressors, activators, methylation, acetylation) the cell is determined. • Morphogenesis is the change of an organism’s phenotype throughout its development of REPRODUCTIVE CLONING • Making an animal with same DNA as a donor • Unfertilized egg cell is replaced by somatic nucleus of an udder • Transcription factors in stem cells are not present in egg cell stage, so fixed determination is un-fixed DOLLY Gene Expression • Gene expression is the act of going from genotype to phenotype • DNA to mRNA to Protein • Genes are regulated by turning on and off transcription The lac operon in E.coli is the method by which E. coli make enzymes that metabolize lactose Regulatory gene – produces the repressor Repressor binds to the operator when lactose is absent No Transcription – RNA polymerase cannot bind to the promoter Figure 18.8-3 Enhancer (distal control elements) Proximal control elements Transcription start site Exon DNA Upstream Intron Exon Intron Downstream Poly-A signal Intron Exon Exon Cleaved 3 end of primary RNA processing transcript Promoter Transcription Exon Primary RNA transcript 5 (pre-mRNA) Poly-A signal Transcription sequence termination region Intron Exon Intron RNA Coding segment mRNA G P AAA AAA P P 5 Cap 5 UTR Start Stop codon codon 3 UTR Poly-A tail 3 When lactose is present, it binds to the repressor pulling it off the operator RNA polymerase binds the promoter – transcription begins Lactose-digesting enzymes are made Regulatory gene DNA Promoter Operator lacI lacZ No RNA made 3 mRNA RNA polymerase 5 Active repressor Protein (a) Lactose absent, repressor active, operon off lac operon DNA lacI lacZ lacY lacA RNA polymerase 3 mRNA 5 mRNA 5 -Galactosidase Protein Allolactose (inducer) Inactive repressor (b) Lactose present, repressor inactive, operon on Permease Transacetylase Another example – positive feedback Activator regulatory protein – CAP is activated by cAMP When glucose is up, cAMP levels are down, CAP is inactive When glucose is absent, cAMP is up, CAP is active and activates the lac operon to produce enzymes that break down lactose Traditional lac operon is negative regulation Know table on pg. 138 Figure 18.5 Promoter DNA lacI lacZ CAP-binding site cAMP Operator RNA polymerase Active binds and transcribes CAP Inactive CAP Allolactose Inactive lac repressor (a) Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized Promoter DNA lacI CAP-binding site lacZ Operator RNA polymerase less likely to bind Inactive CAP Inactive lac repressor (b) Lactose present, glucose present (cAMP level low): little lac mRNA synthesized Trp operon. E.coli will make tryptophan from scratch, but if it is in the surroundings, the E.coli will absorb it. Different from the lac operon trp operon Promoter Promoter Genes of operon DNA trpE trpR trpD trpC trpB trpA C B A Operator Regulatory gene 3 RNA polymerase Start codon Stop codon mRNA 5 mRNA 5 E Protein Inactive repressor D Polypeptide subunits that make up enzymes for tryptophan synthesis (a) Tryptophan absent, repressor inactive, operon on DNA No RNA made mRNA Protein Active repressor Tryptophan (corepressor) (b) Tryptophan present, repressor active, operon off Proximal control elements are located close to the promoter Distal control elements, groupings of which are called enhancers, may be far away from a gene or even located in an intron Some transcription factors function as repressors, inhibiting expression of a particular gene by a variety of methods A particular combination of control elements can activate transcription only when the appropriate activator proteins are present Promoter Activators DNA Enhancer Distal control element Gene TATA box General transcription factors DNAbending protein Group of mediator proteins RNA polymerase II RNA polymerase II Transcription initiation complex RNA synthesis 1. 2. 3. Multicellularity Chromosome complexity Uncoupling of transcription and translation Enhancer Control elements Promoter Albumin gene Crystallin gene LENS CELL NUCLEUS LIVER CELL NUCLEUS Available activators Available activators Albumin gene not expressed Albumin gene expressed Crystallin gene not expressed (a) Liver cell Crystallin gene expressed (b) Lens cell 1. 2. 3. DNA methylation – when CH3 groups attach, represses transcription Histone acetylation – activates transcrition by attaching acetyl groups Histone methylation – represses at the histone. 4. Transcription initiation • General transcription factors – present in all transcription events • Attaches RNA polymerase to the promoter region • Target the TATA box • Specific Trans. Factors – activators and repressors specific to each cell type (ex. Liver and eye cells), bind to enhancer region on gene. 5. RNA processing • Each cell splices the primary mRNA transcript differently 6. RNA interference (RNAi) • Short RNA molecules that bind to mRNA and prevent their translation • microRNA (miRNA) and short interfering RNA (siRNA) Animation: RNA Processing Right-click slide / select “Play” © 2011 Pearson Education, Inc. Animation: Blocking Translation Right-click slide / select “Play” © 2011 Pearson Education, Inc. 7. mRNA degradation • Degradation of the polyA tail and 5’ cap • Degradation of areas rich in A and U 8. Protein degradation • 3-D stage of protein changes shape as protein ages, marked by ubiquitin for destruction Animation: mRNA Degradation © 2011 Pearson Education, Inc. Right-click slide / select “Play” Animation: Protein Processing Right-click slide / select “Play” © 2011 Pearson Education, Inc. Animation: Protein Degradation Right-click slide / select “Play” © 2011 Pearson Education, Inc. Figure 18.14 Ubiquitin Proteasome Protein to be degraded Ubiquitinated protein Proteasome and ubiquitin to be recycled Protein entering a proteasome Protein fragments (peptides)